Investigator-initiated study management, explained.
A doctor has an idea for a study, and a drug company agrees to pay for it and send the medicine. Signing that deal starts years of work. Someone at the company has to read a report from every doctor each quarter, pay each invoice only for work that was done, track every vial and see trouble coming while there is still time to fix it.
This guide is for anyone who runs, funds, pays for or audits these studies: ESR managers (ESR stands for externally sponsored research), global ESR leads, medical directors, finance approvers, clinical supply coordinators, transparency analysts, and leaders deciding whether to automate the work. No background needed.
Imagine you are an ESR manager at Northwind Bio, a drug company, looking after 38 studies that doctors asked it to support. One is KESTREL-IgAN: Dr. Sofia Lindqvist at Calder Ridge Medical Center is testing weekly home injections of Northwind's Renquira in 24 adults with IgA nephropathy, a kidney disease. She is the study's legal sponsor. Northwind funds it and ships the vials.
On Wednesday, October 28, 2026, at 9:12 am her three-page progress report arrives. Page 2 says 9 patients were enrolled by September 30, and the plan you agreed said 16. In the same inbox, a vendor's packing list says the next 40 vials come from a manufacturing batch, called a lot, that expires September 30, 2028. At the pace in the report, the last patient's last visit falls on November 20, 2028.
The plan in the contract
Enrolled by Sep 30
16
Last patient in
Mar 31, 2027
Q3 report, page 2
Enrolled by Sep 30
9
At this pace
Oct 25, 2027
30 weeks late, and a lot that runs out 7 weeks too soonA second study site, a later lot, the next scheduled payment helddecided this week, with time left to act.
Good study management catches both from documents that were already in the mailbox, a quarter or two before a contract date is missed.
Funded studies from contract to final report: the duties, the rules, the numbers and the people
Who holds which duty when a doctor sponsors a study and a company funds it, how to work out how late a study will be, what product and payment records must show, and what Open Payments asks of a research payment, explained without selling anything. If you are new to externally sponsored research, start here.
01 · In plain words
What happens after a drug company says yes to a doctor's study idea
Doctors often have questions a drug company never planned to test. Does this injection work at home as well as in the clinic? Does it help the patients the big trials left out? A doctor writes the idea down and asks the company for help, usually money, the medicine, or both.
A study born this way is called an investigator-initiated study, or IIS. Companies also call it investigator-sponsored research or, in many medical affairs teams, externally sponsored research, ESR. The company's medical team reviews the idea, and if it says yes, the two sides sign a research agreement.
The signature changes who does what. In a trial the company designs itself, the company is the sponsor, the party legally answerable for the study. Here the doctor or the hospital usually takes that role, and the company becomes a supporter. The hospital running the study is called the site, and the written plan it follows is the protocol.
The company still has plenty to do. It agreed to pay at set points, called milestones, such as the first patient enrolled or the final report accepted. It agreed to send a set amount of product. It wants a progress report every quarter, and it has to tell regulators about the money it spent.
The person who keeps all of this moving is the ESR manager. At a large company one ESR manager may hold dozens of studies, each on its own calendar, with its own contract, its own invoices and its own shipments. Each study is planned at the start as a list of dates, called the baseline. Each quarter the real world pulls away from that list a little more. The gap is the drift.
Most of the job is reading. A progress report arrives as a PDF, a shipping reply as an email, an invoice as a scan. The numbers inside them get typed into a spreadsheet or a grants database. The typing takes the time, and because it comes late, the warning comes late too. A study that will finish seven months behind plan looks fine until the milestone it misses, and by then the choices that could have saved it are gone.
One funded study, from a signed contract to its final report
The proposal is approved and the contract signedScientific review is finished. The agreement fixes the budget, the payment schedule, the enrollment plan and the product quantity. KESTREL-IgAN's was signed March 3, 2025.
The baseline is confirmedSeven dates become the plan: contract, first patient, interim analysis (a planned early look at the data), last patient in, last visit, final study report and manuscript.
The study is run, quarter by quarterReports are read, enrollment is compared with plan, product ships, invoices are matched and payments classified. This is where the 9 against 16 is found, and it is the subject of this guide.
The plan changes when the study changesAmendments move dates and money, and a study that drifts gets a recovery plan or, sometimes, an early close.
The study closesFinal report, manuscript, registry results, product reconciled, last payment made and every payment and shipment reported as a transfer of value.
Step 3 is the center of this guide. The people, companies and figures in this example are fictional.
Four surprises about funded studies: the sponsor, the vial's value, the recruitment gap and a missing count
The doctor can be the legal sponsor
US rules define a sponsor-investigator as one individual who both starts and conducts a study, and who carries the duties of both roles.1 The company writing the checks may have no sponsor duties at all, which changes what it may ask for and what it must leave alone.
US reporting asks for no set price on study drug
You might expect every vial to carry a dollar value in Open Payments, the public US database of what drug and device makers give doctors and teaching hospitals. An answer from CMS, the Centers for Medicare & Medicaid Services, which runs it, says manufacturers "are not required to assign a specific value to clinical study drugs" given to principal investigators, and should report the total research payment.2 A company may still value product by a rule of its own, as the sample company in this guide does.
Investigator-sponsored trials stop for poor recruitment far more often
Among 1,017 randomized trials approved in 2000 to 2003, 26.5% of investigator-sponsored ones were discontinued for poor recruitment, against 8.4% of industry-sponsored ones.3 These are the studies an ESR team watches.
Nobody publishes how many of these studies exist
We found no public count of funded studies, no figure for what companies spend on them and no time study of the work. CMS's research payment file holds $9.5 billion for 2025, with no field that marks a record as investigator-initiated.4,5
Baseline, drift, milestone, in-kind: the words this work runs on
Baseline
The dates, budget and product quantity agreed when the study started. It changes only with approval.
Drift
The gap, in weeks, between a baseline date and today's actual or forecast date.
Milestone payment
Money owed when a named event happens, such as twelve patients enrolled or the final report accepted.
In-kind support
Help given as goods or services. In this work it usually means the study product itself.
Who holds which duty when a doctor sponsors the study and a company funds it
In shortThe sponsor answers for the study. In an investigator-initiated study that is normally the doctor or the institution. The company answers for what it promised: money, product and its own reporting. Every part of an ESR manager's job sits on one side of that line, and the research agreement draws it.
The US definition is short. A sponsor is the person who "takes responsibility for and initiates a clinical investigation". A sponsor-investigator is an individual who "both initiates and conducts" it, under whose immediate direction the drug is given, and the term excludes any person other than an individual.1 ICH E6(R3), the international good clinical practice guideline, uses nearly the same words and adds that the obligations "include both those of a sponsor and those of an investigator".6
When a hospital or university takes the role, it is the sponsor and the doctor is its investigator.
The European definition puts the same idea differently. A sponsor is "an individual, company, institution or organisation which takes responsibility for the initiation, for the management and for setting up the financing of the clinical trial".7 That word, financing, is one reason a European agreement needs care. It has to be clear who set up the money and who merely gave some.
Companies say this in public. One device maker's research program page states it is a "supporter" of such studies "but is not the study 'sponsor'", and that the sponsor-investigator "is responsible for conducting the study and assuring the validity of the study data".8
The words get used loosely. A short 2024 paper separates them: "initiated" is about who conceived the study, "sponsored" about who takes on the regulatory responsibilities, and the second word is "often used inaccurately to describe the funding source".9 Check which arrangement your agreement describes before you apply anything in this guide.
The study's conduct sits with the sponsor; money, product and reporting to CMS sit with the company
Who usually holds each duty when the investigator or institution is the sponsor. The research agreement can move items.
NoneSupportsHolds
Sponsor-investigator or institutionSupporting companyProtocol and study conductHoldsNoneEthics approval and consentHoldsNoneFiling with the regulator (IND or trial application), when one is neededHoldsSupportsRegistry entry and resultsHoldsNoneProduct use and records at the siteHoldsSupportsProduct manufacture and shipmentNoneHoldsBudget and payment termsSupportsHoldsOpen Payments and EFPIA disclosureNoneHolds
Filing with the regulator (IND or trial application), when one is needed
Holds
Supports
Registry entry and results
Holds
None
Product use and records at the site
Holds
Supports
Product manufacture and shipment
None
Holds
Budget and payment terms
Supports
Holds
Open Payments and EFPIA disclosure
None
Holds
Two ways a marketed product gets studied without the company's own IND
A US study of a drug usually needs an investigational new drug application, an IND, unless it meets a list of conditions. A study of a lawfully marketed drug is exempt only if it will not support a new indication or a significant labeling change, will not support a significant advertising change, does not significantly raise the risks of the drug through its dose, route or patient group, follows the ethics committee and consent rules, and stays within the ban on promoting an investigational drug.13
KESTREL-IgAN takes the other route: it runs under an IND held by the investigator's side. The doctor rarely writes the whole file from scratch. FDA's guidance for sponsor-investigators, a May 2015 draft that is still a draft, describes a letter of cross-reference authorization: the company lets FDA read the manufacturing and earlier study information in its own file, so the doctor need not supply it again.14 The letter gives FDA access, and the same draft notes that it does not give the sponsor-investigator a right to read the company's confidential content.
An ESR manager often has to track this letter as one more item in the contract's list of commitments.
Why the line matters day to day. An ESR manager who asks for a progress report is checking what the company paid for. An ESR manager who tells a site how to recruit or rewrites its protocol is doing the sponsor's work. A recovery plan is written as a request and agreed with the investigator, and every change to the protocol stays with the investigator and the ethics committee.
03 · Rules and dates
The rules around a funded study, and where each one stood in November 2026
In shortNo single rule covers investigator-initiated studies. Good clinical practice, FDA's IND rules, the EU Clinical Trials Regulation, CMS Open Payments, fraud and abuse guidance, and the results rules each govern one piece. Several moved in 2025 and 2026.
Good clinical practice changed in 2025 and 2026, and more of it takes effect in January 2027
Jan 6, 2025ICH E6(R3) finalized
Principles and Annex 1 adopted at ICH's Step 4.
Jul 23, 2025E6(R3) in effect in the EU
Principles and Annex 1.
Sep 2025FDA publishes E6(R3)
Final guidance on principles and Annex 1.
Jun 3, 2026Annex 2 adopted by ICH
Covers decentralized and pragmatic elements and real-world data.
Jul 27, 2026AI Omnibus in force
EU high-risk AI dates move out to December 2027 and August 2028.
Oct 2026Three new FDA notices
ClinicalTrials.gov Notices of Noncompliance reach 11.
Financial aspects go in an agreement; product accountability rests with the investigator or institution; oversight and systems are proportionate and fit for purpose6
In effect in the EU since July 23, 2025; FDA final September 2025; Annex 2 in the EU from January 15, 202715,16
21 CFR Part 312
Sponsor-investigator duties, the IND exemption, label wording, product records1,13,21,22,10
In force, CFR 2025 edition
FDA sponsor-investigator guidance
How a doctor prepares an IND, and the cross-reference letter14
Draft since May 2015, not for implementation
EU Regulation 536/2014
Sponsor definition, results within a year, 25-year archive, labeling of authorized products7,23,24,25
In force
42 CFR Part 403 Subpart I
Open Payments: research payments, delayed publication, the 90th-day report11,26,17
The code of EFPIA, the European Federation of Pharmaceutical Industries and Associations: R&D transfers of value disclosed in aggregate27
Final consolidated version 2026; applies through national codes
OIG guidance
From the US health department's Office of Inspector General: research funding at fair market value, kept apart from sales and marketing28
The 2003 text now sits in OIG's archive; the General Compliance Program Guidance of November 6, 2023 is current; no date for an update on drug makers29
42 CFR Part 11
Registration and results on ClinicalTrials.gov, the US trial registry; the responsible party30,12,31
In force, CFR 2025 edition
Two different rules share the number 11. 42 CFR Part 11 covers ClinicalTrials.gov. 21 CFR Part 11 covers electronic records and signatures, and section 13 returns to it.
