Wednesday, May 29, 2019

Very Brief Blog: CMS Updates Test Agenda for June 24 Pricing Meeting - Newest PLA Codes

Every summer, CMS holds public meetings that result in setting prices for new lab codes. 

Regular CPT codes are usually priced the summer before the January when they become effective.  In contrast, PLA codes are released quarterly, so they come into use before they hit the CMS pricing process.

On May 28, CMS updated the agenda of codes to be reviewed in its June 24, 2019 meeting.   See the main webpage here.   See the CMS website zip file of codes on the agenda, here.   I've also made my own cloud copy of the Excel, here

CMS includes codes on the June agenda that were just submitted to the AMA CPT in early April and voted in early May.   Congrats to both AMA CPT staff and CMS staff on keeping up this speedy schedule. 

95 Tests To Be Priced

The prior agenda had 48 items, through 0104U.  The newest agenda has 95 items, through 0148U.

Webcast and Attendance

The CMS CLFS meeting will be webcast, but if last year is example, the webcast may not be archived.  (Several years prior to 2018 had been both webcast and archived).  As of May 29, 85 seats were available (here).

Friday, May 24, 2019

Very Brief Blog: HHS to Reverse Obama-Era Definition of "Sex" within ACA Regs That Included "Transgender" Issues

As reported by Politico on May 24, 2019, the administration has released rulemaking that will role back what is framed as an error of legal interpretation in prior HHS regulations.
  • See Politico article here.  The Hill here.  NYT here.  WSJ here. WaPo here.  Breitbart here.
  • See the Notice of Proposed Rulemaking online at HHS here.
    • 204 pages.
    • The proposed rule has not yet appeared in Federal Register.
    • CMS fact sheet released with the rule, here.
  • The previous (currently effective) final rule appeared May 18, 2016, 81FR31375, here.
    • The 2016 regulations defined "sex" as appears in ACA Section 1557 to include transgender issues.
    • The text of ACA Section 1557 is concise (codified as 42 USC 18116, here.)
    • As of May 24, HHS website still referred to the May 2016 final rule, here, including a 64-question FAQ on the 2016 rule.  Cloud copy here.  
    • The HHS 1557 webpage notes that the May 2016 rule was under an injunction since December 2016 regarding those parts that pertained to gender (Franciscan Alliance).
  • CMS published a proposed rule that also touched on transgender issues specifically within Medicare/Medicaid programs, June 16, 2016, 81FR39447, online here.  This was a proposed rule, not a finalized or effective one.
Regarding transgender issues, the new proposed rule states that in the old May 2016 final rule: " the Department defined discrimination “on the basis of sex” to cover, among other things, discrimination on the basis of sex stereotyping [and] gender identity..."    The May 2016 rule covered additional areas such as multi-lingual services (where most of the regulatory costs lie).   

The rule covers litigation history (including Franciscan Alliance).  The rule notes that on April 5, 2019, DOJ filed a brief stating that "Since the 1557 rules was issued, the United States has returned to its longstanding position that the term 'sex' in Title VII does not refer to gender identity, and there is no reason why Section 1557, which incorporates [analogous prohibition] should be treated differently."  HHS notes that the proposed rule being released now in May 2019 would bring HHS regulations into line with the position taken in court by DOJ in April 2019.  In contrast, the 2016 final rule "created confusion regarding Title IX's definition of discrimination on the basis of sex."

Total savings due to decreased regulatory burden are estimated at $3.5B over 5 years (page 124).

The new rule posits $3.5B in 5-year savings whereas the original rule projected only $1B in 5-year costs.  The new rule cites a range of resources for which HHS says it had previously severely underestimated costs (p. 122-123).

HHS adds, "Covered entities would enjoy increased freedom to adapt their Section 1557 compliance programs to most efficiently address their particular needs, benefiting both covered entities and individuals....Covered entities would be free under the proposed rule to implement policies and procedures that comply with Federal civil rights laws in creative, effective, and efficient ways that are tailored to the covered entities and to the communities they serve. (p. 125)."


Numerous court filings both pro and con Franciscan Alliance online here.

The rulemaking refers to the Attorney General's role in supervising implementation of Title IX. which is applied here (see Executive Order 12250, Jimmy Carter, 1980).  The rulemaking also refers to Executive Order 13771 (see Reducing Regulation and Controlling Costs, Donald Trump, 2017).

For an October 2018 NYT article on Title IX, here.

For a concurrent discussion of CDC and LGBT issues, here.

Thursday, May 23, 2019

Brief Curiousity: DOJ Issues Opinion on FDA and Lethal Injections

Over the past several years, states that impose the death penalty by lethal injection have frequently had difficulty obtaining drugs through commercial pathways. 

FDA has also imposed regulatory restrictions. 

This month, in a ruling that former FDA head Scott Gottlieb opposed (video interview here), DOJ has issued a 26 page opinion that FDA authority doesn't extend to drugs used for lethal injection. 

Article at Politico here.

The article has a quite interesting entry point.  It opens by noting that the FDA has authority regulate "drugs and devices...other than food...intended to affect the structure or any function of the body."   However, FDA has not regulated electric chairs and firearms for firing squads - which are devices tht do "affect the structure or function of the body."   However, of course, it does regulate drugs, and it is drugs which come into the question of lethal injection executions.

