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High-Accuracy HLA Type Inference from Whole-Genome Sequencing Data Using Population Reference Graphs

Alexander T. Dilthey, Pierre-Antoine Gourraud, Alexander J. Mentzer, Nezih Cereb, Zamin Iqbal, Gil McVean, Andre Franke
2016 PLoS Computational Biology  
We conclude that HLA*PRG for the first time achieves accuracies comparable to gold-standard reference methods from standard whole-genome sequencing data, though high computational demands (currently~30  ...  Extensive hyperpolymorphism and sequence similarity between the HLA genes, however, pose problems for accurate read mapping and make HLA type inference from wholegenome sequencing data a challenging problem  ...  We would also like to thank Adrian V Hill, Manj Sandhu and Alison M Elliott alongside the High-Accuracy HLA Type Inference from Whole-Genome Sequencing Data Analyzed the data: ATD AJM NC.  ... 
doi:10.1371/journal.pcbi.1005151 pmid:27792722 pmcid:PMC5085092 fatcat:y5jdvexhr5hmzcnwv6x32eybum

HLA*PRG:LA – HLA typing from linearly projected graph alignments [article]

Alexander T Dilthey, Alexander J Mentzer, Raphael Carapito, Clare Cutland, Nezih Cereb, Shabir A. Madhi, Arang Rhie, Sergey Koren, Seiamak Bahram, Gil McVean, Adam M Phillippy
2018 bioRxiv   pre-print
It enables accurate HLA type inference from whole-genome (99% accuracy) and whole-exome (93% accuracy) Illumina data; from long-read Oxford Nanopore and Pacific Biosciences data (98% accuracy for whole-genome  ...  AbstractSummary:HLA*PRG:LA implements a new graph alignment model for HLA type inference, based on the projection of linear alignments onto a variation graph.  ...  Louis for public release of the PacBio NA12878 data.  ... 
doi:10.1101/453555 fatcat:juirt2e2qzgrhidqmeyonc6ty4

HLA*LA – HLA typing from linearly projected graph alignments

Alexander T Dilthey, Alexander J Mentzer, Raphael Carapito, Clare Cutland, Nezih Cereb, Shabir A Madhi, Arang Rhie, Sergey Koren, Seiamak Bahram, Gil McVean, Adam M Phillippy, Bonnie Berger
2019 Bioinformatics  
It enables accurate HLA type inference from whole-genome (99% accuracy) and whole-exome (93% accuracy) Illumina data; from long-read Oxford Nanopore and Pacific Biosciences data (98% accuracy for whole-genome  ...  HLA*LA implements a new graph alignment model for human leukocyte antigen (HLA) type inference, based on the projection of linear alignments onto a variation graph.  ...  Louis for public release of the PacBio NA12878 data.  ... 
doi:10.1093/bioinformatics/btz235 pmid:30942877 pmcid:PMC6821427 fatcat:kw4v46i6mffc3hgdzqlskkrg2a

Improved genome inference in the MHC using a population reference graph

Alexander Dilthey, Charles Cox, Zamin Iqbal, Matthew R Nelson, Gil McVean
2015 Nature Genetics  
Project, we demonstrate, using simulations, SNP genotyping, short-read and long-read data, how the method improves the accuracy of genome inference and reveals regions where the current set of reference  ...  We introduce a population reference graph, which combines multiple reference sequences and catalogues of variation.  ...  Summary of read alignment to a single reference (GRCh37 without alternative loci, containing the 'PGF' haplotype in the xMHC) for a single sample (CS1) in the MHC Class II region (around HLA-DRB1) showing  ... 
doi:10.1038/ng.3257 pmid:25915597 pmcid:PMC4449272 fatcat:joascvqf6nh5jpy2pm56j7sxz4

Kourami: graph-guided assembly for novel human leukocyte antigen allele discovery

Heewook Lee, Carl Kingsford
2018 Genome Biology  
We have developed a graph-guided assembly technique for classical HLA genes, which can construct allele sequences given high-coverage whole-genome sequencing data.  ...  Our method delivers highly accurate HLA typing, comparable to the current state-of-the-art methods. Using various data, we also demonstrate that our method can type novel alleles.  ...  The WGS data for 14 individuals from the 1000 Genomes Project [57] and the WES data of 29 HapMap samples [35] are available through the data portal of the International Genome Sample Resource website  ... 
doi:10.1186/s13059-018-1388-2 pmid:29415772 pmcid:PMC5804087 fatcat:unnww2jscnbixjwp5you2gficq

