JULY 3RD, 2019

The shortest bi-weekly genomics research report in the world. Curated by the Emedgene Research Division.

Beyond SNPs

A deletion in the noncoding region reveals a gene that is critical for intestinal function. Researchers studied 8 infants with intractable congenital diarrhea from 7 unrelated families, where a previous WES yielded no results. WGS identified a common deletion region on chromosome 16 that they called the intestine-critical region (ICR). Mouse models support the discovery.
Nature

In this WGS study, a recessively inherited intronic repeat expansion in RFC1 was identified in 18 out of 22 CANVAS-affected families.
AJHG

MNVs anyone? An evaluation of their functional impact and contribution to disease, using data from 6688 exomes. MNVs were found to be more damaging than SNVs even when both induce missense changes.
Genome Research


Dynamic eQTLs

RNA sequencing data captured 16 time points during the differentiation of induced pluripotent stem cells to cardiomyocytes, in 19 human cell lines. Hundreds of dynamic eQTLs identified that change over time, including some that only affect intermediate stages of differentiation, and cannot be found by using data from mature tissues.
Science


WES+RNA

Improving the diagnostic yield of exome sequencing using RNA-seq data to predict gene–phenotype associations. Found novel genes for 10 out of 61 unsolved rare disease cases.
Nature Communications


SNPs+Regulatory elements

Screening the effects of 5.9 million SNPs on enhancer and promoter activity, the researchers identified more than 30,000 SNPs that alter the activity of putative regulatory elements.
Nature Genetics


Quiz Break !

Can you name 4 of the 7 elements that make a trustworthy AI according to EU guidelines?


Predictive AI

A new deep-learning model can predict from a mammogram if a patient is likely to develop breast cancer as much as five years in the future. Using information from more than 90,000 mammograms, the model detected patterns too subtle for the human eye to detect.
MIT News


Fetal WES

Fetal WES yield is high after abnormal ultrasound in families with relevant history, and when US has abnormal brain, renal or musculoskeletal findings.
Frontiers in Genetics


Back to diversity

Large-scale multi-ethnic biobanks and population studies can provide new opportunities for genomic discovery and a better understanding of population disease risk.
Nature Reviews Genetics

And these new population-specific studies:

  • Germline pathogenic variants reported in Japanese patients with prostate cancer a Journal of the Cancer Institute
  • GWAS of QRS duration identifies new loci specific to Hispanic/Latino populations PLOS One
  • T2D in 433,540 East Asian individuals bioRxiv

Back to reanalysis

MedSeq examined the effort and value of reanalysis for monogenic diseases, PGX and polygenic scores. 14 variants were reclassified and, upon reanalysis, 18 new variants met criteria for reporting, highlighting the need for periodic reanalysis.
AJHG


Somatic mosaicism in normal tissues

Somatic mutations were detected in nearly all individuals and across many normal human tissues. Interestingly, the skin, lung, and esophagus exhibited the most mutations, suggesting that the environment generates many human mutations.
Science


Significant singles:

Ada Reports

(Ada is our AI engine, she likes to add an interesting new factoid she discovered in every issue)

The first known case of autoimmune arthritis associated with a mutation in GATA3. This study expands the phenotypic spectrum of GATA3 mutations.
Arthritis Research and Therapy


Answer: 1. Human agency and oversight 2. Technical robustness and safety 3. Privacy and data governance 4. Transparency 5. Diversity, non-discrimination and fairness 6. Societal and environmental well-being 7. Accountability. You can read more about each of these and how Emedgene implements them on our blog.


Questions? Comments? Corrections? Please email us at hello@emedgene.com

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