NDLI: Variation analysis and gene annotation of eight MHC haplotypes: The MHC Haplotype Project

Content Provider	Springer Nature Link
Author	Horton, Roger Gibson, Richard Coggill, Penny Miretti, Marcos Allcock, Richard J. Almeida, Jeff Forbes, Simon Gilbert, James G. R. Halls, Karen Harrow, Jennifer L. Hart, Elizabeth Howe, Kevin Jackson, David K. Palmer, Sophie Roberts, Anne N. Sims, Sarah Stewart, C. Andrew Traherne, James A. Trevanion, Steve Wilming, Laurens Rogers, Jane Jong, Pieter J. Elliott, John F. Sawcer, Stephen Todd, John A. Trowsdale, John Beck, Stephan
Copyright Year	2007
Abstract	The human major histocompatibility complex (MHC) is contained within about 4 Mb on the short arm of chromosome 6 and is recognised as the most variable region in the human genome. The primary aim of the MHC Haplotype Project was to provide a comprehensively annotated reference sequence of a single, human leukocyte antigen-homozygous MHC haplotype and to use it as a basis against which variations could be assessed from seven other similarly homozygous cell lines, representative of the most common MHC haplotypes in the European population. Comparison of the haplotype sequences, including four haplotypes not previously analysed, resulted in the identification of >44,000 variations, both substitutions and indels (insertions and deletions), which have been submitted to the dbSNP database. The gene annotation uncovered haplotype-specific differences and confirmed the presence of more than 300 loci, including over 160 protein-coding genes. Combined analysis of the variation and annotation datasets revealed 122 gene loci with coding substitutions of which 97 were non-synonymous. The haplotype (A3-B7-DR15; PGF cell line) designated as the new MHC reference sequence, has been incorporated into the human genome assembly (NCBI35 and subsequent builds), and constitutes the largest single-haplotype sequence of the human genome to date. The extensive variation and annotation data derived from the analysis of seven further haplotypes have been made publicly available and provide a framework and resource for future association studies of all MHC-associated diseases and transplant medicine.
Starting Page	1
Ending Page	18
Page Count	18
File Format	PDF
ISSN	00937711
Journal	Immunogenetics
Volume Number	60
Issue Number	1
e-ISSN	14321211
Language	English
Publisher	Springer-Verlag
Publisher Date	2008-01-10
Publisher Place	Berlin, Heidelberg
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Major histocompatibility complex Haplotype Polymorphism Retroelement Genetic predisposition to disease Population genetics Cell Biology Allergology Immunology
Content Type	Text
Resource Type	Article
Subject	Genetics Immunology

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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