04 · The documents
Eight documents that carry a funded study, and the numbers buried in each
In shortAlmost every number an ESR manager needs already exists on paper, written by somebody else: enrollment in a progress report, lots in a packing list, money in an invoice. The work is getting each number out of its document, tying it to the agreement and keeping a pointer back to the page.
A follow-up change that moves money and dates, seen only by the science team
Quarterly progress report
Study coordinator, signed by the investigator
Screened, enrolled, treated and completed; why patients failed screening; outlook; product on hand
Different formats per site; arrives late; retyped by hand
Product request
Site
Quantity, need-by date, stock on hand
Sent by email to the wrong team; above the approved total
Dispatch email and packing list
Depot, order desk or relabeling vendor
Ship date, quantity, lot, expiry, tracking, temperature logger
Lot and expiry copied by hand, checked against nothing
Receipt acknowledgment
Site
Quantity received, condition, temperature in range
Forgotten, and chased by hand weeks later
Invoice
Institution's research finance office
Line items, milestone claimed, amounts
Arrives before the milestone; repeats an earlier invoice
Final study report and manuscript
Investigator
Results against the protocol's objectives
A section missing, noticed only after the final payment
The research agreement touches all four columns, and each other document is the direct source for one or two
Which document is the first-hand source for what the ESR team tracks
Not at allSomeDirect
MilestonesMoneyProductTransparencyResearch agreementSomeDirectSomeSomeProtocol and amendmentsDirectSomeSomeNot at allQuarterly progress reportDirectSomeSomeNot at allDispatch email and packing listNot at allNot at allDirectSomeInvoiceNot at allDirectNot at allDirectFinal study reportDirectSomeNot at allNot at all
Even a modest portfolio creates a lot of these. Take 40 studies, four reports a year each, four invoices each, a shipment every other month and a handful of amendments. That is well over 500 documents a year for one person, and our arithmetic is illustrative: use your own volumes. The sample company in this guide estimates about 2,400 reports, 1,100 invoices and 380 shipments a year across 640 studies, and those figures are fictional.
Each document also has a home outside the ESR team. The agreement sits in contract management, the invoice in accounts payable, the lot in clinical supply, the report in a grants system or a mailbox. So the study's true state lives in five places, and the spreadsheet is somebody's attempt to pull it together.
The research agreement and the company's quality system list further duties for each party during the study. They are the authority on those duties, and a team should follow them as written. This guide stays with dates, product, money and deliverables.
05 · Forecasting a study
Working out how late a study will be from one quarterly report
In shortTake the patients still needed, divide by the recent enrollment rate, and add that to today. For KESTREL-IgAN that is 15 patients at 1.17 a month, which lands on October 25, 2027, 30 weeks after plan. The method is simple. The judgment lies in which rate you believe, and in reading why patients failed screening.
Here is the calculation on the example's numbers. The plan was 24 patients between October 1, 2025 and March 31, 2027, a straight line of 16 by September 30, 2026. The report says 9.
Step
Working
Result
Compare with plan
16 planned − 9 enrolled
7 behind, 44% short
Recent rate
3 in Q2 + 4 in Q3 = 7 in 6 months
1.17 a month
Patients still needed
24 − 9
15
Time to enroll them
15 ÷ 1.17
12.9 months
Forecast last patient in
Sep 30, 2026 + 12.9 months
Oct 25, 2027
Drift
Oct 25, 2027 − Mar 31, 2027 = 208 days
30 weeks, about 7 months
Everything after it
Last visit, final report and manuscript keep their planned gaps
Last visit Nov 20, 2028; final report May 28, 2029
At the last two quarters' pace, KESTREL-IgAN reaches 24 patients about seven months after its plan date
Cumulative patients enrolled at each quarter end
PlanReportedForecast at 1.17 a month
0102030
Q4 25Q2 26Q4 26Q2 27Q4 27
Fictional example from this guide · The plan is the straight line in the sample contract. Forecast points are 3.5 patients a quarter, capped at 24.
Show the numbers
Plan
Reported
Forecast at 1.17 a month
Q4 25
4
2
—
Q1 26
8
2
—
Q2 26
12
5
—
Q3 26
16
9
9
Q4 26
20
—
12.5
Q1 27
24
—
16
Q2 27
24
—
19.5
Q3 27
24
—
23
Q4 27
24
—
24
Why one enrollment rate is never the whole answer
The rate you pick moves the date by months. Over the whole study so far, 9 patients in under 11 months is about 0.84 a month. Over the last quarter alone it is 1.33. And a recovery plan changes the rate itself, so a forecast is a statement of what happens if nothing changes. A range says that out loud: the sample forecast gives August 2027 to January 2028.
To hit the original date the study would need more than double its recent pace
Months to enroll the remaining 15 patients, counted from September 30, 2026
Rate since first patient: 0.84 a month17.9 months
Last two quarters: 1.17 a monththe rate behind the forecast12.9 months
Last quarter only: 1.33 a month11.3 months
If a second site doubles the pace: 2.33 a monthour illustration6.4 months
What the plan needs: 2.5 a month6 months
Fictional example from this guide · Our arithmetic on the fictional example. The doubling is an illustration, with no promise that a second site delivers it.
Show the numbers
Item
Value
Rate since first patient: 0.84 a month
17.9 months
Last two quarters: 1.17 a month
12.9 months
Last quarter only: 1.33 a month
11.3 months
If a second site doubles the pace: 2.33 a month
6.4 months
What the plan needs: 2.5 a month
6 months
Reading the screen failures, where the fix usually hides
A screen failure is a patient checked for the study who does not qualify. Page 2 of the report says 14 patients were screened and 5 failed, and three of the five failed because their kidney function, measured as eGFR, fell below the study's entry limit of 45. Five of 14 is 36%. That single line suggests a question for the investigator: would widening the limit to 30 fit the study's science? Page 3 adds that four patients are in screening and that the clinic's referrals come only from its own patients.
The two findings together point to a recovery plan: more referrals, a second site, and a conversation about the entry criterion. The investigator decides, because the protocol is hers.
Keep the rule for a band simple enough to argue with. The sample company sorts studies into three bands: on track within 4 weeks, drifting at 5 to 12 weeks, and at risk over 12 weeks or with a forecast past a deliverable date. A person can override a band with a reason. A rule people can recite gets used, and an unexplained score gets ignored.
06 · Why studies miss enrollment
The evidence that investigator-led trials miss enrollment more often, in three data sets
In shortStudies from 2014 and 2015 found failed recruitment far more often outside industry. Our own count of ClinicalTrials.gov for 2015 to 2021 starts, using a stand-in group, shows the same pattern: about the same share terminated, twice the share of those terminated citing low enrollment, and many more records left with unknown status.
Carlisle and colleagues examined 2,579 phase 2 and 3 trials closed in 2011. Nineteen percent, 481 trials, were terminated for failed accrual, meaning too few people enrolled, or finished under 85% of planned enrollment. Non-industry funding was among the factors tied to failure, at 25% against 16%.32
Kasenda and colleagues followed 1,017 randomized trials from ethics committee files in three countries. A quarter were discontinued. Poor recruitment was the most common reason, at 26.5% for investigator-sponsored trials and 8.4% for industry-sponsored ones.3 Both studies are old. We wanted a current check, so we asked ClinicalTrials.gov directly.
Three data sets, one direction: recruitment fails more often when an investigator leads
Share of trials in each study, on three different measures
IndustryInvestigator-led or non-industry
Failed accrual, phase 2 and 3 trials closed in 201116%25%
Discontinued for poor recruitment, randomized trials approved 2000 to 20038.4%26.5%
Low-enrollment wording among terminated trials, 2015 to 2021 starts (our count)21.4%46.4%
Our reading of the sources32,3,33 · The three measures differ, so compare within a row. The first two rows are published. The third is our count: a word search of the why-stopped field, with the method printed below.
Show the numbers
Measure
Industry
Investigator-led or non-industry
Failed accrual, phase 2 and 3 trials closed in 2011
16%
25%
Discontinued for poor recruitment, randomized trials approved 2000 to 2003
8.4%
26.5%
Low-enrollment wording among terminated trials, 2015 to 2021 starts (our count)
21.4%
46.4%
What the registry shows for 2015 to 2021 starts, read in November 2026
The registry has no field called investigator-initiated. Our closest proxy is an interventional study whose lead sponsor is classed as "other", meaning a university, hospital or individual, with an industry collaborator. It misses a funded study that names no company as a collaborator, and it takes in other partnerships. We compared those 9,896 studies with 35,255 led by industry. Everything in this part of the section is our count.33
How we made these counts, and what they cover. Our count, from the ClinicalTrials.gov API, version 2, read November 3, 2026. Interventional studies by start date. First group: lead sponsor class OTHER with a collaborator of class INDUSTRY. Second group: lead sponsor class INDUSTRY. The low-enrollment share is the terminated studies whose why-stopped text holds the word stems enrol, accru or recruit. Then we read records by hand. Of 30 records drawn at random from the first group, 18 name a drug or biologic maker and 12 a device, food, consumer, software or service company, and none says who paid. So this group is a stand-in that tracks funded studies loosely, and it counts no funded study as such. Of 30 word-search matches in each group, 26 and 29 really describe low enrollment. Of 40 non-matches in each group, 3 and 0 describe it in other words. Scaled up, that hand read gives roughly 44% and 21%, close to the search and with the same gap. Counts shift by a few from day to day.
Studies led outside industry with an industry collaborator finish less often, and one in six records has gone quiet
Status in November 2026 of interventional studies started 2015 to 2021
CompletedTerminatedWithdrawnUnknown statusStill under way or other
Investigator-led, industry collaborator (9,896)53.9%12.4%16.3%12.2%
Industry-led (35,255)69%12%9.9%
Our reading of the sources33 · Our count, method above. Unknown status means the record has not been verified for two years and its last status was open.
Show the numbers
Completed
Terminated
Withdrawn
Unknown status
Still under way or other
Investigator-led, industry collaborator (9,896)
53.9%
12.4%
5.2%
16.3%
12.2%
Industry-led (35,255)
69%
12%
3.4%
9.9%
5.6%
Terminated studies run at about the same share in both groups, 12.4% and 12.0%. The reasons differ. Among terminated studies with the investigator in the lead, 567 of 1,223 used the words enrollment, accrual or recruitment when explaining why, or 46.4%, against 910 of 4,245 among industry-led studies, 21.4%. That is our count. It reads only what sponsors typed, 198 of those records give no reason, and a study with low enrollment described in other words is missed, so treat those shares as an indication.
The share in unknown status is the finding that most concerns an ESR lead. It reads 16.3% against 9.9%, and each of those records is a study whose public entry stopped being kept up.
About 1,200 to 1,600 studies with a non-industry lead and an industry collaborator start each year
Interventional studies with a non-industry lead and an industry collaborator, by start year
05001,0001,5002,0001,262
201520172019202120232025
Our reading of the sources33 · Our count, November 3, 2026, method above. The peak is about 1,570 in 2021. Recent years may still gain late registrations.
