NOVEMBER 21ST, 2019

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

The Reviews

There were two reviews this week that we particularly liked.

Structural variation
The challenges in the detection and interpretation of SVs. New approaches, such as ensemble algorithms, and single-molecule & connected-molecule strategies, as well as studies integrating biological information, will be essential for the comprehensive understanding of SVs.
Nature Reviews Genetics

Long non-coding RNAs
A thorough review discussing various mechanisms by which cis-acting long non-coding RNAs (lncRNAs) regulate expression of target genes. The paper also covers methodological advances that enable characterization and identification.
Nature Reviews Genetics


Mosaic Y chromosome loss

Researchers identified 137 novel susceptibility loci of LOY in UK Biobank participants and indicated the value of studying clonal mosaicism to unravel underlying mechanisms of cancer and other aging-related diseases.
Nature


The AI Corner

How to read articles that use machine learning is a user’s guide to machine learning literature. We particularly like Liu et al’s emphasis on repeatability and reproducibility, as critical aspects of measuring the consistency of machine learning model performance.
JAMA

An example of why is this important is in this publication. An AI assistant (for pathologists) was developed, to differentiate between two subtypes of primary liver cancer, hepatocellular carcinoma (HCC) and cholangiocarcinoma (CC). Although the model performed well on the test and validation set, it did not improve pathologist performance, while also influencing their decisions.
arXiv

A review of AI in clinical and genomic diagnostics by Torkmani and Dias covers emerging AI solutions & some of the hurdles that need to be addressed for the successful deployment of AI in genomics.
Genome Medicine


Invitation Break !

While we’re on the topic of AI, and the importance of clinical validation, we’d like to invite you to our webinar on the topic:

Breaking the interpretation bottleneck:
Examining the utility of an automated genomic interpretation algorithm in a clinical genetic lab

Our guest, Linyan Meng, PhD, Director at Baylor Genetics, will present the results of a joint Baylor Genetics-Emedgene study demonstrating the utility of machine learning for interpretation in a 180-case cohort.

Please register in advance. The webinar will be held on November 26th, at 11:30AM CT.


Delineating pathomechanism of Down syndrome

Down Syndrome (DS) joins the pantheon of neurological disorders that are caused by dysregulated ISR signaling. Researchers provide compelling evidence to show that overactivation of IRS signaling account for cognitive dysfunction in DS. Targeting PKR or other mediates of this pathway can be an effective treatment approach.
Science


Long reads

Long-read sequencing of 1,817 Icelanders identifies ~23,111 autosomal structural variants per individual and provides insight into their impact in human disease.
bioRxiv


ACMG Panel Guidelines

Technical standards by ACMG for designing, offering, and reporting gene panel testing to harmonize procedures across diagnostic laboratories and ensure clinical sensitivity, specificity, and validity of outcomes.
Genetics in Medicine


Genomics in the clinic

An interview of 23 healthcare professionals involved in the 100 000 genomes project: most of them are positive towards clinical utility of GS, however, they have concerns about training medical professionals that don’t have a genetics background.
BMJ Open

Is testing newborns for adult-onset-only conditions is a violation of their privacy and right to an “open future”? Authors Ross & Clayton take into consideration the case study of BabySeq and highlighted the ethical and moral dilemmas in reporting the outcomes of Pediatric genomic sequencing.
Pediatrics

The Netherlands launched the TRIDENT-2 study, a national level genome-wide non-invasive prenatal testing as a first-tier screening test. However, the debate on whether the benefits outweighs the risks associated with these tests is unresolved.
AJHG


Significant Singles:
  • CHRNA3 and congenital anomalies of the kidney and urinary tract (CAKUT) AJHG
  • TMX2 and severe brain developmental abnormalities AJHG
  • ZNF292 and neurodevelopmental disorder with or without ASD Genetics in Medicine
  • PSMC3 and neurosensory syndrome combining deafness and cataract bioRxiv
  • TTC29 and asthenozoospermia and male infertility AJHG

Ada Reports

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

Biallelic pathogenic variants in VPS35L cause 3C/Ritscher-Schinzel-like syndrome through dysfunction of retriever complex that plays a vital role in fetal development.
Journal of Medical Genetics


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

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