Genome-wide detection of somatic mosaicism at short tandem repeats.

MOTIVATION: Somatic mosaicism has been implicated in several developmental disorders, cancers, and other diseases. Short tandem repeats (STRs) consist of repeated sequences of 1-6 bp and comprise >1 million loci in the human genome. Somatic mosaicism at STRs is known to play a key role in the pathogenicity of loci implicated in repeat expansion disorders and is highly prevalent in cancers exhibiting microsatellite instability. While a variety of tools have been developed to genotype germline variation at STRs, a method for systematically identifying mosaic STRs is lacking. RESULTS: We introduce prancSTR, a novel method for detecting mosaic STRs from individual high-throughput sequencing datasets. prancSTR is designed to detect loci characterized by a single high-frequency mosaic allele, but can also detect loci with multiple mosaic alleles. Unlike many existing mosaicism detection methods for other variant types, prancSTR does not require a matched control sample as input. We show that prancSTR accurately identifies mosaic STRs in simulated data, demonstrate its feasibility by identifying candidate mosaic STRs in Illumina whole genome sequencing data derived from lymphoblastoid cell lines for individuals sequenced by the 1000 Genomes Project, and evaluate the use of prancSTR on Element and PacBio data. In addition to prancSTR, we present simTR, a novel simulation framework which simulates raw sequencing reads with realistic error profiles at STRs. AVAILABILITY AND IMPLEMENTATION: prancSTR and simTR are freely available at https://github.com/gymrek-lab/trtools. Detailed documentation is available at https://trtools.readthedocs.io/

Oil Pulling: A Review

Oil pulling is extensively used traditional Indian folk remedy to prevent decay, bleeding gums, oral malodor, dryness of throat, cracked lips and for strengthening teeth, gums, and jaws. In this procedure, the practitioners rinse their mouth with approximately one tablespoon of an ordinary cooking oil for 3-20 min, then spits it. This practice is usually performed on a daily basis. This technique is believed to cure more than thirty systemic diseases when practiced regularly and as directed. As a result of  side effects to modern medicines and oral hygiene products, people are increasingly attracted towards such traditional practices. The present article attempts to review and discuss this ancient practice and its effects on one’s oral and general health

LongTR: genome-wide profiling of genetic variation at tandem repeats from long reads.

Tandem repeats are frequent across the human genome, and variation in repeat length has been linked to a variety of traits. Recent improvements in long read sequencing technologies have the potential to greatly improve tandem repeat analysis, especially for long or complex repeats. Here, we introduce LongTR, which accurately genotypes tandem repeats from high-fidelity long reads available from both PacBio and Oxford Nanopore Technologies. LongTR is freely available at https://github.com/gymrek-lab/longtr and https://zenodo.org/doi/10.5281/zenodo.11403979

gymrek-lab/TRTools: v5.1.0

<p>New features:</p> <ul> <li>Added prancSTR for mosaicism detection</li> <li>Added simTR for simulating NGS reads with stutter errors at TRs</li> </ul&gt

gymrek-lab/TRTools: v5.0.2

Toolkit for genome-wide analysis of tandem repeat

gymrek-lab/TRTools: v5.1.1

<p>Bug fixes:</p> <ul> <li>Remove stray files from source distribution (#195)</li> </ul&gt