Show the numbers
Studies started
2015
1,215
2016
1,401
2017
1,436
2018
1,441
2019
1,427
2020
1,406
2021
1,570
2022
1,364
2023
1,333
2024
1,239
2025
1,262
Study size explains part of the fragility. A review of 5,834 kidney, bladder and prostate cancer trials found most investigator-initiated trials were open-label phase 2 studies of 20 to 49 people, open-label meaning everyone knows which treatment each patient gets.34 In a study of 24, a single site's staffing change can move the whole forecast. Money is the other part: 48 people interviewed in Switzerland described a systemic problem of these trials being underfunded, with budgets often inaccurate because of poor planning and limited oversight.35
07 · Product supply
Three fulfillment routes, one expiry date and the records behind every vial
In shortProduct reaches a funded study by one of three routes, depending on how it must be labeled. For each shipment someone must check the request against the approved total, capture the lot and expiry from the reply, make sure the lot outlasts the study and collect the site's receipt. All of it has to be on record.
One request passes through five hands before it is closed
KESTREL-IgAN's shipment of 40 vials, from request to receipt
1Requested
Study coordinator asks for 40 vials. 1,560 approved, 320 shipped so far.
Owen Marsh, siteOct 19
2Reviewed
ESR manager checks the request against the approved total.
Nadia BrooksOct 21
3Approved
A second person approves, and the route is chosen by supply type.
Sam Patel, supplyOct 21
4Packed
The vendor relabels and sends a dispatch email and packing list.
VendorOct 28
5Received
The site acknowledges quantity, condition and temperature.
SiteAfter Oct 29
Fictional example from this guide
Show the numbers
Step
What happens
Who
Time
Requested
Study coordinator asks for 40 vials. 1,560 approved, 320 shipped so far.
Owen Marsh, site
Oct 19
Reviewed
ESR manager checks the request against the approved total.
Nadia Brooks
Oct 21
Approved
A second person approves, and the route is chosen by supply type.
Sam Patel, supply
Oct 21
Packed
The vendor relabels and sends a dispatch email and packing list.
Vendor
Oct 28
Received
The site acknowledges quantity, condition and temperature.
Site
After Oct 29
Choosing among clinical kits, commercial packs and relabeled packs
Route
When it fits
Who ships
What to check
Clinically labeled kits
Product already made for studies
Company's R&D depot
Stock against other trials' demand
Commercial packs, in bulk
The site may use marketed packs as labeled
Commercial order desk
That the order is kept apart from sales, and recorded as research support
Relabeled commercial packs
The study needs investigational labels the site cannot apply
Relabeling vendor
Exact label wording, and a lot that lasts
Label wording is a rule. The immediate package of a US investigational drug "shall bear a label with the statement 'Caution: New Drug—Limited by Federal (or United States) law to investigational use.'"21 In the EU, authorized products used in a trial may be labeled under the trial rules or under the normal marketing rules, with additional particulars on the pack where the protocol's circumstances require them.25 If a study runs under an IND exemption, ask regulatory affairs what your packs need.
Checking a lot's expiry against today's forecast, and again when it moves
The example's packing list shows 40 vials, lot RQ26-1187, expiry September 30, 2028. That date looks fine on its own, two years out. It stops looking fine beside the forecast: enrollment has slipped, so the last patient's last visit has moved to November 20, 2028, seven weeks after the lot expires. Against the original plan, April 26, 2028, the lot would have been fine. So this check has to run against today's forecast, and it has to be rerun whenever the forecast moves.
Forecast slippage turned a comfortable expiry date into one that falls seven weeks short
Apr 26, 2028Last visit, original plan
Lot RQ26-1187 would have lasted.
Sep 30, 2028Lot RQ26-1187 expires
The first lot the vendor packed.
Nov 20, 2028Last visit, forecast
Seven weeks after that expiry.
Mar 31, 2029Later lot RQ26-1342 expires
The lot the vendor swapped in.
Fictional example from this guide
Show the numbers
When
What
Apr 26, 2028
Last visit, original plan
Sep 30, 2028
Lot RQ26-1187 expires
Nov 20, 2028
Last visit, forecast
Mar 31, 2029
Later lot RQ26-1342 expires
Whose records prove where each vial went
In an investigator-held IND, FDA's rules put these records on the sponsor-investigator. A sponsor keeps records "showing the receipt, shipment, or other disposition" of the drug, with the investigator's name and the date, quantity and batch of each shipment.22 An investigator keeps records of the "dates, quantity, and use by subjects", and returns or disposes of unused supply when a study ends.10,36
E6(R3) says responsibility for product accountability rests with the investigator or institution, and that a sponsor may facilitate it.6 The company keeps its own shipping records, because it shipped the product and because it may have to report it as a transfer of value. In FDA's fiscal 2024 inspection summary, failing to maintain accountability records appears among the common sponsor-investigator observations.37
The study's agreement decides what the site reports back about stock on hand, so the company can see a shortage coming. Record retention runs two years after approval, or two years after the investigation ends if no application follows, under US rules, and 25 years for the master file under the EU regulation.10,24
08 · Paying for research
Paying for research only when the work that earns it is on file
In shortA research payment should be fair market value for real work, kept away from sales, and tied to evidence. Each invoice line needs a line in the schedule, a document that proves the event happened, and a check of what was already paid and the cap. The government has treated research grants without that discipline as kickbacks.
E6(R3) asks only that "the financial aspects of the trial" be documented in an agreement between sponsor and investigator or institution.6 The harder rules come from fraud and abuse law.
The 2003 guidance for drug makers from the US health department's Office of Inspector General, OIG, said payments for research services "should be fair market value for legitimate, reasonable, and necessary services". It said grants linked to product purchases can be misused, and that "manufacturers should insulate research grant making from sales and marketing influences".
It also listed research "initiated or directed by marketers" and post-marketing research used as a pretense to promote product among the signs of questionable research.28 That text now sits in OIG's archive, and no replacement for drug makers has a date.29 Compliance teams still build on it.
What a real case looked like. In 2020 Pacira Pharmaceuticals paid about $3.5 million to resolve a whistleblower suit.38 The United States contended that 28 grants were typically started by sales or marketing staff, were conditioned on formulary acceptance, meaning an institution adding the drug to its approved list, were approved with little or no documented description of the research or fair market value assessment, and got "little or no follow-up", with some research never carried out as proposed. The agreement states it is no admission of liability, and Pacira denied the allegations.39 Read the list as a checklist of what your file should be able to disprove.
Tying each invoice to a milestone, with the arithmetic
KESTREL-IgAN's sample contract is worth $684,800: seven milestones totaling $524,000, plus $6,700 per enrolled patient, up to 24, which is $160,800. Here is where the money stood on October 28, 2026.
Under a third of the study's money has been paid, and the next $96,000 is now on hold
KESTREL-IgAN's $684,800 contract, October 28, 2026, after the recovery plan
PaidInvoice in reviewHeldLater milestonesPer-patient fees not yet earned
Contract$193.5K$96K$268K$100.5K
Fictional example from this guide · Paid: milestones 1 and 2 plus 5 patients. In review: 4 patients × $6,700. Held: milestone 3. Later: milestones 4 to 7.
Show the numbers
Paid
Invoice in review
Held
Later milestones
Per-patient fees not yet earned
Contract
$193.5K
$26.8K
$96K
$268K
$100.5K
Check
Question
Sample result
Schedule
Is this line in the contract?
$6,700 per enrolled patient, up to 24: yes
Evidence
Did the event happen, on a document someone confirmed?
4 enrolled in Q3, report page 2: $26,800 earned once the report is confirmed
Not yet earned
Is a milestone claimed early?
A last-patient-in invoice of $54,000 with 22 of 24 enrolled: hold it
Duplicate
Was this paid before?
$31,500 for a milestone paid on September 14 under another invoice number: reject it
Completeness
Does the deliverable meet the contract?
$72,000 for a final report with 11 of 12 sections: wait for the missing one
Cap
Does the running total stay inside the budget line?
$33,500 paid + $26,800 against a $160,800 cap: inside
Why these budgets drift: what the real costs of 93 trials showed
Griessbach and colleagues collected real costs from 93 investigator-sponsored randomized trials in Switzerland, Germany and the UK. The median total cost was $645,824, and over a quarter of it went on planning, which is typically not fully funded. Of the 66 with an original budget available, 46 exceeded it by more than 50%.40 So a budget amendment request may trace back to a budget that was never realistic.
Seven in ten investigator-sponsored trials overran their budget by more than half
46 of 66
trials with an available budget exceeded it by more than 50% (69.7%)
trials with an available budget exceeded it by more than 50% (69.7%)
70 of 100
Separation of duties is the plain control behind all this. The person who reviews an invoice should never approve it. Holding a payment is also a legitimate tool, provided the agreement allows it: a recovery plan can hold the next milestone until a new site opens, and the investigator should hear about the hold from a person, in advance.
09 · Open Payments and EFPIA
What Open Payments and the EFPIA Code ask of a research payment and a shipped vial
In shortUS makers report research payments to CMS once a year, by the 90th day, with the institution, the study, the product and the principal investigators. CMS answers that study drug needs no specific value. Europe's EFPIA Code discloses R&D transfers of value in aggregate. Classifying each record when it is approved saves the year-end hunt.
Research is about two-thirds of all the money reported to Open Payments
Program Year 2025, published 2026, in billions of US dollars
The fields a research record needs, and the special rules that apply
Any payment "made in connection with an activity that meets the definition of research" and subject to a written agreement or protocol follows special rules. It is reported separately, with the name of the receiving institution or person, the total research payment "including all research-related costs", the study name, the related product, the principal investigators and, optionally, the ClinicalTrials.gov number.11
CMS allows up to five covered principal investigators per payment, and a payment to a non-teaching institution is still reportable when a physician who is a covered recipient, the rule's term for the clinicians and teaching hospitals it tracks, is a principal investigator.2
Publication may be delayed for new products and new applications of existing ones, for up to four years or until FDA approval.26 Reports are due by the 90th day of the year, so Program Year 2026 is due March 31, 2027.17
The dollar value of study drug. CMS FAQ 9118 asks what value a manufacturer should assign to study drugs given to principal investigators under a research agreement. The answer: manufacturers "are not required to assign a specific value" and "should report the total amount of the research payment, including all research-related costs".2 A company may still record a value by an internal rule, using for example wholesale acquisition cost or standard cost; the FAQ names no method. Write your rule down, have your counsel agree it and apply it the same way every time. The FAQ file we read was current as of July 1, 2024.
In-kind research support has held between $1.7 and $2.1 billion a year since 2021, beside rising cash
Open Payments research payments by form, Program Years 2019 to 2025
Cash or cash equivalentIn-kind items and services
$0$2B$4B$6B$8B$7.6B$1.9B
2019202020212022202320242025
Our reading of the sources5 · Our count: total amount summed by form of payment in CMS's research files for each year, datasets dated June 30, 2026, read November 3, 2026. All research, company-run included: no field isolates funded studies.
