New York Times Coverage of the Obama Precision Medicine Initiative

In the State of the Union Speech on January 20, 2015, the President mentioned he would soon unveil an initiative in precision medicine.  The unveiling came on January 30, with both a detailed White House press release and a 20-minute televised speech by Obama.   For more on the Precision Medicine Initiative, see here.

Between January 20 and January 30, there were two interesting pieces in the New York Times, one a news report and the other an Op-Ed.   Discussion below.

White House Details $215M Initiative in Precision Medicine

In the President's State of the Union Speech, January 20, 2015, one sentence referred to a precision medicine initiative:

21st century businesses will rely on American science, technology, research and development. I want the country that eliminated polio and mapped the human genome to lead a new era of medicine -- one that delivers the right treatment at the right time. In some patients with cystic fibrosis, this approach has reversed a disease once thought unstoppable. Tonight, I'm launching a new Precision Medicine Initiative to bring us closer to curing diseases like cancer and diabetes -- and to give all of us access to the personalized information we need to keep ourselves and our families healthier.

On January 30, the White House describes the initiatives tied to this proposal (here).  The President's 20 minute press conference streams on CNN (here).  Some talk highlights here.  Details after the break.

Metrics about MOLDX Code Coverage - A Snapshot for January 28, 2015

Recently, I was asked to do an analysis of MolDX coverage by CPT code, and I pulled some of its current data into Excel spreadsheets, available (here; look for small 'down arrow' to download).

Note that MolDX coverage may change at any time, so the cloud spreadsheet just provided represents one day's snapshot of MolDX current coverage and non-coverage webpages.

Details after the break.

21st Century Cures: A Health Policy Legislation Smorgasbord

Throughout 2014, the House Energy & Commerce special task force, "21st Century Cures," has held hearings on topics as diverse as orphan drug incentives, telemedicine, and the regulation of LDTs, all tied to the theme of U.S. competitiveness in biomedical innovation.

On January 27, 2015, the committee released an example of draft legislation, covering dozens and dozens of diverse topics, and including more than a few empty "placeholder" sections (such as text affecting FDA regulation of lab-developed tests.)   The website is here; I've uploaded texts like a committee "one pager" and other committee summary documents to the cloud, here.  See an early summary of the 393-page legislative draft (discussion) text at Science, here.  RAPS, the Regulatory Affairs Professionals Society, has a blow by blow discussion online, here.  Their discussion tends to skip over Medicare sections, so I highlight some of those below.  Pink Sheet has a table of explanation of the document, here (subscription).  FaegreBD Consulting discusses where the bill might go, here.

The 21st Century Cures document is not literally a "legislative proposal," but rather a centerpiece to help organize ongoing discussion.  For example, some of the topics may be included just for "airing" and might be very unlikely to be included in final legislation. Modern Healthcare quickly ran a headline, "Dems Balk at Bill" (here).  For the Association of Molecular Pathologists comment, here.

The Senate Finance Committee released a parallel report on medical product innovation on January 29, 2015 (109 pages; SFC website here, 109 page PDF report, here.)  The Senate report is clearly meant to be generally favorable and supportive of the House-side 21CC effort.

Further comments after the break.

Fifty Shades of Blog

At the one year anniversary of this Discoveries in Health Policy blog, there have been 50 postings.  In a year, there were 17,000 page views (about half are real and about half are search engines).  I was tickled that both Nature and the New York times reached out for quotes recently ( New York Times, here.)

Review of most-popular first year entries, after the break.

MOLDX LCD for Comprehensive Genomic Profiling in NSCLC

Palmetto GBA has published a draft LCD to provide coverage for large-scale gene panel tests in non small cell lung cancer.   The LCD is available here at the CMS website.  A public comment period is open from February 10 to March 27, 2015.  Details after the break.

CMS Announces MEDCAC on Molecular Prognostic Tests - March 24, 2015

CMS has announced a MEDCAC (advisory panel) public meeting on prognostic molecular tests, focused on breast cancer and colorectal cancer molecular tests.   Such meetings often kick off with a technology assessment subcontracted by AHRQ.

Update [March 25]: Early trade press after MedCAC suggests it went exactly as predicted in this blog many weeks ago.  An advance copy of the transcript is available here.

Details after the break...

The Backdoor to JP Morgan: Symposia and Presentations On Line.

Every winter, the annual JP Morgan life sciences conference brings Wall Street and the U.S. pharma, biotech, and medtech community to San Francisco for four hectic days.   Admission to the actual conference - which locks down the St Francis Hotel at Union Square - is very strictly controlled.   The conference is for Wall Street and for CEOs/CFOs.

