SEPTEMBER 5TH, 2019
The shortest bi-weekly genomics research report in the world. Curated by the Emedgene Research Division.
Should we CNV?
Researchers map the landscape of CNV burden & associations w/ 3000+ phenotypes in the UK Biobank.
Targeted NGS of 500 IRD patients reveals that copy-number variations account for ~9% of pathogenicity in the inherited retinal degenerations.
CNV analysis in 83 children with early-onset developmental and epileptic encephalopathy indicates the significant involvement of rare CNVs in the manifestation of these disorders.
Journal of Human Genetics
And in brief
- Expanding the phenotype of 16p11.2 microdeletion in a genome-wide multi-ethnic study AJHG
- Novel rare pathogenic variants identified in CDC45 on the non-deleted region in patients with 22q11.2DS & craniosynostosis. Genetics in Medicine
The Long AI Corner
Let’s start off with drug discovery and AI. Researchers used a generative AI model to discover new target molecules for DDR1 kinase inhibitors in just 21 days. This is not a drug, just a target molecule, and is proving grounds for the molecule generation-screening algorithm.
For a peek beyond the hype, it’s worth reading Derek Lowe’s commentary.
We want to use ML, but integrating even the most promising technology into clinical care is a separate challenge.
We’re going to hop in with our own news showing that our decision-support platform is actually quite easy to integrate into labs, and highly beneficial.
Ethics & ML
- Do no harm: a roadmap for responsible machine learning for healthcare Nature Medicine
- The global landscape of AI ethics guidelines Nature Machine Intelligence
The latest hereditary cancer screening research
A group of researchers evaluated gene-specific cancer associations in 165,000 high-risk patients & recommend expanding BRCA & Lynch syndrome testing criteria by including additional clinically actionable genes with overlapping phenotypes to improve the diagnostic yield.
Genetics in Medicine
Clinical & therapeutic utility of germline testing for patients with metastatic breast cancer. In a study conducted on 100 patients with metastatic breast cancer, researchers found 14 patients carrying P/LP variant, however 43% of them did not meet NCCN genetic testing criteria. The study recommends genetic testing for inherited cancer predisposition among all patients with metastatic breast cancer.
Cancer risks in the patients carrying pathogenic mismatch repair variants are influenced by gene, age, and gender, in a study performed in 6350 carriers from the Prospective Lynch Syndrome Database. Novel clinical guidelines are required to address these gene & gender-specific risks of Lynch syndrome.
Genetics in Medicine
This soda is dangerous!
If you get it from the NYPD. Last year they gave a 12-year-old boy charged with a felony a soda, and then tested the straw for DNA. The NYPD database contains the DNA of over 80k+ people, not all of whom are aware their genetic data has been captured by law enforcement.
Via The New York Times
Low concordance between variant data aggregators
The pathogenicity of 55 CFTR variants of known significance was assessed by a group of experts. Concordance between the databases evaluated was only 50%, reminding all of us to remain cautious in interpreting and disclosing incidental findings.
Lifestyle vs Genetics 2
One more research showing that apart from genetics, modifiable risk factors influence the development of dementia. Adoption of a healthy lifestyle can mitigate the risk of dementia in individuals with low or intermediate predisposed genetic risk. However, these factors might not be very beneficial for high-risk individuals.
(We previously published a similar finding in JAMA)
- Leveraging European infrastructures to access 1 million human genomes by 2022 Nature Reviews Genetics
- The eMERGE study accomplished integration of structured genomic results into multiple EHR systems, setting the stage for clinical decision support to enable genomic medicine. AJHG
Genome-wide PheWAS or phenome-wide GWAS?
In-depth analysis of 4,155 GWASs and 558 traits provides insights into the extent of pleiotropy of loci, genes, SNPs, characteristics of trait-associated variants & the polygenicity of complex traits.
- ALDH3A2 and Sjögren–Larsson syndrome Journal of Human Genetics
- TANGO1 and a novel syndromal disease due to hampered cellular collagen secretion bioRxiv
- Novel ZRS variant and preaxial polydactyly type I Genetics in Medicine
- CHD4, CNOT3 & SETD5 and moyamoya angiopathy Genetics in Medicine
(Ada is our AI engine, she likes to add an interesting new factoid she discovered in every issue)
New gene-disease connection: Variants in ZGRF1 implicated for a rare sensory reflex epilepsy, hot water epilepsy. The study was performed on a 4-generation family with multiple affected members.
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