Round up April 24th – May 9th

Astra-Zeneca are co-ordinating the sequencing of 2m genomes, with multiple partners, including Venter’s HLI, the Sanger, and Genomics England: https://www.genomeweb.com/sequencing-technology/astrazeneca-launches-genomics-initiative-drive-drug-discovery-and-development

Geisinger Health System are sequencing 100,000 exomes (to be expanded to 250,000) – this is an interesting read on a healthcare systems’ genomics ambitions. One advantage they have is the ability to recontact patients to help resolve VUSs: https://www.genomeweb.com/molecular-diagnostics/geisinger-mycode-results-reengagement-patients-may-clarify-variant

Foundation Medicine launched a liquid biopsy test, for those cancer patients for whom a tumor sample is unobtainable. https://www.genomeweb.com/molecular-diagnostics/foundation-medicine-partners-astrazeneca-launches-liquid-biopsy-test-acquires

NantHealth is filing for an IPO https://www.genomeweb.com/sequencing-technology/personalized-healthcare-firm-nanthealth-files-ipo

The National Human Genome Research Institute will spend $21.8M to assess the cost effectiveness and clinical utility of sequencing https://www.genomeweb.com/sequencing-technology/clinical-sequencing-evidence-consortium-gets-218m-commitment-nhgri

A study that did WGS on 560 breast cancer tumor samples concludes that “the genes harbouring the substantial majority of driver mutations are now known” — there’s about 90 of them. They also identify “genetic signatures” of the cancer– “Each mutational process will leave its own specific pattern on the genome or mutational signature”. A consequence of this is that “statistical models involving mutability cannot assume uniform genomic mutation rates and must consider signature dependent variation as a factor in all future analyses”. BBC write-up: http://www.bbc.com/news/health-36168717. Driver genes: http://www.nature.com/nature/journal/vaop/ncurrent/full/nature17676.html, Signatures: http://www.nature.com/ncomms/2016/160502/ncomms11383/full/ncomms11383.html

Memorial Sloan Kettering have announced some of the effects of their MSK-IMPACT tumor-normal panel. They now report on germline variants, and about 20% of patients have pathogenic hereditary cancer variants. Data on the proportion of patients with clinically relevant information returned is not available, except for lung cancer, where it is ~77%. https://www.genomeweb.com/molecular-diagnostics/mskcc-cancer-sequencing-team-shares-first-data-risk-variants-clinical-germline

An overview of hereditary cancer risk, as provided by the American Society of Clinical Oncology for their oncologist members: http://www.asco.org/practice-guidelines/practice-management-issues/genetics-toolkit#/welcome

Before the ACMG guidelines were published, the International Agency for Research on Cancer (IARC) had a probabilistic framework for interpreting VUSs. A paper that used the two alongside each other found only “slight agreement” between the two methods: http://www.nature.com/gim/journal/vaop/ncurrent/full/gim201639a.html

ClinGen have developed a framework for the actionability of disease-gene pairs, and have published the results of applying this framework to the 56 incidental finding genes (see Table 3): http://www.nature.com/gim/journal/vaop/ncurrent/full/gim201640a.html

A description from AstraZeneca on how they define actionability in somatic samples that are part of early stage clinical trails: http://www.nature.com/nrc/journal/v16/n5/full/nrc.2016.35.html

De novo assembly of a human genome without long reads? 10X and BioNano have joined forces to produce a high quality such assembly based on Ilumina tech: https://www.genomeweb.com/sequencing-technology/ucsf-10x-genomics-bionano-genomics-team-describes-new-de-novo-genome-sequence

An easy read on Oxford Nanopore’s technology, http://www.theatlantic.com/science/archive/2016/04/this-technology-will-allow-anyone-to-sequence-dna-anywhere/479625/, and a more scholarly take on the history of nanopore sequencing: http://www.nature.com/nbt/journal/v34/n5/full/nbt.3423.html

A Huffington Post blog on the current relevance of genetic testing on mental disorders argues that we are nowhere near ready for prime time: http://www.huffingtonpost.com/allen-frances/what-you-need-to-know-abo_34_b_9812922.html. Another blog on personalised medicine in cancer states we are only pursuing this in cancer because ““you are selling hope in a bottle, and you cannot refuse people who are dying”: http://www.star2.com/health/wellness/2016/05/01/the-over-hyping-of-precision-medicine/

The beautiful story of how Thailand have implemented a simple wallet card for the results of a pharmacogenomics test, for which 8% of their population will test positive. The card indicates whether the patient will succumb to an often fatal disease if given a particular drug. http://www.futuremedicine.com/doi/full/10.2217/pgs-2015-0009

A study that shows that ethnically based Genetic Risk Scores (using aggregates of individual variant effects to predict disease risk) do better than non-ethnically based ones: http://www.ncbi.nlm.nih.gov/pubmed/27140652?dopt=Abstract

A study using ENCODE data to try and elucidate function of intergenic SNPs that are associated with disease: http://www.nature.com/articles/npjgenmed20166. Another study that looks at the combined effects of SNPs on disease risk, focused on Coronary Artery Disease  http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3561.html

A review on modeling propensity for common diseases, including environmental factors: http://www.nature.com/nrg/journal/vaop/ncurrent/full/nrg.2016.27.html

Two alleles associated with having twins have been discovered via GWAS, with large effect sizes: http://www.cell.com/ajhg/abstract/S0002-9297(16)30043-X

And finally, how do your genes influence your politics? http://www.scientificamerican.com/article/the-genes-of-left-and-right/

 

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