News from the AGBT Conference, Feb 10th – Feb 13th
- Note this is the first year that they’ve separated Research and Tech (just happened) and Clinical Applications (to be held in September)
- 10X unveiled new pipeline (machine plus application platforms), Chromium, full release due in May. Reminder: synthetic long-reads sequencing can do some things, like long-range phasing, well. Chromium can do Phase blocks which average >10MB, and requires similar coverage to standard Ilumina runs. Phased reads enables much better calling of copy number regions and large indels. They’ve also made good progress towards the first diploid de novo assemblies. Cost for whole genome is $450 on top of $1000. Press release on co-marketing with Ilumina (“10 X on X Ten”): http://www.illumina.com/company/news-center/press-releases/press-release-details.html?newsid=2137067&linkId=21145087.Press release on their new shiny exome: http://www.10xgenomics.com/news/agilent-technologies-and-10x-genomics-announce-collaboration-to-develop-a-premium-exome/
- Nanostring, a no library prep or amplification sequencing technology, still far from commercialization: http://core-genomics.blogspot.com/2016/02/agbt16-day-4-new-sequencing-chemistry.html
- Foundation Medicine released details of their circulating tumor DNA (ctDNA) assay: https://www.genomeweb.com/sequencing-technology/foundation-medicine-describes-ctdna-assay-validation-agbt
- The 100K Genome Asia project was announced, first aim is to make reference genomes for each of the major Asian ethnic groups: http://www.prnewswire.com/news-releases/genomeasia-100k-initiative-announced-to-sequence-100000-genomes-in-south-north-and-east-asia-568523301.html. Note: Macrogen are involved
- Some details of NASA’s twins study (one in space, one earth bound), which I’m mentioning just because I’d never heard of it, and its cool: http://www.nasa.gov/mission_pages/station/research/experiments/2108.html
Research and Reviews
- On Clinical Utility. The ACMG believes that diagnoses, and corresponding changes in disease management, should be sufficient demonstration of clinical utility — even in the absence of evidence for improved clinical outcomes (http://www.nature.com/gim/journal/vaop/ncurrent/full/gim2015153a.html). Payors disagree, e.g. see this lawsuit of a genetic testing company taking a payor to court for not covering their test: https://www.genomeweb.com/molecular-diagnostics/exact-v-humana-lawsuit-reflects-genetic-testing-firms-deepening-adversarial. This week the Office of Public Health Genomics published a position http://www.nature.com/gim/journal/vaop/ncurrent/full/gim2015153a.html, which is a good short read on the complexities of what “clinical utility” means, ultimately arguing for something that is highly context specific.
- On testing of minors. Current ASHG guidelines say there should be no predictive genetic testing of minors (http://www.ncbi.nlm.nih.gov/pubmed/26140447). This short piece outlines the opposing view, http://www.nature.com/gim/journal/vaop/ncurrent/full/gim2015191a.html, drawing on a study just published concerning lack of adverse effects of such testing.
- So, we know that all non-African humans have Neanderthal DNA. But the picture of which other homonoid species we interbred with, and how, just got a whole lot more complicated: http://www.sciencemag.org/news/2016/02/humans-mated-neandertals-much-earlier-and-more-frequently-thought
- Some of the genetic basis of musical ability uncovered: http://www.nature.com/articles/srep21198— highlighting many genes (including novel ones) that make sense, e.g. involved in inner ear development, cognition, memory, auditory processing, and genes known to be related to bird song in birds. I find this interesting as a glimpse at a possible future — something not disease related (musical aptitude, other types of ability…), but just as amenable to genetic burden report as a disease area.
- A competitor to algorithms that use phenotype to rank variants, OMIMGeneExplorer: http://www.ncbi.nlm.nih.gov/pubmed/26838676. It incorporates “a simple interface for translating free-text clinical notes into HPO terms”
- Heidi Rehm et al on strategies for Academic Medical Centers: http://www.mdpi.com/2075-4426/6/1/8/htm. In a nutshell: forge commercial partnerships; try and consolidate onto one genomics based test for rare diseases; look to support research projects.
- A review of the current state of the art of single-cell sequencing: http://www.nature.com/nrg/journal/v17/n3/full/nrg.2015.16.html
- PheWas are the younger sibling of the better known GWAS. In Genome Wide Association Studies, you start with cases and controls and find genetic variation that segregates. In a Phenome Wide Association Study, you use phenotype data from EHRs to explore the phenomic consequences of particular genetic variants. PheWAS can be more powerful if you have rich phenotype data. Review of current state of the art: http://www.nature.com/nrg/journal/v17/n3/full/nrg.2015.36.html.
- A study using 23andMe data to look at penetrance (the often missing piece of the puzzle), in this case of prion disease. Write-up here: http://www.nature.com/nrg/journal/v17/n3/full/nrg.2016.9.html. The authors of the paper are a husband and wife team, who got into this research when they found out she had a prion disease, with no current treatment, that will kill her at age 50ish, unless there are major breakthroughs shortly. Read their story here: http://www.bostonglobe.com/magazine/2016/02/17/husband-and-wife-race-cure-her-fatal-genetic-disease/
- 49% of Americans believe in human evolution, but 75% of Americans believe in elephant evolution http://www.sciencemag.org/news/2016/02/americans-knowledge-evolution-isn-t-bad-if-you-ask-them-about-elephants
- Sure Genomics — who launched a whole genome, more or less direct to consumer product earlier this month — had been planning to get around FDA regs: “Sure Genomics loops in a physician from its network to gather information about your family history and order the sequencing that intends to answer your specific questions about your health. The physician then prescribes the sequencing, meaning they technically have oversight of the information you’re about to get back.” There’s also a genetic counsellor involved in the return of results: http://www.businessinsider.com/sure-genomics-genomic-sequencing-test-2016-2.But they just received an FDA letter saying: “If you do not believe that you are required to obtain FDA clearance for the SureDNA test, please provide us with the basis of that determination.”
- Sophia Genetics (variant calling, annotation,algorithms, reporting, http://www.sophiagenetics.com/hospitals/sophia-ddm/sophia-ddmtm-details.html) partner with Swift Biosciences (sequencing), aiming to capture European market: https://www.genomeweb.com/informatics/sophia-genetics-partners-swift-biosciences-offer-mdx-solution
- LabCorp are doing well, largely thanks to their Covance acquisition: https://www.genomeweb.com/molecular-diagnostics/boosted-covance-acquisition-labcorp-posts-48-percent-revenue-growth-q4
- Genomics England announced partnerships with
- Icon, for data management: https://www.genomeweb.com/informatics/genomics-england-taps-icon-manage-100k-genomic-data
- Ilumina, for genome interpretation https://www.genomeweb.com/business-news/illumina-genomics-england-partner-improve-genomic-interpretation. This was not an expected announcement.
- Invitae is selling far more tests than last year, but lost $90m in 2015. This year they will introduce a panel aimed at healthy individuals: https://www.genomeweb.com/molecular-diagnostics/invitaes-q4-revenues-increase-more-threefold
- Seven Bridges, who do bioinformatics in the cloud for genomics, have raised $45m. That will go on head count, especially in their new SF office: https://www.genomeweb.com/informatics/seven-bridges-genomics-raises-45-million-series
- Military personnel (active and veteran) can now get a genetic test designed to look at mental health genetics (“pharmacogenetic test for psychiatry”) for free: https://genomind.com/news/genetic-testing-for-mental-health-approved-as-new-ally-for-military-personnel-and-veterans/