Although the new legal brief distinguishes its approach, there was a related FDA Supreme Court case brought by opponents of the death penalty in 1985, Heckler v Cheney, pdf of that case here.  In addition, following decisions Beaty and Cook, there is an injunction based on FDA law prohibiting importation of sodium thiopental into the US (it is not manufactured in the US), for any purpose.  (Refs. inside new DOJ brief, p. 7).

In one of many examples, DOJ points out that pesticides impact the human body as defined under FDA law, but are clearly meant to be regulated only under another body of law (federal insecticide act, FIFRA).


In an interview at CNBC health conference "Healthy Returns," May 22, 2019, Scott Gottlieb discussed this DOJ document.  But he also noted that FDA was under a current active injunction requiring it to forbid importation of execution drugs.   Therefore, DOJ would have to take this new memo, go back to the injunction court, get the injunction lifted (so that FDA could "stop" forbidding importation of execution drugs), which itself would get appealed by various parties up to the Supreme Court over four years.

Very Brief Blog: Agenda and Hot Topics from Advamed's SF Digital Health Conference

Just completed: AdvaMed's annual Digital Health Conference in San Francisco, May 22-23, 2019.

See trade press here.   See agenda still online here for priorities and hot topics.

For archival purposes, I've also clipped the agenda below the break.

The AdvaMed digital conference held in SF exactly overlapped on the same days with a Big Data healthcare conference at Stanford (here).  Their keynote speaker was Jeff Dean, SVP for AI at Google.

Monday, May 20, 2019

Scott Gottlieb Gives Major Speech on Reimbursement Issues (May 10, 2019)

A Scott Gottlieb speech at the National Press Club on May 10, 2019.   New to me, today. 

Gottlieb speaks at length about reimbursement issues and dysfunctional payment policies and how they are maladapted to innovation.   Discussion that investors are forced to use arcane reimbursement rules to guide investments and what products can be brought to market - not medical science and best clinical advances and outcomes.

Find it here:

He builds to this conclusion:
Our biggest obstacles may be policy.   Our biggest challenges may be our inability to devise coverage schemes that can enable the efficient, and when appropriate the rapid adoption of these innovations; allow for a return on capital that maintains investment in these high-risk endeavors; and most important, enables equal access to a cure regardless of a person’s wealth.
We must address these challenges directly. We must be willing to start over with new payment schemes when it comes to these paradigm leaps like cell and gene therapy.
There’s no need to try and fit a cure into the existing payment schemes, when we already know those structures have struggled to keep pace with this innovation.

If of interest, I've included a lightly annotated/highlighted version below the break.

See also an OpEd article by Gottlieb on CNBC, May 20, here.

In a March 2019 speech to the Federation of American Hospitals, the notable senior White House health policy expert Joe Grogan similarly decried a health financing system too dependent on gaming and coding.  Summary here.

Gottlieb 8 minute interview with CNBC, May 21, here.
Gottlieb 24 minute interview during CNBC health conference, May 22, here.

In Unusual Move, CMS Delays Final NCD For CAR-T Therapies

In a very uncommon move, CMS announced on May 17 that it was delaying release of a final version of its National Coverage Determination on CAR-T therapies.

CMS made the announcement in a press release that was only a few words long, here.  They simply state, "A decision is [still] forthcoming."

See coverage at Fierce Healthcare, here.  At Modern Healthcare here.  For a May 10 speech on CMS CAR-T policy by prior FDA commissioner Dr. Scott Gottleib, here.


CMS released a proposed CAR-T decision on February 15, with a final decision normally appearing in 90 days or less, but usually on the 90th day.  See the proposed decision here.

NCDs can include a puzzling mix of obvious and subtle criteria.  For example, the CMS NCD for next generation sequencing requires testing to be provided via a CLIA-certified lab, but other parts of national law also require that.   The NCD proposal for CAR-T requires provision "when prescribed by the treating oncologist" and must have "one physician experienced in cellular therapy" and "a designated care area that protections the patient from transmission of infectious agents."

More to the point, even when the therapy is FDA-on-label, the inpatient or outpatient beneficiary must be enrolled in a registry with follow-up at 3, 6, 12, and 24 months.  Patient-related outcomes must be measured, as well as metrics like disease free survival and overall survival.  If patients are under an indication with NCCN (but not FDA) endorsement, the patient must be in "a CMS approved trial."

Policy Issues

Commenters have raised issues as to whether CMS can/should require clinical trials for patients getting an on-label FDA-approved therapy.   Commenters have also raised issues as to whether the clinical studies required would limit access.   For an open access article on CMS CAR-T policies, here.

CMS determined to pay for inpatient CAR-T via the "New Technology Add-on Payment" process, which pays 50% of the additional costs of a new, costly technology.   Numerous articles have pointed out this may leave hospitals in the red for over $150,000 per patient.  In April 2019, CMS proposed to raise the payment from 50% to 65% beginning with the October 2019 fiscal year (CY2020).  Article at BioPharmaDive here.  Scott Gottlieb discussed CAR-T including CMS policy at some length in a May 10 speech, here.


The tracking sheet for the NCD is here.  The NCD was requested by United Healthcare here.

To read a summary of a May 2019 speech by CMS administrator Seema Verma on Medicare's approach to new technologies and innovation, here.

