Literature DB >> 28674023

Fast and accurate HLA typing from short-read next-generation sequence data with xHLA.

Chao Xie1, Zhen Xuan Yeo2, Marie Wong2, Jason Piper2, Tao Long3, Ewen F Kirkness3, William H Biggs3, Ken Bloom3, Stephen Spellman4, Cynthia Vierra-Green4, Colleen Brady4, Richard H Scheuermann5,6, Amalio Telenti3, Sally Howard3, Suzanne Brewerton2, Yaron Turpaz2,3, J Craig Venter7,5.   

Abstract

The HLA gene complex on human chromosome 6 is one of the most polymorphic regions in the human genome and contributes in large part to the diversity of the immune system. Accurate typing of HLA genes with short-read sequencing data has historically been difficult due to the sequence similarity between the polymorphic alleles. Here, we introduce an algorithm, xHLA, that iteratively refines the mapping results at the amino acid level to achieve 99-100% four-digit typing accuracy for both class I and II HLA genes, taking only [Formula: see text]3 min to process a 30× whole-genome BAM file on a desktop computer.

Entities:  

Keywords:  MHC; autoimmune diseases; transplantation

Mesh：

Year:  2017        PMID： 28674023      PMCID： PMC5544337          DOI： 10.1073/pnas.1707945114

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN： 0027-8424            Impact factor:   11.205


  23 in total

1.  The IPD-IMGT/HLA Database - New developments in reporting HLA variation.

Authors:  James Robinson; Anup R Soormally; James D Hayhurst; Steven G E Marsh
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2.  In chronic condition: experiences of patients with complex health care needs, in eight countries, 2008.

Authors:  Cathy Schoen; Robin Osborn; Sabrina K H How; Michelle M Doty; Jordon Peugh
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3.  Isaac: ultra-fast whole-genome secondary analysis on Illumina sequencing platforms.

Authors:  Come Raczy; Roman Petrovski; Christopher T Saunders; Ilya Chorny; Semyon Kruglyak; Elliott H Margulies; Han-Yu Chuang; Morten Källberg; Swathi A Kumar; Arnold Liao; Kristina M Little; Michael P Strömberg; Stephen W Tanner
Journal:  Bioinformatics       Date:  2013-06-04       Impact factor: 6.937

4.  OptiType: precision HLA typing from next-generation sequencing data.

Authors:  András Szolek; Benjamin Schubert; Christopher Mohr; Marc Sturm; Magdalena Feldhahn; Oliver Kohlbacher
Journal:  Bioinformatics       Date:  2014-08-20       Impact factor: 6.937

5.  HLA diversity in the 1000 genomes dataset.

Authors:  Pierre-Antoine Gourraud; Pouya Khankhanian; Nezih Cereb; Soo Young Yang; Michael Feolo; Martin Maiers; John D Rioux; Stephen Hauser; Jorge Oksenberg
Journal:  PLoS One       Date:  2014-07-02       Impact factor: 3.240

6.  Fast and accurate long-read alignment with Burrows-Wheeler transform.

Authors:  Heng Li; Richard Durbin
Journal:  Bioinformatics       Date:  2010-01-15       Impact factor: 6.937

7.  Derivation of HLA types from shotgun sequence datasets.

Authors:  René L Warren; Gina Choe; Douglas J Freeman; Mauro Castellarin; Sarah Munro; Richard Moore; Robert A Holt
Journal:  Genome Med       Date:  2012-12-10       Impact factor: 11.117

8.  The IMGT/HLA database.

Authors:  James Robinson; Jason A Halliwell; Hamish McWilliam; Rodrigo Lopez; Peter Parham; Steven G E Marsh
Journal:  Nucleic Acids Res       Date:  2012-10-17       Impact factor: 16.971

9.  The HLA Region and Autoimmune Disease: Associations and Mechanisms of Action.

Authors:  S C L Gough; M J Simmonds
Journal:  Curr Genomics       Date:  2007-11       Impact factor: 2.236

10.  MUSCLE: a multiple sequence alignment method with reduced time and space complexity.

Authors:  Robert C Edgar
Journal:  BMC Bioinformatics       Date:  2004-08-19       Impact factor: 3.169
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  36 in total

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2.  Neoadjuvant and Adjuvant Pembrolizumab in Resectable Locally Advanced, Human Papillomavirus-Unrelated Head and Neck Cancer: A Multicenter, Phase II Trial.

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Journal:  Clin Cancer Res       Date:  2020-07-14       Impact factor: 12.531

3.  ALPHLARD-NT: Bayesian Method for Human Leukocyte Antigen Genotyping and Mutation Calling through Simultaneous Analysis of Normal and Tumor Whole-Genome Sequence Data.

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Journal:  J Comput Biol       Date:  2019-04-03       Impact factor: 1.479

4.  T cell receptor-β J usage, in combination with particular HLA class II alleles, correlates with better cancer survival rates.

Authors:  Blake M Callahan; Wei Lue Tong; George Blanck
Journal:  Immunol Res       Date:  2018-04       Impact factor: 2.829

5.  Evolutionary Pressure against MHC Class II Binding Cancer Mutations.

Authors:  Rachel Marty Pyke; Wesley Kurt Thompson; Rany M Salem; Joan Font-Burgada; Maurizio Zanetti; Hannah Carter
Journal:  Cell       Date:  2018-09-20       Impact factor: 41.582

Review 6.  Next-generation computational tools for interrogating cancer immunity.

Authors:  Francesca Finotello; Dietmar Rieder; Hubert Hackl; Zlatko Trajanoski
Journal:  Nat Rev Genet       Date:  2019-09-12       Impact factor: 59.581

Review 7.  A long road/read to rapid high-resolution HLA typing: The nanopore perspective.

Authors:  Chang Liu
Journal:  Hum Immunol       Date:  2020-05-01       Impact factor: 2.211

8.  Whole-exome sequencing reveals common and rare variants in immunologic and neurological genes implicated in achalasia.

Authors:  Quanlin Li; Weifeng Chen; Cheng Wang; Zuqiang Liu; Yayun Gu; Xiaoyue Xu; Jiaxing Xu; Tao Jiang; Meidong Xu; Yifeng Wang; Congcong Chen; Yunshi Zhong; Yiqun Zhang; Liqing Yao; Guangfu Jin; Zhibin Hu; Pinghong Zhou
Journal:  Am J Hum Genet       Date:  2021-06-30       Impact factor: 11.025

9.  Benchmarking HLA genotyping and clarifying HLA impact on survival in tumor immunotherapy.

Authors:  Xiangyong Li; Chi Zhou; Ke Chen; Bingding Huang; Qi Liu; Hao Ye
Journal:  Mol Oncol       Date:  2021-01-24       Impact factor: 6.603

10.  Genetic risk, dysbiosis, and treatment stratification using host genome and gut microbiome in inflammatory bowel disease.

Authors:  Ahmed Moustafa; Weizhong Li; Ericka L Anderson; Emily H M Wong; Parambir S Dulai; William J Sandborn; William Biggs; Shibu Yooseph; Marcus B Jones; J Craig Venter; Karen E Nelson; John T Chang; Amalio Telenti; Brigid S Boland
Journal:  Clin Transl Gastroenterol       Date:  2018-01-18       Impact factor: 4.488
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