Show the numbers
Cash or cash equivalent
In-kind items and services
2019
$5.3B
$1.4B
2020
$5.5B
$1.5B
2021
$6.2B
$2.1B
2022
$6.4B
$1.8B
2023
$7B
$1.7B
2024
$7B
$1.9B
2025
$7.6B
$1.9B
By our count, in Program Year 2025 the in-kind share came to $1.91 billion on 128,187 records, against $7.58 billion in cash on 803,772 records.5 These totals include every kind of research a maker funds. They show the scale of in-kind support and say nothing about funded studies on their own. Small-payment thresholds of $13.82 and $138.13 for 2026, and $14.31 and $143.01 for 2027, apply to very small transfers, so they rarely touch a research record.18
The penalties, and the one case that set the record
Failing to report brings civil penalties of $1,443 to $14,432 per item, capped at $216,490 a year, and for knowing failures $14,432 to $144,329, capped at $1,443,275. Those are the 2025 levels, and HHS made no adjustment for 2026.41,42 In August 2026 the Justice Department announced a Veloxis settlement of more than $46 million, including a $1.55 million penalty it called "the largest Sunshine Act recovery since the law was passed in 2010". That case concerned meals and attendee lists, and it shows that reporting records get read closely.43
Final reports, manuscripts and registry results: the dates and who owes each one
In shortFunded studies owe a chain of deliverables, some to the company under contract and some to the public under law. A sponsor-investigator normally owes the registry results personally. FDA has now sent 11 public notices, 2 of them to individual physicians, and by our count one in six records in our registry group has gone quiet.
Deliverable
Owed to
Set by
Usual date
Progress report
Company
Agreement
Sample: 30 days after quarter end
Interim analysis report
Company
Agreement, protocol
Moves with enrollment
Abstracts and posters
Company for review, then a congress
Publication plan
Congress deadline
Final study report
Company, and any regulator as required
Agreement
Sample: 6 months after last visit
Primary manuscript
A journal, after company review
Agreement
Sample: 6 months after the report
ClinicalTrials.gov results
The public
42 CFR 11.44
1 year after primary completion, for applicable trials30
EU results summary
The public, through CTIS, the EU's Clinical Trial Information System
Regulation 536/2014, Article 37
1 year from the end of the trial in all Member States concerned; shortened to 6 months for subjects aged 0 to 17 or a pediatric plan trial23,45
On the US side, the responsible party is the sponsor, unless and until a principal investigator has been designated.12 When a doctor holds the IND, the doctor normally is that party. Status changes must reach the registry within 30 calendar days, and so must the actual primary completion date, the day the last patient has the final exam or treatment used to collect the main outcome's data.31 The company doesn't own these filings, but a missing result reflects on the product and the program, so ESR teams track them as if they did.
FDA's public notices are rare, but 2026 has already matched its highest year
ClinicalTrials.gov Notices of Noncompliance by year, 11 in all, 2 of them to individual physicians
32021
12022
12023
12024
22025
32026
Source19 · FDA's page, content current October 30, 2026. It lists no civil money penalty imposed in these cases.
Show the numbers
Period
Value
2021
3
2022
1
2023
1
2024
1
2025
2
2026
3
A Notice gives 30 days to fix the problem. After that FDA may seek penalties of up to $15,107, plus up to $15,107 for each day the violation goes uncorrected, at 2025 levels.41,19 In Germany, a late or missing Article 37 document can bring a fine of up to 25,000 euros, though we found no published case of one.46
The wider record is poor: in a 2020 Lancet study, 1,722 of 4,209 trials due to report, 40.9%, met the one-year deadline, and 63.8% had reported at any time. Industry sponsors had about three times the odds of complying that non-industry, non-government sponsors had.47
Four in ten trials reported on time when the US results rule was first measured
1,722 of 4,209
due trials reported results within the one-year deadline, as of September 2019 (40.9%)
due trials reported results within the one-year deadline, as of September 2019 (40.9%)
41 of 100
For the ESR team the practical move is to compute each date from the current forecast, and to chase it through the investigator. Our count of registry records, method in section 6, found results posted for 36.1% of completed studies in the proxy group and 44.3% of industry-led ones, which is no legal test, since many of these are not applicable clinical trials.33 It does point to where to look first.
A final report needs reading too. Check it against the protocol's objectives, section by section. A report missing the table for a secondary endpoint, a lesser outcome the study measures, is an unfinished deliverable, and the contract's milestone usually says "accepted", which gives the company grounds to wait for the missing section.
11 · Amendments and early closes
Re-baselining after an amendment, and closing a study that cannot recover
In shortA protocol amendment is a scientific document with financial consequences: dates, budget, product and contract may all move. Someone has to work those out and get them approved. And some studies should stop. A clean close needs the enrollment history, recovery attempts, final payment, product reconciliation and registry updates in one place, with two signatures.
One amendment worked through: twelve more months of follow-up in a rare kidney disease
GLOM-DURA is a sample study of Glomira in 24 adults with C3 glomerulopathy, a rare kidney disease. Amendment 3 extends follow-up from 12 to 24 months after the core period, with two more visits, to study how long the response lasts. Working out the new dates, budget and product, and getting them approved, is called a re-baseline.
Item
Baseline
Proposed
Working
Last patient last visit
Jun 30, 2027
Jun 30, 2028
+12 months
Final study report
Dec 31, 2027
Dec 29, 2028
+12 months
Primary manuscript
Jun 30, 2028
Jun 30, 2028
Month-12 results, unchanged
Budget
$590,000
$674,000
2 visits × 24 patients × $1,250 = $60,000, plus $24,000 for data management; +14.2%
Product
864 bottles
1,152 bottles
1 bottle a month × 24 patients × 12 months = 288
Because the budget moves more than the sample company's 10% rule, the contract needs an amendment as well. Amendments are common everywhere: a Tufts study of phase I to IV protocols found 76% had at least one, up from 57%, with an average of 260 days from identifying the need to the last oversight approval, and 215 days during which sites ran under different versions. The authors deemed 77% of amendments unavoidable.48 Those figures come from company-run protocols; no one publishes the same for funded studies.
An early close on a pediatric study that reached 3 of 20 patients
GLOM-KIDS, a sample study in children with C3 glomerulopathy, had enrolled 3 of 20 in 22 months. Two recovery attempts failed: a second site withdrew, and an amendment widening the age range never went in. On October 14, 2026 the investigator agreed to stop enrolling and let the three children finish their 52 weeks. The case has to balance on every line.
Every one of 60 shipped bottles needs a destination before the study can close
GLOM-KIDS product reconciliation
DispensedKept for the 3 children to finishTo destroy at the site, with a certificate
$512,000 − $186,400 − $18,200; milestones 4 to 7 canceled
An early close carries its own obligations. Status updates reach the registry within 30 days.31 Discontinued trials are more likely to go unpublished, 55.1% against 33.6% in Kasenda's cohort, and only 37.9% of the discontinuations in that cohort were reported to the ethics committees.3 A good close plan names who will write up what was learned. Unused supply is returned or disposed of, with written records of the disposition.36,22
12 · What goes wrong
Eight ways a funded study goes wrong after signature, and what each one costs
In shortThe failures are mostly ordinary: a late warning, a payment before the work, a lot that runs out, a classification done from memory in January. No public source counts them, so your baseline has to come from your own files. A sample of 30 closed studies will show you which ones you have.
A grant nobody follows up does the widest damage, and late warning costs the most time and science
Our judgment of how each failure hits money, timeline, legal exposure and science
LittleSomeSerious
MoneyTimelineLegal exposureScientific valueDrift found after a milestone is missedSomeSeriousLittleSeriousMilestone paid before it is earnedSeriousLittleSeriousLittleDuplicate invoice paidSeriousLittleSomeLittleGrant with no follow-up on the researchSeriousSomeSeriousSeriousLot expires before the last visitSomeSeriousSomeSomeShipment above the approved totalSomeLittleSomeLittleTransfer classified at year end from extractsLittleSomeSeriousLittleRegistry results late or missingLittleSomeSeriousSerious
Why these happen: five causes behind almost every entry on that grid
Cause
How it does the damage
Retyping
A number copied by hand from a PDF carries no pointer back to its page. A mistake surfaces only if someone rereads the source, and the trace back to the original is hard to show an auditor from a spreadsheet.
Long gaps between looks
A report arrives quarterly and an overworked team reads it weeks later, so a study has already lost a quarter by the time anyone reacts.
Shared mailboxes
Requests and dispatch notices live in inboxes that have no owner, and no one is warned about a reply that never comes.
Separated systems
The contract, the invoice and the enrollment count are held by different teams, so nobody compares them at the moment of payment.
One form for all
One business unit cares about temperature loggers and lot release, and another about registry entries. A single form makes teams work around it in side spreadsheets.
FDA inspects only about ten sponsor-investigators a year, so internal checks carry the weight
Sponsor-investigator inspections with a final classification, fiscal years 2020 to 2024
14FY2020
5FY2021
10FY2022
13FY2023
10FY2024
Source37 · Fiscal 2024 also shows 609 clinical investigator and 99 sponsor or CRO inspections. Remote record reviews are counted apart. FDA's deck was the newest listed on June 4, 2026.
Show the numbers
Period
Value
FY2020
14
FY2021
5
FY2022
10
FY2023
13
FY2024
10
FDA's inspection summary for sponsor-investigators lists common observations that include failing to maintain the Form FDA 1572, on which an investigator commits to follow FDA's rules, inadequate case histories, not following the plan and missing accountability records.37 Most of those fall on the investigator. Yet a company that funds a study and ships its product has a real interest in whether the file holds up, and a clean paper trail on its own side is what it controls.
Find out which of these you have. Pull 30 studies that closed in the last three years. For each, record how long the first missed milestone lagged the first late report, whether any invoice was paid before its evidence, whether a lot came close to expiry, and when each transfer of value was classified. No published benchmark exists, so this file is your baseline.
13 · Software and AI
What software can read, what people must decide, and what regulators say about AI in this work
In shortSoftware does well at reading documents, matching lines and doing date arithmetic. It should draft recovery plans and leave every decision on money, product, baselines and closes to a named person. No regulator has written AI rules for this work, and the general texts are drafts, delayed, or scoped elsewhere. Part 11 and data integrity rules still apply to the records.
The more rule-bound the task and the cheaper the error, the more software can carry
Cost of a wrong answer →
People decide
Second signer
Person edits
Person confirms
Early closePayment releaseRecovery planLot checkRecovery messageReading figuresCopying lots
How rule-bound the task is →
Our reading of the sources6,28,49 · Top left, software assembles the evidence. Top right, software checks. Bottom left, software drafts. Bottom right, software reads and fills. Transparency category and report chasing sit near the payment and copying points.
Show the numbers
Item
How rule-bound the task is (0–1)
Cost of a wrong answer (0–1)
Early close
0.12
0.64
Payment release
0.78
0.76
Recovery plan
0.20
0.52
Lot check
0.80
0.58
Recovery message
0.12
0.28
Reading figures
0.78
0.32
Copying lots
0.62
0.12
Text
What it says
Where that leaves ESR work
FDA draft guidance on AI, January 2025
Covers AI that produces information to support regulatory decisions on drugs and biologics, and leaves out operational efficiencies that do not affect patients, drug quality or study reliability50
Reading invoices and packing lists is operational. Any result used in a submission would need another look. Still a draft
Draft EU GMP Annex 22
Static models in critical GMP uses; generative AI and large language models "should not be used" in critical GMP applications. Consultation July 7 to October 7, 202551
A manufacturing text and still a draft. EMA's report of a June 30, 2026 workshop records comments for widening it, with no revised text52
EU AI Act, after the AI Omnibus
Annex III high-risk rules from December 2, 2027; Annex I product rules from August 2, 202820
Back-office document reading is unlikely to fall in either list. Ask your counsel to confirm
ICH E6(R3)
Computerized systems should be fit for purpose, proportionate to their importance6
Binds the sponsor's trial systems, and a sensible yardstick for a supporter's
21 CFR Part 11
Secure, time-stamped audit trails, and signatures that show name, date and time, and meaning49,53
Applies to electronic records kept under FDA rules. Software can supply controls that support your compliance; your own validation and procedures complete it
The limits to hold on to when you evaluate document-reading software or a forecast
Reading software can misread a scanned table, so each value needs a link to its page and a person who confirms it. A forecast built on few patients has wide error, so it should show a range, and nobody should present it as a prediction of what the site will do after a change.