Saturday, May 18, 2019

Very Brief Blog: Tuesday, May 21, Webinar on CMS NGS NCD and also NGS in Europe

On Tuesday, May 21, 2019, Boston Healthcare Associates hosts a national and international webinar on policies and utilization for next generation sequencing.   It's at 11 eastern, 8 pacific, 4 pm UK, 5 pm Europe.

The first part of the webinar is led by myself - talking about the CMS NCD for next-generation sequencing.   Boston Healthcare Associates presents new data on US/European NGS utilization and coming trends.

Register here before Tuesday.   See the Boston Healthcare Associates homepage here.

Webinar description:

Even though next-generation sequencing (NGS) cancer testing has moved from a rarity to a common feature of clinical practice in recent years, reimbursement policies for NGS testing still vary widely among private and public insurers across different countries 
In the United States, both large commercial labs and large health systems offer NGS tumor testing, and it is anticipated that this landscape will change the availability of a US Food and Drug Administration (FDA)-approved NGS tumor panel. Meanwhile, healthcare systems in Europe are taking what is, in many ways, a very different approach to reimbursement of clinical sequencing with NGS. In France, for example, a network of regional laboratories will be reimbursed to provide molecular testing services. Similarly, genomic laboratory hubs will provide access to whole genome sequencing in the UK beginning in 2019. 
In this free webinar, the featured speakers will shed light on the clinical and commercial reality of NGS in oncology, with predictions for what lies ahead in the United States and Europe.

Speakers will be Bruce Quinn, and Joseph Ferraro, President and CEO of Boston Healthcare Associates.

Very Brief Blog: World Biomarker Conference, Boston (June 17-20, 2019)

Today's mail brought a snailmail brochure for the 15th Annual World Biomarker Congress in Boston, held in conjunction with World Pharma Week. 

The agenda looked quite interesting.   Read more online here.

  • June 17 highlights "Internet of Diagnostics Things" (IoDT)
  • June 18-20 include a several-day track offering an A-to-Z view of immuno-oncology biomarkers, a complex and rapidly moving area.
    • Separately, see a DeciBio article on digital pathology and immuno-oncology, here.
  • June 20 shifts to "Digital Biomarkers" - sensors, wearables, m-health.
Go straight to the full PDF brochure download here (email registration required).


Footnote.  I won't be there; I'll be making my third annual trip to a two-day health innovation congress in Berlin sponsored by the Charite' health center; here. Twitter here.

Wednesday, May 15, 2019

Rapid Advances in Germline and Tumor Genomic Information, Services, Companies

In an excellent posting at Dark Daily on May 15, 2019, Andrea Downing Peck reviews expansion of the Cancer Gene Consensus, part of the UK-based COSMIC program (Catalogue of Somatic Mutations in Cancer).
  • See Dark Daily article here.
  • See COSMIC main website here.
  • See website for Cancer Gene Consensus (CGC) here.
  • See an October 2018 article on CGC by Sondka et al. at Nature Reviews Cancer, here.
  • Together, COSMIC and CGC provide a wealth of tabular, searchable, and graphically presented information on oncogenes both germline and somatic.  If you haven't heard of these resources, worth looking at their content and approach.

Larger Context

Public Databases
  • Association for Molecular Pathology manages a website of Validation Resources and Interpretation Guidelines, online here and here.
    • See also Oza et al. at PubMed and, in the right-hand panel, publications PubMed sees as similar.  Find Oza et al. here, go straight into listing of its related articles here.
  • Increasingly, the FDA will be able to use public databases as part of genomic test clearance/approvals: see April 2018 FDA guidance here.
CancerMine: Public Literature Database

A searchable database based on public oncology literatur is CancerMine.  See a new publication by Lever et al. in Nature Methods, May 2019, here.   See the open access database here,  See references early in the Lever et al. paper to CGC  and COSMIC, but also to Network of Cancer Genes, IntOGen, TCGA, ONGene, TSGene, and CIViC.

Increased Use of Functional Data in Clinical Diagnostics

Increasingly, genomic interpretation involves big databases, clinical curation, but also goes back and forth between the interpretation suite and an actual wetlab for molecular studies (such as rapid in vitro CRISPR studies, Moses et al. open access here, and transcriptome sequencing as in Cummings et al., 2017 here, and Kremer et al. 2017 here, Gonorazky et al., 2019, here).

In parallel, look for more attention to intronic mutations or intronic epigenomic changes like methylation, coupled with transcriptomic studies to resolve novel driver or risk mutations - see Dvinge 2015 here, Pique 2019 here.

Pipeline Analysis Coming Into Its Own

In addition to setting up clinical variant databases per se, how we get from the patient sample to the variant report follows a long and complex genomic pipeline.

Few papers have compared approaches along the whole A-to-Z clinical pipeline.   This spring, AstraZeneca in collaboration with genomic software company SolveBio published a first-of-its-kind review of the complete clinical variant pipeline, from raw BAM file to final report, for four different clinical ctDNA tests.
  • The website for SolveBio here.
  • See article by Stetson here
  • Coverage in Genomeweb here.
Note than an EVP at AstraZeneca recently joined the board of directors of Guardant, here.

Machine Learning for Whole Genome Analysis in the NICU

In April 2019, Clark et al. from Rady Children's Hospital and collaborators published a landmark paper usig machine learning to automate phenotyping and interpretation.  See the Science Translational Medicine article here.

This project was picked up for a laudatory blog by NIH director Francis Collins, here.  (See also Genomeweb here, and a trade journal highlighting the incorporation of natural language processing, here.) 

