Round-up Sept 30th – Nov 8th

It has been too long since the last round-up, so here is a birds eye view of some of the more eye catching developments.

  • ASHG 2016 happened
  • The 4th Global Alliance for Genomics and Health happened
  • CMS has updated CPT codes, which is relatively good news for reimbursement potential of NGS tests.
  • Illumina and PacBio shares fall on Q3 earnings reports
  • PacBio suing Oxford Nanapore
  • When genetic testing goes wrong – the misdiagnosis of a family of 20

I am going to try to shift to weekly updates as of now!

ASHG 2016, some of my highlights (which you would have seen if you’d been following me on Twitter…):

  • Daniel MacArthur announces Genome Aggregation Database, contains 120k+ exomes and 15k+ genomes, gnomAD. Wow. #ASHG16
  • gnomAD, initial focus on analysis of protein-truncating regions; pilot studies involving recontact of individuals with “extreme genotypes” #ASHG16
  • Your age written in your genome – age predicted mean error 11 years from NGS data, using telomere length and mosaic chromosome loss. #ASHG16
  • Method to integrate 10k+ functional genomics datasets, can predict about half of conserved non-exonic bases #ASHG16

Global Alliance for Genomics and Health, 4th Plenary Session, some of my highlights:

  • The guiding principle of data sharing not protection from harm, but activating the right to benefit from science (UDHR 27) – B Knoppers @ #GA4GH2016
  • Improving care of individuals and families through “share, compare, resolve” framework for variant curation, BRCA Exchange #GA4GH2016
  • Match Maker Exchange as “a dating service for lonely exomes”, a federated network of databases for finding similar patients #GA4GH2016
  • We should call out those not sharing data, and be on the watch for those “sharewashing”. Voices of industry at #GA4GH2016
  • Data Working group mantra “collaborate on interface; compete on implementation”; data schema and API now available #GA4GH2016
  • #GA4GH2016incoming head Ewan Birney says we have to raise our game, got to make stuff that works practically, will bribe volunteers with chocolate

 

Market news:

CMS has upped the reimbursement for certain CPT codes covering NGS tests, though not enough for some: https://www.genomeweb.com/molecular-diagnostics/medicare-bumps-final-pricing-certain-ngs-tests-and-maaas-not-enough-some-say

On Oct 11th Illumina announced lower than expected Q3 earnings, driven by a “larger than anticipated year-over-year decline in high-throughput sequencing instruments”. Shares fell by 25% and have not recovered since. https://www.genomeweb.com/sequencing/illuminas-q3-revenues-fall-short-guidance-shares-tumble

PacBio’s shares also fell on its Q3 financial reports, despite revenue jumping 80%. It has launched a patent battle with Oxford Nanapore, seeking to ban ONT’s presence in the US: https://www.genomeweb.com/sequencing/pacbios-q3-revenue-jumps-80-percent-files-complaint-against-oxford-nanopore

PierianDX bought Tute Genomics. Pierian had been focusing its efforts on software in daignostic somatic testing, and Tute was primarily focused on germline. https://www.genomeweb.com/informatics/pieriandx-buys-tute-genomics-improve-clinical-informatics-workflow-constitutional

23andMe have abandoned NGS testing, instead focusing on their chip technology – NGS was too complex and the consumer price point not achievable. https://www.buzzfeed.com/stephaniemlee/23andme-anne-wojcicki-next-generation-sequencing

Veritas, who have a $999 genome on the market, have raised a $30m Series B: https://www.genomeweb.com/sequencing/veritas-genetics-raises-30m-series-b-financing-round

Illumina have launched a new 170 gene panel that uses a hybrid capture technique for DNA and RNA simultaneously. First only for research use, Illumina anticipate its use as a companion diagnostic by pharma companies: https://www.genomeweb.com/sequencing/illumina-expects-pharma-firms-leverage-new-tumor-profiling-panel-companion-dx

