JANUARY 2ND, 2020
The shortest bi-weekly genomics research report in the world. Curated by the Emedgene Research Division.
Keeping up with genomes
Genome Medicine has a special issue devoted to ‘Clinical interpretation of genome variation’.
In the lead editorial, guest editors Rehm and Fowler reiterate the need for diverse training sets, robust pipelines & effective analysis tools for the detection and interpretation of clinically significant variants, in order to provide quality care to all patients.
We covered several publications included in the issue in the past. Some interesting new ones:
- Recommendations for the collection and use of multiplexed functional data for clinical variant interpretation
- Recommendations for application of the functional evidence PS3/BS3 criterion using the ACMG/AMP sequence variant interpretation framework (which has been available on the ClinGen website since October)
1 Million ClinVar
On December 20th ClinVar announced 1,000,000 variants submitted, 568,000 unique. Congrats to all contributing members! This is an outstanding achievement for the entire community.
The AI Corner
In a large study published in Nature, Google Health/DeepMind demonstrates an AI system that outperforms specialists at diagnosing breast cancer. The study used representative datasets from the USA and the UK, and indicates an absolute reduction of 5.7% and 1.2% (USA and UK) in false positives and 9.4% and 2.7% in false negatives.
Also worth reading this Twitter thread from author Jeffrey De Fauw
Happy 2020 Break !
De novo mutations arising on the paternal chromosome make the largest known contribution to autism risk, and correlate with paternal age at the time of conception. Quantification of sperm mosaicism can stratify autism spectrum disorder recurrence risk in offspring.
Combining family history with genetic testing
Assessing VUS in BRCA1/2 using personal and family history
Genetics in Medicine
Using SNP and patient age in addition to family history in order to assess prostate cancer risk.
Gene therapy for Hemophilia A
A multiyear follow-up of AAV5-hFVIII-SQ gene therapy for haemophilia A reveals sustained & clinically relevant benefit of the therapy with substantial decrease in annualized rates of bleeding events & complete cessation of prophylactic factor VIII use in all participants.
Genomic medicine in primary care
An assessment of family physicians’ current involvement and confidence in genomic medicine (GM). FPs lack confidence in GM skills needed for practice, particularly in emerging areas of GM. They see their role as making appropriate referrals, are somewhat optimistic about the contribution GM may make to patient care, but express caution about its current clinical benefits.
Frontiers in Genetics
- KDR and pulmonary arterial hypertension bioRxiv
- NDUFAF8 and Leigh syndrome with an isolated complex I deficiency AJHG
- SYCP2 and human male infertility AJHG
- RIPOR2 and adult-onset hearing loss bioRxiv
- PPP1R12A and congenital malformations affecting embryogenesis of brain and genitourinary systems AJHG
- NADSYN1 and multiple organ defects AJHG
(Ada is our AI engine, she likes to add an interesting new factoid she discovered in every issue)
Homozygous gain-of-function germline variants in STAT2 are associated with severe type I interferonopathy and unrestrained interferon signaling. The loss of USP18 (the negative regulator of IFNα/β signaling) activity is the suggestive mechanism for the disease manifestation. Published in both Science Immunology and bioRxiv.
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