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:

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:

Foundation Medicine launched a liquid biopsy test, for those cancer patients for whom a tumor sample is unobtainable.

NantHealth is filing for an IPO

The National Human Genome Research Institute will spend $21.8M to assess the cost effectiveness and clinical utility of sequencing

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: Driver genes:, Signatures:

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%.

An overview of hereditary cancer risk, as provided by the American Society of Clinical Oncology for their oncologist members:

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:

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):

A description from AstraZeneca on how they define actionability in somatic samples that are part of early stage clinical trails:

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:

An easy read on Oxford Nanopore’s technology,, and a more scholarly take on the history of nanopore sequencing:

A Huffington Post blog on the current relevance of genetic testing on mental disorders argues that we are nowhere near ready for prime time: 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”:

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.

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:

A study using ENCODE data to try and elucidate function of intergenic SNPs that are associated with disease: Another study that looks at the combined effects of SNPs on disease risk, focused on Coronary Artery Disease

A review on modeling propensity for common diseases, including environmental factors:

Two alleles associated with having twins have been discovered via GWAS, with large effect sizes:

And finally, how do your genes influence your politics?



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