Monday, March 25, 2024

ASM Responds to FDA LDT Rule

At the House E&C hearing on FDA LDT on 3/21/2024, there were two or three paragraph-long comments on the adverse effect on microbiology.   (Other specialty interests including tox testing and rare diseases and pediatric special cases).

ASM submitted a written comment to the hearing.

https://asm.org/Press-Releases/2024/March/ASM-Statement-in-Response-to-Health-Subcommittee-H#:~:text=ASM%20submitted%20comments%20on%20the,LDTs%20for%20infectious%20disease%20testing.

ASM submitted 12/2023 comments to FDA:

https://asm.org/articles/policy/2023/december/asm-responds-to-fda-proposed-rule-on-laboratory-de

See also 9p pdf which includes a supplemental 3-page section of information and graphics (p 7-8-9).

https://asm.org/getmedia/6d94930b-10e1-4b77-bbae-bcae1d1a07ad/PDF_Comments-to-FDA-on-Regulation-of-LDTs_Dec-2023.pdf

IDSA had a highly negative public blog on 11/2023:

https://www.idsociety.org/science-speaks-blog/2023/fda-proposal-threatens-access-to-critical-id-diagnostic-tests/#/+/0/publishedDate_na_dt/desc/


####

Here are some quotes from the March 21 hearing.


Thank you, ma'am. Dr. Eisner. You know, I've heard worries that FDAs proposal could make it

more difficult to treat antibiotic resistant infections and address antimicrobial resistance and

currently FDA has no pathway for off label antibiotic test. And at Vanderbilt University Medical

Center ICUs roughly 60% of antibiotics prescribed are for off label organisms or off label

indications and use of off label antibiotics are made possible by LD T testing for antibiotic

susceptibility. How would the loss of such test affect the management of patients including those

with compromised immune systems or facing extremely rare infections?


Speaker 9 2:19:48

Thank you for the question. I think that it's quite evident that the FDA rule as proposed would

clamp down on LDTs in a way that would bring testing such as antimicrobial resistance testing

to a halt, that could leave hospitalized patients without a pathway to exiting their infectious

status. It could lead to overtreatment with multiple antibiotics in an attempt to eradicate which

can lead to kidney failure, liver failure, etc. I think that it is a huge challenge to understand the

global impact of LDTs because it is not just about oncology genetics, it's about infectious

disease. It's about rare disease. It's about anatomic pathology, it's about there isn't a field of

medicine, where LDTs aren't part of the picture. And I think it is. It is understandable that we are

talking a lot about oncology today. I for one, appreciate that perspective. But I think when you

look at the larger landscape of laboratory testing LDTs plays such a pivotal role across every

specialty.

###

Thank you for yielding. I just have a follow up question I was someone asked question about

Anna my antimicrobial resistant efforts, which is a long standing issue we've been trying to

address and Mr. Rothstein under that, under that, how do you how would you see a framework

like valid handle new anti microbial resistance tests that might come available?


Speaker 6 2:36:30

Thank you for the question. And this is a topic that's actually very well suited for the technology

certification program contemplated in VALID right now anti microbial testing, which is so

important for our nation, but for patients and for ensuring that we have antibiotics available. For

the long term requires for each test of whether it's a bacteria or a fungus, each of those tests

has to go through FDA one at a time. Under the technology certification program in valid a

manufacturer or a laboratory could develop a platform in which FDA looks at once, and then any

subsequent bacteria, fungus or other type of micro organism that needs to be detected, could

go through that platform without going to FDA as long as the parameters are met within the

agreement between FDA and the industry. And it would make the process for antimicrobial

resistance products to come to market in an extremely efficient mechanism matter. Thank

 

Monday, March 18, 2024

scraping amazon orders

 Until March 2023, you could download your year of amazon orders in Excel for taxes.

Then they stopped.

There is still a way to request data on your orders (or other data), but you get back an email "it may take a month."  https://www.amazon.com/gp/help/customer/display.html?nodeId=TP1zlemejtTn6pwYKS

  ####

There is a chrome plug in that will "scrape" your order history for ten minutes and then give you a CSV table.

