Genomic characterization of MICA gene using multiple next generation sequencing platforms: A validation study.

HLA : Immune Response Genetics
Yizhou ZouDimitri S Monos

Abstract

We have developed a protocol regarding the genomic characterization of the MICA gene by next generation sequencing (NGS). The amplicon includes the full length of the gene and is about 13 kb. A total of 156 samples were included in the study. Ninety-seven of these samples were previously characterized at MICA by legacy methods (Sanger or sequence specific oligonucleotide) and were used to evaluate the accuracy, precision, specificity, and sensitivity of the assay. An additional 59 DNA samples of unknown ethnicity volunteers from the United States were only genotyped by NGS. Samples were chosen to contain a diverse set of alleles. Our NGS approach included a first round of sequencing on the Illumina MiSeq platform and a second round of sequencing on the MinION platform by Oxford Nanopore Technology (ONT), on selected samples for the purpose of either characterizing new alleles or setting phase among multiple polymorphisms to resolve ambiguities or generate complete sequence for alleles that were only partially reported in the IMGT/HLA database. Complete consensus sequences were generated for every allele sequenced with ONT, extending from the 5' untranslated region (UTR) to the 3' UTR of the MICA gene. Thirty-two MICA sequences ...Continue Reading

References

Jul 5, 1994·Proceedings of the National Academy of Sciences of the United States of America·S BahramT Spies
Jun 17, 1999·Immunogenetics·E W PetersdorfJ A Hansen
Jun 8, 2001·Human Immunology·Y ZhangP Stastny
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Sep 28, 2007·The New England Journal of Medicine·Yizhou ZouGerhard Opelz
Jan 31, 2009·American Journal of Transplantation : Official Journal of the American Society of Transplantation and the American Society of Transplant Surgeons·B Suárez-AlvarezC López-Larrea
Feb 16, 2010·Trends in Molecular Medicine·Mun-Kit Choy, Maude E Phipps
Jun 6, 2012·Methods in Molecular Biology·Yizhou Zou, Peter Stastny
Jun 8, 2019·The Journal of Molecular Diagnostics : JMD·Jamie L DukeDimitri S Monos

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Citations

Oct 31, 2020·International Journal of Immunogenetics·Steven G E Marsh
Nov 28, 2020·HLA : Immune Response Genetics·Steven G E Marsh
Feb 10, 2021·International Journal of Immunogenetics·Steven G E Marsh
Feb 10, 2021·HLA : Immune Response Genetics·Steven G E Marsh

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Methods Mentioned

BETA
genotyping
PCR
3730 Sequencing
electrophoresis
Illumina sequencing

Software Mentioned

NGSengine
ONT
Pysam
msa
CHOP
HLA Fusion
Bioconductor
MAFFT
ONT MinION
Omixon Twin

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