Virus Expression Database

GSE48918

Impact of genomic polymorphisms on the repertoire of human MHC class I-associated peptides

Submitted by Diana Paola Granados (IRIC, Canada) on Jul 16 2013

Platform: ngs – Illumina HiSeq 2000 (Homo sapiens)

Pubmed: 24714562

Summary We developed a novel approach combining next generation sequencing, bioinformatics and mass spectrometry to assess the impact of non-MHC polymorphisms on the repertoire of MHC I-associated peptides (MIPs). We compared the genomic landscape of MIPs eluted from B lymphoblasts of two MHC-identical siblings and determined that MIPs mirror the genomic frequency of non-synonymous polymorphisms but they behave as recessive traits at the surface level. Moreover, we showed that 11.7% of the MIP coding exome is polymorphic at the population level. Our method provides fundamental insights into the relation between the genomic self and the immune self and accelerates the discovery of polymorphic MIPs (also known as minor histocompatibility antigens), which play a major role in allo-immune responses.

2 Samples

ID Title Cell Type Timepoint Reported Virus Virus Species Exclusion Reason
GSM1186811 B-LCL-2.1 lymphoblastoid cell line  Human gammaherpesvirus 4
GSM1186812 B-LCL-2.2 lymphoblastoid cell line  Human gammaherpesvirus 4