I got one that is 600 lines long, first digital orders then other orders  (We get a lot of groceries etc via Amazon).

###

There is also a Chrome web store order scraper

https://chromewebstore.google.com/detail/amazon-order-history-repo/mgkilgclilajckgnedgjgnfdokkgnibi

it takes a while for the years table to appear, when it does and you tap 2023 it immediatley starts “scraping” it may give odd nearlhy empty pages but updates tiny print

it seems to keep running and reducing PENIDNGS despite periodic ERROR PAGES SORRY that pop up.

just wait ten minutes

When it stops runninng, the top bar will say DOWNLOAD CSV (several iminutes)


There is ALSO a $14 app,
Amazon Order History Exporter,
which worked smoother but costs $14.



Sunday, March 17, 2024

CMS Staff Discuss ADLTs

 CMS staff discuss ADLTs @ meeting.

##


AI RE WRITE


Understanding the ADLT Application Process


Jason Bennett, who oversees the office of new technology coding and pricing at Medicare, provided insights into the Advanced Diagnostic Laboratory Tests (ADLT) application process. He emphasized the relatively low application volume, with approximately 20 to 22 products reviewed over time. Bennett noted that about two-thirds of these applications meet the criteria for approval.

A key challenge in the ADLT application process, as Bennett described, is demonstrating the uniqueness and clinical utility of the test compared to existing options. The evaluation team, which includes clinicians, focuses on understanding the new information the test provides and its implications for patient care. Bennett advises applicants to clearly articulate how their test delivers unique, actionable insights that can improve patient outcomes.

Bennett also mentioned that some applications are denied for straightforward reasons, such as not being conducted in a single laboratory. However, the primary challenge remains proving the test's unique value and clinical relevance.

Addressing Timelines and Resource Constraints

Bruce Quinn, a consultant specializing in Medicare technology, raised concerns about delays in the ADLT decision-making process. Bennett acknowledged that FDA-based decisions tend to be more streamlined due to fewer criteria. He highlighted the broader issue of resource constraints at CMS, noting the contrast with the FDA's user fee system that supports its operations.

Bennett explained that the Medicare Trust Fund does not provide the same level of resource flexibility for CMS, which relies on annual appropriations. These budgetary constraints, combined with the need to prioritize tasks and manage a growing workload against flat or limited resources, lead to variability in review timelines. He stressed that current environmental factors might increase this variability, underscoring the challenges of managing the agency's mission within these constraints.


CONCLUSION

In conclusion, Bennett's discussion sheds light on the complexities of the ADLT application process and the impact of resource limitations on CMS's ability to maintain timely reviews. Applicants are advised to focus on clearly demonstrating their test's unique value and clinical utility to navigate these challenges successfully.

 

###

AUTO TRANSCRIPT (LOW QUALITY, UNEDITED)

Speaker 1  11:33 


Well, that's helpful. No, thank you. So, Jason, you know, I know and part of your work is in review of the advanced diagnostic laboratory tests, ADLT  and can you help us understand that process, and market stakeholders can do to, in your view, would be a better approach to going to apply for a ADLT? And perhaps some tips, and then also maybe what some mistakes to avoid? In your view? Yeah,


 


Speaker 3  12:01 


there's not been a lot of application for the pathway. We've had around 2022 or so products, I think we've seen over the years. So it's not a high utilization, or kind of kind of high approach pathway. And I think we've had around two thirds or so that have met the criteria for it's really important to, to take the time to look at the criteria and assess how how the test relates to those criteria.


 


And then really be prepared to help us understand your perspective or your business's perspective on that.


 


One of the complexities that I think we see is around that kind of concept of telling us what new information there is that the test is bringing to market relative to other tasks.


 


And the team that will look at it will include clinicians who are kind of trying to understand how to interpret those results as they would in clinical practice. And so it's important to be able to kind of describe, in many respects, what the test is saying about the patient. And then how is that supposed to affect the care that the decision right that the physician is making? Or, or, or sort of what that's why there isn't somewhere else, they would have gone to receive that same type of information.