In silico tools for accurate HLA and KIR inference from clinical sequencing data empower immunogenetics on individual-patient and population scales

Jieming Chen, Shravan Madireddi, Deepti Nagarkar, Maciej Migdal, Jason Vander Heiden, Diana Chang, Kiran Mukhyala, Suresh Selvaraj, Edward E Kadel, Matthew J Brauer, Sanjeev Mariathasan, Julie Hunkapiller (+3 others)
2020 Briefings in Bioinformatics  
Here, we report an evaluation of recently published algorithms to computationally infer complex immunogenetic variation in the form of HLA alleles and KIR haplotypes from whole-genome or whole-exome sequencing  ...  For both HLA allele and KIR gene typing, we identified tools that yielded >97% overall accuracy for four-digit HLA types, and >99% overall accuracy for KIR gene presence, suggesting the readiness of in  ...  Whole-genome and whole-exome sequencing WGS and WES were performed for the samples in the HLA and KIR reference datasets, on Illumina HiSeq instruments using paired-end reads of 150 bp.  ... 
doi:10.1093/bib/bbaa223 pmid:32940337 pmcid:PMC8138874 fatcat:evcvd3rlvje45b6pmb4niinomq

Graphtyper: Population-scale genotyping using pangenome graphs [article]

Hannes P. Eggertsson, Hakon Jonsson, Snaedis Kristmundsdottir, Eirikur Hjartarson, Birte Kehr, Gisli Masson, Florian Zink, Aslaug Jonasdottir, Adalbjorg Jonasdottir, Ingileif Jonsdottir, Daniel F. Gudbjartsson, Pall Melsted (+2 others)
2017 bioRxiv   pre-print
Graphtyper genotyped 89.4 million sequence variants in whole-genomes of 28,075 Icelanders using less than 100,000 CPU days, including detailed genotyping of six human leukocyte antigen (HLA) genes.  ...  Graphtyper realigns short-read sequence data to a pangenome, a variation-aware graph structure that encodes sequence variation within a population by representing possible haplotypes as graph paths.  ...  OptiType: precision HLA typing from next-generation sequencing data. 25 Bioinformatics 30, 3310-6 (2014). 26 33. Bentley, D. R. et al.  ... 
doi:10.1101/148403 fatcat:zixpkqovrndfvh2zfsxaujbgim

Assembly and analysis of 100 full MHC haplotypes from the Danish population

Jacob M. Jensen, Palle Villesen, Rune M. Friborg, Thomas Mailund, Søren Besenbacher, Mikkel H. Schierup
2017 Genome Research  
Here, we reconstruct full MHC haplotypes from de novo assembled trios without relying on a reference genome and perform evolutionary analyses.  ...  We report 100 full MHC haplotypes and call a large set of structural variants in the regions for future use in imputation with GWAS data.  ...  This work was supported by funding from The Danish Council for Independent Research, Centre for Integrative Sequencing (iSeq), and Innovation Fund Denmark.  ... 
doi:10.1101/gr.218891.116 pmid:28774965 pmcid:PMC5580718 fatcat:jgswcvh64jeu5ikci6vc66aw34

Multi-Population Classical HLA Type Imputation

Alexander Dilthey, Stephen Leslie, Loukas Moutsianas, Judong Shen, Charles Cox, Matthew R. Nelson, Gil McVean, Sharon Browning
2013 PLoS Computational Biology  
We present an HLA type imputation model, HLA*IMP:02, designed to operate on a multi-population reference panel. HLA*IMP:02 is based on a graphical representation of haplotype structure.  ...  HLA*IMP:02 supports imputation of HLA-DPB1 and HLA-DRB3-5, is highly tolerant of missing data in the imputation panel and works on standard genotype data from popular genotyping chips.  ...  We also acknowledge use of genotype data from the British 1958 Birth Cohort DNA collection, funded by the Medical Research Council grant G0000934 and the Wellcome Trust grant 068545/Z/02.  ... 
doi:10.1371/journal.pcbi.1002877 pmid:23459081 pmcid:PMC3572961 fatcat:ub4yupdu3vhbvok72gkzhjcayy

Graph-Guided Assembly For Novel HLA Allele Discovery [article]

Heewook Lee, Carl Kingsford
2017 bioRxiv   pre-print
high accuracy from whole genome sequencing data.  ...  haplotype sequences of typing exons given high-coverage (>30-fold) whole genome sequencing data.  ...  High-accuracy HLA type inference from whole-genome sequencing data using popula-480 tion reference graphs.  ... 
doi:10.1101/138826 fatcat:jsbe7nha4fh2jga2vofao2pvse

