Understanding the genetic basis of human diseases and related physiological traits is the main objective of the programme. Many of the disease phenotypes we focus on are complex diseases whose genetic risk factors are multi-factorial and work in concert with a number of environmental forces. Using both hypothesis-driven investigations and unbiased genome-wide interrogations, we are working towards identifying genomic regions or genes whose natural variations influence disease predisposition, progression and treatment outcomes.
Disease Gene Discovery
By building up a common set of high-throughput genotyping and sequencing technologies and statistical methods through collaborative efforts, our investigation of disease inheritance and susceptibility covers diverse disease areas, including cancers (breast cancer, nasopharyngeal carcinoma, non-Hodgkin lymphoma), neuropsychiatric disorders (Parkinson Disease, schizophrenia), infectious diseases (tuberculosis, leprosy, meningococcal disease, Kawasaki disease and dengue), immunity and inflammation diseases (psoriasis, SLE, ankylosing spondylitis, IgA nephropathy, IBD), and eye diseases (age-related macular degeneration, glaucoma, pseudoexfoliation syndrome, and extreme myopia) and optic traits (central corneal thickness, optic nerve heard parameters, and intraocular pressure). We have extensive research programmes on interrogating common risk variants by genome-wide association study (GWAS) and are increasing our efforts on deciphering the contribution of low frequency and rare genetic variants to human diseases by carrying out targeted or whole exome sequencing analysis of patient cohorts, particularly the ones with either severe phenotypes or strong family inheritance. Availability and affordability of high throughput sequencing have made possible the generation of a plethora of sequencing data in a large collection of patients affected with complex and rare diseases, which will help us to achieve a good understanding on the whole spectrum of disease-related genetic variants.
Functionalisation of Disease Risk Loci
We are also interested in understanding biological mechanisms that underlie these genetic risk loci by pinpointing causal variants through fine-mapping analysis and characterising their functional impacts using in vitro and in vivo model systems. By combining comprehensive association analysis and functional annotation of all the variants within the critical region of a disease risk locus, we are searching for functional variants that are the primary driver and thus the causal event of disease association. Our effort has also gone beyond regional fine mapping analysis into whole genome interrogation, for example, by analysing all the genetic variants within various transcriptional binding sites in large clinical cohorts of diseases. The importance of regulatory polymorphisms in disease development has already been clearly suggested by the fact that the disease susceptibility loci discovered by GWAS are enriched for DNA elements regulating transcriptional activities. Intersection between the new genome-wide knowledge of regulatory sequences and the rapid development of high-throughput sequencing and genotyping technologies will allow the comprehensive investigation of the role of regulatory variation in human disease development. In addition, banking on the great number of novel disease risk loci discovered by our genetic studies of common and rare diseases, we are collaborating, with other research
programmes at the GIS, to pursue the functional investigation of these genetic risk loci by building up in vitro cellular models of disease where genetic risk variants are introduced into disease-relevant cells derived from either embryonic stem cells (ES) or induced pluri-potent stem cells (iPS) for functional interrogation. As a complementary effort, we are also collaborating to establish in vivo model animals for the functional investigation of disease risk-associated genes or genetic variants.
Population and Evolutionary Genomics and Statistical Genetics
Since the extent and distribution of disease predisposing genetic variation in the human species today is the result of a long and complicated evolutionary, migratory, and demographic history, we are interested in investigating population and evolutionary processes affecting genetic variations in modern human populations. We have been working on assessing the extent of inter- and intra-population genomic variation and detecting signatures of positive natural selection as well as investigating genomic variation across multiple global and regional populations. In addition, we are also interested in understanding the history of introgression from archaic sister species and their distribution into extant human populations as well as the convergent evolution between domesticated species (e.g. dogs) and human beings. Such population and evolutionary genomic studies provide a unique opportunity to look at disease genetics at a much broader scale. Furthermore, we are also interested in developing novel statistical methodologies to progress beyond searching for disease association in the genome at individual SNP level, to incorporate regional or gene-based evidences and to pursue pathway analysis. To control for population stratification in disease association studies, we have also been developing methods to provide efficient and accurate ancestry estimation for both sequencing (including target sequencing, exome sequencing, and whole genome sequencing) and array-genotyping data as well as exploring novel strategies to control for population stratification and to boost statistical power for rare variant association studies by integrating information from large amounts of existing genetic data, expression data, and functional annotation data.
Featured Publications
- Tan DE, Foo JN, Bei JX, Chang J, Peng R, Zheng X, Wei L, Huang Y, Lim WY, Li J, Cui Q, Chew SH, Ebstein RP, Kuperan P, Lim ST, Tao M, Tan SH, Wong A, Wong GC, Tan SY, Ng SB, Zeng YX, Khor CC, Lin D, Seow AL, Jia WH, Liu J. Genome-wide association study of B cell non-Hodgkin lymphoma identifies 3q27 as a susceptibility locus in the Chinese population. Nature Genetics. 2013;45(7):804-7.