Invitae will offer the ACMG Incidental Findings 56 gene panel on the Helix platform: https://www.genomeweb.com/molecular-diagnostics/invitae-helix-bring-medical-genetic-testing-broader-market-through-apps

The UK government has made NIPT for trisomies 13, 18 and 21 standard of care. Although abortions are expected to rise, this number will be smaller than the number of miscarriages prevented because the use of amnios will go down: https://www.theguardian.com/society/2016/nov/04/new-prenatal-test-for-downs-syndrome-will-not-lead-to-more-terminations-nipt

You can now order a genomics test on Amazon: https://www.genomeweb.com/molecular-diagnostics/good-start-genetics-selling-carrier-screening-tests-through-amazon

Science:

HLI have published the results of deep sequencing of 10,000 individuals. They find that 84% of human genome can be reliably sequenced via Illumina technology. Each individual contributes ~8,500 novel variants. http://www.prnewswire.com/news-releases/researchers-from-human-longevity-inc-publish-paper-detailing-results-of-deep-sequencing-of-10545-human-genomes-300338937.html

Using Complete Genomics long reads technology, researchers at the Personal Genomes Project have published 100 haplotyped genomes, with associated phenotype data: http://gigascience.biomedcentral.com/articles/10.1186/s13742-016-0148-z

A study from Ambry makes the case for the continued need for Sanger confirmation, because achieving a satisfactory Specificity/Sensitivity for clinical applications with NGS is impossible, particularly in certain regions. They argue that training pipelines to assess variants in these regions is impossible except with vast validation sets, which labs are unlikely to be able to do. https://www.genomeweb.com/sequencing/ambry-genetics-study-indicates-continued-need-sanger-confirmation-ngs-testing

The BabySeq project, which aims to sequence both healthy and sick newborns, is having surprisingly low uptake, even in the sick baby cohort: http://www.sciencemag.org/news/2016/10/surprisingly-few-new-parents-enlist-study-have-baby-s-genome-sequenced

CRISPR potential for sickle cell disease. “What we have right now, if we can scale it up and make sure it works well, is already enough to form the basis of a clinical trial to cure sickle cell disease with gene editing,” first author Mark DeWitt told the LA Times.: http://stm.sciencemag.org/content/8/360/360ra134

A survey of the practices of clinical diagnostic labs finds large discrepancies particularly in “use of phenotypic data to inform case analysis and interpretation and reporting of case-specific quality metrics and methods”: http://www.nature.com/gim/journal/vaop/ncurrent/full/gim2016152a.html

An accessible discussion of the graph based genome. https://www.statnews.com/2016/10/07/dna-genome-sequencing-new-maps/:

— The first open access graph of ~1000 people will be available by the end of the year

— Seven Bridges unveiled a beta proprietary graph earlier this year – the NCI and the VA are both down to use it

— A competition is being set up by the Global Alliance to “find out who has got the best graph”

— Suspicion of proprietary tools and patents in the space

— Likes of MacArthur (of ExAC fame) thinks long term it will be a thing, but not in a hurry to make the transition away from tried and tested reference based tools

Also in the news:

A family of 20 was mis-diagnosed with a cardiac issue, with at least one very invasive procedure carried out. “When the pursuit of the genotype gets in front of the establishment of the phenotype, bad things happen.” http://www.frontlinegenomics.com/news/8153/family-study-wrong-genetic-diagnoses/http://www.sciencedirect.com/science/article/pii/S0025619616304633

There are over a dozen companies doing DTC genetic analysis of sports performance. This article is from a woman who ordered several of them and was very unimpressed by both the lack of concordance between tests, and the type of data that she received: https://www.statnews.com/2016/11/02/genetic-testing-sports/

J Lo will star in a new NBC series based in a world where CRISPR’s use is rampant: http://www.hollywoodreporter.com/live-feed/jennifer-lopez-sets-futuristic-bio-939509