 


So that's probably you know, at a high level, the area where we see the most complexity, and often where there's most engagement back and forth, as we tried to kind of refine our understanding of that and and hear from your from the laboratories about what was behind that test and why they're there other issues that that have occurred, but that resulted in denials. But those are usually more straightforward.


 


For instance, if it's not a single laboratory, that that can be a disqualifying reason. But the primary one tends to come around that aspect of what's unique what's different about this test? And how is that clinically useful to to improve the patient's outcomes or potential for for future outcomes?




###


Hi, my name is Bruce Quinn, I work full time on Medicare technology consulting. . Jason, I work with different companies in the lab industry. And I've been hearing where people have been talking that the ADL T decisions seem to be coming out on a longer timetable than they used to. And I just wondered if that was true? 

And if so, are the FDA based ADLT still a fairly clean decision?


Speaker 3  41:32  

Certainly the FDA ones are the cleanest decision, I think that we that we have. There's there's the fewest criterion. So that's a more straightforward decision. You know, one of the things that I think is helpful for everyone to understand, and it's timely, right, because we're potentially a week away from our annual budget, having that many of you work with the FDA, and they have a user fee system that helps support them and helps them have a robust agency to stay on top of the technologies. Think a lot of people assume that the trust fund the Medicare trust fund does the same thing for us from a resource standpoint. It did you hear your Tamarack? chuckling it does not. A lot of folks, I think think that we just have from that and pull the resources that the agency wants or needs to do the mission that we've been called to do by statute. And that's not the case. So we, most of our staff, are very much funded out of a primary administration appropriation line that is annually funded. And as we all see the environment that we're in, we know that the environment that we're in, and that's not different for CMS, as it is for many other federal agencies. So we have to take the workforce that we have and stretch them across everything that we possibly can do. We have to prioritize between the musters by certain dates, the really like to dues and the other commitments that we've made as an agency. And, and so there will be variability in that. And I do think that this immediate time is one of those with which the variability is probably going to increase relative to maybe the last few years as we, as we sort of see where, where our final appropriation comes in. But, but as you all know, if you work from a flat budget, you still have inflation. So that that means that there are in our appropriations lines notionally fund the types of things you would think of people are contracts, and our facilities.


 And so you have to make adjustments to to accommodate that. And if the workload is growing, at the same time, your resources are flat, or otherwise, you have to make trade offs.

Friday, March 15, 2024

Pathologist Ordering Diagnostic Tests: The "Pathology Exception" - and Lung Cancer Papers

Periodically, questions arise whether pathologists can order genomic tests (e.g. lung cancer gene panels).

My reading of Medicare regulations, is "NO."  There are two sources.  In 42 CFR 410.32, CMS regulations state that diagnostic tests must be ordered by the treating physician who uses the test in the management of the patient's disease.   For me, the only natural reading is that this was intended to excluded pathologists and radiologists (by intention, not by accident.) 

Further, the origin of the rules is 62 Fed Reg 59048, 1997, where they discuss for example an IDTF physician cannot order tests, but the primary physician "treating the patient" can. (59071).  This despite the fact the IDTF radiologist is "managing" the patient to the extent of reading out the imaging. (See also 410.33(d).) See also p. 59058.  CMS remarks that, "[in a radiology example,] provision could be made for an emergency situation. We are trying to address situations in which there is a pattern of the testing entity’s adding procedures [tests] to those ordered by the patient’s personal physician."

Second, the Benefits Policy Manual, Chapter 15, 80.6.4, has several pages about when a pathologist or radiologist can order or alter a diagnostic test.   They carefully distinguish not just between diagnostic and interventional radiologists, but between "therapeutic" and "diagnostic" interventional radiology procedures.   (I assume they didn't mention pathologists here because the term "therapeutic interventional pathologist" isn't even availalble.)   

In short, my reading of 410.32 and 80.6.4 is that the only natural reading of the author's intent was to exclude pathologists. '

Admittedly, there is a bit of gray area.  A pathologist can order tests required to complete a case, such as a gram stain when bacteria are seen.   

See my 2022 discussion here:

https://www.discoveriesinhealthpolicy.com/2022/04/the-exception-for-pathologists-ordering.html


###

###

While attending a March 2024 meeting where this was discussed, I ran across some further citations.

