OCTOBER 24TH, 2019

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

The Other Structural Variations: UPD & Retrotransposition

Prevalence of uniparental disomy in general population: UPD is twice as common as previously thought. Study identifies 675 instances of UPD across 23andMe & UK Biobank databases using a machine-learning framework.
AJHG

Contribution of retrotransposition to developmental disorders: assessment of 9738 DDD study trios indicates transposable elements account for ~0.04% of developmental disorders.
Nature Communications


Utility of RNAseq

Diagnostic utility of transcriptome sequencing for undiagnosed rare Mendelian diseases. Integration of RNAseq with genome or exome sequencing can significantly increase the molecular diagnostic rate.
Genetics in Medicine

RNAseq as a supplement in cases where likely pathogenic or VUS were identified, associated with an improved outcome of hereditary cancer predisposition genetic testing and could affect medical management in at least 1 in 43 patients if performed concurrently.
JAMA Network Open


Reinterpretation

Is there a duty to reinterpret genetic data? The ethical dimensions. The likelihood of substantial patient benefit from a systematic approach to reinterpretation suggests the importance for the genetics community to reach consensus on this issue.
Genetics in Medicine

Variant classification changes over time in BRCA1 and BRCA2. During a 5-year period, 32.9% (398/1209) of variants were reassessed and 12.4% (150/1209) were reclassified. The majority of reclassified variants were downgraded (112/150, 74.7%).
Genetics in Medicine

In our own news, we just announced Pathorolo, the first machine learning algorithm developed to assess the likelihood of solving a genomics clinical case with currently available information. In the reanalysis of large unsolved past cohorts, the Pathorolo model will allow the geneticist to manually analyze only the cases that are likely to be solved.
The Emedgene Blog


Break !

What were the top genes and diseases presented at ASHG 2019?
We text mined all 3364 posters to find out.

topdiseasesashg19

Interestingly, 85% of genes only appeared in a single poster, and an additional 12% in two posters.
See our findings.


The AI Corner

A free smartphone app for the autonomous early diagnosis of childhood eye diseases, specifically engineered to detect photographic leukocoria.
Science Advances

A machine learning model identifies patients with familial hypercholesterolemia from health encounter data. Of those reviewed, ~87% in the national database & ~77% in the health-care delivery system dataset were found to have high enough clinical suspicion of FH.
The Lancet Digital Health


Enhancers/promoters, less distinct than we thought

Enhancers & promoters are not mutually exclusive & share several properties & functions. Hence, more inclusive models are needed to study these regulatory elements. A review of emerging models.
Nature Reviews Genetics


Contribution of VUS

Expanded preconception carrier screening to identify at-risk couples for multiple diseases. Researchers estimated possible contribution of P/LP*cVUS matings to ECS yield in an Ashkenazi Jewish cohort.
Genetics in Medicine


Effect of parental age on offspring

Human germline de novo mutations pla vital role in the manifestation of genetic diseases. Research indicates there is a positive correlation between parental age and the number of de novo mutations in offspring, with a more pronounced effect for paternal age.
Trends in Genetics


Significant Singles:
  • TMEM63A and infantile-onset transient hypomyelination AJHG
  • CDH2 and syndromic neurodevelopmental disorder AJHG
  • NKAP and Marfanoid habitus & cognitive Impairment AJHG
  • RNF170 and hereditary spastic paraplegia Nature Communications
  • TANC2 and neurodevelopmental disorder Nature Communications
  • RPL13 and spondyloepimetaphyseal dysplasia AJHG

Ada Reports

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

A recurrent start codon variant in UGP2 can cause novel autosomal recessive developmental and/or epileptic encephalopathies by altering glycosylation & sensitivity to ER stress.
bioRxiv


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