See a 25 minute May 2019 conference presentation online, by program director Dr. Stephen Kingsmore, here.

The network of collaborators on the Rady paper includes Fabric Genomics, Diploid, Alexion, Codified Genomics, Tessella, and Clinithink.  Sequencing via Illumina NovaSeq.

Mix of Public, Institutional, and Commercial Sources

The field of genomics advances by a mix of platform advances, clinical databases, novel chemistry studies (e.g. transcriptomics for variant calls to reduce VUS), and commercial companies.   I've called the field "Digital Genomics" as a nascent industry, in a December 2017 article in Journal of Precision Medicine (here, here).  In that 2017 article, I laid out a possible conceptual map of digital genomic industry players as here:

click to enlarge; demonstration chart from 2017

PierianDx Webinar Online: A Company Applies Digital Genomics to Clinical Sign-outs

A few weeks ago, PierianDx (with whom Illumina established a formal collaboration last winter, here), held a webinar on its 2019 suite of services to support clinical sign-outs.
  • The video, as well as the deck and the transcript, are online at Pierian here.   
  • Worth checking out.
PierianDx integrates a suite of databases, sources, and services into a licensed service.   The webinar is designed to show genomic clinicians how PierianDx can support them, but it's also worth reviewing as a model and case study of how the genomics industry structure is rapidly evolving through a mix of public database, wetlab, platform, and SaaS resources.

The TruSight 500 Illumina panel is under FDA review as a breakthrough device (here).



PubMed Expertise.  When you look up an article on PubMed, the website shows you "related articles" on the right-hand margin.  ubMed lists several related articles, below which, it gives you little text hyperlinks to "see reviews" (that are related) or "see all" (related articles in their own screen).

It's not a direct fit with the other digital genomics topics in this blog, such as SolveBio and Pierian, but see a very nice article from the consultancy DeciBio on digital pathology and spatial digital analysis in pathology for immuno-oncology - May 2019, here.  They also flag about ten relevant abstracts from the upcoming ASCO2019 meeting.

Wednesday, May 8, 2019

Very Brief Blog: HHS Finalizes Rule to Require Drug Prices in TV Ads

Last fall, HHS announced a number of possible initiatives regarding drug prices, including requiring prices in TV ads and linking US CMS prices to European prices (via a CMMI demonstration).

On May 8, 2019, CMS finalized the rule requiring TV ads for drugs (costing >$35) to include WAC prices for either "30 days" or "a typical course of treatment."
  • Endpoints blog here.
  • Federal Register webpage here.
  • Early copy of rule here. (CMS-4187-F, modifying 42 CFR 403.1200ff.)
    • Original proposal here.
    • Discussion at Foley Hoag, here.
The regulation does not include any direct penalties, but Endpoints notes that CMS proposes that other companies might sue a non-compliant scofflaw company under the Lanham Act.   ("We anticipate that the primary enforcement mechanism will be the threat of private actions under the Lanham Act...")

The regulation contains a clause over-riding state or city laws that attempted to be either more stringent or more lenient than this regulation:
No State or political subdivision of any State may establish or continue in effect any requirement concerning the disclosure in a television advertisement of the pricing of a prescription drug or biological product which is different from, or in addition to, any requirement imposed by this subpart. 403.1204(b).

They mention that CMS doesn't have explicit authority to regulate drug price TV advertising.  ("Many commenters stated that the proposal is beyond the authority of CMS to promulgate these regulations under a reasonable interpretation of sections 1102 and 1871 of the Social Security Act...")   For that matter, CMS staff also don't have explicit authority to regulate what States do (states rights!) regarding drug price advertising.

CMS notes in discussion they considered making a special carve-out counseling code payable when the physician discusses drug pricing with patients.  They deferred action for now.  Someone commented that were such a code to be created, it should be available to pharmacists also.


For a May 2019 article in Health Affairs on Euro reference pricing for Medicare - Yang et al., here.  And for Pharma pushback to international reference pricing, Stat-Plus here.

Tuesday, May 7, 2019

Brief Blog: UBIOME - What Did They Actually Do?

With the flurry of press this month about FBI and legal actions against UBIOME, I recalled I got a UBIOME test out of curiousity last November

I hadn't looked closely at the email chains and paperwork until now.

This blog discusses (1) Email chains and (2) Lab methods report.  Link to Zip file at bottom.

(1) Email Chains

I opened a "uBiome Account" on October 15, 2018, and they confirmed to my email that I had.  Also on October 15, I completed a uBiome Request online (it includes questions like your history of milk intolerance, gas, diarrhea, cramps, etc).   uBiome then sent me a collection kit by mail.  (Hint: You tap their swab to your TP.)

