Round-up Feb 19th-Feb 25th

Illumina have sued Oxford Nanopore Technologies for patent infringement. This is based on Illumina holding two patents for the use of the MspA pore. ONT have historically used a different pore, but they have perhaps switched to MspA. GenomeWeb report Oxford Nanopore’s CEO Gordon Sanghera saying, “It is gratifying to have the commercial relevance of Oxford Nanopore products so publicly acknowledged by the market monopolist for NGS.”. All this in the context of ONT soon to have their IPO, and old industry hands pointing out that Illumina launched a patent suit against Complete Genomics just before their IPO.  https://www.genomeweb.com/sequencing-technology/update-illumina-sues-oxford-nanopore-patent-infringement. Additional commentary on the unfolding drama: http://www.opiniomics.org/shots-fired-nanopore-wars-part-ii/.

Paper calling for the end of race in genetics http://science.sciencemag.org/content/351/6273/564, and a useful summary: http://www.newsworks.org/index.php/local/the-pulse/91075-scientists-call-for-the-removal-of-race-in-genetics-research- . “We believe the use of biological concepts of race in human genetic research—so disputed and so mired in confusion—is problematic at best and harmful at worst. It is time for biologists to find a better way.” One better way suggested is the use of the term “ancestry”.

Ultimately, many people born with severe genetic disease have excellent lives. So how much effort should we go to eliminate them? A very interesting read: http://www.nature.com/news/should-you-edit-your-children-s-genes-1.19432.

Robert Califf has been confirmed as the new head of the FDA, https://www.genomeweb.com/scan/califf-confirmed. He wants the FDA to be more proactive in removing bad products from the market.

Highly accurate Muscular Dystrophy diagnoses off of Ion Torrent sequencing: http://www.nature.com/jhg/journal/vaop/ncurrent/full/jhg20167a.html

For NGS data, methods that aggregate variation over genes in order to pick up on associations from case-control studies (e.g. VAAST) are all the rage. These are supplanting the variant-by-variant analyses that dominated the SNP chip world. Burden tests can be followed by procedures to identify actual causal variants (e.g. remove a variant if excluding this variant can lead to a smaller P-value for the gene). Another approach is to continue to score each variant separately, but test for association using “adaptive combination of P-values (ADA)” to pinpoint causal variants: http://www.nature.com/articles/srep21824

Grow sperm in a dish, from stem cells: http://www.sciencemag.org/news/2016/02/new-method-grows-sperm-dish. Post male world, anyone?

 

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Round-up Feb 9th – Feb 18th

News from the AGBT Conference, Feb 10th – Feb 13th

 

Research and Reviews

Market News

 

Round-up, Feb 2nd – Feb 8th

23andMe links being a morning person and genetics. The GWAS type analysis found 15 regions, several near known circadian rhythm genes. http://www.nature.com/ncomms/2016/160202/ncomms10448/full/ncomms10448.html

Oxford Nanopore’s MinION has been at work, producing “real time, portable sequencing for Ebola surveillance”: http://www.nature.com/nature/journal/vaop/ncurrent/full/nature16996.html Using the MinION (which weighs less than 100g), “We were able to generate results less than 24 h after receiving an Ebola-positive sample, with the sequencing process taking as little as 15–60 min. We show that real-time genomic surveillance is possible in resource-limited settings and can be established rapidly to monitor outbreaks.”

Last February, the UK approved the creation of three person embryos, where the mitochondria came from a third donor. The FDA had requested an Institute of Medicine report on the technique. Published this week, the report concluded with various caveats that it could be ethical — but limited to male embryos for the moment (males do not pass on mitochondria, so the changes made would affect only the individual in question). http://www.nap.edu/catalog/21871/mitochondrial-replacement-techniques-ethical-social-and-policy-considerations. However, the latest federal budget “prevents the FDA from using funds to review applications in which a human embryo is intentionally created or modified to include” changes that could be passed down to future generations.

A link between genes near an individual’s disrupted transcription factor binding sites and their phenotype data is established in this paper, in a further foray beyond the exome: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1004711. This mutational load/burden style approach used data from five individuals who have made both their whole genomes and medical histories public.

