American Journal of Life Sciences
Volume 4, Issue 6, December 2016, Pages: 146-151
Received: Nov. 29, 2016;
Published: Dec. 1, 2016
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Yuanwei Zhang, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China; BGI-Shenzhen, Shenzhen, China
Tao Zhang, BGI-Shenzhen, Shenzhen, China
Zuhong Lu, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
The major histocompatibility complex (MHC) is recognized as the most variable region in the human genome and has susceptibility to > 100 diseases. We constructed a complete MHC haplotype sequence of MCF cell line by gap filling based on whole genome sequencing (WGS) data. Gaps spanning ~ 1 Mb were filled and 31 genes were annotated in these gaps. This sequence could be used as reference to identify disease associations within this haplotype or similar haplotypes. The method for gap filling can be applied to other MHC haplotypes or other genomic region.
Gap Filling for a Human MHC Haplotype Sequence, American Journal of Life Sciences.
Vol. 4, No. 6,
2016, pp. 146-151.
The, M. H. C. s. c., Complete sequence and gene map of a human major histocompatibility complex. The MHC sequencing consortium. Nature, 1999. 401 (6756): p. 921-923.
Stewart, C. A., et al., Complete MHC haplotype sequencing for common disease gene mapping. Genome research, 2004. 14 (6): p. 1176-1187.
Burton, P. R., et al., Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature, 2007. 447 (7145): p. 661-678.
Horton, R., et al., Variation analysis and gene annotation of eight MHC haplotypes: the MHC Haplotype Project. Immunogenetics, 2008. 60 (1): p. 1-18.
Yeo, T. W., et al., A second major histocompatibility complex susceptibility locus for multiple sclerosis. Annals of neurology, 2007. 61 (3): p. 228-236.
Miller, F. W., et al., Genome-wide association study identifies HLA 8.1 ancestral haplotype alleles as major genetic risk factors for myositis phenotypes. Genes and immunity, 2015. 16 (7): p. 470-480.
Lagha, A., et al., HLA DRB1/DQB1 alleles and DRB1‐DQB1 haplotypes and the risk of rheumatoid arthritis in Tunisians: a population‐based case–control study. HLA, 2016. 88 (3): p. 100-109.
De Sá, P. H., et al., GapBlaster—A Graphical Gap Filler for Prokaryote Genomes. PloS one, 2016. 11 (5): p. e0155327.
Piro, V. C., et al., FGAP: an automated gap closing tool. BMC research notes, 2014. 7 (1): p. 1.
Ramos, R. T. J., et al., Graphical contig analyzer for all sequencing platforms (G4ALL): a new stand-alone tool for finishing and draft generation of bacterial genomes. Bioinformation, 2013. 9 (11): p. 599.
Boetzer, M. and W. Pirovano, Toward almost closed genomes with GapFiller. Genome biology, 2012. 13 (6): p. 1.
Luo, R., et al., SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience, 2012. 1 (1): p. 1.
Kent, W. J., BLAT—the BLAST-like alignment tool. Genome research, 2002. 12 (4): p. 656-664.
Robinson, J., et al., The IPD and IMGT/HLA database: allele variant databases. Nucleic acids research, 2014: p. gku1161.
Li, H. and R. Durbin, Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics, 2009. 25 (14): p. 1754-1760.
Li, H., et al., The sequence alignment/map format and SAMtools. Bioinformatics, 2009. 25 (16): p. 2078-2079.
Li, H., A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics, 2011. 27 (21): p. 2987-2993.
Speir, M. L., et al., The UCSC Genome Browser database: 2016 update. Nucleic acids research, 2016. 44 (D1): p. D717-D725.
Altschul, S. F., et al., Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic acids research, 1997. 25(17): p. 3389-3402.
Morioka, M. S., et al., Filling in the Gap of Human Chromosome 4: Single Molecule Real Time Sequencing of Macrosatellite Repeats in the Facioscapulohumeral Muscular Dystrophy Locus. PloS one, 2016. 11 (3): p. e0151963.