Literature DB >> 23775738

Next-generation HLA sequencing using the 454 GS FLX system.

Elizabeth A Trachtenberg1, Cherie L Holcomb.   

Abstract

Next-generation sequencing (NGS) of HLA class I and II loci (HLA-A, HLA-B, HLA-C, DRB1, DRB3, DRB4, DRB5, DQA1, DQB1, DPB1) is described here in detail using the 454 Life Sciences GS FLX System and Titanium chemistry. An overview of the protocol with our experience on sequence performance efficiencies, read depth and ambiguity analyses using the GS FLX System are also presented. A total of 14 HLA primer pairs with multiplex identifiers (MIDs) are used in clonal, amplicon-based pyrosequencing of up to 44 samples per plate using the GS FLX. Genotype assignment and ambiguity reduction -analysis is performed using Conexio Assign ATF 454 software. Clonal NGS gives a significant reduction in genotyping ambiguity during analysis of the highly complex HLA system.

Entities:  

Mesh：

Substances：

Year:  2013        PMID： 23775738      PMCID： PMC4196724          DOI： 10.1007/978-1-62703-493-7_10

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  5 in total

1.  Multi-locus HLA class I and II allele and haplotype associations with follicular lymphoma.

Authors:  C F Skibola; N K Akers; L Conde; M Ladner; S K Hawbecker; F Cohen; F Ribas; H A Erlich; D Goodridge; E A Trachtenberg; M T Smith; P M Bracci
Journal:  Tissue Antigens       Date:  2012-02-02

2.  Genome sequencing in microfabricated high-density picolitre reactors.

Authors:  Marcel Margulies; Michael Egholm; William E Altman; Said Attiya; Joel S Bader; Lisa A Bemben; Jan Berka; Michael S Braverman; Yi-Ju Chen; Zhoutao Chen; Scott B Dewell; Lei Du; Joseph M Fierro; Xavier V Gomes; Brian C Godwin; Wen He; Scott Helgesen; Chun Heen Ho; Chun He Ho; Gerard P Irzyk; Szilveszter C Jando; Maria L I Alenquer; Thomas P Jarvie; Kshama B Jirage; Jong-Bum Kim; James R Knight; Janna R Lanza; John H Leamon; Steven M Lefkowitz; Ming Lei; Jing Li; Kenton L Lohman; Hong Lu; Vinod B Makhijani; Keith E McDade; Michael P McKenna; Eugene W Myers; Elizabeth Nickerson; John R Nobile; Ramona Plant; Bernard P Puc; Michael T Ronan; George T Roth; Gary J Sarkis; Jan Fredrik Simons; John W Simpson; Maithreyan Srinivasan; Karrie R Tartaro; Alexander Tomasz; Kari A Vogt; Greg A Volkmer; Shally H Wang; Yong Wang; Michael P Weiner; Pengguang Yu; Richard F Begley; Jonathan M Rothberg
Journal:  Nature       Date:  2005-07-31       Impact factor: 49.962

3.  Next-generation sequencing can reveal in vitro-generated PCR crossover products: some artifactual sequences correspond to HLA alleles in the IMGT/HLA database.

Authors:  C L Holcomb; M Rastrou; T C Williams; D Goodridge; A M Lazaro; M Tilanus; H A Erlich
Journal:  Tissue Antigens       Date:  2014-01

4.  A multi-site study using high-resolution HLA genotyping by next generation sequencing.

Authors:  C L Holcomb; B Höglund; M W Anderson; L A Blake; I Böhme; M Egholm; D Ferriola; C Gabriel; S E Gelber; D Goodridge; S Hawbecker; R Klein; M Ladner; C Lind; D Monos; M J Pando; J Pröll; D C Sayer; G Schmitz-Agheguian; B B Simen; B Thiele; E A Trachtenberg; D B Tyan; R Wassmuth; S White; H A Erlich
Journal:  Tissue Antigens       Date:  2011-03

5.  High-resolution, high-throughput HLA genotyping by next-generation sequencing.

Authors:  G Bentley; R Higuchi; B Hoglund; D Goodridge; D Sayer; E A Trachtenberg; H A Erlich
Journal:  Tissue Antigens       Date:  2009-11
  5 in total
  2 in total

Review 1.  The impact of next-generation sequencing technologies on HLA research.

Authors:  Kazuyoshi Hosomichi; Takashi Shiina; Atsushi Tajima; Ituro Inoue
Journal:  J Hum Genet       Date:  2015-08-27       Impact factor: 3.172

2.  The use of haplotype-specific transcripts improves sample annotation consistency.

Authors:  Nicole Hartmann; Evert Luesink; Edward Khokhlovich; Joseph D Szustakowski; Lukas Baeriswyl; Joshua Peterson; Andreas Scherer; Nirmala R Nanguneri; Frank Staedtler
Journal:  Biomark Res       Date:  2014-09-30
  2 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.