Round-up August 23rd – September 29th

 

Highlights

Europe is launching a “Million Genomes initiative’, partly in response to the US’s Precision Medicine Initiative, and partly to combat the fragmentation of research along national lines currently seen in Europe: https://www.genomeweb.com/informatics/million-european-genomes-alliance-proposed-response-obamas-precision-medicine-initiative

Zuckerberg and Chan have committed $3bn to curing all the world’s diseases. As some have pointed out, the sum pales in comparison to what is spent on biomedical research, but the ambition is admirable: http://www.popsci.com/lets-talk-about-how-small-3-billion-is-compared-to-total-scientific-funding

Meanwhile, Microsoft have set their intention to “solve cancer” within the decade, using AI. I’m including this blog post from someone skeptical partly because it has such an on point XKCD comic: http://scienceblogs.com/insolence/2016/09/23/microsoft-vows-to-solve-cancer-in-a-decade-hubris-ensues/

Should babies be sequenced at birth? $25m of new projects announced by the NIH will study the practicalities: https://www.nih.gov/news-events/news-releases/nih-program-explores-use-genomic-sequencing-newborn-healthcare

A “population-based health intervention effort ” in Nevada had thousands of registrants within the first 24 hours of launch, and all registrants will receive free 23andMe reports. The project is a colloboration of Renown Health (an ACO, with rick phenotype data), the Desert Research Initiative (who have environmental data) and 23andMe. https://www.genomeweb.com/molecular-diagnostics/thousands-join-nevada-population-study-get-free-23andme-genetic-tests

Interesting papers

How rare is rare enough to be concerning for a variant? A new paper by the ExAC team suggests some thresholds for the “maximum credible population AF” for different conditions. Spoiler: much less than 5% http://biorxiv.org/content/early/2016/09/02/073114

Using a genomic test to identify which breast cancer patients can skip chemo: http://www.nytimes.com/2016/08/25/science/gene-tests-identify-breast-cancer-patients-who-can-skip-chemotherapy-study-says.html  “The main goal of the study (of 6693 early stage breast cancer patients) was to find out whether women with a high clinical risk but a low genomic risk (23%) could safely forgo chemo… After five years, among those who did not receive chemotherapy, 94.4 percent had no distant spread. Those who received chemo fared slightly better: 95.9 percent had no distant spread.”

The future of baby making became even more exotic with the report of the unnecessary nature of the egg cell (in mice at least): http://www.nature.com/articles/ncomms12676

A good illustration of the importance of gene-environment interactions: children with a particular variant were not more likely to develop asthma than average. But children with the variant who had a viral respiratory infection when an infant are 12 times as likely to develop asthma. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0157848

Genomiser, an extension of Exomiser, has been published. It prioritizes non-coding variation in the context of phenotype. http://www.cell.com/ajhg/abstract/S0002-9297(16)30278-6

The Middle East is an interesting population from a genetic point of view because of high levels of consanguinity (100 times higher than the US) and large families. A study looking at 1111 exomes, found e.g. “rare homozygous putative loss-of-function variants in 301 genes, of which a substantial proportion were novel,”: http://www.nature.com/ng/journal/v48/n9/full/ng.3652.html

A delightful paper that dwells on some of the inconsistent uses of language in genomics. e.g. “It is the phenotype or trait that exhibits a given inheritance pattern, not the pathogenic variant. Thus, it is incorrect to say that a variant “is” autosomal recessive (or dominant, etc.) but correct to say it is associated with an autosomal recessive (or dominant) pattern of inheritance.” And calling it Next Generation Sequencing is so yesteryear, now we’re calling it “Massively Parallel Sequencing”. http://www.nature.com/gim/journal/vaop/ncurrent/full/gim2016139a.html

A study of how direct to consumer companies handled data privacy and sharing showed most came up short. The study is also of interest for listing the breadth of concerns that such a company needs to address: https://www.ncbi.nlm.nih.gov/pubmed/27657678

5.6% of people who took a direct to consumer pharmacogenomics test have had prescriptions altered based on the results: http://www.nature.com/gim/journal/vaop/ncurrent/full/gim2016141a.html

You’ve heard of GWAS, you’ve probably heard of PheWAS, but what about EWAS? Epigenome Wide Association Studies are starting to be a thing, such as this one on Schizophrenia, which discovered hundreds of sites differentially methylated in those with the condition, some overlapping with sites previously identified via GWAS: http://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1041-x

And in another win for omics, a Metabolomic study has shown clear differences in those suffering from Chronic Fatugue Syndrome – their metabolomes resemble those who have infections. The signal is clear enough to suggest a much needed diagnostic method: http://www.pnas.org/content/early/2016/08/24/1607571113.full

The ACMG are planning on updating their list of 56 genes for incidental findings by year end. Subsequent iterations will likely involve pharmacogenomics genes. https://www.genomeweb.com/molecular-diagnostics/acmg-plans-update-secondary-findings-gene-list-year-end-considers-pgx-genes

A new database for DNA modification: http://biorxiv.org/content/early/2016/08/26/071712

Industry News

Health Nucleus, “powered by Human Lengevity Inc” (Craig Venter’s latest project) – an “interactive health platform” completely personalized to you, using your genome. https://www.healthnucleus.com/purpose

Tute Genomics recently launched a campaign via Kickstarter offering DTC genomic services. The FDA swiftly sent them a letter and yesterday the campaign was suspended. The whole exome (~$400) or whole genome (~$1000) service would have not only given customers access to their raw data, but also reports on carrier status, ACMG incidental findings, pharmacogenomics, and “information on well-characterized variant-disease risks for different common or complex diseases”: https://www.genomeweb.com/informatics/tute-genomics-launches-kickstarter-gauge-market-interest-dtc-whole-genome-exome. The note on cancellation: http://www.geneticdirect.com/?p=1749

IDbyDNA, a company that shares a significant overlap of brain power with us at Omicia, has raised a $9m Series A. Their tech enables rapid and exact pathogen detection. https://www.genomeweb.com/business-news/idbydna-raises-9m-series-financing-round

Sophia Genetics and Illumina have started a partnership to address the CLinical Diagnostics European market: https://www.genomeweb.com/informatics/illumina-sophia-genetics-comarket-ngs-solutions-clinical-dx

GenomOncology will work with Genomics England on their cancer samples: https://www.genomeweb.com/cancer/genomics-england-use-genomoncology-data-management-system-100k-genomes-project

Color Genomics, who offer a $250 hereditary cancer test, have raised a $45m Series B. https://www.genomeweb.com/cancer/color-genomics-raises-45m-series-b-financing-offers-patient-families-discounted-testing

A fairly good overview of what Illumina is up to these days, including Helix: https://www.fastcompany.com/3061591/body-os/illumina-owns-the-dna-sequencing-market-now-its-building-an-app-store-too “In the case of Flatley’s own malignant hypothermia, which can result in sudden death while under general anesthesia, a user might query this before deciding on surgery for instance. Or a family might check for an MT-RNR1 m.1555A>G mutation before their child is being treated with gentamicin saving the 1:500 kids with this particular variant from going deaf while in the ICU.”

 

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