An article published in GenomeBiology presents STRling—a fast and accurate method to detect short tandem repeat expansions from short-read sequencing data. Critically, it can detect novel expansions, those that are missing from the reference genome.
Illumina reads containing substantial repetitive content are frequently mis-mapped or left unmapped by alignment algorithms []. The first task is to recover STR-containing reads and determine their most likely genomic origin. STRling first makes an index of large uninterrupted STR loci in the reference genome, by searching for perfect repeats in 100 bp windows, sliding by 60 bp at a time. Reads aligning to these STR “sink” regions are considered to have unreliable mapping locations.
We consider the alignment location of high STR content reads unreliable. Therefore, STRling uses paired information to localize these reads where possible. Specifically, if a read contains at least 80% STR content and has a well-mapped mate , STRling uses the mapping position of the mate to relocate the STR read to a position that is the median fragment length away in the direction concordant with the orientation of the mate. This is called an “anchored pair” .
For joint-calling, locus discovery is performed using reads from all samples using the merge subcommand, and the resulting positions are provided to the call subcommand for individual genotyping. By default, STRling discards any loci where less than five of these reads come from the same sample.
To estimate the size of alleles greater than the read length, STRling counts the number of STR k-mers in all anchored and overlapping reads assigned to that locus. As an experiment, we edited the reference genome at the Huntington’s Disease locus to add 300 alleles of varying length between 0 bp and 1800 bp insertion then simulated paired end reads using an empirical insert-size distribution.
United States Latest News, United States Headlines
Similar News:You can also read news stories similar to this one that we have collected from other news sources.
Multidrug-resistant Acinetobacter pittii is adapting to and exhibiting potential succession aboard the International Space Station - MicrobiomeBackground Monitoring the adaptation of microorganisms to the extreme environment of the International Space Station (ISS) is crucial to understanding microbial evolution and infection prevention. Acinetobacter pittii is an opportunistic nosocomial pathogen, primarily impacting immunocompromised patients, that was recently isolated from two missions aboard the ISS. Results Here, we report how ISS-associated A. pittii (n=20 genomes) has formed its own genetically and functionally discrete clade distinct from most Earth-bound isolates (n=291 genomes). The antimicrobial susceptibility testing of ISS strains and two related clinical isolates demonstrated that ISS strains acquired more resistance, specifically with regard to expanded-spectrum cephalosporins, despite no prediction of increased resistance based on genomic analysis of resistance genes. By investigating 402 longitudinal environmental and host-associated ISS metagenomes, we observed that viable A. pittii is increasing in relative abundance and therefore potentially exhibiting succession, being identified in |2X more metagenomic samples in back-to-back missions. ISS strains additionally contain functions that enable them to survive in harsh environments, including the transcriptional regulator LexA. Via a genome-wide association study, we identified a high level of mutational burden in methionine sulfoxide reductase genes relative to the most closely related Earth strains. Conclusions Overall, these results indicated a step forward in understanding how microorganisms might evolve and alter their antibiotic resistance phenotype in extreme, resource-limited, human-built environments. Video Abstract
Read more »
Prince Louis' Christmas outfit sparks criticism of Royal Familythe Royal Family members walked the short distance from Sandringham House to St Mary Magdalene Church
Read more »
Patriots Report Card: Rhamondre Stevenson, Pats Offense Come Up Short Vs. BengalsThe Patriots defense stepped up to give the team a chance at a Christmas miracle, but Rhamondre Stevenson and the offense didn’t hold up their end of the bargain. Phil Perry hands out his grades after another crushing loss.
Read more »
Actor Stephen Greif, known for roles in The Crown & EastEnders, dies at 78THE Crown actor Stephen Greif has died aged 78, his agent announced today. The star most recently played Speaker of the House Sir Bernard Weatherill in the Netflix drama in 2020, and also appeared …
Read more »
Sheffield DJ's lockdown chart challenge keeps spinningA DJ who started a lockdown challenge to play every single chart record since the 1950s says he has developed a world-wide audience.
Read more »