PMID- 25087472
OWN - NLM
STAT- MEDLINE
DCOM- 20150331
LR  - 20211021
IS  - 1471-2164 (Electronic)
IS  - 1471-2164 (Linking)
VI  - 15
IP  - 1
DP  - 2014 Aug 4
TI  - A Bead-based Normalization for Uniform Sequencing depth (BeNUS) protocol for 
      multi-samples sequencing exemplified by HLA-B.
PG  - 645
LID - 10.1186/1471-2164-15-645 [doi]
LID - 645
AB  - BACKGROUND: Human leukocyte antigen (HLA) is a group of genes that are extremely 
      polymorphic among individuals and populations and have been associated with more 
      than 100 different diseases and adverse drug effects. HLA typing is accordingly 
      an important tool in clinical application, medical research, and population 
      genetics. We have previously developed a phase-defined HLA gene sequencing method 
      using MiSeq sequencing. RESULTS: Here we report a simple, high-throughput, and 
      cost-effective sequencing method that includes normalized library preparation and 
      adjustment of DNA molar concentration. We applied long-range PCR to amplify HLA-B 
      for 96 samples followed by transposase-based library construction and multiplex 
      sequencing with the MiSeq sequencer. After sequencing, we observed low variation 
      in read percentages (0.2% to 1.55%) among the 96 demultiplexed samples. On this 
      basis, all the samples were amenable to haplotype phasing using our phase-defined 
      sequencing method. In our study, a sequencing depth of 800x was necessary and 
      sufficient to achieve full phasing of HLA-B alleles with reliable assignment of 
      the allelic sequence to the 8 digit level. CONCLUSIONS: Our HLA sequencing method 
      optimized for 96 multiplexing samples is highly time effective and cost effective 
      and is especially suitable for automated multi-sample library preparation and 
      sequencing.
FAU - Hosomichi, Kazuyoshi
AU  - Hosomichi K
FAU - Mitsunaga, Shigeki
AU  - Mitsunaga S
FAU - Nagasaki, Hideki
AU  - Nagasaki H
FAU - Inoue, Ituro
AU  - Inoue I
AD  - Division of Human Genetics, National Institute of Genetics, 1111 Yata, Mishima, 
      411-8540 Shizuoka, Japan. itinoue@nig.ac.jp.
LA  - eng
SI  - SRA/DRA001289
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20140804
PL  - England
TA  - BMC Genomics
JT  - BMC genomics
JID - 100965258
RN  - 0 (HLA-B Antigens)
SB  - IM
MH  - Cost-Benefit Analysis
MH  - HLA-B Antigens/*genetics
MH  - High-Throughput Nucleotide Sequencing/economics/*methods
MH  - Humans
MH  - Polymerase Chain Reaction
MH  - Sequence Analysis, DNA/economics/*methods
PMC - PMC4133082
EDAT- 2014/08/05 06:00
MHDA- 2015/04/01 06:00
PMCR- 2014/08/04
CRDT- 2014/08/05 06:00
PHST- 2014/01/28 00:00 [received]
PHST- 2014/07/30 00:00 [accepted]
PHST- 2014/08/05 06:00 [entrez]
PHST- 2014/08/05 06:00 [pubmed]
PHST- 2015/04/01 06:00 [medline]
PHST- 2014/08/04 00:00 [pmc-release]
AID - 1471-2164-15-645 [pii]
AID - 6340 [pii]
AID - 10.1186/1471-2164-15-645 [doi]
PST - epublish
SO  - BMC Genomics. 2014 Aug 4;15(1):645. doi: 10.1186/1471-2164-15-645.