A novel RNAseq–assisted method for MHC class I genotyping in a non-model species applied to a lethal vaccination-induced alloimmune disease

BMC Genomics

Research Article

Frieder Hadlich¹  Rosemarie Weikard¹  Wiebke Demasius¹  Christa Kühn²  Johannes Buitkamp³ 

[1] Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196, Dummerstorf, Germany;Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196, Dummerstorf, Germany;Faculty of Agricultural and Environmental Sciences, University Rostock, 18059, Rostock, Germany;Institute of Animal Breeding, Bavarian State Research Center for Agriculture, 85586, Grub, Germany;

关键词: MHC class I;    MHC typing;    Expression levels;    Cattle;    RNAseq;    Bovine neonatal pancytopenia (BNP);   

DOI  :  10.1186/s12864-016-2688-0

 received in 2015-12-04, accepted in 2016-04-30,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundMHC class I genotyping is essential for a wide range of biomedical, immunological and biodiversity applications. Whereas in human a comprehensive MHC class I allele catalogue is available, respective data in non-model species is scarce in spite of decades of research.ResultsTaking advantage of the new high-throughput RNA sequencing technology (RNAseq), we developed a novel RNAseq-assisted method (RAMHCIT) for MHC class I typing at nucleotide level. RAMHCIT is performed on white blood cells, which highly express MHC class I molecules enabling reliable discovery of new alleles and discrimination of closely related alleles due to the high coverage of alleles with reads. RAMHCIT is more comprehensive than previous methods, because no targeted PCR pre-amplification of MHC loci is necessary, which avoids preselection of alleles as usually encountered, when amplification with MHC class I primers is performed prior to sequencing. In addition to allele identification, RAMHCIT also enables quantification of MHC class I expression at allele level, which was remarkably consistent across individuals.ConclusionsSuccessful application of RAMHCIT is demonstrated on a data set from cattle with different phenotype regarding a lethal, vaccination-induced alloimmune disease (bovine neonatal pancytopenia), for which MHC class I alleles had been postulated as causal agents.

【 授权许可】

CC BY   
© Demasius et al. 2016