I hadn't noticed before, on October 15 they emailed that "your SmartGut Test has been prescribed."   Apparently this is a teledoc or doc-by-wire situation; I didn't even recall knowing that it happened.  The ordering doc, it turns out, was a [name], National City, CA, NPI 1750358768.  National City is on the south side of San Diego.  This provider billed Medicare for a handful of anesthesia sessions and short office visits in CY2016.
Note that this type of order disqualifies for Medicare, since Medicare requires a payable test to be ordered by the patient's treating physician (42 CFR 410.32).  
At least as of CY2016 public CMS data, uBiome (which has an NPI) had no payments from Medicare.  If the ordering physician had been valid, my case and probably a lot of others wouldn't have met Medicare's public rules for medical necessity; in a cloud zip file here.
My uBiome kit was "on its way" to my house on October 16.  It was received back by uBiome on November 5 (hey, I travel alot for work.)  uBiome refers to the collection date as October 27.  This includes a link (I don't recall ever opening this email) to their Billing FAQ for billing insurers.  The 2019 version of that webpage is here (see also Zip at bottom).  An email says:

On November 8, I got an email asking for my feedback:

  • Do you think uBiome is a TRUSTWORTHY company?   
  •    (A) Not really, (B) kind of, or (C) Yes.

I don't recall a paper explanation of benefits from my insurer, but if they had paid $1000 or $2000 to uBiome and I found out about it I would have complained loudly (or blogged or tweeted.)

In fact, by checking online, there were some denied claims from uBiome to my insurer, Blue Shield CA.  It doesn't provide CPT codes but does say that "information was requested from the provider" which apparently never appeared.   BS-CA also classes some of the claims as "duplicates" (a common term in insurance for same provider, same date of service.)  Sterilized (redacted) cloud EOB here.  There are various bills for $135, $1080, $1755, $2835, $2970.  Score: BCBS 1, Lab 0.

My uBiome lab report is dated November 20, which is after the insurance billing events memorialized by BCBS.  They appeared to use my collection date or postmark date of October 27 as the "date of service" although it didn't reach the lab til November 5 nor be signed out til November 20, and in between, November 12 is memorialized by BCBS as the claims submission date for services in October.


The report is in a cloud copy in the zip file at the bottom of this blog.  In addition, I've been told a sample John Doe report is online at uBiome.

Methods and Limitations are on Page 15-16.

In the SmartGut test, microbial DNA is extracted and marker genes are amplified by polymerase chain reaction (PCR) and then sequenced using the Illumina® NextSeq 500 sequencer. The sequence data is processed using a proprietary phylogenetic analysis algorithm. On average, the sensitivity, specificity, precision, and negative predictive value for the microorganisms on our target list are 97.7%, 99.9%, 98.0%, 100.0% for the species, and 97.2%, 99.9%, 99.1%, 99.9% for the genera,  respectively.
This test detects the presence of the following microorganisms: Alistipes, Alloprevotella, Bacteroides, Barnesiella, Bifidobacterium,
Blautia, Butyricimonas, Campylobacter, Catenibacterium, Clostridium, Collinsella, Coprococcus, Dialister, Escherichia/Shigella,
Faecalibacterium, Flavonifractor, Fusobacterium, Gelria, Holdemania, Lactobacillus, Odoribacter, Oscillibacter, Oscillospira,
Parabacteroides, Paraprevotella, Phascolarctobacterium, Prevotella, Roseburia, Ruminococcus, Streptococcus, Tyzzerella, Veillonella,
Akkermansia muciniphila, Anaerotruncus colihominis, Bacillus coagulans, Bacteroides fragilis, Bifidobacterium animalis,
Bifidobacterium bifidum, Butyrivibrio crossotus, Clostridium butyricum, Clostridium difficile, Collinsella aerofaciens, Desulfovibrio
piger, Dialister invisus, Enterococcus italicus, Lactobacillus brevis, Lactobacillus coryniformis, Lactobacillus delbrueckii, Lactobacillus
fermentum, Lactobacillus helveticus, Lactobacillus kefiranofaciens, Lactobacillus kunkeei, Lactobacillus rhamnosus, Lactobacillus
salivarius, Lactococcus lactis, Leuconostoc kimchii, Methanobrevibacter smithii, Oxalobacter formigenes, Pediococcus pentosaceus,
Propionibacterium freudenreichii, Ruminococcus albus, Ruminococcus flavefaciens, Salmonella enterica, Vibrio cholerae, and Weissella
Some of these microorganisms may not be considered pathogenic but are included as they reflect the state of the patient's microbiome. The microbiome and its clinical relevance is an area of active investigation. This sample has passed all laboratory and sample quality metrics.
For more information about the methods underlying uBiome's SmartGut test, please see Almonacid et al., 2017 (  [also in zip file below]

Detection of a microorganism by this test does not imply a diagnosis. Similarly, a lack of detection does not exclude the presence of a disease-causing microorganism or a diagnosis of disease. Please consult your healthcare provider to interpret the results provided in this report. 
The SmartGut test was developed, and its performance characteristics were determined, by uBiome, Inc. For more information about the methods underlying uBiome's SmartGut test, please see Almonacid et al., 2017 (
This test has not been cleared or approved by the U.S. Food and Drug Administration (FDA). The FDA has determined that such clearance or approval is not necessary.
This test may be used for clinical purposes and should not be regarded as investigational or for research only. uBiome's clinical reference laboratory is accredited by the internationally recognized College of American Pathologists (CAP) and is certified under the Clinical Laboratory Improvement Amendments of 1988 (CLIA) as qualified to perform high complexity clinical laboratory testing.
This test is a next-generation sequencing-based assay that can identify 33 species and 32 genera of gastrointestinal microbiomerelated microorganisms from a stool swab sample, including 5 pathogenic organisms. The detection (or lack thereof) of
microorganisms is reported to the medical professional in this report. The report should be considered in context with other clinical criteria (e.g. patient history, physical exam), as well as other studies (such as laboratory, pathology, and imaging) by a qualified
medical professional prior to initiating or changing a patient diagnostic work-up or treatment plan.
Patient management decisions must be based on the independent medical judgment of the treating medical professional. The test and accompanying report are not intended to be used as the sole means for clinical diagnosis or patient management decisions.
The report may include information on the relevance of reported microorganisms. This information is derived from peer-reviewed studies and other publicly available databases and may include associations between the microorganism and a health condition.
Careful consideration must be made by the medical professional when using this information, as it may or may not be relevant to this patient. Organisms not included in this test may also have an effect on the mentioned health conditions. The organisms on this test may affect additional health conditions not mentioned on this report.
SmartGut is a clinical test, successfully validated using samples collected from individuals of mainly adult age, with a subset of minors. When ordered for minors, the results may still provide valuable information about the minor's health; however, the
accuracy of the results will differ from what was validated for the adult age range.
The reference range for each organism was established using 865 samples from self-reported healthy individuals.