Classification follows rules that CMS and your counsel set, and an exception should go to the transparency analyst. Separately, we found no independent test of any ESR software's reading accuracy. Ask a vendor to measure it on your documents.
And keep the line from section 2 in view. Automation helps a supporter see what it paid for. It should not start managing a study the investigator sponsors, so what the software sends a site should stay within what the agreement allows, and should go out only when a person sends it.
14 · How teams do it today
How ESR teams run funded studies today: the roles, the hand-offs and the minutes each quarter
In shortAn ESR manager carries the portfolio and hands off to finance, supply, medical and transparency colleagues, mostly by email, around a grants database and a spreadsheet. Most time goes to reading and retyping. We found no public time study, so the numbers below are an estimate for you to replace with your own.
ESR manager to QA auditor: who touches a funded study
EM
ESR manager
Runs a set of studies by country or therapeutic area: reads reports, chases sites, reviews invoices and shipments, proposes changes.
Cares about: knowing which study needs a call this week.
GL
Global ESR lead
Owns the portfolio and its budget, approves re-baselines and co-signs early closes.
Cares about: which studies will miss their final report, and why.
MD
Medical director
The scientific owner. Decides whether a change still answers the question the company agreed to support.
FA
Finance payment approver
Approves research payments as the second person and releases payment files to accounts payable.
CS
Clinical supply coordinator
Approves shipments and works with the depot, the order desk and the relabeling vendor.
TA
Transparency analyst
Checks each payment and shipment category before the reporting files go out.
PI
Investigator and study coordinator
Outside the company. Write the reports, send invoices, request product and acknowledge receipt.
QA
Quality assurance auditor
Audits the system and prepares inspections: who signed, what it meant and what they saw.
By hand, a quarter's report and invoice take five steps, and the last comes months later
A common by-hand flow, drawn from how the work is described; there is no public time data
1Report due
Reminders go out by email near quarter end.
ESR managerDay 0 to 30
2Report read
Figures are retyped into a tracker, and the plan compared by eye.
ESR managerDays later
3Medical told
A late study gets raised in a meeting or an email.
Medical directorWhen noticed
4Invoice checked
The PDF contract is opened, and the line checked against paid-to-date.
ESR manager, financeOn arrival
5Year-end classification
Finance extracts are classified for reporting.
Transparency analystJanuary to March
Illustrative · replace with your own numbers
Show the numbers
Step
What happens
Who
Time
Report due
Reminders go out by email near quarter end.
ESR manager
Day 0 to 30
Report read
Figures are retyped into a tracker, and the plan compared by eye.
ESR manager
Days later
Medical told
A late study gets raised in a meeting or an email.
Medical director
When noticed
Invoice checked
The PDF contract is opened, and the line checked against paid-to-date.
ESR manager, finance
On arrival
Year-end classification
Finance extracts are classified for reporting.
Transparency analyst
January to March
Where an ESR manager's minutes go on one study in one quarter
Reading and checking take more of a manager's quarter than chasing or classifying
About 165 minutes per study per quarter by hand: our estimate, unmeasured
Reading the progress report and keying the figures40 minutes
Checking the invoice against the schedule and what is paid35 minutes
Comparing enrollment with plan and working out how late30 minutes
Chasing missing reports and receipts25 minutes
Copying ship date, quantity, lot and expiry20 minutes
Classifying the payment and the product15 minutes
Illustrative · replace with your own numbers · At 38 studies that is about 105 hours a quarter. Time a sample of your own.
Show the numbers
Item
Value
Reading the progress report and keying the figures
40 minutes
Checking the invoice against the schedule and what is paid
35 minutes
Comparing enrollment with plan and working out how late
30 minutes
Chasing missing reports and receipts
25 minutes
Copying ship date, quantity, lot and expiry
20 minutes
Classifying the payment and the product
15 minutes
Spreadsheets, grants tools and outsourcing: three ways teams run it
Way
Where the work lives
Fits when
What it leaves open
Spreadsheets and shared mailboxes
One workbook per team
A few dozen studies, one country
No audit trail, no signatures, no forecast
Grants or ESR tracking software
Request records with forms, milestones and reports
Global programs that need one process from proposal to close
Records what staff type. Reading reports, shipping replies and invoices stays by hand
A trial management system, stretched
A tool built for company-run trials
Companies with one such system everywhere
Investigator-sponsor roles, portals and in-kind product fit awkwardly
Outsourced administration
A vendor runs tracking and payments
Small portfolios or a new country
The oversight and the signatures stay with you
We found no public market size for this category and no reliable count of programs. Commercial software for it exists under the names investigator-initiated study management, grants management and research management.
Part B · See it working
Botminds Investigator-Initiated Study Management on one kidney study's third quarter
Part A described the work without naming a product. This part shows how Botminds does it, for a fictional company running 38 studies for one ESR manager. Every company, site, person, product, number and document in the screens is sample data.
15 · One quarter, start to finish
KESTREL-IgAN's quarter: a three-page report read, a study moved to At risk, a later lot, a signed plan and a payment held
In shortThis is the example from the top of the page, inside the product. Dr. Lindqvist's report arrives at 9:12 am. Agents read it, cite every figure, forecast the last patient 30 weeks late and draft a recovery plan. In the same hour the supply tracer flags a lot. Nadia Brooks asks for a later lot and approves the plan, and milestone 3 is held. Finance approves the invoice as the second person.
1
Nadia opens 38 studies drawn as one river
Each study is one row. Hollow marks are its baselined milestones, solid marks are actual or forecast ones, and the colored stretch between them is the drift, printed in weeks at the end of the row.
On the morning of October 28 she has 2 studies At risk and 10 Drifting. KESTREL-IgAN sits at +11 weeks with a chip that says its Q3 report is in. A line across the top lists the work waiting on her: 4 reports, 3 shipments and 6 invoices, plus a new study, an amendment and a close-out.
The portfolio river. Sample studies in nephrology, hepatology and neuromuscular disease. The river scopes to one manager, one business unit or the whole portfolio.
2
The quarterly report reader works through the three pages in 6.4 seconds
Seven steps run in view: received, read the enrollment table, compared with the plan, forecast the last patient, moved the band, drafted the recovery, and handed to Nadia.
Each step says what it found. Three steps turn amber: 7 behind plan (44%), the rate of 1.17 a month giving October 25, 2027, and the rule that moves the study from Drifting to At risk.
The reader at work. 6.4 seconds is what this sample run shows; your documents will set your own figure.
3
Every figure links back to its page
Screened 14, enrolled 9 of 24, treated 9, completed 2. Each tile carries a page tag. Click one and the passage lights up in the report on the left, so Nadia checks it and types nothing.
The left pane is Dr. Lindqvist's own report, unaltered. Three screen failures for eGFR below 45 and the note about a limited referral base are highlighted, because the recovery plan rests on them.
Figures with their pages. Sample report. Tiles and the highlighted table agree.
4
A forecast with a range, a band with its rule, a plan with owners
The chart draws plan, actual and forecast together: last patient in on October 25, 2027, with an 80% range of August 2027 to January 2028, and the interim analysis, final report and manuscript moving with it.
Below it sit the band change with its rule, a message to Dr. Lindqvist and a plan of five actions: a second site by January 15, 2027, referral letters to 6 clinics by November 30, a protocol amendment to the ethics committee by December 15, a monthly call and a hold on milestone 3. The message waits for Nadia, and investigators never see bands or forecasts.
Plan, actual and forecast. The forecast assumes the recent rate continues. The amendment and the second site remain the investigator's decisions.
5
In the same hour, a packing list shows a lot that will not last
The vendor's dispatch email and packing list reach the supply mailbox. The supply tracer fills ship date, quantity, lot, expiry, tracking, logger and labels, each with a link to its line, and nothing is typed.
It then checks the lot against today's forecast. Lot RQ26-1187 expires September 30, 2028, seven weeks before the last visit, now forecast for November 20, 2028, so it raises a flag. It also records the shipment as a research payment, in-kind items.
Filled, flagged and classified. The $194,000 is the sample company's own rule, 40 vials at wholesale acquisition cost. CMS does not require a specific value for study drug.2
6
Nadia asks for a later lot, and the record refills itself
One click sends a drafted message to the vendor, asking for a lot that expires after November 20, 2028. The reply offers lot RQ26-1342, expiry March 31, 2029, same ship date. The tracer reads it, updates both fields, clears the flag and logs the change.
Nadia confirms the shipment record, and the site sees lot and expiry in its portal.
The later lot. The change is recorded in the audit trail with both emails behind it.
7
One signature confirms the figures and approves the plan
Nadia signs once, with the statement in front of her: the Q3 figures are confirmed, the five actions go to their owners and milestone 3, $96,000, is held until the second site opens. The signature records her name, the date and time, and its meaning, which here is Approved.
The study page shows the hold straight away, and the investigator's portal shows the milestone on hold until the second site opens.
The payment schedule after approval. Milestone 3 shows Held. The $584,300 header adds the fees earned so far to the milestones; the sample contract's full $684,800 counts the 15 patients not yet enrolled.
8
Finance approves the invoice as the second person
Confirming the report makes the per-patient invoice payable: 4 × $6,700 = $26,800, tied to the schedule and to page 2. Nadia marks it reviewed.
She cannot approve it herself. Marcus Webb, the finance approver, sees the line, the evidence and the cap, and signs. The payment joins that afternoon's file to accounts payable, and the transfer of value is already classified.
Second person. The screen separates reviewer from approver by role, and records both signatures.
The solution reads and proposes; named people confirm, approve and sign. It does not change a baseline, release a payment, ship product or message an investigator on its own.
16 · The other screens
The rest of an ESR manager's week: chased reports, blocked shipments, unearned invoices, re-baselines and closes
In shortBeyond the one case above, the same pattern repeats: agents read and match, then a person decides. Here are reports confirmed in bulk, a request above its approved total, exceptions in payments, a re-baseline, an early close, final report checks, the investigator's view and the administrator's settings.
Reports confirmed together, and the ones that never came
Clean reports. Eight reports match their plan within 10% at a confidence of at least 0.95. One signature confirms them, and any report can still be opened first.
Reports still missing. Reminders go out on day 0 and day 7, with escalation to the medical director on day 14. One study has missed two quarters.
A mark on the river. Hover any mark for its dates, its range and the source behind them.
Ask the portfolio. Questions in plain words get named studies with their sources: here, which studies will miss their final report date.
Product requests routed by supply type, and stopped when they exceed the total
Totals and path. The tracer picks the path from the supply type and says why. Requested 40 of 1,560 approved, with 320 shipped.
Over the approved total. 720 approved, 640 shipped, 120 requested. The tracer will not route it as asked, and a person chooses among approving 80, raising an increase or rejecting.
Invoices that were not earned, and files that reach accounts payable
The match. Line, schedule, evidence, paid and cap, all on one row, with the page cited.
Not earned. A $54,000 last-patient-in invoice against 22 of 24 enrolled. Nadia can hold it and tell the site.
Duplicate. $31,500 already paid on September 14 under another invoice number.
Payment files. Payments leave by API or SFTP CSV, by country. A rejected row shows the payment system's reason and how it was fixed.