See LOSK 2017

https://ascopubs.org/doi/10.1200/JOP.2017.023788

Losk et al  (2017) Implementation of Surgeon-Initiated Gene Expression Profile Testing (Oncotype DX) Among Patients With Early-Stage Breast Cancer to Reduce Delays in Chemotherapy Initiation.  J Onco Pract 13:e815.  PMID 28858535

Finding:

The introduction of standardized criteria and workflows reduced time between surgery and Onco type DX ordering, and time from surgery to receipt of result, by 7.3 days ( P < .001) and 6.3 days ( P < .001), respectively. The mean number of days between surgery and initiation of chemotherapy was also reduced by 6.4 days ( P = .004).

The authors open with a number of citations to Oncotype causing downstream delays in decision-making.   The authors do not discuss CMS rules.

I used a subscription data resource, SCITE, to pull later papers citing LOSK.  It had been cited 14 times.  These include:

Natsuhara (& Losk), 2018, The Ooncologist.  Impact of genomic assay testing and clinical factors on chemotherapy use after implementation of standardized testing criteria.  

https://academic.oup.com/oncolo/article/24/5/595/6439227

Zipkin 2021  Cancer Med.  Surgeon and medical oncologist peer network effects on the uptake of the 21‐gene breast cancer recurrence score assay.  

https://onlinelibrary.wiley.com/doi/10.1002/cam4.3720

Trapani 2023  JCO  Identifying Patterns and Barriers in OncotypeDX Recurrence Score Testing in Older Patients With Early-Stage, Estrogen Receptor–Positive Breast Cancer: Implications for Guidance and Reimbursement.

https://ascopubs.org/doi/10.1200/OP.22.00731 [not open access]

Gregg 2019.  Tranl Lung Ca Res.   Molecular testing strategies in non-small cell lung cancer: optimizing the diagnostic journey.   

https://tlcr.amegroups.org/article/view/29030/21559

Pruneri 2023  NPJ Breast Cancer.  The central role of pathology labs in breast cancer precision oncology: a call for action

https://www.nature.com/articles/s41523-023-00506-5

###

A Linked In Post and a new "Oncology & Therapy" article by Nesline et al.

The Impact of Prior Single-Gene Testing on Comprehensive Genomic Profiling Results for Patients with Non-Small Cell Lung Cancer, NESLINE et al., March 2024.

https://link.springer.com/article/10.1007/s40487-024-00270-x

See a cover note at Linked In by Rebecca Previs MD of LabCorp..

https://www.linkedin.com/posts/rebecca-previs-190bb422b_experts-sound-the-alarm-on-lack-of-comprehensive-activity-7180567156835651584-6MPw/?utm_source=share&utm_medium=member_ios

See J Clin ONcol, March 17, 2024, Subbiah et al.   See section, "Where is the evidence" with a number of timely major links.  Universal Germline and Tumor Genomic Testing Needed to Win the War Against Cancer: Genomics Is the Diagnosis.

https://ascopubs.org/doi/full/10.1200/JCO.22.02833



###
See also news  from PMC about lung cancer and health equity,

https://www.msm.edu/RSSFeedArticles/2024/March/Lung-Cancer-Inequity.php

https://www.ajc.com/opinion/from-diagnosis-to-denial-breaking-chains-of-lung-cancer-inequity/GIUYCEKONVA35A7BOWL6LFE44Y/

Original source (2nd link) is firewaled, top source (MSM.edu) is not.

ALso mirrored:  https://www.personalizedmedicinecoalition.org/op-ed-from-diagnosis-to-denial-breaking-the-chains-of-lung-cancer-inequity-for-black-men/

PMC Report, 41pp, on disparities in personalized medicine and underserved communities

https://www.personalizedmedicinecoalition.org/wp-content/uploads/2024/02/report-1.pdf

See also Turna Ray April 3, Lung cancer EGFR treated with PDL1

https://www.precisionmedicineonline.com/precision-oncology/nsclc-patients-who-should-get-first-line-egfr-inhibitors-are-immunotherapy