Zip file of cited materials here.

Thursday, May 2, 2019

Administration Releases Rules for Health Workers Conscientious Objections

On May 2, 2019, President Trump announced new rules from HHS regarding the strength of workers' rights to decline to provide health services that cross their religious beliefs.  The regulations cover both "individuals and entities."
  • NYT here.
  • Politico here.
  • CNN here.  
  • Health Affairs rapid analysis of the final rule, here.  MedPageToday here.
  • The 440-page rule, not yet in Federal Register, in a preview version at HHS.
    • Here.
    • The earlier proposed rule, 1/2018, is here. It received 72,000 comments.
  • City of San Francisco sues HHS, here, here.

In June 2016, the Obama administration released proposed rules that would (if enacted) specifically protect the rights of gay/LGBT persons receiving healthcare.   

Those 2016 proposed rules were apparently put on hold by the Trump administration and will expire, assuming they are non-finalized, in June.  See the HHS 2016-era proposal, here.  Access comments here.  

That earlier rule - CMS-3295-P - at 81 FR 39448, also proposed to require hospitals to have antibiotic stewardship committees, and that hasn't been finalized, either.  The antibiotic crisis has been in the news lately (here) and was discussed in April by PAC-CARB, the President's Advisory Commission on antibiotics (here).

In his autobiography, presidential candidate Pete Buttigieg raised concerns about an Indiana law that would have strengthened religious reasons for not providing services (healthcare or other), which he felt could have limited services to gay persons by some entities (e.g. see the Colorado gay cake case here).  The law existed for a few days in Indiana under then-Governor Pence.


On a personal note, since this HHS position pivots on religion, one should note that the Supreme Court has said that "no official...can prescribe what shall be orthodox in matters of...religion."  (WV Bd of Ed v Barnette, 1943; cited in Masterpiece Cakeshop, 2018).  While Masterpiece Cakeshop also stated that there remains "the delicate question of when freedom of religion must yield to an otherwise valid exercise of state power," it also quoted that under Barnette, the state can't include any judgment of what is a valid religion - maybe one person's personally-valid religion, which is not to be questioned, prohibits interracial marriage, for example.

CMS Speech on Tech Innovation; Focus on LCD Process Revisions With New Documents

Last fall, CMS published a new and heavily revised version of the LCD Manual for MACs - also known as "PIM Chapter 13."  Here.

CMS Releases Q&A on New LCD Process

On May 2, 2019, CMS posted an interesting 5-page Q&A on the new LCD process.   The CMS LCD homepage is here and the PDF is currently online here

LCD Q&A Is Tied to Seema Verma Speech on Medicare & Innovation

It seems to be timed with a speech today at the Medical Device Manufacturers (MDMA) annual meeting by CMS chief Seema Verma. 

Press release here, 2600-word speech here.  (That's half as long as the 2019 State of the Union Speech.)

The speech is worth reading; for example, I learned about changes for novel DME technology pricing that I didn't know about (see 83 FR 56922, p.57046, 11/14/2018).  She also highlights advances under her leadership, such as covering continuous glucose meters and finally ensuring insulin "pod" devices are covered under Part D (here, here). 

(Though not so focused on innovation and medtech, see also Verma's lengthy speech to Federation of American Hospitals, March 4, 2019, here.)

Summary of LCD Changes for 2019

Enjoy the reading.   Here is a summary of the LCD changes (using both the program manual revision and the new detailed Q&A document).
  • CAC meetings are no longer required for each new LCD, but are at the discretion of MACs.
  • CAC meetings are open to the public to listen or watch, and recordings will be preserved online.
  • CAC meetings can be held to review and discuss a particular proposed LCD (as in the past) or for informational purposes ahead of LCD creation (to discuss a topic in a general way.)
  • CAC meetings can be live, or webinar, or teleconference.
  • CAC meetings can span a contractor with multiple states (e.g. Noridian has "JE" and "JF") or multi-MAC.   
    • CMS held two multi-MAC meetings already, one for DME MACs to discuss a brain tumor therapy, and one for all the MACs to let their CAC members hear about and discuss a spinal surgery procedure.  Example of "national scope MAC CAC meeting" is here.  See also here with multi MAC kyphoplasty transcript here.
    • So far, no LCDs have yet been released on the topics in the two informational CACs.

  • Public meetings have to be held for each new set of LCDs.  This means LCDs will probably continue to be released in batches.   Public comment is 45 days.

