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San Lucas FA, Rosenberg NA, Scheet P. Haploscope: a tool for the graphical display of haplotype structure in populations. Genet Epidemiol 2011; 36:17-21. [PMID: 22147662 DOI: 10.1002/gepi.20640] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Revised: 09/14/2011] [Accepted: 09/21/2011] [Indexed: 11/11/2022]
Abstract
Patterns of linkage disequilibrium are often depicted pictorially by using tools that rely on visualizations of raw data or pairwise correlations among individual markers. Such approaches can fail to highlight some of the more interesting and complex features of haplotype structure. To enable natural visual comparisons of haplotype structure across subgroups of a population (e.g. isolated subpopulations or cases and controls), we propose an alternative visualization that provides a novel graphical representation of haplotype frequencies. We introduce Haploscope, a tool for visualizing the haplotype cluster frequencies that are produced by statistical models for population haplotype variation. We demonstrate the utility of our technique by examining haplotypes around the LCT gene, an example of recent positive selection, in samples from the Human Genome Diversity Panel. Haploscope, which has flexible options for annotation and inspection of haplotypes, is available for download at http://scheet.org/software.
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Affiliation(s)
- F Anthony San Lucas
- Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
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Wong SH, Gochhait S, Malhotra D, Pettersson FH, Teo YY, Khor CC, Rautanen A, Chapman SJ, Mills TC, Srivastava A, Rudko A, Freidin MB, Puzyrev VP, Ali S, Aggarwal S, Chopra R, Reddy BSN, Garg VK, Roy S, Meisner S, Hazra SK, Saha B, Floyd S, Keating BJ, Kim C, Fairfax BP, Knight JC, Hill PC, Adegbola RA, Hakonarson H, Fine PEM, Pitchappan RM, Bamezai RNK, Hill AVS, Vannberg FO. Leprosy and the adaptation of human toll-like receptor 1. PLoS Pathog 2010; 6:e1000979. [PMID: 20617178 PMCID: PMC2895660 DOI: 10.1371/journal.ppat.1000979] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2010] [Accepted: 06/02/2010] [Indexed: 01/06/2023] Open
Abstract
Leprosy is an infectious disease caused by the obligate intracellular pathogen Mycobacterium leprae and remains endemic in many parts of the world. Despite several major studies on susceptibility to leprosy, few genomic loci have been replicated independently. We have conducted an association analysis of more than 1,500 individuals from different case-control and family studies, and observed consistent associations between genetic variants in both TLR1 and the HLA-DRB1/DQA1 regions with susceptibility to leprosy (TLR1 I602S, case-control P = 5.7×10−8, OR = 0.31, 95% CI = 0.20–0.48, and HLA-DQA1 rs1071630, case-control P = 4.9×10−14, OR = 0.43, 95% CI = 0.35–0.54). The effect sizes of these associations suggest that TLR1 and HLA-DRB1/DQA1 are major susceptibility genes in susceptibility to leprosy. Further population differentiation analysis shows that the TLR1 locus is extremely differentiated. The protective dysfunctional 602S allele is rare in Africa but expands to become the dominant allele among individuals of European descent. This supports the hypothesis that this locus may be under selection from mycobacteria or other pathogens that are recognized by TLR1 and its co-receptors. These observations provide insight into the long standing host-pathogen relationship between human and mycobacteria and highlight the key role of the TLR pathway in infectious diseases. Mycobacterium leprae is an obligate intracellular pathogen that causes leprosy, a disease that shares a long history with the human population but which remains endemic in many parts of the world. Despite the fact that the genome of M. leprae has been sequenced, our understanding of its pathogenesis and interaction with the human host is limited, in part due to the inability to culture the bacterium in vitro. In this gene-centric microarray study, we have genotyped SNPs in over 2,000 genes and identified TLR1 and HLA-DRB1/DQA1 as major leprosy susceptibility genes. Studying the geographical distribution of this hypo-functional TLR1 variant demonstrated extreme population differentiation at this locus. These results suggest that leprosy may have contributed to the evolution of this genomic region, and provide insight into the long history of the host-pathogen relationship between humans and M. leprae.
