Pipeline release! nf-core/oncoanalyser v2.3.0 - 2.3.0 - Spotted Nightjar!
A comprehensive cancer DNA/RNA analysis and reporting pipeline
Please see the changelog: https://github.com/nf-core/oncoanalyser/releases/tag/2.3.0
#cancer #clinical #dna #exome #ngs #panel #rna #targeted #wgs #wigits #wts #nfcore #openscience #nextflow #bioinformatics
Whole genome sequencing (WGS) at high-depth (30X) allows the accurate discovery of variants in the coding and non-coding DNA regions and helps elucidate the genetic underpinnings of human health and diseases. Yet, due to the prohibitive cost of high-depth WGS, most large-scale genetic association studies use genotyping arrays or high-depth whole exome sequencing (WES). Here we propose a cost-effective method which we call “Whole Exome Genome Sequencing” (WEGS), that combines low-depth WGS and high-depth WES with up to 8 samples pooled and sequenced simultaneously (multiplexed). We experimentally assess the performance of WEGS with four different depth of coverage and sample multiplexing configurations. We show that the optimal WEGS configurations are 1.7–2.0 times cheaper than standard WES (no-plexing), 1.8–2.1 times cheaper than high-depth WGS, reach similar recall and precision rates in detecting coding variants as WES, and capture more population-specific variants in the rest of the genome that are difficult to recover when using genotype imputation methods. We apply WEGS to 862 patients with peripheral artery disease and show that it directly assesses more known disease-associated variants than a typical genotyping array and thousands of non-imputable variants per disease-associated locus.
https://www.nature.com/articles/s41588-023-01637-y
"Public platform with 39,472 #exome control samples enables association studies without genotype sharing"
We provide access to a library of 39,472 exome sequencing controls at http://dnascore.net enabling association studies for case cohorts lacking control subjects. Using this approach, control sets can be selected from this online library with a prespecified matching accuracy, ensuring well-calibrated association analysis for both rare and common variants.
A new method allows selection of matched controls from an external pool of samples without genotype sharing. This method has been implemented in an online repository containing 39,472 exome sequencing controls that can be used for association analyses.
The Mexico City Prospective Study is a prospective cohort of more than 150,000 adults recruited two decades ago from the urban districts of Coyoacán and Iztapalapa in Mexico City. Here we generated genotype and exome-sequencing data for all individuals and whole-genome sequencing data for 9,950 selected individuals. #isogg #dna #mexico #geneadons #nature #genetics #exome #indigenous #wholegenomesequencing
Genotype and exome sequencing of 150,000 participants and whole-genome sequencing of 9,950 selected individuals recruited into the Mexico City Prospective Study constitute a valuable, publicly available resource of non-European sequencing data.
A genomics company is providing precision medicine analytics from its databases with generative A.I. based on large language models from Amazon Web Services.
https://sciencebusiness.technewslit.com/?p=45227
#News #Press #Science #Business #Biotechnology #ArtificialIntelligence #Genome #Exome #MachineLearning #LargeLanguageModels #GenerativeAI #Sequencing #Software #Analytics
nf-core
Anna Szala
Daniel Hoffmann 🌼
Pierre Lindenbaum
ISOGG
Alan Kotok