However, under SEC open information laws, most of the conferences stream online, just like quarterly earnings calls.  This isn't much advertised, but it's a public website and this is the link for the 33rd annual conference:

http://jpmorgan.metameetings.com/confbook/healthcare15/ondemand.html

(Registration is free with your email).

There were four keynote events in addition to the dozens of corporate presentations.  Francis Collins, the head of NIH, gave his outlook for genomics and biotech.   There were also three panels featuring national thought leaders on the topics of pricing and value-based genomic tests, next-generation sequencing, and disruptive DHealth technologies.   More details after the break.

FDA posts Videos, Presentations, From Jan 8-9 LDT Workshop

The FDA has released both two days of video and all publication presentations from the January 8-9, 2015 public workshop on FDA regulatory of laboratory developed tests.

See:  Here.

Agenda and links after the break.  82 presentations were calendared, although a few were withdrawn.

HHS Says Court Case Fighting the NCD on Amyloid PET Scans Isn't Valid; Defendants Fire Back

Summary:

• Three beneficiaries, supported by Lilly, filed for summary judgement against the CMS beta-amyloid NCD in September 2014.
• CMS filed a lengthy motion to dsmiss in December 2014.
• The plaintiffs filed a renewed request to invalidate the NCD and enjoin enforcement in January 2015.

Details after the break.

ACLA Releases New Position Paper against FDA LDT Regulation; AMA Weighs in Too

On January 7, the American Clinical Laboratory Association (ACLA) released a detailed legal white paper on why the FDA does not have the authority to regulate laboratory developed tests.   The press release is here, the legal white paper here.  

ACLA released, on the web here,  its oral comments at the January 8-9,2015 FDA public workshop on LDT regulation.

Last summer, the FDA responded to three Citizen's Petitions for and against FDA LDT regulation, with the petitions and the FDA's responses to each clipped below. 

'06, '08, '13 Petition	7/2014 FDA Response
2006 Washington Legal Foundation	Response
2008 Genentech	Response
2013 ACLA	Response

The subscription website Genomeweb interviews the ACLA legal authors, here, and a counterpoint, here.

• Also this week, the AMA publicly released its letter to the House "21st Century Cures" group, which requested public feedback on the FDA LDT issue by this week.  
• AMA document, here.

Theranos: A Library of Articles and Links 2006-2016

This blog began in December 2014, when a no-longer-existing blog ran a critical review of the favorable New Yorker article on Elizabeth Holmes and Theranos.

From December 2014-December 2016, this blog entry records an informal log of online news articles about Theranos.   I do not review it for the dead links that likely accumulate over time.

The original lead paragraphs of this blog, written back in December 2014, were archived here.
For an update on the March 2018 SEC action against Theranos, here.

I'll add one note from June 2018 - an article that, "Pathologists predicted the Theranos debacle, but their voices were missing from most news coverage"!!  Here.  (Archived here).

FDA to hold workshop on NGS regulation: February 20, 2015; Publishes 9-p white paper

The FDA has announced a workshop on regulation of genetic tests and next-generation sequencing, to be held in Bethesda on February 20, 2015.  The FDA announcement is here.  The FDA conference page is here.

The agenda for the day has not yet been announced.  However, FDA has published a nine page white paper outlining the agency's view of key topics and issues in NGS regulation, here.

• Update 2/23/2015: The meeting was held on February 20; for the Genomeweb meeting review by Turna Ray, see here (subscription).

Key points are:

SUMMARY: 
The Food and Drug Administration (FDA) is announcing the following public workshop entitled “Optimizing FDA’s Regulatory Oversight of Next Generation Sequencing Diagnostic Tests.” (here) The purpose of this workshop is to discuss and receive feedback from the community on the questions in the discussion paper on diagnostic tests for human genetics or genomics using next generation sequencing (NGS) technology.

WHEN:  February 20, 2015, from 8:30 a.m. to 5 p.m.
ADDRESS:  Natcher Center at the National Institutes of Health Campus, 9000 Rockville Pike, Bldg. 45 Auditorium, Bethesda, MD 20814.

WHITE PAPER:  Section 1 is a brief introduction, Section 2 discusses the FDA's regulation of laboratory tests.  Section 3 is a two-page overview of "challenge and opportunities" raised by NGS.  It also notes FDA's several workshops and prior efforts in this area, and the clearance of Illumnia cystic fibrosis NGS tests.  The longest section, Section IV, discusses NGS analytical validity topics (IV-A) and clinical validity topics (IV-B).  There is a discussion of CLINVAR and other public data repositories, and a discussion of how the FDA, clinicians, and public should handle variants of uncertain significance.  There is a short closing section V.

