Dilthey, Alexander T. (2021). State-of-the-art genome inference in the human MHC. Int. J. Biochem. Cell Biol., 131. OXFORD: PERGAMON-ELSEVIER SCIENCE LTD. ISSN 1878-5875

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Abstract

The Major Histocompatibility Complex (MHC) on the short arm of chromosome 6 is associated with more diseases than any other region of the genome; it encodes the antigen-presenting Human Leukocyte Antigen (HLA) proteins and is one of the key immunogenetic regions of the genome. Accurate genome inference and interpretation of MHC association signals have traditionally been hampered by the region's uniquely complex features, such as high levels of polymorphism; inter-gene sequence homologies; structural variation; and long-range haplotype structures. Recent algorithmic and technological advances have, however, significantly increased the accessibility of genetic variation in the MHC; these developments include (i) accurate SNP-based HLA type imputation; (ii) genome graph approaches for variation-aware genome inference from next-generation sequencing data; (iii) long-read-based diploid de novo assembly of the MHC; (iv) cost-effective targeted MHC sequencing methods. Applied to hundreds of thousands of samples over the last years, these technologies have already enabled significant biological discoveries, for example in the field of autoimmune disease genetics. Remaining challenges concern the development of integrated methods that leverage haplotype-resolved de novo assembly of the MHC for the development of improved MHC genotyping methods for short reads and the construction of improved reference panels for SNP-based imputation. Improved genome inference in the MHC can crucially contribute to an improved genetic and functional understanding of many immune-related phenotypes and diseases.

Item Type: Journal Article
Creators:
CreatorsEmailORCIDORCID Put Code
Dilthey, Alexander T.UNSPECIFIEDUNSPECIFIEDUNSPECIFIED
URN: urn:nbn:de:hbz:38-572656
DOI: 10.1016/j.biocel.2020.105882
Journal or Publication Title: Int. J. Biochem. Cell Biol.
Volume: 131
Date: 2021
Publisher: PERGAMON-ELSEVIER SCIENCE LTD
Place of Publication: OXFORD
ISSN: 1878-5875
Language: English
Faculty: Unspecified
Divisions: Unspecified
Subjects: no entry
Uncontrolled Keywords:
KeywordsLanguage
MAJOR HISTOCOMPATIBILITY COMPLEX; CLASSICAL HLA ALLELES; CLASS-I; HIGH-RESOLUTION; GENETIC-VARIATION; WIDE ASSOCIATION; EVOLUTION; MAP; ALIGNMENT; DISEASEMultiple languages
Biochemistry & Molecular Biology; Cell BiologyMultiple languages
URI: http://kups.ub.uni-koeln.de/id/eprint/57265

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