###

CA Blue Shield rolls back MRD coverage in cancer, via Laura Housman,

https://www.linkedin.com/feed/update/urn:li:activity:7178526955921715200?commentUrn=urn%3Ali%3Acomment%3A%28activity%3A7178526955921715200%2C7178764131209007105%29&replyUrn=urn%3Ali%3Acomment%3A%28activity%3A7178526955921715200%2C7179473466461450240%29&dashCommentUrn=urn%3Ali%3Afsd_comment%3A%287178764131209007105%2Curn%3Ali%3Aactivity%3A7178526955921715200%29&dashReplyUrn=urn%3Ali%3Afsd_comment%3A%287179473466461450240%2Curn%3Ali%3Aactivity%3A7178526955921715200%29

Genomeweb - pro's con's of MRD

https://www.precisionmedicineonline.com/liquid-biopsy/failed-trial-suggests-circulating-tumor-dna-monitoring-not-universally-applicable





Another pivotal article was:

Roberts MC et al. (2016) Int J Tech Assmt HealthCare 32:355.  PMID 27958190.  ONCOLOGISTS' BARRIERS AND FACILITATORS FOR ONCOTYPE DX USE: QUALITATIVE STUDY

https://pubmed.ncbi.nlm.nih.gov/27958190/

According to SCITE, this has been cited 10 times.

Citations included

Roberts, 2015, Racial variations in adjuvant chemotherapy initiation among breast cancer patients receiving oncotype Dx testing. Br Ca Res Tx.  (No diff found).

https://link.springer.com/article/10.1007/s10549-015-3518-9

McVeigh 2016, CLinical use of the Oncotype Dx genomic test...  Br Ca  Targets & Therapy.  Primarily a review up to 2016.    https://www.dovepress.com/clinical-use-of-the-oncotype-dx-genomic-test-to-guide-treatment-decisi-peer-reviewed-fulltext-article-BCTT

A small study, appearing in Cancers, looked at machine learning with clinical variables for recurrence risk..   Sukhadia et al, 2023, open access.  https://www.mdpi.com/2072-6694/15/15/3960 


##

Medicare, as I recall, has public cloud databases that include ordering physicians for DME, but not for other services.  To get the type of physicians ordering, say, a Foundation Medicine or an Oncotype Dx test, I don't think FOIA would work, since FOIA releases only available documents and precludes any filtering or research work.  But one could do a work order for CMS data on ordering physician for key diagnostic codes like Foundation or Oncotype.  I suspect it would show none or next-to-none are ordered by radiologists or pathologists.   Whether this is good or bad is a policy issue to debate or revise.

Sunday, March 10, 2024

FDA Cites Crazy Stats, Misuses Stats, on PPV or FP FN of "Probabilistic tests"

 The Genomic Health Oncotype test gives out ranges mostly from 5% cancer reccurence risk to 40% cancer recurrence risk.   So if you get the former, and recur, is that a False Negative?  If you get the latter and do NOT recur, is that 60% FP?   I don't think so, it's simply statistics.

FDA seems to deliberately misunderstand this, logging Oncotype Dx and other probalbilistic calls as being either right or wrong and thus either FN or FP.  

I mean to explain in a blog.  here are links.


###

  1. FDA LDT Proposal: Now that this is under review at OMB,  

 

  1. There’s a point of view that, given the large number of substantive comments received and the relatively quick turnaround from the agency, it’s unlikely that FDA would have made significant revisions from the proposal.

 

  1. Given the workload this would entail for FDA, however, it would seem that something would need to be grandfathered in, which leaves the key question being which tests / type FDA views as posing the greatest risk (e.g., prenatal screening, cancer treatment decisions) and is therefore less likely to grandfather in.

 

  1. To that point, I managed to find this Sept. 22, 2023 FDA memorandum on specific testing examples “that raise public health concerns,” which was listed as a footnote citation in that joint FDA / CMS statement from a few weeks ago

The "few weeks ago" is FDA CMS press release.
THe second is this memo which I discussed above briefly

I've filed hard copy as 
2023 FDA 1003 Shuck Goofy Memo on FP FN on Probabilistic LDTs 14p.pdf



Wednesday, March 6, 2024

3 6 2024; FOCR HRD Email

 Email from FOCR on HRD on March 6, 2024.

