PMID- 19845894
OWN - NLM
STAT- MEDLINE
DCOM- 20100201
LR  - 20211020
IS  - 1399-0039 (Electronic)
IS  - 0001-2815 (Print)
IS  - 0001-2815 (Linking)
VI  - 74
IP  - 5
DP  - 2009 Nov
TI  - High-resolution, high-throughput HLA genotyping by next-generation sequencing.
PG  - 393-403
LID - 10.1111/j.1399-0039.2009.01345.x [doi]
AB  - The human leukocyte antigen (HLA) class I and class II loci are the most 
      polymorphic genes in the human genome. Hematopoietic stem cell transplantation 
      requires allele-level HLA typing at multiple loci to select the best matched 
      unrelated donors for recipient patients. In current methods for HLA typing, both 
      alleles of a heterozygote are amplified and typed or sequenced simultaneously, 
      often making it difficult to unambiguously determine the sequence of the two 
      alleles. Next-generation sequencing methods clonally propagate in parallel 
      millions of single DNA molecules, which are then also sequenced in parallel. 
      Recently, the read lengths obtainable by one such next-generation sequencing 
      method (454 Life Sciences, Inc.) have increased to >250 nucleotides. These clonal 
      read lengths make possible setting the phase of the linked polymorphisms within 
      an exon and thus the unambiguous determination of the sequence of each HLA 
      allele. Here we demonstrate this capacity as well as show that the throughput of 
      the system is sufficiently high to enable a complete, 7-locus HLA class I and II 
      typing for 24 or 48 individual DNAs in a single GS FLX sequencing run. Highly 
      multiplexed amplicon sequencing is facilitated by the use of sample-specific 
      internal sequence tags (multiplex identification tags or MIDs) in the primers 
      that allow pooling of samples yet maintain the ability to assign sequences to 
      specific individuals. We have incorporated an HLA typing software application 
      developed by Conexio Genomics (Freemantle, Australia) that assigns HLA genotypes 
      for these 7 loci (HLA-A, -B, -C, DRB1, DQA1, DQB1, DPB1), as well as for DRB3, 
      DRB4, and DRB5 from 454 sequence data. The potential of this HLA sequencing 
      system to analyze chimeric mixtures is demonstrated here by the detection of a 
      rare HLA-B allele in a mixture of two homozygous cell lines (1/100), as well as 
      by the detection of the rare nontransmitted maternal allele present in the blood 
      of a severe combined immunodeficiency disease syndrome (SCIDS) patient.
FAU - Bentley, G
AU  - Bentley G
AD  - Department of Human Genetics, Roche Molecular Systems Inc, Pleasanton, CA 94588, 
      USA.
FAU - Higuchi, R
AU  - Higuchi R
FAU - Hoglund, B
AU  - Hoglund B
FAU - Goodridge, D
AU  - Goodridge D
FAU - Sayer, D
AU  - Sayer D
FAU - Trachtenberg, E A
AU  - Trachtenberg EA
FAU - Erlich, H A
AU  - Erlich HA
LA  - eng
GR  - U01 AI067068/AI/NIAID NIH HHS/United States
PT  - Evaluation Study
PT  - Journal Article
PL  - England
TA  - Tissue Antigens
JT  - Tissue antigens
JID - 0331072
RN  - 0 (HLA Antigens)
SB  - IM
MH  - Alleles
MH  - Base Sequence
MH  - *Family Characteristics
MH  - Female
MH  - Gene Frequency
MH  - Genotype
MH  - HLA Antigens/analysis/*genetics
MH  - High-Throughput Screening Assays/*methods
MH  - Histocompatibility Testing/methods
MH  - Humans
MH  - Male
MH  - Parents
MH  - Polymorphism, Genetic
MH  - Sequence Analysis, DNA/*methods
MH  - Severe Combined Immunodeficiency/genetics/immunology
PMC - PMC4205125
MID - NIHMS635466
EDAT- 2009/10/23 06:00
MHDA- 2010/02/02 06:00
PMCR- 2014/10/21
CRDT- 2009/10/23 06:00
PHST- 2009/10/23 06:00 [entrez]
PHST- 2009/10/23 06:00 [pubmed]
PHST- 2010/02/02 06:00 [medline]
PHST- 2014/10/21 00:00 [pmc-release]
AID - TAN1345 [pii]
AID - 10.1111/j.1399-0039.2009.01345.x [doi]
PST - ppublish
SO  - Tissue Antigens. 2009 Nov;74(5):393-403. doi: 10.1111/j.1399-0039.2009.01345.x.