BACKGROUND: Comprehensive sequence characterization across the MHC is important for successful organ transplantation and genetic association studies. To this end, we have developed an automated sample preparation, molecular barcoding and multiplexing protocol for the amplification and sequence-determination of class I HLA loci. We have coupled this process to a novel HLA calling algorithm to determine the most likely pair of alleles at each locus. RESULTS: We have benchmarked our protocol with 270 HapMap individuals from four worldwide populations with 96.4% accuracy at 4-digit resolution. A variation of this initial protocol, more suitable for large sample sizes, in which molecular barcodes are added during PCR rather than library construction, was tested on 95 HapMap individuals with 98.6% accuracy at 4-digit resolution. CONCLUSIONS: Next-generation sequencing on the 454 FLX Titanium platform is a reliable, efficient, and scalable technology for HLA typing.
BACKGROUND: Comprehensive sequence characterization across the MHC is important for successful organ transplantation and genetic association studies. To this end, we have developed an automated sample preparation, molecular barcoding and multiplexing protocol for the amplification and sequence-determination of class I HLA loci. We have coupled this process to a novel HLA calling algorithm to determine the most likely pair of alleles at each locus. RESULTS: We have benchmarked our protocol with 270 HapMap individuals from four worldwide populations with 96.4% accuracy at 4-digit resolution. A variation of this initial protocol, more suitable for large sample sizes, in which molecular barcodes are added during PCR rather than library construction, was tested on 95 HapMap individuals with 98.6% accuracy at 4-digit resolution. CONCLUSIONS: Next-generation sequencing on the 454 FLX Titanium platform is a reliable, efficient, and scalable technology for HLA typing.
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
Authors: Andrew M Waterhouse; James B Procter; David M A Martin; Michèle Clamp; Geoffrey J Barton Journal: Bioinformatics Date: 2009-01-16 Impact factor: 6.937
Authors: Roger Horton; Laurens Wilming; Vikki Rand; Ruth C Lovering; Elspeth A Bruford; Varsha K Khodiyar; Michael J Lush; Sue Povey; C Conover Talbot; Mathew W Wright; Hester M Wain; John Trowsdale; Andreas Ziegler; Stephan Beck Journal: Nat Rev Genet Date: 2004-12 Impact factor: 53.242
Authors: Paul I W de Bakker; Gil McVean; Pardis C Sabeti; Marcos M Miretti; Todd Green; Jonathan Marchini; Xiayi Ke; Alienke J Monsuur; Pamela Whittaker; Marcos Delgado; Jonathan Morrison; Angela Richardson; Emily C Walsh; Xiaojiang Gao; Luana Galver; John Hart; David A Hafler; Margaret Pericak-Vance; John A Todd; Mark J Daly; John Trowsdale; Cisca Wijmenga; Tim J Vyse; Stephan Beck; Sarah Shaw Murray; Mary Carrington; Simon Gregory; Panos Deloukas; John D Rioux Journal: Nat Genet Date: 2006-09-24 Impact factor: 38.330
Authors: James Robinson; Matthew J Waller; Sylvie C Fail; Hamish McWilliam; Rodrigo Lopez; Peter Parham; Steven G E Marsh Journal: Nucleic Acids Res Date: 2008-10-05 Impact factor: 16.971
Authors: Roger Horton; Richard Gibson; Penny Coggill; Marcos Miretti; Richard J Allcock; Jeff Almeida; Simon Forbes; James G R Gilbert; Karen Halls; Jennifer L Harrow; Elizabeth Hart; Kevin Howe; David K Jackson; Sophie Palmer; Anne N Roberts; Sarah Sims; C Andrew Stewart; James A Traherne; Steve Trevanion; Laurens Wilming; Jane Rogers; Pieter J de Jong; John F Elliott; Stephen Sawcer; John A Todd; John Trowsdale; Stephan Beck Journal: Immunogenetics Date: 2008-01-10 Impact factor: 2.846
Authors: Michelle M A Fernando; Christine R Stevens; Emily C Walsh; Philip L De Jager; Philippe Goyette; Robert M Plenge; Timothy J Vyse; John D Rioux Journal: PLoS Genet Date: 2008-04-25 Impact factor: 5.917
Authors: J Pham; C Oseroff; D Hinz; J Sidney; S Paul; J Greenbaum; R Vita; E Phillips; S Mallal; B Peters; A Sette Journal: Clin Exp Allergy Date: 2016-07-26 Impact factor: 5.018
Authors: Cecilia S Lindestam Arlehamn; Richard Copin; Shay Leary; Steven J Mack; Elizabeth Phillips; Simon Mallal; Alessandro Sette; Gretta Blatner; Heather Siefers; Joel D Ernst Journal: Hum Immunol Date: 2017-03-16 Impact factor: 2.850
Authors: Zaza M Ndhlovu; Lori B Chibnik; Jacqueline Proudfoot; Seanna Vine; Ashley McMullen; Kevin Cesa; Filippos Porichis; R Brad Jones; Donna Marie Alvino; Meghan G Hart; Eleni Stampouloglou; Alicja Piechocka-Trocha; Carl Kadie; Florencia Pereyra; David Heckerman; Philip L De Jager; Bruce D Walker; Daniel E Kaufmann Journal: Blood Date: 2012-12-11 Impact factor: 22.113
Authors: Michael Wittig; Jarl A Anmarkrud; Jan C Kässens; Simon Koch; Michael Forster; Eva Ellinghaus; Johannes R Hov; Sascha Sauer; Manfred Schimmler; Malte Ziemann; Siegfried Görg; Frank Jacob; Tom H Karlsen; Andre Franke Journal: Nucleic Acids Res Date: 2015-03-09 Impact factor: 16.971
Authors: Daniela Weiskopf; Alba Grifoni; Cecilia S Lindestam Arlehamn; Michael Angelo; Shay Leary; John Sidney; April Frazier; Steven J Mack; Elizabeth Phillips; Simon Mallal; Cristhiam Cerpas; Angel Balmaseda; Eva Harris; Alessandro Sette Journal: Hum Immunol Date: 2017-11-07 Impact factor: 2.850
Authors: Ti-Cheng Chang; Kelly M Haupfear; Jing Yu; Evadnie Rampersaud; Vivien A Sheehan; Jonathan M Flanagan; Jane S Hankins; Mitchell J Weiss; Gang Wu; Sunitha Vege; Connie M Westhoff; Stella T Chou; Yan Zheng Journal: Blood Adv Date: 2020-09-22