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Computational Molecular Biology
2011, Vol.1, No.3, 12-19 http://cmb.sophiapublisher.com
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CDRH: A Database of Complex Disease-related Haplotypes in Human
Ruijie Zhang , Yongshuai Jiang , Hongchao Lv , Xuehong Zhang , Peng Sun , Yan Zhang , Jin Li ,
Mingming Zhang , Zhenwei Shang , Xia Li
College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150086, China
Corresponding Author email: zhangruijie2013@gmail.com;
Author
Computational Molecular Biology, 2011, Vol.1, No.3 doi: 10.5376/cmb.2011.01.0003
Copyright
© 2013 Zhang et al. This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted
use, distribution, and reproduction in any medium, provided the original work is properly cited.
Abstract
Many common variations in DNA sequences and their specific combinations (haplotypes) may be the underlying causes
of differences in individual susceptibility to complex diseases. Great progress has been made in accumulating abundant resources
relating to complex disease-related haplotypes. However, these resources are scattered among different literature, resulting in reduced
utilization of the information. Therefore, we developed a database of complex disease-related haplotypes in human (CDRH). To date,
a total of 1 125 haplotypes involved in 114 complex diseases, such as breast cancer, type 2 diabetes, and rheumatoid arthritis, have
been manually extracted from 274 papers. After careful review of the literature, we obtained detailed information on haplotypes and
diseases. Furthermore, we integrated gene- and SNP- (and/or microsatellite-) related information from external databases to facilitate
further analysis. Via a user-friendly interface, users can query the CDRH by disease name, gene name, chromosome number, or SNP
ID (rs#). We hope that CDRH will enrich our knowledge of haplotypes and promote research into the relationship between
haplotypes and heritable risk for complex diseases. The CDRH database is freely available at http://bioinfo.hrbmu.edu.cn/cdrh.
Keywords
CDRH; Haplotypes; Complex diseases
Introduction
A haplotype comprises a specific allele set observed
on a single chromosome, or part of a chromosome
(HapMap, 2003; LIN and ZENG, 2006). Haplotypes
can provide critical insights into complex traits,
population histories, and natural selection (Tishkoff et
al., 2000; Daly et al., 2001; Gao et al., 2009).
Importantly, there is increasing evidence from
empirical and simulation studies that, in some
circumstances, haplotypes in a chromosomal region of
interest can be more powerful than using individual
markers in the identification of complex disease
susceptibility (Zhao et al., 2003; Gabriel et al., 2002).
Many studies based on haplotypes have successfully
detected genetic susceptibilities to complex human
diseases (Berger et al., 2008; Soma et al., 2008), such
as prostate cancer (Yaspan et al., 2008), breast cancer
(Slattery et al., 2008), type 1 diabetes (Santiago et al.,
2008), and rheumatoid arthritis (Hung et al., 2007).
With the exponential increases in the scale and density
of genetic variation data sets, haplotype analyses have
become more important in genetic studies of human
diseases, and large amounts of haplotype data have
been accumulated. Some haplotype-related databases
have been developed for collecting and preserving
haplotype information in past decades. D-HaploDB
(Higasa et al., 2007) is a genome-wide definitive
haplotypes database constructed by a collection of
completely genotyped hydatidiform mole samples.
YHRD (Kayser et al., 2002) aims to deposit
Y-chromosomal short tandem repeat haplotypes for
U.S. populations. mtDB (Ingman and Gyllensten,
2006) provides mitochondrial haplotypes search
functions for medical and human population genetic
researchers. However, there is no specific database
compiling studies of haplotypes associated with
complex diseases.
Computational
Molecular Biology
Preferred citation for this article:
Zhang et al., 2011, CDRH: A Database of Complex Disease-related Haplotypes in Human, Computational Molecular Biology, Vol.1, No.3 12-19 (doi:
10.5376/cmb.2011.01.0003)
Received: 11 Oct., 2011
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Accepted: 09 Nov., 2011
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Published: 28 Nov., 2011