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Integrated genomic analysis reveals mutated ELF3 as a potential gallbladder cancer vaccine candidate

Nature Communications, volume 11, Article number: 4225 (2020)

Gallbladder cancer (GBC) is an aggressive gastrointestinal malignancy with no approved targeted therapy. Here, we analyze exomes (n = 160), transcriptomes (n = 115), and low pass whole genomes (n = 146) from 167 gallbladder cancers (GBCs) from patients in Korea, India and Chile. In addition, we also sequence samples from 39 GBC high-risk patients and detect evidence of early cancer-related genomic lesions. Among the several significantly mutated genes not previously linked to GBC are ETS domain genes ELF3 and EHF, CTNNB1, APC, NSD1, KAT8, STK11 and NFE2L2. A majority of ELF3 alterations are frame-shift mutations that result in several cancer-specific neoantigens that activate T-cells indicating that they are cancer vaccine candidates.

  https://www.nature.com/articles/s41467-020-17880-4

Transcriptomic profile of adverse neurodevelopmental outcomes after neonatal encephalopathy

Nature Genetics, Sci Rep 10, 13100 (2020).

A rapid and early diagnostic test to identify the encephalopathic babies at risk of adverse outcome may accelerate the development of neuroprotectants. We examined if a whole blood transcriptomic signature measured soon after birth, predicts adverse neurodevelopmental outcome eighteen months after neonatal encephalopathy. We performed next generation sequencing on whole blood ribonucleic acid obtained within six hours of birth from the first 47 encephalopathic babies recruited to the Hypothermia for Encephalopathy in Low and middle-income countries (HELIX) trial.

  https://www.nature.com/articles/s41598-020-70131-w

Human ACE2 receptor polymorphisms predict SARS-CoV-2 susceptibility

bioRxiv, 2020.04.07.024752

Eric W Stawiski, Devan Diwanji, Kushal Suryamohan, Ravi Gupta, Frederic A Fellouse, Fah Sathirapongsasuti, Jiang Liu, Ying-Ping Jiang, Aakrosh Ratan, Monika Mis, Devi Santhosh, Sneha Somasekar, Sangeetha Mohan, Sameer Phalke, Boney Kuriakose, Aju Antony, Jagath R Junutula, Stephan C Schuster, Natalia Jura, Somasekar Seshagiri

In this study, we assessed if ACE2 polymorphisms might alter host susceptibility to SARS-CoV-2 by affecting the ACE2 S-protein interaction. Our comprehensive analysis of several large genomic datasets that included over 290,000 samples representing >400 population groups identified multiple ACE2 protein-altering variants, some of which mapped to the S-protein-interacting ACE2 surface.

  https://www.biorxiv.org/content/10.1101/2020.04.07.024752v1

The Indian cobra reference genome and transcriptome enables comprehensive identification of venom toxins.

Nature Genetics, volume 52, pages106–117 (2020)

Kushal Suryamohan, Sajesh P. Krishnankutty, Somasekar Seshagiri

Snakebite envenoming is a serious and neglected tropical disease that kills ~100,000 people annually. High-quality, genome-enabled comprehensive characterization of toxin genes will facilitate development of effective humanized recombinant antivenom. We report a de novo near-chromosomal genome assembly of Naja naja, the Indian cobra, a highly venomous, medically important snake.

  https://www.nature.com/articles/s41588-019-0559-8
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