Bioinformatics Strategies, Challenges, and Opportunities for Next Generation Sequencing-Based HLA Genotyping

Steffen Klasberg, Vineeth Surendranath, Vinzenz Lange, Gerhard Schöfl
2019 Transfusion Medicine and Hemotherapy  
NGS has led to a dramatically increased sequencing throughput at high accuracy, while being more time and cost efficient than precursor technologies.  ...  This review surveys the different modalities involved in generating NGS HLA profiling sequence data.  ...  The increased feasibility of sequencing genomes (WGS) [37, 38] using short-read and long-read platforms, or a combination of both, has led to availability of whole-genome data from which HLA genotypes  ... 
doi:10.1159/000502487 pmid:31832057 pmcid:PMC6876610 fatcat:ivikwrauwnf4zkydz6nn75aega

arcasHLA: high-resolution HLA typing from RNAseq

2019 Bioinformatics  
Here, we present arcasHLA: a fast and accurate in silico tool that infers HLA genotypes from RNA-sequencing data.  ...  Recent improvements in the quality and accessibility of next-generation sequencing have made HLA typing from standard short-read data practical.  ...  Additionally, we thank arcasHLA: HLA typing from RNAseq Ruthie Birger, Marta Galanti, Erik Ladewig, Haruka Morita and Minhaz Ud-Dean for useful discussions.  ... 
doi:10.1093/bioinformatics/btz474 pmid:31173059 pmcid:PMC6956775 fatcat:vx7ln7y2nfgb7dydcn5pc2u6ua

A high-resolution HLA reference panel capturing global population diversity enables multi-ethnic fine-mapping in HIV host response [article]

Yang Luo, Masahiro Kanai, Wanson Choi, Xinyi Li, Kenichi Yamamoto, Kotaro Ogawa, Maria Gutierrez-Arcelus, Peter K Gregersen, Philip E Stuart, James T Elder, Jacques Fellay, Mary Carrington (+18 others)
2020 medRxiv   pre-print
To enable such studies, we constructed a large (N=21,546) high resolution HLA reference panel spanning five global populations based on whole-genome sequencing data.  ...  We jointly analyzed genome-wide association studies (GWAS) of HIV-1 viral load from EUR, AA and LAT populations.  ...  Results Performance evaluation of inferred classical HLA alleles To build a large-scale multi-ethnic HLA imputation reference panel, we used high-coverage whole genome sequencing (WGS) datasets [17]  ... 
doi:10.1101/2020.07.16.20155606 fatcat:qrchys3anfgldhoyhnv6qafity

Technical Performance of a 430-Gene Preventative Genomics Assay to Identify Multiple Variant Types Associated with Adult-Onset Monogenic Conditions, Susceptibility Loci, and Pharmacogenetic Insights

Ari Silver, Gabriel A. Lazarin, Maxwell Silver, Meghan Miller, Michael Jansen, Christine Wechsberg, Erin Dekanek, Stav Grossfeld, Tim Herpel, Dinura Gunatilake, Alexander Bisignano, Malgorzata Jaremko
2022 Journal of Personalized Medicine  
Validation was performed against reference DNA from three sources: 1000 Genomes Project (n = 3), Coriell biobank (n = 105), and previously molecularly characterized biological specimens: blood (n = 15)  ...  This study demonstrates the validity of an NGS assay for genetic screening and the broadening of access to preventative genomics.  ...  HLAII uses a program which uses a graph-based method with high accuracy on exome and lowcoverage whole genome sequencing data [19] .  ... 
doi:10.3390/jpm12050667 fatcat:sscqezbtzzewffs3ydmmrwubxe

SweHLA: the high confidence HLA typing bio-resource drawn from 1000 Swedish genomes

Jessika Nordin, Adam Ameur, Kerstin Lindblad-Toh, Ulf Gyllensten, Jennifer R. S. Meadows
2019 European Journal of Human Genetics  
There is a need to accurately call human leukocyte antigen (HLA) genes from existing short-read sequencing data, however there is no single solution that matches the gold standard of Sanger sequenced lab  ...  SweHLA demonstrates a way to use existing NGS data to generate a population resource agnostic to individual HLA software biases.  ...  Acknowledgements We thank Mats Pettersson from Uppsala University for discussions around methodological biases.  ... 
doi:10.1038/s41431-019-0559-2 pmid:31844174 fatcat:umg5h6vt2nbxtb755sxjfbleum
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