JULY 18TH, 2019
The shortest bi-weekly genomics research report in the world. Curated by the Emedgene Research Division.
Deeper into the human genome
We love it when genomics make it into NEJM, getting attention from the wider medical community. This well-written and interesting review by Evan Eichler out of UW takes clinicians beyond SNPs and the coding regions (and even beyond short-reads) to diagnose diseases.
Roughly 40% of the genome is located in intronic regions, compared to 1% of coding regions. Therefore the number of intronic variants is significantly higher than in coding regions, which is a technological challenge. Since they’re not translated into proteins, understanding their impact on disease, usually through their effect on splicing, increases the challenge of identifying significant introns.
This week brought us 2 new publications linking rare diseases with deep intronic variants:
- The FECH locus and erythropoietic protoporphyria (EPP) Genetics in Medicine
- ANAPC1 and Rothmund-Thomson syndrome type 1 AJHG
The AI Corner
This week’s star performer, gaining over 3500 tweets and quite a few news pieces, was this article on extracting information from publications in material sciences. Extracting knowledge from articles is one of our key ML focus areas, we firmly believe that lit research should be assisted by AI, given the massive growth in knowledge.
Here, researchers used an unsupervised approach, and were able to extract both entities and relations successfully. The Word2Vec algorithm they used did cool things like learn the periodic table and even predict functional materials papers.
Continuing on the theme of massively growing data and our ability to automate learnings from it, these researchers looked at Facebook posts, and successfully predicted medical conditions including diabetes, anxiety, depression, and psychoses.
What’s in a name?
Men and women are equally likely to have mutations in #BRCA genes and develop cancer, but men are much less likely to get screened. Dr. Colin C. Pritchard suggests giving HBOC a gender-neutral name to encourage testing.
Quiz Break !
Super humans exist! At least a human with supervision.
Can you name the condition that causes tetrachromancy, or the ablity to see 100 million different colors? We’ll give you a hint, they have an extra retina cone.
The largest GWAS to date on Anorexia Nervosa patients, 17k strong, was published this week. Researchers individuals found 8 genome-wide significant loci, implicating metabo-genetic origins for the illness.
Peripheral artery disease (PAD) is a leading cause of cardiovascular morbidity and mortality. A GWAS in the Million Veteran Program testing identifies 18 novel loci and 4 disease-specific variants, and provides insights on differences between PAD and other forms of ASCVD.
Genotyping vs NGS
A comprehensive review out of UK Biobank finds SNP-chip genotype accuracy is high overall, but the likelihood of a true positive result reduces substantially with decreasing allele frequency (only 16% for variants with a frequency of <0.001%). Make sure your family and friends are treating consumer genotyping products with caution.
Nature vs Nurture
- Lifestyle matters more: Dementia JAMA
- Environmental factors had a greater influence on education & cognitive traits than on other traits, such as height, BMI, ADHD, or schizophrenia AJHG
- POU3F3 (AKA Brain-1) and neurodevelopmental disorder AJHG
- JAG1 and FEVR (familial exudative vitreoretinopathy), blindness-causing retinal vascular disease Genetics in Medicine
- DYRK1A and ID-related congenital anomalies of the kidney and urinary tract Genetics in Medicine
- PISD and Liberfarb syndrome Genetics in Medicine
(Ada is our AI engine, she likes to add an interesting new factoid she discovered in every issue)
Jumping on the diversity bandwagon this week! ARMC5 shows an association with hypertension in blacks in this study. Interestingly, a protective variant was also identified, and confirmed in vitro.
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