Transfers of value. Monthly figures by category, sent by file to the transparency reporting system, which files the report. Sample values use the company's own rule for product.
A re-baseline with three approvers, and an early close with two
The re-baseline. Amendment 3 compared with the baseline: dates, budget up 14.2%, product up 288 bottles, each cited.
Who approves. The budget move triggers a contract amendment. The proposer can't approve, and this unit also requires the medical director.
Collaboration. Where the company co-authors, obligations such as a 30-day manuscript review are tracked as well.
The close case. 3 of 20 in 22 months, two recovery attempts, and the investigator's agreement cited.
Reconciled and signed. Every bottle accounted for, $307,400 released, registry dates set, and two signers who are not the preparer.
The final report check, the investigator's view and the settings behind it all
Deliverables. 11 of 12 sections found, with section 9.3 missing, and the $72,000 milestone waits. Registry dates are worked out from the rules.
The portal. What Dr. Lindqvist sees: her own study, tasks and payments. She never sees bands, forecasts, confidence or internal notes.
One process, many units. Each sample business unit sets its own required fields and steps. Every change becomes a new version that a second administrator approves.
Rules, as settings. Your thresholds, including the rule used to value product for transparency.
Roles and duties. Roles, and the rule that a person cannot approve what they prepared.
Integrations. Systems of record by API, file or email, each with its last run and any error.
Agents under control. Each agent is versioned, with a threshold and its last test on gold records. Overrides need a reason code.
The audit trail. Who, what, when, the signature's meaning and the evidence, ready to export as an inspection pack. Records cannot be edited or deleted.
At go-live, the portfolio import mapper maps an existing portfolio file's columns to fields, checks each row against its business unit's rules and prepares a dry run. In the sample, 598 studies came in on February 3, 2025.
17 · Who reads, who signs
Seven ESR agents, the five people who sign and what the solution reads and writes
In shortSeven agents do the clerical half of active study management, and each has something it must never do. Five roles confirm, approve and sign, and the person who prepares never approves. Documents come in from the portal, email and your systems, and cited records and files go out.
Report reader to import mapper: each agent's job and its limit
Quarterly report reader
Reads each progress report, extracts screened, enrolled, treated and completed with the page cited, forecasts last patient in with a range, sets the band and drafts the recovery.
Never changes a baseline or sends a message.
Supply tracer
Checks each request against approved and shipped totals, routes it to one of three paths, fills ship date, quantity, lot and expiry from the reply, flags a lot that will not last and chases the receipt.
Never approves a shipment or ships more than approved.
Invoice matcher
Ties each line to the schedule and its evidence, checks what is paid, the cap and duplicates, and classifies the transfer of value for Open Payments and EFPIA.
Never approves or releases a payment.
Amendment reader
Compares a protocol or contract amendment with the baseline, proposes the re-baseline and flags when the contract must change.
Never applies a re-baseline.
Close-out assembler
Builds the early close or termination case: enrollment, recovery attempts, spend, product, final payment, registry update and notices.
Never closes a study.
Deliverables tracker
Tracks reports, abstracts, posters, manuscripts and registry results against due dates, and reads a final report against the protocol.
Never accepts a deliverable.
Portfolio import mapper
Maps a legacy file's columns at go-live, validates each row and prepares a dry run.
Never imports without approval.
Who signs what: the second-person rule across five roles
Confirms and proposesESR managerConfirms figures and shipment records, reviews invoices, approves recovery plans and proposes re-baselines.
Second person on productClinical supply coordinatorApproves shipments. The person who reviewed a request never approves it.
Second person on moneyFinance approverApproves payments and releases payment files. The reviewer never approves.
Second person on the planGlobal ESR leadApproves re-baselines and co-signs early closes and terminations.
Scientific ownerMedical directorSigns scientific changes and early closes, and is told when a study moves to At risk.
The transparency analyst alone can change a classification, with a reason kept in the audit trail, and a second administrator approves each configuration version. A confidence below 0.95 sends a figure to a person. Signatures carry the printed name, the date and time, and the meaning, and the trail exports as an inspection pack. These are controls that support your compliance with 21 CFR Part 11; your validation and procedures complete it.49
From reports, replies and invoices to cited records: what goes in and what comes out
From the site, through the portal
Quarterly progress reports
Invoices
Product requests and receipt acknowledgments
Protocol amendments and final study reports
From your company and vendors
The approved study and baseline, at contract signature
Research agreements and payment schedules
Dispatch emails and packing lists
Agents read, match and draftEach document, against the baseline and the agreement
A named person decides
Every figure cites its source
Outputs
The portfolio river: baseline against forecast, drift in weeks, three bands
Cited quarterly figures and a forecast with a range
Recovery plans, re-baselines and close cases for signature
Shipment records with lot, expiry and receipt
Matched, approved payments to accounts payable by API or SFTP CSV
Transfer-of-value classifications for Open Payments and EFPIA
Systems an ESR program already runs, connected by API or flat file
Study review toolThe approved study, at signature
Contract managementAgreements, amendments
ERP accounts payablePayments out, status back
Clinical supplyOrders, dispatch, lots
Commercial order deskBulk orders, dispatch
Relabeling vendorsOrders, packing lists
Transparency reportingMonthly files
Trial registriesClinicalTrials.gov, EU CTIS
Publication planningAbstracts, manuscripts
Document managementGxP archive
The outcomes this was designed for
Design target
What it means
2 quarters earlier
Warning that a study will miss its milestones comes at the first late report, ahead of the missed milestone
0 shipment fields typed
Ship date, quantity, lot and expiry are read from the fulfillment reply, each cited
100% classified on approval
Payments and product shipments carry their Open Payments and EFPIA class when approved, ahead of the year-end file
These are design targets, to be measured in your own pilot. The sample screens show 640 active studies at the portfolio level. This solution classifies each transfer of value and hands it to your transparency reporting system; the transparency team files the report. Proposal intake and scientific review belong to a separate review solution.
Part C · Are you ready to automate?
Automating funded study management: what late warning costs, what it returns and how to test it
You run an ESR program, or manage the people who do, or sign its payments. This part is written for you: what errors and delays cost you today, what automating the clerical half could return, whether your team is ready, and what to ask any vendor of this software, including us.
18 · What late warning costs
What a late warning, an unearned payment or a lost study costs your ESR program
In shortPublished figures frame the question: how often recruitment fails, how much these trials cost, how often results run late. What matters to your decision is your own count of late warnings, wrong payments and hours spent retyping, and no one publishes those. A week with your closed studies will give you your first numbers.
26.5%
of investigator-sponsored randomized trials in one cohort were discontinued for poor recruitment, against 8.4% of industry-sponsored ones.3
Kasenda et al., JAMA 2014
$645,824
was the median total cost of 93 investigator-sponsored randomized trials in three European countries. Money you may lose if yours stops early.40
Griessbach et al., 2024
40.9%
of trials due to report under the US rule met its one-year results deadline, as of September 2019.47
DeVito et al., Lancet 2020
Reading, checking and copying are where an ESR manager's quarter can shrink
Minutes for one study in one quarter, 165 by hand and 23 with the solution
By hand (our estimate)With the solution (our estimate)
Reading the report and keying figures40 min5 min
Checking the invoice against the schedule35 min5 min
Comparing with plan, working out how late30 min5 min
Chasing reports and receipts25 min3 min
Copying ship date, quantity, lot and expiry20 min3 min
Classifying payment and product15 min2 min
Illustrative · replace with your own numbers · Neither column is a measurement. Time a sample of your own, then measure the second column in a pilot.
Show the numbers
Step
By hand (our estimate)
With the solution (our estimate)
Reading the report and keying figures
40 min
5 min
Checking the invoice against the schedule
35 min
5 min
Comparing with plan, working out how late
30 min
5 min
Chasing reports and receipts
25 min
3 min
Copying ship date, quantity, lot and expiry
20 min
3 min
Classifying payment and product
15 min
2 min
Reading 30 closed studies to find your own ESR baseline
Cost
Where it hides
How to find your number in a week
Late warning
Between the first late report and the first missed milestone
For 30 closed studies, count the quarters between the two
Lost studies
Money paid on studies that closed without an answer
Sum what you paid on every study closed early in three years
Hours on reading and retyping
Quarter ends, spread among local managers
Time five reports, five invoices and five shipments from arrival to recorded
Payments before they were earned
Milestones paid with the evidence filed later, or not at all
Sample 50 paid milestones and match each to a dated document
Duplicates and overruns
Same milestone under a new invoice number
Run paid invoices by study and amount across three years
Product trouble
Lots replaced at a site, destroyed stock
Count lots that expired at sites, and vials destroyed unused
Year-end classification
January to March, in the transparency team
Hours spent on research records, and corrections made after submission
Results owed
Registry entries with unknown status
Search your funded studies on ClinicalTrials.gov and count overdue or stale entries
The investigator lost, the question left unanswered, and other costs a return calculation misses
The question that never gets answeredA closed study may leave a gap the company wanted filled and can't refill quickly.
The patients already enrolledPeople who joined a study that could not reach its answer, a cost no invoice shows.32
The investigator's goodwillA doctor who waited months for a payment or an answer may not propose a second study.
Your medical director's attentionTime spent on status meetings comes out of the science.
An inspection or audit requestThe afternoon spent rebuilding a study's history from a mailbox.
19 · Your return
What automating funded study management returns when you count ESR hours and wrong payments against the tool's cost
In shortPut in your own numbers. Every default marked illustrative is an assumption to replace. The calculator values manager time and payments not made in error, and shows recovered studies on a separate line, because that value is real and much harder to prove.
Hours, payments, warning and classification: where ESR automation can save
Manager time
Reports read before anyone opens them
Figures arrive cited, so the manager confirms them and goes to the studies in trouble.
studies × 4 × minutes saved ÷ 60 × hourly cost
Wrong payments
Unearned and duplicate invoices caught
Every line meets the schedule, the evidence and the paid-to-date check before review.
invoices × error share × average invoice
Earlier warning
Studies recovered in time
A warning at the first late report leaves room for a site, a referral plan or a protocol discussion.
studies recovered × their cost × share saved
Product
Lots that outlast the study
Each lot is checked against today's forecast, ahead of the shipment.
lots replaced at sites × replacement cost
Transparency
Classified on approval
Your analyst checks exceptions through the year, and the January hunt shrinks.
records × minutes saved at year end × hourly cost
Inspection
History ready to export
Who signed, what it meant and what they saw, for any study, in one pack.
requests a year × hours to rebuild × hourly cost
The ESR return calculator: studies, invoices and your hourly cost
The 165 minutes a quarter is our estimate. The study cost is the median from Griessbach and colleagues.40 Every input marked illustrative is an assumption.
Your portfolioPaymentsYour cost, and recovered studies
Illustrative yearly value
Report and invoice time today, valued$0
Time released, valued$0
Payments not made in error$0
After your yearly cost$0
ESR hours released a year0
Separate, not in the total: studies recovered$0
Formulas, per year: Time today = studies × 4 quarters × minutes today ÷ 60 × hourly cost Time released = studies × 4 × (minutes today − minutes with automation) ÷ 60 × hourly cost Payments not made in error = invoices × error share × average invoice After your cost = time released + payments not made in error − yearly cost Studies recovered = studies recovered × cost of a study × share saved
Not counted: product replaced at sites, year-end transparency hours or inspection preparation. A wrongly paid invoice may be recoverable, so count only what you would have lost. Released hours are value only when you decide what they are for: more studies per manager, faster answers to investigators or more time for the science.