##


Homologous Recombination Deficiency (HRD) is a complex biomarker that can help identify patients likely to respond to certain therapies. Friends of Cancer Research's (Friends) HRD Harmonization Project Harmonization Project is a unique research partnership to find alignment among different assays that measure HRD, to support its use as a biomarker in clinical research and care, and to serve as a foundational approach to inform future areas of research.

Friends worked with leading diagnostic test developers and other key stakeholders to evaluate a common set of tumor samples. The project assessed variability across 17 different HRD tests and identified opportunities for future alignment.  

View initial findings here

Optimizing assay alignment improves interpretation of HRD outputs from different tests, ultimately helping patients and healthcare providers to make the best treatment decisions. 


A panel discussion with project partners during Friends recent public meeting, “The Future of Diagnostic Tests: New Data & Modern Policy” held in Washington, DC and broadcast virtually focused on findings from the research partnership and their implications. The session, “Aligning on Approaches to Measuring HRD: Findings from the HRD Harmonization Project,” opened with a presentation from Friends' Director, Regulatory and Research Partnerships, Hillary Andrews, discussing the intricacies of HRD as a biomarker and noting its significance in identifying patients suitable for a PARP inhibitor, a type of targeted cancer drug used as a treatment across various cancers.  

She also described the final findings from the project, demonstrating moderate variability among HRD outputs across 17 assays that assessed a common dataset. Click to watch the full meeting

Dr. Andrews' presentation was followed by a panel conversation with Project work group members. This diverse set of panelists spoke to the recent developments within the project and next steps.  

One of the key take aways from the discussion is the need for assay alignment. This was addressed early on in the conversation by NCI project partner Lisa McShane. 


This importance of assay development and assay alignment segway into the role that providers play in supporting the work to reach a gold standard. Project partner Rebecca Arend at the University of Alabama Birmingham spoke to the implications of not having further develop assay alignment on doctors and patients. 

 

This critical point reaffirmed why continued work communicating and creating consistency in assay development is vital. 

An exciting recent development within the field is the application of machine-based learning. This was a closing remark from Pfizer's Douglas Laird as we look to the future use cases of HRD. 


The HRD Harmonization Project serves as a foundation to support future research to: 

  • Explore how disease context impacts association between HRD and clinical outcomes. 

  • Identify approaches for the development of clinical evidence to support development of HRD Assays. 
     

To learn more about the project visit: https://friendsofcancerresearch.org/hrd/     
 

Watch our recent HRD meeting here

 
Interested in staying up to date with HRD Harmonization Project news?  
Click here 

 

Project Partners
 
ACT Genomics, AmoyDx, AstraZeneca, Bayer, Bionano Genomics, Inc., BostonGene Corporation, Bristol Myers Squibb, Burning Rock, Diagnostic Laboratory Services, Inc., DNAnexus, EMD Serono, Inc., European Organization for Research and Treatment of Cancer (EORTC), Foundation Medicine, Inc., Genentech, Inc., Guardant Health, Inc., Illumina, Inc., Invitae Corp., Laboratory Corporation of America (Labcorp), MD Anderson Cancer Center, Merck & Co., Inc. (MSD), Molecular Characterization Laboratory (MoCha) at Frederick National Laboratory, the National Cancer Institute (NCI), NeoGenomics Neogenomics Laboratories, Inc., PathAI, Pfizer, Pillar Biosciences, SOPHiA Genetics, Tempus, Thermo Fisher Scientific, the U.S. Food and Drug Administration (FDA), University of Alabama at Birmingham, and the University of Heidelberg. 

About Friends of Cancer Research

Friends of Cancer Research (Friends) is working to accelerate policy change, support groundbreaking science, and deliver new therapies to patients quickly and safely. We unite scientists, pharmaceutical companies, and policy makers with shared trust and guide them toward meaningful cooperation. This collaboration among partners from every healthcare sector ultimately drives advances in science, policy, and regulation that speed life-saving treatments to patients. For more information, please visit https://friendsofcancerresearch.org/.