OCTOBER 3RD, 2019
The shortest bi-weekly genomics research report in the world. Curated by the Emedgene Research Division.
FLet’s get the latest hot news out of the way. A technical artifact resulted in deviation from the Hardy-Weinberg Equilibrium (HWE), negating previous findings associating CCR5-Δ32 with increased mortality.
Noteworthy variant research
Extensive disruption of protein interactions by genetic variants across broad allele frequency ranges. Functional analysis finds that ~10.5% of these variants – per individual – can be disruptive, affecting 669 human protein interactions.
Frequency cutoffs below 1% may not be applicable in all clinical cases: a lesson from fibrillinopathies
On the bioinformatics side, but interesting results. New tool to identify evolutionary signatures of protein-coding regions, PhyloCSF, identifies 118 GWAS protein-altering variants that were previously thought to be noncoding.
The AI Corner
Humans vs Machines!
A meta-analysis of 25 studies over 13 specialties found similar performance between deep learning and humans. BUT only a limited number of studies evaluate the performance of AI models in the presence of a-priori knowledge about the patient, and AI cannot yet replicate the essence of the diagnostic process.
Ditch the labels
Large hand-labeled training sets for machine learning, are expensive and time-consuming to produce. But what if we didn’t need them?
Researchers were able to develop a weakly supervised deep learning method that successfully identified patient outcomes from clinical notes.
npj Digital Medicine
A different team was able to extract evidence of supplement-drug interactions from the literature. They used labels of the closely related task of identifying drug-drug interactions for supervision.
Houston, we’re coming for you!
If you’re at ASHG this year, come say hello:
- Platform presentation: ‘Breaking the interpretation bottleneck: Examining the utility of an automated genomic interpretation algorithm in a clinical genetic lab’, Saturday, October 19th @ 11:00AM
- Booth #1108 throughout exhibition hours
And just to let you know, we won’t be publishing during ASHG, and will be back to our usual schedule after the show.
Overcoming unhealthy genes
Can one overcome the deleterious effects of “unhealthy genes”? This article highlights how strong genetic predisposition, of a complex condition like ASCVD, can be subdued by simple interventions, such as change in lifestyle & use of safe generic medications.
npj Genomic Medicine
Long-read sequencing is nearing practical levels for the analysis of SV and tandem repeats, and accuracy and affordability is improving.
Journal of Human Genetics
- The transferability of lipid loci across African, Asian and European cohorts Nature Communications
- Ancestry-dependent enrichment of deleterious homozygotes in Runs of Homozygosity AJHG
- Enrichment of multiple sclerosis susceptibility genes across major immune cells. The study identified 233 significant risk loci for MS & explains ~48% of the estimated heritability of the disease. Science
- Trans-ancestry GWAS of serum urate identified 183 genetic loci (147 previously unknown), variants, tissues & transcriptional pathways. Nature Genetics
- MYH9 and platelet disorder Human Mutation
- ABCC9 and ABCC9-related intellectual disability myopathy syndrome (AIMS) Nature Communications
- NPM1 and dyskeratosis congenita Nature Genetics
- RHOA and neuroectodermal syndrome Nature Genetics
- MESD and osteogenesis imperfecta AJHG
(Ada is our AI engine, she likes to add an interesting new factoid she discovered in every issue)
New gene-disease connection: Bi-allelic variants in METTL5 cause autosomal-recessive intellectual disability and microcephaly by impairing brain development and neuronal function.
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