  • There is now a formal process to submit a request that a New LCD be created.  (Previously, this happened commonly, but wasn't a manualized procedure.)   
    • However, this could cause MACs to have a large backlog of acceptable requests for new LCDs ( but lack the bandwidth to produce them.
    • Similarly, requests for existing LCD reconsiderations may be ruled "valid" (13.3.2) but there is no limit to the potential backlog.
  • There is a formal process to have (at MAC's discretion) an Informal Meeting with stakeholders about their LCD idea.   It's still elective for the MAC.   
    • In the past, some MACs gave these meetings pretty readily, and other MACs just about never.   ("When can we meet to discuss your new product and an LCD?  How about never?  Is never good for you?")   
    • While the meeting has a "name" now, it's still elective on the par of the MAC.

  • LCDs must have a listing of the evidence considered and a discussion of the MAC's rationale.  Frankly, this has been a program manual instruction for twenty years or more, but apparently CMS is taking it more seriously now. (13.5.3)
  • LCD finalization must include a public posting of all comments received, with responses.  There is always a risk the answer will be tangential or telegraphic or obtuse (this is also true of NCD comments and responses.)   
  • CMS emphasizes in the Q&A that MACs can't post LCDs that ban payment for PLA codes, Category III codes, etc, without a public notice and a discussion of the evidence.
Some things haven't changed, e.g. final LCDs should be posted 45 days before they are active.

In the past, LCDs could be "expanded" without public comment.   Now, an "expansion" of the LCD language requires public notice, public comment, response to Q&A, etc.  Assuming, as I've heard, new LCDs are reviewed at CMS for a few weeks "to be sure it doesn't conflict with an NCD," a simple expansion could take 3 weeks at CMS, be posted 2 weeks ahead of a public meeting (, then enter 6 weeks public comment (, and a 3 week turnaround time in review, and a 6 week final public notice (13.2.6).  I tally 20 weeks for something that used to be as fast as 2 weeks.

ICD-10 and CPT codes will be moved outside the LCDs and into attached articles.   (The attached articles can be freely revised as CPT codes change, without following the rules for LCDs.)   However, when this change happens, CMS will ensure that an LCD and its coding article are tightly linked since users need to search CPT codes to find out if there is a germane LCD.   


There used to be a recommended list of CAC members, but it's been deleted.  Now it's just "representatives of medical specialties, beneficiaries, and medical associations."

Some of the new PIM is duplicative.  For example, an instruction to take 45 days of public comment on proposed LCDs appears similarly at 13.5.5 and at

In the UK, NHS also shows high interest in the topic of "faster access to new treatments," e.g. 5/3/2019, here.

Very Brief Blog: Attack on the ACA; What Happens to CMMI and Other Policy Provisions?

Over the past several months, another legal case against the Affordable Care Act has been rolling forward.   In brief, several years ago the Supreme Court ruled that Congress had constitutional authority to create the Affordable Care Act health programs not due to the Commerce clause, but do the taxing power.  Recently, Congress repealed the taxing authority inside the ACA.  This has led to a new round of court cases that now, unlike previously, the ACA is unconstitutional. 

This week, the Department of Justice filed its 75-page brief with the Fifth Circuit Court.   DOJ now takes the position that yes, with the tax authority line item being repealed, the ACA as a whole is unconstitutional.  (This is the position a Dallas judge took in 2018).

For policy watchers, this immediately raises issues.  The ACA contained a great number of provisions unrelated to health insurance, such as creating the Center for Innovation (CMMI) at Medicare.  In addition, remember that in 2010, modern biosimilars law was also rolled into the ACA.   Are these all repealed because the ACA must be viewed as a whole and its parts are "inseverable?"

Health Affairs and Link to DOJ Case

Health Affairs has a detailed open-access analysis of the case so far, here.  And the 75-page DOJ brief is online here.

DOJ handles the severability issue on pages 37-38.   The current Trump DOJ argument is that all the ACA provisions should be jettisoned, except, only where the "provisions actually injure the individual plaintiffs."

DOJ notes that ACA amended criminal statutes around healthcare fraud.   DOJ states that these are one example of parts of ACA that do not harm the plaintiffs, and therefore, plaintiffs have no standing to raise them in court nor see them thrown out.   Presumably CMMI and biologicals law would also be "severable" meaning they could stand if the rest of ACA was struck down.   For example, Trump Administration proposed creating a future policy to tie Medicare drug prices to European drug prices, a showpiece idea which turns out to hinge on the CMMI, which is embedded as part of the ACA.

Survival of CMMI or Biosimilars Would Be Decided by Local Judge on Remand

DOJ doesn't go into detail, but on page 38 notes, "The district court can determine the precise scope of judgement on remand" (e.g. just which paragraphs of the 1000-page law go, and which stay.) 

The judge there, however, initially did throw out the whole of the ACA, from the first word to the last, without regard to needing to read all its diverse parts and without regard to this "standing of plaintiffs" issue.



Few Sign

LA Times here.  "Legal nuttery...".    One commenter I read noted that the DOJ filing was signed only by two lower level DOJ attorneys (Joseph Hunt and August Flentje) and considered that unusual.


The standing to bring suit against the ACA has gotten thinner.  Originally, plaintiffs could complain the ACA forced them to pay a tax if they did not have health insurance, but that provision is gone.

