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Application of high-resolution, massively parallel pyrosequencing for estimation of haplotypes and gene expression levels of swine leukocyte antigen (SLA) class I genes

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Application of high-resolution, massively parallel pyrosequencing for estimation of haplotypes and gene expression levels of swine leukocyte antigen (SLA) class I genes

Content Provider	Springer Nature Link
Author	Kita, Yuki F. Ando, Asako Tanaka, Keiko Suzuki, Shingo Ozaki, Yuki Uenishi, Hirohide Iko, Hidetoshi Kulski, Jerzy K. Shiina, Takashi
Copyright Year	2011
Abstract	The swine is an important animal model for allo- and xeno-transplantation donor studies, which necessitates an extensive characterization of the expression and sequence variations within the highly polygenic and polymorphic swine leukocyte antigen (SLA) region. Massively parallel pyrosequencing is potentially an effective new 2ndGen method for simultaneous high-throughput genotyping and detection of SLA class I gene expression levels. In this study, we compared the 2ndGen method using the Roche Genome Sequencer 454 FLX with the conventional method using sub-cloning and Sanger sequencing to genotype SLA class I genes in five pigs of the Clawn breed and four pigs of the Landrace breed. We obtained an average of 10.4 SLA class I sequences per pig by the 2ndGen method, consistent with the inheritance data, and an average of only 6.0 sequences by the conventional method. We also performed a correlation analysis between the sequence read numbers obtained by the 2ndGen method and the relative expression values obtained by quantitative real-time PCR analysis at the allele level. A significant correlation coefficient (r = 0.899, P < 0.01) was observed between the sequence read numbers and the relative quantitative values for the expressed classical SLA class I genes SLA-1, SLA-2, and SLA-3, suggesting that the sequence read numbers closely reflect the gene expression levels in white blood cells. Overall, five novel class I sequences, different haplotype-specific expression patterns and a splice variant for one of the SLA class I genes were identified by the 2ndGen method at greater efficiency and sensitivity than the conventional method.
Starting Page	187
Ending Page	199
Page Count	13
File Format	PDF
ISSN	00937711
Journal	Immunogenetics
Volume Number	64
Issue Number	3
e-ISSN	14321211
Language	English
Publisher	Springer-Verlag
Publisher Date	2011-09-20
Publisher Place	Berlin, Heidelberg
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Swine MHC Genotyping Haplotype Real-time PCR Pyrosequencing Gene Function Human Genetics Immunology Allergology Cell Biology
Content Type	Text
Resource Type	Article
Subject	Genetics Immunology

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