Common disease: the product of many common variants, or a few rare ones? GWAS, which only look at common variants, have not been able to explain much genetic predisposition. This study looked at both common and rare variants for AMD http://www.ncbi.nlm.nih.gov/pubmed/26691988: “Our results support the hypothesis that rare coding variants can pinpoint causal genes within known genetic loci and illustrate that applying the approach systematically to detect new loci requires extremely large sample sizes.” Also see a writeup at MassGenomics http://massgenomics.org/2016/02/rare-variant-studies-of-common-disease.html.

Two reasons senescent cells (those that no longer undergo cell division) have been in the news.

 

In a follow on to the case of the child who was forced to leave a Palo Alto school because he was a CF carrier, the U.S. Departments of Education and Justice have filed a brief siding with the family and against Palo Alto school district, arguing that the decision violoated both his first ammendament prviacy rights and the Americans with Disabilities Act http://www.paloaltoonline.com/news/2016/02/08/feds-weigh-in-on-palo-alto-dna-privacy-case

A Nature Editorial draws attention to how hard it is to get a paper corrected or retracted, even if it is clearly wrong, and even by the authors of the study: http://www.nature.com/news/reproducibility-a-tragedy-of-errors-1.19264

 

Round-up, Jan 27th – Feb 1st

In the biggest genetics discovery of the week, the first link between molecular processes and the onset of schizophrenia has been reported. Previously, case-control studies had pointed to the major histocompatibility complex on chromosome 6. This study pins down structurally diverse alleles of the complement component 4 genes, which are involved in tagging synapses for pruning during brain development. http://www.nature.com/nature/journal/vaop/ncurrent/full/nature16549.html, and a NYT write-up http://www.nytimes.com/2016/01/28/health/schizophrenia-cause-synaptic-pruning-brain-psychiatry.html
A write up of a fascinating case of a boy who was removed from a Palo Alto school because he had a cystic fibrosis genetic marker: http://www.buzzfeed.com/stephaniemlee/this-boy-was-thrown-out-of-school-because-of-his-dna-parents
And while on legal matters, GINA is the legislation that protects what can be done with your genetic material, and there’s a proposal to somewhat loosen it, to better enable Affordable Care Act type wellness plans: http://www.eeoc.gov/laws/regulations/qanda-gina-wellness.cfm. The Genetic Alliance is opposing, here’s a blog post that outlines their opposition: http://www.genomicslawreport.com/index.php/2016/01/25/eeoc-tries-to-harmonize-acas-promotion-of-employer-wellness-programs-with-ginas-ban-against-employer-access-to-genetic-information-of-employees-and-employees-family-members/
A British scientist has been given the go ahead to modify human embryos using CRISPR-Cas9, in an effort to ultimately help improve IVF success rates: http://news.yahoo.com/britain-gives-scientist-ahead-genetically-modify-human-embryos-111100612.html. Queue talk of designer babies.
And on research ethics, just in case you hadn’t spotted it, this NEJM editorial about “research parasites” has been causing a twitter storm: http://www.nejm.org/doi/full/10.1056/NEJMe1516564. Research parasites are those “people who had nothing to do with the design and execution of the study but use another group’s data for their own ends, possibly stealing from the research productivity planned by the data gatherers, or even use the data to try to disprove what the original investigators had posited.”
A report of the first patient identified with three independent autosomal-recessive single-gene disorders.  “We propose that blended phenotypes resulting from several concomitant single-gene disorders in the same patient likely account for a proportion of presumed monogenic disorders of currently unknown cause and contribute to variable genotype-phenotype correlations.” http://www.nature.com/ejhg/journal/vaop/ncurrent/full/ejhg2015285a.html
An interesting company that takes the output of a cancer screening test as input to not only help find clinical trials, but others with the same mutation profile, and easily digestible “stories” about particular mutations: http://www.cureforward.com/#/viewstory
A study making the case for the cost effectiveness of population wide carrier screening based on NGS over SNP genotyping, or no testing at all (no prices for guessing line of business of study writers): http://onlinelibrary.wiley.com/doi/10.1002/mgg3.204/abstract
A Geisinger based team have done a literature aggregation exercise to produce a database of genes involved in neurodevelopmental disorders: http://geisingeradmi.org/care-innovation/studies/dbd-genes/