Round-up, May 10th – May 22nd

George Church is back in the news, this time for the plan to write a human genome within the next 10 years: https://www.statnews.com/2016/05/16/george-church-profile/

In January, the Department of Health and Human Services updated  what data can be requested by patients about themselves, to cover most things: http://www.hhs.gov/hipaa/for-professionals/privacy/guidance/access/index.html. This was published on a blog and went somewhat unnoticed, but has just come into the limelight as several individuals asked Myriad for all their genetic variants (including benign variants). Myriad initially said No, and although complied after they became aware of the new regulations, the plaintiffs have not dropped their HIPAA complaint. The individuals wanted the benign variants so that they could upload them to ClinVar. Science’s write-up is a must read: http://www.sciencemag.org/news/2016/05/after-prominent-gene-testing-firm-declined-give-patients-their-complete-data-aclu-filed

The White House is targeting Mircobiomes for a bold new funding push, with an emphasis on going beyond findings correlations to building tools to get at causation: http://www.sciencemag.org/news/2016/05/earth-s-microbes-get-their-own-white-house-initiative

The US Equal Employment Opportunity Commission (EEOC) just updated regulations that the ASHG argues means that “employees who decide to keep their own and their spouses’ health information private may have to pay “significantly higher health insurance premiums” than those who share their information”; “”The new EEOC rules mean that Americans could be forced to choose between access to affordable healthcare and keeping their health information private”: https://www.genomeweb.com/policy-legislation/genetic-privacy-protection-weakened-recently-revised-eeoc-regulations-ashg-says

A fascinating read about the relationship between study designers, their participants, the journalists who report on them, and the public reaction: http://www.sciencemag.org/news/2016/05/cholesterol-study-volunteer-unsettling-discovery-science-paper-herself

Natera are finding they are starting to see good reimbursement for average risk pregnancies for their Non-invasive prenatal screening test: https://www.genomeweb.com/sequencing-technology/natera-says-bet-average-risk-pregnancies-paying-it-faces-changing

UK start-up PetaGene has a business model based on compressing sequence files, so their customers spend less on storage: https://www.genomeweb.com/informatics/uk-based-petagene-building-business-around-sequence-file-compression-software-suite

A GenomeWeb interview with the head of BGI Research, focusing on Clinical Tests. One of their projects is a cloud based computer  platform, “we are not just going to offer kits and instruments but also software in the future”: https://www.genomeweb.com/molecular-diagnostics/qa-mao-mao-new-chief-scientific-officer-bgi-genomics-developing-clinical

Happy 10th birthday, Next Generation Sequencing! A review: http://www.nature.com/nrg/journal/v17/n6/full/nrg.2016.49.html

A study that looked at concordance between WES and Sanger found the big issue for WES remains poor coverage of certain areas, for which Sanger is still needed — 42 of 51 genes analyzed had “adequate” coverage (over 75% of sequence with coverage of greater than 20×), and for these concordance was very high (97.3%, with not all discrepancies due to WES data): http://onlinelibrary.wiley.com/doi/10.1002/mgg3.223/full

A study of various labs variant classification using the AMCG/AMP guidelines found high discordance, but that the criteria gave a good framework for talking about differences. The paper does a good job at illustrating how the criteria are being interpreted, including when they are being altered: http://www.cell.com/ajhg/fulltext/S0002-9297%2816%2930059-3?date=051316&u=115

A big data-mining project representing joint work from the New York Genomes Center and 23-and-Me has found many variants involved in multiple traits, and some pairs of variants linked causally: http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3570.html

Illumina’s MiSeq does not do well with the sequence ‘CCCGCC’: http://www.nature.com/articles/srep26314

A platform to aggregate patient level clinical trail data, Vivli, is gathering steam: http://www.sciencemag.org/news/2016/05/industry-backed-project-aims-become-one-stop-shop-clinical-research-data

An overview of several studies show human evolution at work: http://www.sciencemag.org/news/2016/05/humans-are-still-evolving-and-we-can-watch-it-happen. On the shortest of time scales, selection in the middle of the 20th century for an allele that makes it harder to quit smoking has been shown in the UK population.

A method proposed to replace the need to find controls for matched case-control studies, using publicly available data — the concept is termed the Universal Control Repository Network (UNICORN): http://www.cell.com/ajhg/fulltext/S0002-9297(16)30035-0

Various studies of cancer outcomes from patients who underwent somatic genetic testing have shown less than stellar results, but often on small sample sizes. A meta-analysis of 13,000 patients has shown clear benefit: https://www.genomeweb.com/cancer/precision-medicine-oncology-gets-more-support-13k-patient-meta-analysis.

The NIH is funding four new studies on the ethical, social, legal implications of genomics: https://www.nih.gov/news-events/news-releases/nih-funds-new-studies-ethical-legal-social-impact-genomic-information

 

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