Here, DOJ believes the ACA hurts the plaintiffs because it limits range of choice in insurance markets (at page 18, page 24, etc.)  DOJ cites the the word "choice" appears 10 times.  For example, under ACA, health plans must cover preventive services like mammography and you don't have a choice to get a non-mammography health plan.   You're thus injured; take it to the Supreme Court!

I'm not an attorney, but there are lots of state laws that have lots of restrictions on how insurance or other sales and products operate.  And federal laws restrict your ability to buy a car without airbags.   Maybe the state can regulate health plans moreso than the federal government.  Cases back in the 1890s ruled that Congress couldn't interfere with racial discrimination at private schools and clubs and employers, for example, striking down parts of the prior 1875 Civil Rights Act.   And parts of the New Deal in the 1930s were struck down as exceeding the authority of Congress, well, until they weren't any more.  Maybe the attempted posture here will be that states can require state health insurance (say) to require mammography, but Congress can't, since Congress can't place any limits on health plans under this theory.  Of course, the plaintiffs might have standing to sue as "injured" because of the "limits of choice" on their health plan purchases, but they might not win, because the limits serve some overriding federal purpose (just like air bags).

Wednesday, May 1, 2019

Medicare Byways: The DME Ordering Provider Database

Medicare provides a range of cloud-based provider utilization data via a home page here

In my work, I frequently use the national physician and lab database organized by CPT billing codes.  For example, you can look up your own family physician, see his name, address, and NPI, and see every CPT code that Medicare paid him for (1,000 office visits, 500 chest x-rays, 200 urinalyses, etc).   Here.   (You click through to a cloud database view, where the key tabs to play with are FILTER (e.g. by a HCPCS code) and EXPORT (e.g. to Excel).)

That database doesn't include DME suppliers.

DME Ordering Physicians

However, you can get into a database for "referring DME providers."  Here

This database logs every physician who has ordered a DME item, which item, and how many.   (DME seems to be an area with regular fraud stories, e.g. here.)

While DME has long been a somewhat sleepy field, innovation is picking up as more and more innovators are taking traditional DME devices (orthotic braces, scales, sleep apnea air pumps) and making them cloud-enabled - the internet of medical things IoMT or here, IoDME. 

So, for example, you can look up the name and address of every doc who ordered a sleep apnea air pump in CY2016.   (2017 data will be released around May 2019).

Example L1833

For example, a question came in about orthotic knee braces.  These include L1833 (and a dizzying range of other orthotics codes). 

CMS tells us that about 777 physicians or other professionals order about 49,531 of these in CY2016.   Five doctors ordered over 1000 units each, totalling 14% of all US orders.   (Full identifying info available at CMS; the docs were in Maryland, Pennsylvania, Arkansas, California, and Minnesota, for example).   You could take those 5 doctors, from the DME ordering database, and look them each up by his NPI number in the physician services database and see what services they were providing for Medicare patients. 

Orthotics Policy for Summer Beach Reading

There's also a 75-page online policy (including many pages of ICD-10 codes) for when and how these orthotic devices can be ordered - here.   Who knew?

NYT Highlights Crazy Range of Payer Payments ($11-$1000) For Same Lab Tests

On April 30, 2019, Margot Sanger-Katz at NYT highlights the wide (or wild) discrepancies in payment rates for common lab tests.  Article here.
  • Update: for a May 9 NYT follow up article on hospital payments from private payers vs Medicare fee schedules, here.  Trade press here.
    • While much is made of the "opaque health market," everyone can look up all the Medicare fees, and every self-insured firm knows (or can easily know) what it pays, and every payer knows what it pays, so it's the variances are the world's worst kept secret.  
    • OK, yes, it's opaque if you just cut your hand and have to go to the E.R. in five minutes. 
    • But, if you are a self-insured employer and want to know your 2018 rates paid vs CMS rates, you could figure most of it out in an hour.
The NYT article is a window into data published by the "Health Care Cost Institute" - here.  For example, prices for a comprehensive 14-analyte metabolic panel (80053) range from about $10 to $1000.  Sanger-Katz emphasizes this aren't charges, but paid prices in actual data across a range of real insurers.  One of the take-home lessons is that some cities have narrow price bands (Knoxville, Cleveland) and others have crazy-wide price bands (Boston, San Francisco).

You Saw This in PAMA Nationwide Lab Price Data

New CMS CLFS PAMA prices became effective in January 2018, based on reported private payer data (reported by labs) in 1H2017 and released by CMS in September 2017.    While CMS released summary median price tables, they also put the full reported lab data into a giant cloud data archive that can be searched online. 

This CMS data showed all the payment rates, for every lab test reported, so with a little effort, you could see similar data to the NYT article this week, in September 2017 for free on the CMS website.

It takes a little practice to use it (see the FILTER tab and then use the EXPORT tab) but the CMS PAMA raw cloud data is here.


For example, if you go to the cloud interface and filter for HCPCS 80053, you get 106,651 lines of data.  This gives a 1.5MB Excel file with payments running from the low pennies to $65,000.  Even assuming the last number represents 4,440 claims at $14.65 each, there were still for example 20,000 payments between $100 and $200. 


Also for CY2016 (actually 1HCY2016), BRCA 81211 payments numbered 94,977 (implying about 180,000 payments for a full year).   Common prices included $3,123 and $3,173 but there were dozens of payments between $4000 and $17,000.