I've also provided online the full-text of the FDA discussion paper on NGS, after the break.

For an NIH workshop on Precision Medicine and whole genome sequencing, Feb 11-12, 2015, see here.

On February 18, 2015, Eric Lander of the President's Council of Advisors on Science and Technology (PCAST) published an Op Ed in the NEJM on the need for special FDA treatment of NGS (here.)  Trade press at Genomeweb (here, subscription).

Can “Clinical Utility" Vary For Two Tests, if “Clinical Validity" is the Same?

Last summer, I was discussing molecular tests with a commercial plan medical director, and he referred to two gene panel breast cancer tests. In his opinion, he felt that the two tests had equal clinical validity, or if anything, the second test had higher clinical validity. However, he felt the first test had “greater clinical utility."

This puzzled me, because I had just published a paper with coauthor Felix Frueh on bringing some structure and order to communications about clinical utility. It had never occurred to me that a test could have greater clinical validity than another, similar test, yet lower clinical utility. In order to draw this conclusion, I believe there is too much “slippage" in the way clinical validity and clinical utility are defined and used. It is more useful to define them in a way such that clinical utility depends on clinical validity plus a use context. If the clinical validity for one of the tests is higher, and the use context is the same, the clinical utility for the other test cannot be better, although it might be the same.

Returning to the Definitions

In a 2014 comprehensive review, Parkinson and colleagues defined clinical validity as “the association between the biomarker and the pathophysiological state or clinical presentation of illness."1 This is essentially the same as that used by Hayes and colleagues in 2013: clinical validity is “how well the test relates to the clinical outcome of interest, such as survival or response to therapy."2

Following these definitions, the test relates what happens in a test tube (a chemical or molecular analysis) to a clinically relevant phenomenon. To be comprehensive, sometimes the test report is analytical (glucose = 125), sometimes it is genomic (we find mutation BRAF V600E is present), sometimes it is an abstract score (“recurrence score = 35"), and sometimes it is binary (a strep lateral flow immunotest is “positive").

Purely analytical tests are related to clinical states by common knowledge or definitions. For combination diagnostics, a clinical correlation is statistically (BRAF V600E is strongly associated with a high chance of response to sorafenib.) For multiple analyte tests with algorithms (MAAA tests), there is usually a double report, one being algorithmic and one being a clinical variable (recurrence score of 35 correlates with a 23% chance of 10 year recurrence).

Test	Analytical Report	Clinical Validity
Glucose	Glucose = 125	Common knowledge or definitions or protocols (not on report)
BRAF	BRAF mutation = V600E	High correlation with sorafenib response in malignant melanoma (usually on report, “interpretation")
MAAA	Recurrence score = 35	Correlated with 23% risk of 10 year recurrence in ER+, Node- breast cancer if tamoxifen treated (on report)
Strep Test	Binary (immunoreaction positive)	Strep present (on report)

We do something with tests, which brings about their clinical utility. For Parkinson et al. (2014), “the results of the assay lead to a clinical decision that has been shown with a high level of evidence to improve outcomes."3 For Hayes et al. (2013), “whether the results of the test provide information that contributes to and improves current optimal management of the patient’s disease."4

The commercial payer’s question, with which I opened this essay, led me to think that these definitions of clinical validity and clinical utility were not designed to help people agree where the two concepts start and stop, or how they meet at a border zone. However, it is possible to think about these concepts in such a way that there is a bright-line border between them.

The Three Buckets for “AV," “CV," and “CU"

A metaphor that makes the difference clear is this:

• Analytical validity lives in a test tube.
• Clinical validity lives on a report and in a data file.
• Clinical utility lives in a patient.

The simplest concept is probably analytical validity: it relates to expressions in test measurements, repeatability, reproducibility, interfering substances, or analyte sensitivity such as ng/ml. Thus, “analytical validity lives in a test tube," or at least inside the equipment that is doing the measuring.

Clinical validity lives in a report, in a data file, on a chalk board. We know that BRAF V600E is associated with sorafenib response in malignant melanoma because clinical trials showed us this was the case. We know that a range of breast cancer genomic tests – including Mammaprint, Oncotype DX, the BCI, and Prosigna – correlate with breast cancer recurrence rates because well-designed large databases tell us so.