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Affiliation(s)
- Sunny H. Wong
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Sailesh Gochhait
- National Centre of Applied Human Genetics, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Dheeraj Malhotra
- National Centre of Applied Human Genetics, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Fredrik H. Pettersson
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Yik Y. Teo
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Chiea C. Khor
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Host Susceptibility to Infection Program, Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research, Singapore
| | - Anna Rautanen
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Stephen J. Chapman
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Tara C. Mills
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Amit Srivastava
- National Centre of Applied Human Genetics, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Aleksey Rudko
- Research Institute of Medical Genetics, Siberian Branch of Russian Academy of Medical Sciences, Tomsk, Russia
| | - Maxim B. Freidin
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Research Institute of Medical Genetics, Siberian Branch of Russian Academy of Medical Sciences, Tomsk, Russia
| | - Valery P. Puzyrev
- Research Institute of Medical Genetics, Siberian Branch of Russian Academy of Medical Sciences, Tomsk, Russia
| | - Shafat Ali
- National Centre of Applied Human Genetics, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Shweta Aggarwal
- National Centre of Applied Human Genetics, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Rupali Chopra
- National Centre of Applied Human Genetics, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Belum S. N. Reddy
- Department of Dermatology and Sexually Transmitted Diseases, Maulana Azad Medical College, Lok Nayak Jai Prakash Hospital, New Delhi, India
| | - Vijay K. Garg
- Department of Dermatology and Sexually Transmitted Diseases, Maulana Azad Medical College, Lok Nayak Jai Prakash Hospital, New Delhi, India
| | - Suchismita Roy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Sarah Meisner
- Bath Royal United Hospital Trust, Combe Park, Bath, United Kingdom
| | | | - Bibhuti Saha
- Calcutta School of Tropical Medicine, Kolkata, India
| | - Sian Floyd
- Infectious Disease Epidemiology Unit, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Brendan J. Keating
- Institute for Translational Medicine and Therapeutics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Cecilia Kim
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Benjamin P. Fairfax
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Julian C. Knight
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | | | | | - Hakon Hakonarson
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Paul E. M. Fine
- Infectious Disease Epidemiology Unit, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | - Rameshwar N. K. Bamezai
- National Centre of Applied Human Genetics, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Adrian V. S. Hill
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Fredrik O. Vannberg
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- * E-mail:
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Teo YY, Sim X, Ong RTH, Tan AKS, Chen J, Tantoso E, Small KS, Ku CS, Lee EJD, Seielstad M, Chia KS. Singapore Genome Variation Project: a haplotype map of three Southeast Asian populations. Genome Res 2009; 19:2154-62. [PMID: 19700652 DOI: 10.1101/gr.095000.109] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The Singapore Genome Variation Project (SGVP) provides a publicly available resource of 1.6 million single nucleotide polymorphisms (SNPs) genotyped in 268 individuals from the Chinese, Malay, and Indian population groups in Southeast Asia. This online database catalogs information and summaries on genotype and phased haplotype data, including allele frequencies, assessment of linkage disequilibrium (LD), and recombination rates in a format similar to the International HapMap Project. Here, we introduce this resource and describe the analysis of human genomic variation upon agglomerating data from the HapMap and the Human Genome Diversity Project, providing useful insights into the population structure of the three major population groups in Asia. In addition, this resource also surveyed across the genome for variation in regional patterns of LD between the HapMap and SGVP populations, and for signatures of positive natural selection using two well-established metrics: iHS and XP-EHH. The raw and processed genetic data, together with all population genetic summaries, are publicly available for download and browsing through a web browser modeled with the Generic Genome Browser.
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Affiliation(s)
- Yik-Ying Teo
- Centre for Molecular Epidemiology, National University of Singapore, Singapore 117597
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