20 · Readiness check
Eight questions that show whether your ESR program is ready to automate its post-award work
In shortScore each question from 0 to 2. The total places you in one of three bands, each with a next step. Nothing you choose leaves this page.
1
Studies under management
How many active funded studies do you run, and across how many countries?
Why it mattersVolume turns minutes per report into capacity. A few studies rarely pay for new software.
A strong answer"About 300, in 25 countries, with 60 new contracts a year."
2
A baseline for every study
Does each active study have agreed dates, a budget and a product quantity on record?
Why it mattersA forecast needs something to drift from. If the baseline lives in a PDF, importing it is the first project.
A strong answer"Every study has seven dates in one file, confirmed by its manager."
3
Reports you can get at
Do progress reports come through one place, in a form you can collect?
Why it mattersA reader can only read what it receives. Reports scattered across personal inboxes come first.
A strong answer"All through our portal, as PDFs, with reminders."
4
Payment schedules in usable form
Can each invoice line be traced to a schedule you hold in a usable form?
Why it mattersPay-only-what-is-earned needs the schedule, the evidence and the paid-to-date in reach at once.
A strong answer"Schedules are in contract management, and AP gives us paid-to-date by API."
5
A named owner and budget
Who owns ESR post-award operations, and is there a budget for changing them?
Why it mattersWithout one owner, each country keeps its own spreadsheet.
A strong answer"Our global ESR lead owns the process and the budget."
6
Separation of duties agreed
Have finance, supply and medical agreed who reviews and who approves?
Why it mattersSoftware enforces the rule you agree on, and a second person must be available or everything waits.
A strong answer"Reviewer and approver are named by role in the SOP, with backups."
7
Your own baseline
Do you know your late-warning lag, your wrong-payment share and your hours per report?
Why it mattersYou can only claim a return against numbers you measured before you started.
A strong answer"We read 30 closed studies: warnings lag by 2.5 quarters, and 1 in 80 invoices had an error."
8
Quality and IT ready
Have quality and IT looked at validation, Part 11 records, data location and integrations?
Why it mattersA pilot stalls when validation and access questions arrive late.
A strong answer"Quality has a risk-based plan, and data residency is agreed for EU studies."
9
The whole portfolio, on one screen · for reflection
If every funded study showed its true forecast the morning after its report arrived, what decisions would you make differently, and who would you need in the room to make them?
Why it mattersYour answer shows what the warning is worth to you, and who has to act on it.
A strong answerA short, specific list, for example: "we would move two sites in January and stop paying for three studies with no route to an answer."
From one clean baseline file to a rollout by business unit: what each score tells you to do
0–6
Explore
Put every study's seven dates, budget and product quantity in one file, name an owner and read 30 closed studies. That file is useful whether or not you buy anything.
7–11
Ready to pilot
Replay one closed quarter for one unit, with reports, replies and invoices you already checked by hand. Then run one live quarter end in parallel, with people deciding everything.
12–16
Ready to implement
Plan the portfolio import, the integrations and the per-unit fields, then roll out by business unit, starting where reports already come through one place.
21 · Questions for any vendor
What to ask an ESR software vendor about reading, forecasts, supply, money and who decides
In shortAsk every vendor the same questions, us included. Many tools in this category record what staff type. The answers show what the tool reads, how you check it, how it handles the sponsor line, and how you would measure it on your own files.
A
Reading reports, emails and invoices, with citations
A1
Does it read our reports, emails and invoices, or do staff type the values?
Why it mattersThis decides whether the hours go away.
Strong answerA demonstration on your own PDFs and emails, with each value linked to its page.
A2
How accurate is it, measured how?
Why it mattersClaims without a method mean little, and no independent test exists.
Strong answerField-level accuracy on a held-back sample of your documents, by document type.
A3
What happens to a value it is unsure of?
Why it mattersA confident wrong number is the main risk.
Strong answerA threshold you set; anything below it goes to a named person.
B
Enrollment forecasts and drift bands
B1
How is a forecast calculated, and can we see it?
Why it mattersA forecast nobody can explain gets ignored.
Strong answerThe rate, the window and the range on screen, with the rule for each band in your settings.
B2
Can a person override a band?
Why it mattersThe manager knows things the report does not say.
Strong answerYes, with a reason code, kept in the audit trail.
C
Lots, milestones and in-kind product
C1
Does it check a lot against the current forecast?
Why it mattersA fixed check misses a lot that stops lasting when the study slips.
Strong answerA rule rerun whenever the forecast moves.
C2
Can it pay on evidence, and hold a milestone?
Why it mattersPaying on evidence is the control a fraud review looks for.
Strong answerLine, schedule, evidence, paid-to-date and cap on one screen, with reviewer and approver separated.
C3
How does it treat in-kind product for Open Payments and EFPIA?
Why it mattersCMS FAQ 9118 means a company's own rule may apply.2
Strong answerYour valuation rule as a setting, classification at approval, and a file your reporting system accepts.
D
Messages to investigators, Part 11 and your data
D1
What can the tool send to an investigator on its own?
Why it mattersThe company is a supporter, and automated messages can overstep.
Strong answerNothing without a person's click; the site sees only its own study.
D2
How does it support Part 11?
Why it mattersNo product can be certified for Part 11, so be wary of any vendor that says otherwise.
Strong answerAudit trails and signature manifestations shown on screen, with documents for your own validation.49
D3
Where does our data go, and is it used to train anything?
Why it mattersReports and invoices are confidential and may hold personal data.
Strong answerRegional storage, access by role, no training on your data, in writing.
22 · A first pilot
A twelve-week ESR pilot: one business unit, one closed quarter replayed, one live quarter end in parallel
In shortStart with documents you have already checked by hand, so you know the right answers. Then run one quarter end live, with people deciding everything. Decide with five numbers: field accuracy, citation validity, warning lead, exceptions caught and minutes per study.
Build the baseline file for one business unit: dates, budget and product for each study, with a named owner.
Gather one closed quarter: every report, reply and invoice, plus what you decided. Plant a few errors in copies: a duplicate invoice, an early milestone, a short-dated lot.
Replay it and score every field against your own record, by document type.
Run one live quarter end in parallel, with nothing automatic: your team still checks by hand and decides everything.
Decide with your numbers, and set the thresholds you are willing to live with for bulk confirmation.
Twelve weeks is enough to replay one quarter and run one quarter end live
Your teamWith the vendor
Baseline file and owners
Configure fields, rules, roles
Replay a closed quarter
Time reports by hand
Live quarter end in parallel
Score and decide
Week 036912
Illustrative · replace with your own numbers
Show the numbers
Activity
From
To
Baseline file and owners
0
2
Configure fields, rules, roles
1
4
Replay a closed quarter
3
6
Time reports by hand
2
6
Live quarter end in parallel
6
11
Score and decide
10
12
Reading accuracy, warning lead and exceptions: the ESR numbers to score
Measure
How
Why
Field accuracy
Each value against your checked record, by document type
Sets the confidence threshold you can trust
Citation validity
Each cite opens the right page and passage
A person can only confirm what they can check
Warning lead
Quarters between a flagged study and its later missed milestone, on replayed data
Shows how much earlier the warning comes
Exceptions caught
Planted duplicates, early milestones and short lots found
Proves the controls work
Minutes per study
Timed by hand, and in parallel
The business case rests on them
The full working-session questions: 9 questions in three groups
Bring ESR, medical, finance, supply, transparency, quality and IT into one room.
E
Your research agreements and payment structures
E1
Which payment structures do your agreements use?
Why it mattersMilestones, per-patient fees and pass-through costs each need a rule.
Strong answerA short list, with a sample agreement for each.
E2
Which fields does each business unit need?
Why it mattersPer-unit differences are why spreadsheets survive.
Strong answerA table of required, optional and hidden fields by unit.
E3
What does the agreement say about messages, holds and reviews?
Why it mattersA hold or a reminder must fall within what you signed.
Strong answerCounsel has confirmed wording for holds and manuscript review.
F
Where contracts, payments and lot data live
F1
Which systems hold contracts, payments, supply and publications?
Why it mattersIntegrations decide the first months of work.
Strong answerNamed systems, with an API or a file for each.
F2
Do vendors reply by email or by file?
Why it mattersReading depends on the channel.
Strong answerA shared supply mailbox the tool can read.
F3
Where does paid-to-date come from?
Why it mattersDuplicates and caps need it.
Strong answerAn extract or API from accounts payable, refreshed daily.
G
Your rules for valuing product, EU studies and stopping
G1
What rule do you use to value in-kind product?
Why it mattersCMS leaves room, so you need a written choice.2
Strong answerA written rule that counsel has approved.
G2
When does an EU study need different handling?
Why it mattersAggregate disclosure and national rules differ.27
Strong answerA map of countries and their reporting.
G3
Who decides a study should stop?
Why it mattersAn early close needs two signers and a clear path.
Strong answerNamed roles, and criteria the medical team agrees.
23 · Frequently asked questions
What people ask about investigator-initiated studies and how they are run
In shortEach answer stands on its own. For the detail behind it, follow the section it came from.
What is investigator-initiated study management?
It is the work a company's medical affairs team does after approving a doctor's study and signing the contract: tracking milestones against the baseline, reading quarterly progress reports, supplying product, paying invoices against the schedule, classifying each transfer of value and closing the study. It runs for years, usually from spreadsheets, a grants database and email. Teams also call it externally sponsored research, or ESR.
What is the difference between an investigator-initiated study and a company-sponsored trial?
In a company-sponsored trial the company designs the study and answers for it as sponsor. In an investigator-initiated study a doctor or institution proposes it and normally acts as sponsor, while the company supports it with money, product or both. The research agreement states who holds which duty.
What does an ESR manager do?
An ESR manager runs a set of funded studies after contract signature. The job covers reading progress reports, comparing enrollment with plan, checking invoices, reviewing product requests, chasing deliverables and raising problems with the investigator and medical director. A large company may give one manager dozens of studies across a region.
Who is the sponsor of an investigator-initiated study?
Usually the investigator or the institution. US rules define a sponsor-investigator as an individual who both initiates and conducts the study and who carries both sets of duties, and the EU regulation allows an individual, company, institution or organization to be sponsor. A company that only funds and supplies the study often describes itself as a supporter.
Does an investigator-initiated study need an IND?
It depends on the study. A US study of a lawfully marketed drug may be exempt if it will not support a new indication or major labeling change, does not significantly raise the risks through dose, route or patient group, and follows the ethics and consent rules. Otherwise the investigator files an IND, often with a letter from the company letting FDA refer to its existing file.
Are payments for investigator-initiated studies reported to Open Payments?
Yes, when they fall under the research payment rules, and in-kind support counts as a form of payment. Research records carry the receiving institution, the total amount, the study name, the related product and the principal investigators, and are due by the 90th day of the following year. A payment to a non-teaching institution is still reportable when a covered physician is a principal investigator.
How do you value study drug for Open Payments?
CMS FAQ 9118 says manufacturers are not required to assign a specific value to clinical study drugs given to principal investigators, and should report the total research payment including all research-related costs. A company may still set an internal rule, such as wholesale acquisition cost or standard cost. Have counsel agree the rule and apply it the same way every time.
What does fair market value mean for investigator-initiated research?
It means paying for research at what the work is worth, for services that are legitimate, reasonable and necessary. OIG's 2003 guidance also tells makers to keep research grants apart from sales and marketing, and it is now in OIG's archive. A file should show a documented proposal, a fair market value assessment and follow-up on the work.
How do you forecast last patient in for a study?