- Zhang FR, Liu H, Irwanto A, Fu XA, Li Y, Yu GQ, Yu YX, Chen MF, Low HQ, Li JH, Bao FF, Foo JN, Bei JX, Jia XM, Liu J, Liany H, Wang N, Niu GY, Wang ZZ, Shi BQ, Tian HQ, Liu HX, Ma SS, Zhou Y, You JB, Yang Q, Wang C, Chu TS, Liu DC, Yu XL, Sun YH, Ning Y, Wei ZH, Chen SL, Chen XC, Zhang ZX, Liu YX, Pulit SL, Wu WB, Zheng ZY, Yang RD, Long H, Liu ZS, Wang JQ, Li M, Zhang LH, Wang H, Wang LM, Xiao P, Li JL, Huang ZM, Huang JX, Li Z, Liu J, Xiong L, Yang J, Wang XD, Yu DB, Lu XM, Zhou GZ, Yan LB, Shen JP, Zhang GC, Zeng YX, de Bakker PI, Chen SM, Liu JJ "HLA-B*13:01 and the dapsone hypersensitivity syndrome." N Engl J Med 2013 Oct 24 ; 369(17) : 1620-8 Abstract
- Javed A, Agrawal S, Ng PC "Phen-Gen: combining phenotype and genotype to analyze rare disorders." Nat Methods 2014 Sep ; 11(9) : 935-7 Epub 2014 Aug 3 Abstract
- Vithana EN, Khor CC, Qiao C, Nongpiur ME, George R, Chen LJ, Do T, Abu-Amero K, Huang CK, Low S, Tajudin LS, Perera SA, Cheng CY, Xu L, Jia H, Ho CL, Sim KS, Wu RY, Tham CC, Chew PT, Su DH, Oen FT, Sarangapani S, Soumittra N, Osman EA, Wong HT, Tang G, Fan S, Meng H, Huong DT, Wang H, Feng B, Baskaran M, Shantha B, Ramprasad VL, Kumaramanickavel G, Iyengar SK, How AC, Lee KY, Sivakumaran TA, Yong VH, Ting SM, Li Y, Wang YX, Tay WT, Sim X, Lavanya R, Cornes BK, Zheng YF, Wong TT, Loon SC, Yong VK, Waseem N, Yaakub A, Chia KS, Allingham RR, Hauser MA, Lam DS, Hibberd ML, Bhattacharya SS, Zhang M, Teo YY, Tan DT, Jonas JB, Tai ES, Saw SM, Hon DN, Al-Obeidan SA, Liu J, Chau TN, Simmons CP, Bei JX, Zeng YX, Foster PJ, Vijaya L, Wong TY, Pang CP, Wang N, Aung T. Genome- wide association analyses identify three new susceptibility loci for primary angle closure glaucoma. Nature Genetics. 2012 44(10):1142-7.
- Khor CC, Chau TN, Pang J, Davila S, Long HT, Ong RT, Dunstan SJ, Wills B, Farrar J, Van Tram T, Gan TT, Binh NT, Tri le T, Lien le B, Tuan NM, Tham NT, Lanh MN, Nguyet NM, Hieu NT, Van N Vinh Chau N, Thuy TT, Tan DE, Sakuntabhai A, Teo YY, Hibberd ML, Simmons CP. Genome- wide association study identifies susceptibility loci for dengue shock syndrome at MICB and PLCE1. Nature Genetics. 2011;43(11):1139-41.
- Davila S, Wright VJ, Khor CC, Sim KS, Binder A, Breunis WB, Inwald D, Nadel S, Betts H, Carrol ED, de Groot R, Hermans PW, Hazelzet J, Emonts M, Lim CC, Kuijpers TW, Martinon-Torres F, Salas A, Zenz W, Levin M, Hibberd ML; International Meningococcal Genetics Consortium. Genome- wide association study identifies variants in the CFH region associated with host susceptibility to meningococcal disease. Nature Genetics. 2010;42(9):772-6.
- Zhang FR, Huang W, Chen SM, Sun LD, Liu H, Li Y, Cui Y, Yan XX, Yang HT, Yang RD, Chu TS, Zhang C, Zhang L, Han JW, Yu GQ, Quan C, Yu YX, Zhang Z, Shi BQ, Zhang LH, Cheng H, Wang CY, Lin Y, Zheng HF, Fu XA, Zuo XB, Wang Q, Long H, Sun YP, Cheng YL, Tian HQ, Zhou FS, Liu HX, Lu WS, He SM, Du WL, Shen M, Jin QY, Wang Y, Low HQ, Erwin T, Yang NH, Li JY, Zhao X, Jiao YL, Mao LG, Yin G, Jiang ZX, Wang XD, Yu JP, Hu ZH, Gong CH, Liu YQ, Liu RY, Wang DM, Wei D, Liu JX, Cao WK, Cao HZ, Li YP, Yan WG, Wei SY, Wang KJ, Hibberd ML, Yang S, Zhang XJ, Liu JJ. Genomewide association study of leprosy. New England Journal of Medicine. 2009;361(27):2609-18.
- HUGO Pan-Asian SNP Consortium. GIS authors are Chen J, Kumar V, Liu ET, Ong R, Png E, Seistad M, Tan A. Mapping human genetic diversity in Asia. Science. 2009;326(5959):1541-5.