It’s best to view clinical validity and clinical utility as separate categories even when the contents, for a test in question and its use case, are similar. For example, we might say offhand that the clinical validity and the clinical utility of a BRAF test are the same – a V600E mutation is associated with clinical response, and the lack of this mutation is associated with non response. In health technology assessments, tests like BRAF get a fast pass, because the clinical validity and clinical utility are so similar.5 However, we avoid a host of later problems if we take the position that even for these tests, the clinical validity and clinical utility are not “the same."

Test	Analytical Report	Clinical Validity	Clinical Utility
Combination Diagnostics
BRAF	BRAF mutation = V600E	V600E is correlated with increased survival when treated with sorafenib	When V600E patient is treated with sorafenib, he/she lives longer.
Her2Neu	Her2neu Positive	Positive Her2Neu is correlatedwith increased survival if treated with Herceptin	When Her2neu positive patient is treated with Herceptin, she lives longer.

Here, while “clinical validity" and “clinical utility" sound the same, they are not the same thing. Clinical validity is a correlation with an analytical test report and the outside clinical world. Clinical utility is something that really happens as a result of what we “do" for a patient. This carries out the idea that clinical validity “lives" on a test report, on a chalk board, or in a paper, whereas clinical utility “lives" in the patient herself or himself. Another way of using our metaphor is to say that analytical validity happens in the real world – although in a very tiny real world inside a test tube – and clinical validity “lives" on a report that we are confident is true because of various prior data. Clinical utility again lives in the real three dimensional living world of drugs, therapies, and patients. Yet another way of saying this – if only one factory could make Herceptin, and it blew up, and there were no more Herceptin drug supplies, the clinical utility of a Her2neu report for a doctor and his patient would be gone (at least for now, and in regards to prescribing Herceptin). However, the clinical validity would be just as true: her test report is in our hand, and cohorts of test-positive patients were reported to live “N" months longer, and it had varied greatly based on Her2neu status.

A Graphic Model of Clinical Utility

In 2014, Frueh and Quinn published a six-question approach to communications about clinical utility, including a figure that shows a one-way relationship between clinical validity and clinical utility. The model focuses on decision making for new tests, where the clinical utility is comparative to the status quo:

However, there is only an increase in clinical utility for that patient because we did something different than the status quo, a “change in management:"

And there could only be a change in management because there was something different about the information we had with the new test, relative to the status quo with the old test (or no test):

This last graphic, shown above, only makes sense if two tests that had “the same clinical validity" would have the same impact on clinical utility in the same use case. This is easy to see if we have two thermometers, or two glucose meters, that have exactly the same reports. It’s also easy to see if we have two different BRAF tests that have the same (or very nearly the same) V600E mutation or wild type reports. The model shown above is generalized for diagnostic tests. For example, if an old MRI scanner has 0.5 cm resolution, and a new MRI scanner has 0.2 cm resolution, the new scanner may have more accurate radiology reports (clinical validity) which lead to better outcomes (correct surgical decisions and other clinical decisions not misled by false positives and false negatives). On the other hand, if two MRI scanners have exact the same image field size, slice thickness, contrast ratio, and resolution, it would be difficult to imagine that two indistinguishable imaging results from, say, a Siemens and a Philips MRI scanner, would have different diagnoses in the reading room or different clinical actions.

-------------------------

1 Parkinson DR et al. (2014) Evidence of clinical utility: an unmet need in molecular diagnostics for patients with cancer. Clin Cancer Res 20:1428-44.2 Hayes DF et al. (2013) Tumor biomarker diagnostics: Breaking a vicious cycle. Science Translat Med 5:196cm63 Parkinson et al. (ref. 1); citing Olson S, Berger AC (2012) Genome based diagnostics: clarifying pathways to clinical use [Workshop]. Institute of Medicine.4 Hayes et al. (ref. 2).5 The Palmetto MolDX evaluation process provides a “fast track" for combination diagnostics approved with drugs in FDA pivotal drug trials. The BCBS Tech Evaluation Center provided a rapid satisfactory report on BRAF kinase testing in 2011.http://www.bcbs.com/blueresources/tec/vols/26/26_07.pdf

House Energy & Commerce: Committee Wants Feedback on Regulation of Lab Tests

On December 9, 2014, the "21st Century Cures" subcommittee of the House Energy & Commerce Committee released ten questions on which it seeks public feedback by Monday, January 5, 2015.   The 21st Century Cures committee website is here, the feedback request is here.  The request for comments is online as a PDF, here.

The request for comments notes that the committee held a roundtable on personalized medicine on July 23, 2014, and a meeting specific to the FDA's proposal to regulate LDTs on September 9, 2014.  (For my coverage of the latter, see here, including a very detailed discussion report, here.)

I've also cut-pasted the eleven questions in full, below the break.