Divide the patients still needed by the recent enrollment rate and add the result to the date of the latest data. A study with 15 patients to go at 1.17 a month is about 12.9 months out. Show it as a range, and rerun it each quarter, because a second site or a change in entry criteria changes the rate.
Who posts results on ClinicalTrials.gov for an investigator-initiated study?
The responsible party, which is the sponsor unless a principal investigator has been designated. When a doctor holds the IND, that is normally the doctor, and results for an applicable clinical trial are due one year after primary completion. FDA's list of public notices includes individual physicians.
Can AI read investigators' progress reports?
Yes, as a reading and drafting step with people deciding. The useful test is field accuracy on your own documents, with each value linked to its page and low-confidence values sent to a person. No regulator has written AI rules for this work, and the general texts are drafts or are scoped elsewhere.
Does automating this work make us compliant with 21 CFR Part 11?
No product can make you compliant or be certified. Software can supply controls that support your compliance, such as secure audit trails and signatures that show the name, date, time and meaning. Your own validation, procedures and training complete it.
Does the Botminds solution cover every duty in a research agreement?
It covers dates, enrollment, product, payments, classification, amendments, deliverables and close-out. Each research agreement and quality system also lists other duties for each party, and those documents remain the authority on them. Your team should follow them as written, outside this solution.
How long does it take to go live?
Botminds builds the solution from your requirements and documents: research agreements and payment schedules, each business unit's fields and steps, and a sample of past reports, shipping replies and invoices. It goes live once every quality check has passed. Your existing portfolio comes in from a flat file, and a person approves the import.
24 · One-page summary
Funded study management on one page: the method, the November 2026 rules and the terms
Print this page
In shortThe whole guide on one screen: the method, the rules as of November 2026, the readiness bands and the terms.
The method
Confirm the baseline at signature: dates, budget, product.
Read each quarterly report, with every figure tied to its page.
Compare with plan, forecast with a range, and set the band by a written rule.
Agree a recovery plan with the investigator while there is time, and hold money only as the agreement allows.
Check each request against the approved total, and each lot against today's forecast.
Pay each line against its schedule, evidence and cap, with a second person approving.
Classify each transfer of value on approval; track deliverables and results; reconcile at close.
Readiness: score 0–2 on eight questions: 0–6 explore · 7–11 pilot · 12–16 implement.
As of November 2026: ICH E6(R3) in effect in the EU since July 23, 2025; FDA final September 2025; Annex 2 in the EU from January 15, 2027 · FDA sponsor-investigator guidance still a May 2015 draft · Open Payments 2026 thresholds $13.82 and $138.13, reports due March 31, 2027; no specific value required for study drug (FAQ 9118).
ClinicalTrials.gov results one year after primary completion; 11 FDA notices · EU results one year from end of trial · OIG's 2003 guidance in its archive · FDA's AI guidance a draft · draft Annex 22 not adopted, and a manufacturing text · EU AI Act high-risk dates moved to December 2027 and August 2028.
The party that takes responsibility for starting and running a study.
Sponsor-investigator
One individual who both starts and conducts a study.
Supporter
A company that funds or supplies a study without sponsoring it.
Baseline
The agreed dates, budget and product, changed only with approval.
Drift
The gap in weeks between a baseline date and today's date.
Milestone payment
Money owed when a named event happens.
Re-baseline
An approved change to the baseline, usually after an amendment.
In kind
Support given as goods or services, usually the study product.
Research payment
Open Payments' category for money tied to research under an agreement or protocol.
Transfer of value
Anything of value given to a covered recipient or institution.
Responsible party
The one who owes ClinicalTrials.gov its registration and results.
Fair market value
What legitimate, necessary research services are worth.
Lot
A batch of product with one expiry date.
25 · Sources
Sources
Accessed November 2026. Regulatory status statements are as of November 2026. Our own data queries are labeled as ours.
21 CFR 312.3, definitions of sponsor and sponsor-investigator, CFR 2025 edition. govinfo.gov
CMS, Open Payments Frequently Asked Questions, current as of July 1, 2024: FAQ 9118 (value of clinical study drugs), FAQ 2001 (research payment to a non-teaching institution), up to five principal investigators. cms.gov
Kasenda B. et al., Prevalence, characteristics, and publication of discontinued randomized trials, JAMA, 2014;311(10):1045-51, PubMed abstract. pubmed.ncbi.nlm.nih.gov
CMS, Open Payments data overview, modified July 9, 2026: Program Year 2025, 17.07 million records, $14.67 billion, of which research $9.50 billion, general $3.92 billion, ownership $1.25 billion. cms.gov
CMS, Research Payment Data, Program Years 2019 to 2025, datasets modified June 30, 2026; our count, total amount summed by form of payment, November 3, 2026. openpaymentsdata.cms.gov
ICH, E6(R3) Guideline for Good Clinical Practice, Step 4, January 6, 2025: principles, sections 2.10, 3.5, 3.6, 3.9 and the glossary entry for sponsor-investigator. database.ich.org
Regulation (EU) No 536/2014, Article 2(14), definition of sponsor, as published on legislation.gov.uk. legislation.gov.uk
Medtronic, External Research Program page, a published example of a company describing itself as supporter and the investigator as sponsor, read November 3, 2026. medtronic.com
Paleoudis E.G., Pinto C., Investigator-Initiated vs. Investigator-Sponsored Research: Definitions Matter, J Clin Med Res, 2024;16(1):31-32. jocmr.org
21 CFR 312.62, investigator recordkeeping and record retention, CFR 2025 edition. govinfo.gov
42 CFR 403.904, reports of payments or other transfers of value, including paragraphs (d), (f) and the exclusions, CFR 2025 edition. govinfo.gov
21 CFR 312.2(b), studies of a lawfully marketed drug exempt from an IND, CFR 2025 edition. govinfo.gov
FDA, Investigational New Drug Applications Prepared and Submitted by Sponsor-Investigators, draft guidance, May 2015, docket FDA-2015-D-1484; page current August 24, 2018 and still marked draft, read November 2026. fda.gov
EMA, ICH E6 Good Clinical Practice scientific guideline page, read November 3, 2026: principles and Annex 1 in effect July 23, 2025; Annex 2 adopted by ICH June 3, 2026, in effect January 15, 2027. ema.europa.eu
FDA, E6(R3) Good Clinical Practice, final guidance, September 2025, docket FDA-2023-D-1955. fda.gov
42 CFR 403.908, submission by the 90th day of each year, CFR 2025 edition. govinfo.gov
CMS, Open Payments Data Collection, modified September 29, 2026: thresholds for Program Years 2026 and 2027. cms.gov
FDA, ClinicalTrials.gov Notices of Noncompliance, content current October 30, 2026. fda.gov
European Commission, AI Act application timeline after the AI Omnibus (Regulation (EU) 2026/1744), in force July 27, 2026. digital-strategy.ec.europa.eu
21 CFR 312.6, labeling of an investigational new drug, CFR 2025 edition. govinfo.gov
21 CFR 312.57, sponsor recordkeeping and record retention, CFR 2025 edition. govinfo.gov
Regulation (EU) No 536/2014, Article 37, end of trial and summary of results. legislation.gov.uk
Regulation (EU) No 536/2014, Article 58, archiving of the clinical trial master file. legislation.gov.uk
Regulation (EU) No 536/2014, Article 67, labeling of authorized investigational medicinal products. legislation.gov.uk
42 CFR 403.910, delayed publication for research payments, CFR 2025 edition. govinfo.gov
EFPIA, Code of Practice, final consolidated version 2026, definitions and Article 23, Research and Development ToV. efpia.eu
HHS OIG, Compliance Program Guidance for Pharmaceutical Manufacturers, 68 FR 23731, May 5, 2003, sections on research funding. govinfo.gov
HHS OIG, Compliance Guidance page, read November 3, 2026: the 2003 text sits in the archive; General Compliance Program Guidance, November 6, 2023, is listed as current. oig.hhs.gov
42 CFR 11.64, when clinical trial information must be updated, CFR 2025 edition. govinfo.gov
Carlisle B. et al., Unsuccessful trial accrual and human subjects protections, Clinical Trials, 2015;12(1):77-83, PubMed abstract. pubmed.ncbi.nlm.nih.gov
U.S. National Library of Medicine, ClinicalTrials.gov API v2; our count, November 3, 2026: interventional studies by start date; lead sponsor class OTHER with collaborator class INDUSTRY, or lead sponsor class INDUSTRY; overall status; has results; why-stopped text holding enrol, accru or recruit. clinicaltrials.gov
Wong B. et al., Comparison of industry-sponsored and investigator-initiated trials in advanced genitourinary cancers, Clin Genitourin Cancer, 2024;22(6):102210, PubMed abstract. pubmed.ncbi.nlm.nih.gov
McLennan S., Griessbach A., Briel M., Practices and attitudes of Swiss stakeholders regarding investigator-initiated clinical trial funding acquisition and cost management, JAMA Netw Open, 2021;4(6):e2111847, PubMed abstract. pubmed.ncbi.nlm.nih.gov
FDA, Bioresearch Monitoring Fiscal Year 2024 Metrics, the newest deck listed on June 4, 2026. fda.gov
HHS OIG, enforcement action entry, July 28, 2020: Pacira agrees to pay $3.5 million. oig.hhs.gov
United States and Pacira Pharmaceuticals, Settlement Agreement, 2020, recitals D to F: contentions of the United States, no admission of liability, allegations denied. justice.gov
Griessbach A. et al., Resource use and costs of investigator-sponsored randomized clinical trials in Switzerland, Germany, and the United Kingdom, J Clin Epidemiol, 2024;176:111536, PubMed abstract. pubmed.ncbi.nlm.nih.gov
HHS, No Adjustment to HHS Civil Monetary Penalty Amounts for 2026, FR Doc. 2026-21524, October 21, 2026. govinfo.gov
U.S. Department of Justice, Office of Public Affairs, Veloxis Pharmaceuticals release, August 10, 2026. justice.gov
42 CFR 403.902, definitions including research and indirect payments, CFR 2025 edition. govinfo.gov
EMA, Sponsor handbook for the Clinical Trial Information System, Version 6.4, EMA/148347/2026, July 7, 2026, section 5.2.1. ema.europa.eu
Germany, Arzneimittelgesetz, section 97(2d) no. 2 and (3), read November 3, 2026. gesetze-im-internet.de
DeVito N.J., Bacon S., Goldacre B., Compliance with legal requirement to report clinical trial results on ClinicalTrials.gov, Lancet, 2020;395:361-369, PubMed abstract. pubmed.ncbi.nlm.nih.gov
Getz K. et al., New Benchmarks on Protocol Amendment Practices, Trends and their Impact on Clinical Trial Performance, Ther Innov Regul Sci, 2024;58(3):539-548, PubMed abstract. pubmed.ncbi.nlm.nih.gov
21 CFR Part 11, sections 11.10(e) and 11.50, CFR 2025 edition. govinfo.gov
FDA, Considerations for the Use of Artificial Intelligence to Support Regulatory Decision-Making for Drug and Biological Products, draft guidance, January 2025. fda.gov
European Commission and PIC/S, draft EU GMP Annex 22, consultation July 7 to October 7, 2025; EudraLex Volume 4 listed no Annex 22 on November 3, 2026. picscheme.org
EMA, report of the workshop on artificial intelligence guidance (Annex 22), June 30, 2026, EMA/156789/2026. ema.europa.eu
FDA, Part 11, Electronic Records; Electronic Signatures: Scope and Application, guidance, 2003. fda.gov
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