title: A novel RNAseq-assisted method for MHC class I genotyping in a non-model species applied to a lethal vaccination-induced alloimmune disease.
abstract: MHC 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.
  
  
  
  Taking 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.
  
  
  
  Successful 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.
authors.affiliation: Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196, Dummerstorf, Germany.
authors.forename: Wiebke
authors.initials: W
authors.lastname: Demasius
authors.affiliation: Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196, Dummerstorf, Germany.
authors.forename: Rosemarie
authors.initials: R
authors.lastname: Weikard
authors.affiliation: Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196, Dummerstorf, Germany.
authors.forename: Frieder
authors.initials: F
authors.lastname: Hadlich
authors.affiliation: Institute of Animal Breeding, Bavarian State Research Center for Agriculture, 85586, Grub, Germany.
authors.forename: Johannes
authors.initials: J
authors.lastname: Buitkamp
authors.affiliation: Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196, Dummerstorf, Germany. kuehn@fbn-dummerstorf.de.|Faculty of Agricultural and Environmental Sciences, University Rostock, 18059, Rostock, Germany. kuehn@fbn-dummerstorf.de.
authors.forename: Christa
authors.initials: C
authors.lastname: Kühn
mesh_terms: D000483:Alleles; D000818:Animals; D002417:Cattle; D002418:Cattle Diseases / Q000209:etiology*; D002460:Cell Line; D005805:Genes, MHC Class I; D005838:Genotype; D060005:Genotyping Techniques; D005858:Germany; D006239:Haplotypes; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods; D007154:Immune System Diseases / Q000662:veterinary*; D020641:Polymorphism, Single Nucleotide; D014611:Vaccination / Q000009:adverse effects*; D014612:Vaccines / Q000008:administration & dosage / Q000009:adverse effects*; D057188:Workflow
chemical_list: D014612:Vaccines
keywords: Bovine neonatal pancytopenia (BNP); Cattle; Expression levels; MHC class I; MHC typing; RNAseq