Round-up April 4th – April 23rd

Veritas Genomics are offering a $999 genome, ordered through your genome, with results accessible via an App. You can see the list of conditions and traits that they will report on here.

Astra-Zeneca are partnering with Venter’s HLI (which recently raised $220M in venture funding) to analyze 2 million WGS, in a 10 year, $100ms deal.

Kaiser have announced a sequencing initiative for 500,000 of their members, with the aim of drawing actionable information into their members’ EHRs

AncestryDNA have received an undisclosed amount of funding, and are being quiet about what the money will be used for

Wellderly Case-Control analysis published: Wellderly are those with the healthy-aging phenotype, the “disease-free aging in humans without medical interventions.” The cohort of 511 “Wellderly” have a significantly lower genetic risk for Alzheimer disease and coronary artery disease, but no difference for diabetes or cancer risk. One of the first examples of WGS case-control looking at both rare and common variants.

Across nearly 600,000 individuals, 13 were found that should have died from disease — so called genetic superheros. Following up with these 13 is impossible because of how they were consented, and Daniel MacArthur uses this to make a call for “a willingness of participants to donate their genomic and clinical data, and a commitment by researchers and regulators to overcome the daunting obstacles to data sharing on a global scale.”

New development for gene-editing: “the new technique basically means that CRISPR just went from handling DNA like a meat cleaver — to handling it like a scalpel”

A second Chinese group have published the results of using CRISPR on (non-viable) human embryos, attempting to knock out the CCR5 gene, a mutation known to protect against HIV. 4 of the 26 embryos were successfully edited.

AMP has published cost analysis of WGS. Labs reported costs of

  • five to 50 genes for solid tumor samples: $578 to $908.
  • tumor panel with greater than 50 genes: $1,948.
  • hearing loss sequencing analysis: $1,048 and $1,949.
  • exome sequencing: $1,499 to $3,388.

The article also performs a cost-benefit analysis of WGS, with all scenarios they test coming out on the benefit side.

The Broad Institute, who maintains the most frequently used variant-calling pipeline, GATK, is launching GATK in the cloud, across all the main providers.

Envision, a spin-out company from Hudson-Alpha, are offering WGS in a clinical setting for $6500. They claim analysis times of 1-1.5 hours, based on their software, Codi. The group has been controversial in its advocacy of WGS rather than WES. They say the number of variants that end up being analyzed are almost identical for exomes versus genomes, but some diagnoses are possible with WGS and not in WES.

Pharmacogenomics Clinical Annotation Tool (PharmCAT), is being developed as part of a consortia. It will annotate a VCF with all CPIC level-A variants, to be published under Creative Commons

DNAFit, a company that will give you tailored training advice based on your genetics for $140, has published a study claiming that there test makes a difference to performance

A nice write up of the decisions couples face when considering pre-implantation genetic diagnosis, from Genome Magazine

GWAS hits for “subjective well-being”, and for cognitive function

Hypo-methylation at the MAOA locus has been linked to panic disorders. New research shows that those patients who undergo successful Cognitive Behavioral Therapy have their methylation patterns returned to more normal levels

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Round-up March 17th – April 3rd

A review from some GSK scientists arguing for integrating genetic based drug-efficacy into clinical trails, despite the fact that at GSK they have done 17 such GWAS and not found anything clinically actionable. They argue that “only a minority of truly efficacious drugs are likely to have clinically meaningful genetic predictors of efficacy” http://www.nature.com/nrg/journal/v17/n4/full/nrg.2016.12.html

The European Society of Human Genetics has published some musings on expanded carrier screening, which also serves as a useful survey of carrier screening http://www.nature.com/ejhg/journal/vaop/ncurrent/full/ejhg2015271a.html.

  • “Since the stated aim of reproductive screening (including carrier screening) here is not prevention, but rather the provision of options for reproductive decision making, appropriate pre-test information and voluntary decision making becomes an essential requirement rather than a mere side-constraint: without this, the screening cannot fulfil its aim.”
  • Success of programs should be judged on whether “informed choice and reproductive decision making” is optimized (not by birth prevalence of affected children)
  • They suggest that the risk of information overload may limit the type of tests that should be performed.
  • Consent as one of the most challenging issues, and the possibility of “generic consent” should be explored

Some more commentary on the Athena case, highlighting the risk that cases such as this could prevent the fledgling genetic testing field from  really getting off the ground: http://techonomy.com/2016/03/lawsuit-underscores-risk-of-thinking-genetic-tests-authoritative/.

Sequenom’s patent for non-invasive prenatal testing has been struck down, with lower courts citing the influence of the Supreme Court’s “sweeping language” in the Mayo v Prometheus. This case struck down a patent for a personalized medicine based approach to setting drug dosage level https://en.wikipedia.org/wiki/Mayo_Collaborative_Services_v._Prometheus_Laboratories,_Inc. Sequenom will now. appeal to the Supreme Court: https://www.genomeweb.com/molecular-diagnostics/sequenom-files-petition-supreme-court-review-decision-invalidating-nipt-patent

23andMe will be launching “Genotyping Services for Research” in Q2, whereby they will genotype and provide 23andMe accounts to participants in trials. Engaging those involved with research trails is seen as a challenge for many studies, and this is an easy way to give something back to them. https://www.genomeweb.com/molecular-diagnostics/23andme-running-genotyping-research-service-pilot-projects-launch-slated-q2

Qiagen have teamed up with Intel to offer a complete highly-scalable genetic testing pipeline, announcing analysis of a whole genome for $22. Note: “analysis” means variant calling: https://www.qiagenbioinformatics.com/wp-content/uploads/2016/03/White-Paper-Final-Version.pdf

Craig Venter has made a bacteria with 473 genes, which is considered an “MVP” of a genome. 149 of these genes have no known function (though are essential). http://www.sciencemag.org/news/2016/03/synthetic-microbe-lives-less-500-geneshttp://www.theatlantic.com/science/archive/2016/03/the-quest-to-make-synthetic-cells-shows-how-little-we-know-about-life/475053/

A programming language for DNA: http://www.nature.com/news/biology-software-promises-easier-way-to-program-living-cells-1.19671

Some analysis of PacBio’s threat to Illumina: http://www.fool.com/investing/general/2016/03/18/is-this-the-biggest-threat-yet-to-illumina.aspx

Risks in the genetic testing industry, a summary of a set of interviews with genetics professionals. Main risks linked to lack of physician education and pace of technology development: http://www.nature.com/gim/journal/vaop/ncurrent/full/gim201616a.html

A study using the 150k participants in the UK BioBank have quantified the lifespan reduction of having certain SNPs: http://www.eurekalert.org/pub_releases/2016-03/uoe-igc033016.php

Large GWAS meta-analysis of the genetics of cannabis use finds no significant SNPs, but four genes: http://www.nature.com/tp/journal/v6/n3/full/tp201636a.html

On secondary findings, and how not to over interpret them: http://www.nature.com/gim/journal/vaop/ncurrent/full/gim201619a.html

The case continues to grow that the genetic code may be more flexible than we think, with extra codons shown to code for selenocysteine, the 21st amino acid (i.e. just outside the canonical set of 20): https://www.sciencedaily.com/releases/2016/03/160331134413.htm

Making the case for individuals owning their health data, and the risk of the “unpatient”: http://www.nature.com/nbt/journal/v33/n9/full/nbt.3340.html