Current methods and opportunities of next-generation sequencing (NGS) for HLA typing

CTT JOURNAL | VOLUME 5 | NUMBER 4 | DECEMBER 2016 1Youri A. Serov, 1Ildar M. Barkhatov, 1Anton S. Klimov, 2Andrey S. Berkos 1Research Institute of Children Oncology, Hematology and Transplantation, The First State I. Pavlov Medical University, St. Petersburg, Russia 2Russian Research Institute of Hematology and Transfusiology, Federal Medical-Biological Agency, St. Petersburg, Russia Current methods and opportunities of next-generation sequencing (NGS) for HLA typing Cellular Therapy and Transplantation (CTT). Vol.5, No.4 (17), 2016 doi: 10.18620/ctt-1866-8836-2016-5-4-63-70 Submitted: 14 September 2016, accepted: 25 November 2016

[1]  E. Petersdorf.  Optimal HLA matching in hematopoietic cell transplantation. , 2008, Current opinion in immunology.

[2]  Matthew W. Anderson,et al.  A multi-site study using high-resolution HLA genotyping by next generation sequencing. , 2011, Tissue antigens.

[3]  J. Wagner,et al.  Reduced-intensity conditioning transplantation in acute leukemia: the effect of source of unrelated donor stem cells on outcomes. , 2010, Blood.

[4]  E. Weimer,et al.  Performance Characteristics and Validation of Next-Generation Sequencing for Human Leucocyte Antigen Typing. , 2016, The Journal of molecular diagnostics : JMD.

[5]  R Higuchi,et al.  High-resolution, high-throughput HLA genotyping by next-generation sequencing. , 2009, Tissue antigens.

[6]  Effie W Petersdorf,et al.  Effect of T-cell-epitope matching at HLA-DPB1 in recipients of unrelated-donor haemopoietic-cell transplantation: a retrospective study. , 2012, The Lancet. Oncology.

[7]  Bruce R. Blazar,et al.  Advances in graft-versus-host disease biology and therapy , 2012, Nature Reviews Immunology.

[8]  M. Sykes,et al.  Emerging concepts in haematopoietic cell transplantation , 2012, Nature Reviews Immunology.

[9]  R. Blasczyk,et al.  Sequencing of HLA class II genes based on the conserved diversity of the non-coding regions: sequencing based typing of HLA-DRB genes. , 1997, Tissue antigens.

[10]  S. Lank,et al.  A novel single cDNA amplicon pyrosequencing method for high-throughput, cost-effective sequence-based HLA class I genotyping. , 2010, Human immunology.

[11]  James Robinson,et al.  The IPD and IMGT/HLA database: allele variant databases , 2014, Nucleic Acids Res..

[12]  J. Madrigal,et al.  The impact of HLA genotyping on survival following unrelated donor haematopoietic stem cell transplantation , 2010, British journal of haematology.

[13]  D. Monos,et al.  Next-generation sequencing: the solution for high-resolution, unambiguous human leukocyte antigen typing. , 2010, Human immunology.

[14]  M. Metzker.  Sequencing technologies — the next generation , 2010, Nature Reviews Genetics.

[15]  Susan M. Huse,et al.  Accuracy and quality of massively parallel DNA pyrosequencing , 2007, Genome Biology.

[16]  P Liebelt,et al.  Reanalysis of sequence-based HLA-A, -B and -Cw typings: how ambiguous is today's SBT typing tomorrow. , 2007, Tissue antigens.

[17]  R. Blasczyk,et al.  Immunogenetics of HLA null alleles: implications for blood stem cell transplantation. , 2004, Tissue antigens.

[18]  N. Yu,et al.  Resolution of HLA class I sequence-based typing ambiguities by group-specific sequencing primers. , 2011, Tissue antigens.

[19]  Helene Polin,et al.  Rapid, scalable and highly automated HLA genotyping using next-generation sequencing: a transition from research to diagnostics , 2013, BMC Genomics.

[20]  S. Krishnakumar,et al.  High-throughput, high-fidelity HLA genotyping with deep sequencing , 2012, Proceedings of the National Academy of Sciences.

[21]  S. E. Marsh,et al.  Nomenclature for factors of the HLA system, update March 2016 , 2016, International journal of immunogenetics.

[22]  H. Erlich,et al.  HLA DNA typing: past, present, and future. , 2012, Tissue antigens.

[23]  S. Roy,et al.  HAPCAD: An open-source tool to detect PCR crossovers in next-generation sequencing generated HLA data. , 2016, Human immunology.

[24]  P. Dunn.  Human leucocyte antigen typing: techniques and technology, a critical appraisal , 2011, International journal of immunogenetics.

[25]  Vladimir Brusic,et al.  Ultra-high resolution HLA genotyping and allele discovery by highly multiplexed cDNA amplicon pyrosequencing , 2012, BMC Genomics.

[26]  M. Danzer,et al.  High-throughput sequence-based typing strategy for HLA-DRB1 based on real-time polymerase chain reaction. , 2007, Human immunology.

[27]  Olivier Harismendy,et al.  Method for improving sequence coverage uniformity of targeted genomic intervals amplified by LR-PCR using Illumina GA sequencing-by-synthesis technology. , 2009, BioTechniques.

[28]  Jerzy K. Kulski,et al.  Super high resolution for single molecule-sequence-based typing of classical HLA loci at the 8-digit level using next generation sequencers. , 2012, Tissue antigens.

[29]  N. Lennon,et al.  Next-generation sequencing for HLA typing of class I loci , 2011, BMC Genomics.

[30]  Helene Polin,et al.  Rapid high-throughput human leukocyte antigen typing by massively parallel pyrosequencing for high-resolution allele identification. , 2009, Human immunology.

[31]  K. Voelkerding,et al.  Next-generation sequencing: from basic research to diagnostics. , 2009, Clinical chemistry.

[32]  P. Stastny,et al.  Nomenclature for factors of the HLA system, update March , 2008 .

[33]  P. Hufnagl,et al.  Sequence Capture and Next Generation Resequencing of the MHC Region Highlights Potential Transplantation Determinants in HLA Identical Haematopoietic Stem Cell Transplantation , 2011, DNA research : an international journal for rapid publication of reports on genes and genomes.