Utility of long-read sequencing for All of Us
M Mahmoud et a, BIORXIV, January 24, 2023
We compared the performance of traditional short-read sequencing with long-read sequencing in a small cohort of samples from the HapMap project and two AoU control samples representing eight datasets. Our analysis revealed substantial differences in the ability of these technologies to accurately sequence complex medically relevant genes, particularly in terms of gene coverage and pathogenic variant identification. Our results show that HiFi reads produced the most accurate results for both small and large variants.
A one-year genomic investigation of Escherichia coli epidemiology and nosocomial spread at a large US healthcare network
EG Mills et al, Genome Medicine, December 30, 2022
Whole-genome sequencing (WGS), phylogenetic analysis, and antibiotic susceptibility testing were performed for a complete set of 2075 E. coli clinical isolates collected from 1776 patients at a large tertiary healthcare network in the USA between October 2019 and September 2020. The study provides a rare and contemporary survey on the epidemiology and spread of E. coli in a large US healthcare network. While surveillance and infection control efforts often focus on ESBL and MDR lineages, our findings reveal that non-MDR isolates represent a large burden of infections, including those of predicted nosocomial origins.
Parents’ decision-making regarding whether to receive adult-onset only genetic findings for their children: Findings from the BabySeq Project
S Pereira et al, Genetics in Medicine, December 20, 2022
Parents noted several motivations to receive and reasons to decline adult-onset only results. Most commonly, parents cited early intervention/surveillance (n=11), implications for family heath (n=7), and the ability to prepare (n=6) as motivations to receive these results. The most common reasons to decline were protection of the child’s future autonomy (n=4), negative impact on parenting (n=3), and anxiety about future disease (n=3).
RNA Sequencing as a Diagnostic Tool.
Ketkar Shamika et al. JAMA 2022 12
RNA sequencing (RNA-seq) is a new tool in the genetic diagnostic laboratory made possible by the advent of low-cost, high-throughput, next-generation sequencing technology. Historically, RNA studies were limited to gene expression using microarray technology for the detection of gene rearrangements and quantification of gene expression for predefined genes. RNA-seq allows detection of qualitative and quantitative changes in RNA expression across the genome in clinical samples and is increasingly being used as an adjunct to diagnostic exome sequencing and whole-genome sequencing.