Gap Filling for a Human MHC Haplotype Sequence

Yuanwei Zhang; Tao Zhang; Zuhong Lu

doi:doi:10.11648/j.ajls.20160406.12

| Peer-Reviewed

Gap Filling for a Human MHC Haplotype Sequence

Yuanwei Zhang, Tao Zhang, Zuhong Lu

Published in American Journal of Life Sciences (Volume 4, Issue 6)

Received: 29 November 2016 Accepted: Published: 1 December 2016

Views: Downloads:

Download PDF

Share This Article

Twitter
Linked In
Facebook

Abstract

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.

Published in	American Journal of Life Sciences (Volume 4, Issue 6)
DOI	10.11648/j.ajls.20160406.12
Page(s)	146-151
Creative Commons	This is an Open Access article, distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium or format, provided the original work is properly cited.
Copyright	Copyright © The Author(s), 2024. Published by Science Publishing Group

Keywords

Gap Filling, MHC, Haplotype, WGS

References

[1]	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.
[2]	Stewart, C. A., et al., Complete MHC haplotype sequencing for common disease gene mapping. Genome research, 2004. 14 (6): p. 1176-1187.
[3]	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.
[4]	Horton, R., et al., Variation analysis and gene annotation of eight MHC haplotypes: the MHC Haplotype Project. Immunogenetics, 2008. 60 (1): p. 1-18.
[5]	Yeo, T. W., et al., A second major histocompatibility complex susceptibility locus for multiple sclerosis. Annals of neurology, 2007. 61 (3): p. 228-236.
[6]	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.
[7]	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.
[8]	De Sá, P. H., et al., GapBlaster—A Graphical Gap Filler for Prokaryote Genomes. PloS one, 2016. 11 (5): p. e0155327.
[9]	Piro, V. C., et al., FGAP: an automated gap closing tool. BMC research notes, 2014. 7 (1): p. 1.
[10]	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.
[11]	Boetzer, M. and W. Pirovano, Toward almost closed genomes with GapFiller. Genome biology, 2012. 13 (6): p. 1.
[12]	Luo, R., et al., SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience, 2012. 1 (1): p. 1.
[13]	Kent, W. J., BLAT—the BLAST-like alignment tool. Genome research, 2002. 12 (4): p. 656-664.
[14]	Robinson, J., et al., The IPD and IMGT/HLA database: allele variant databases. Nucleic acids research, 2014: p. gku1161.
[15]	Li, H. and R. Durbin, Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics, 2009. 25 (14): p. 1754-1760.
[16]	Li, H., et al., The sequence alignment/map format and SAMtools. Bioinformatics, 2009. 25 (16): p. 2078-2079.
[17]	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.
[18]	Speir, M. L., et al., The UCSC Genome Browser database: 2016 update. Nucleic acids research, 2016. 44 (D1): p. D717-D725.
[19]	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.
[20]	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.

Cite This Article

Plain Text BibTeX RIS

APA Style

Yuanwei Zhang, Tao Zhang, Zuhong Lu. (2016). Gap Filling for a Human MHC Haplotype Sequence. American Journal of Life Sciences, 4(6), 146-151. https://doi.org/10.11648/j.ajls.20160406.12

Copy | Download

ACS Style

Yuanwei Zhang; Tao Zhang; Zuhong Lu. Gap Filling for a Human MHC Haplotype Sequence. Am. J. Life Sci. 2016, 4(6), 146-151. doi: 10.11648/j.ajls.20160406.12

Copy | Download

AMA Style

Yuanwei Zhang, Tao Zhang, Zuhong Lu. Gap Filling for a Human MHC Haplotype Sequence. Am J Life Sci. 2016;4(6):146-151. doi: 10.11648/j.ajls.20160406.12

Copy | Download

@article{10.11648/j.ajls.20160406.12,
  author = {Yuanwei Zhang and Tao Zhang and Zuhong Lu},
  title = {Gap Filling for a Human MHC Haplotype Sequence},
  journal = {American Journal of Life Sciences},
  volume = {4},
  number = {6},
  pages = {146-151},
  doi = {10.11648/j.ajls.20160406.12},
  url = {https://doi.org/10.11648/j.ajls.20160406.12},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.ajls.20160406.12},
  abstract = {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.},
 year = {2016}
}

Copy | Download

TY  - JOUR
T1  - Gap Filling for a Human MHC Haplotype Sequence
AU  - Yuanwei Zhang
AU  - Tao Zhang
AU  - Zuhong Lu
Y1  - 2016/12/01
PY  - 2016
N1  - https://doi.org/10.11648/j.ajls.20160406.12
DO  - 10.11648/j.ajls.20160406.12
T2  - American Journal of Life Sciences
JF  - American Journal of Life Sciences
JO  - American Journal of Life Sciences
SP  - 146
EP  - 151
PB  - Science Publishing Group
SN  - 2328-5737
UR  - https://doi.org/10.11648/j.ajls.20160406.12
AB  - 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.
VL  - 4
IS  - 6
ER  -

Copy | Download

Author Information

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

Download PDF

Sections

Plain Text BibTeX RIS

APA Style

Yuanwei Zhang, Tao Zhang, Zuhong Lu. (2016). Gap Filling for a Human MHC Haplotype Sequence. American Journal of Life Sciences, 4(6), 146-151. https://doi.org/10.11648/j.ajls.20160406.12

Copy | Download

ACS Style

Yuanwei Zhang; Tao Zhang; Zuhong Lu. Gap Filling for a Human MHC Haplotype Sequence. Am. J. Life Sci. 2016, 4(6), 146-151. doi: 10.11648/j.ajls.20160406.12

Copy | Download

AMA Style

Yuanwei Zhang, Tao Zhang, Zuhong Lu. Gap Filling for a Human MHC Haplotype Sequence. Am J Life Sci. 2016;4(6):146-151. doi: 10.11648/j.ajls.20160406.12

Copy | Download

@article{10.11648/j.ajls.20160406.12,
  author = {Yuanwei Zhang and Tao Zhang and Zuhong Lu},
  title = {Gap Filling for a Human MHC Haplotype Sequence},
  journal = {American Journal of Life Sciences},
  volume = {4},
  number = {6},
  pages = {146-151},
  doi = {10.11648/j.ajls.20160406.12},
  url = {https://doi.org/10.11648/j.ajls.20160406.12},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.ajls.20160406.12},
  abstract = {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.},
 year = {2016}
}

Copy | Download

TY  - JOUR
T1  - Gap Filling for a Human MHC Haplotype Sequence
AU  - Yuanwei Zhang
AU  - Tao Zhang
AU  - Zuhong Lu
Y1  - 2016/12/01
PY  - 2016
N1  - https://doi.org/10.11648/j.ajls.20160406.12
DO  - 10.11648/j.ajls.20160406.12
T2  - American Journal of Life Sciences
JF  - American Journal of Life Sciences
JO  - American Journal of Life Sciences
SP  - 146
EP  - 151
PB  - Science Publishing Group
SN  - 2328-5737
UR  - https://doi.org/10.11648/j.ajls.20160406.12
AB  - 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.
VL  - 4
IS  - 6
ER  -

Copy | Download