Research Areas

Bioinformatics

Publications

Wang Y, Mak TSH, Dattani S, Garcia-Barcelo MM, Fu X, Yip KY, Ngan ESW, Tam PKH, Tang CS*, Sham PC*. Whole genome sequencing reveals epistasis effects within RET for Hirschsprung disease. Sci Rep. 2022;12(1):20423.

Ng KM, Ding Q, Tse YL, Chou OHI, Lai WH, Au KW, Lau YM, Ji Y, Siu CW, Tang CS, Colman A, Tsang SY, Tse HF. Isogenic Human-Induced Pluripotent Stem Cell-Derived Cardiomyocytes Reveal Activation of Wnt Signaling Pathways Underlying intrinsic cardiac abnormalities in Rett Syndrome. Int. J. Mol. Sci. 2022, 23(24) (in press). doi: 10.3390/ijms232415609

Chau JFT, Yu MHC, Chui MMC, Yeung CCW, Kwok AWC, Xuehan Z, Lee R, Fung JLF, Lee M, Mak CCY, Ng NYT, Chung CCY, Chan MCY, Tsang MHY, Chan MCK, Chan KYK, Kan ASY, Chung PHY, Yang W, Lee SL, Chan GCF, Tam PKH, Lau YL, Yeung KS*, Chung BHY*, Tang CS*. Comprehensive analysis of recessive carrier status using exome and genome sequencing data in 1543 Southern Chinese. NPJ Genom Med. 2022 Mar 21;7(1):23. doi: 10.1038/s41525-022-00287-z.

Chan YH, Hai JJ, Schooling CM, Au Yeung SL, Zhao J, Thomas GN, Cheng KK, Jiang CQ, Wong YK, Au KW, Tang CS, Cheung CYY, Xu A, Sham PC, Lam TH, Lam KS, Tse HF. Mendelian randomization analysis of vitamin D in the secondary prevention of hypertensive-diabetic subjects: role of facilitating blood pressure control. Genes Nutr. 2022 Jan 29; 17(1):1. doi: 10.1186/s12263-022-00704-z. (in press)

Tang CS†, Mononen M†, Lam WY, Jin SH, Zhuang X, Garcia-Barcelo MM, Lin Q, Yang Y, Sahara M, Eroglu E, Chien K*, Hong H*, Tam PKH*, Gruber PJ*. Sequencing of a Chinese Tetralogy of Fallot cohort reveals clustering mutations in myogenic heart progenitors. JCI Insight. 2022 Jan 25; 7(2):e152198. doi: 10.1172/jci.insight.152198.

Lu X, Liu Z, Liu F, Wang L, Li J, Niu X, Shen C, Hu D, Huang K, Chen J, Liu X, Cao J, Chen S, Ma H, Yu L, Zhao Y, Lu F, Wu X, Wu X, Li Y, Zhang Z, Mo X, Zhao L, Huang J, Wen W, Shu X, Takeuchi F, Kato N, Chang X, Chan MYY, Gao W, Zheng H, Chen K, Chen J, He J, Tang CS, Lam KSL, Tse HF, Cheung CYY, Takahashi A, Kubo M, Kamatani Y, Terao C, Sham PC, Heng CK, Hu Z, Chen YE, Wu T, Shen H, Willer CJ, Gu D. Polygenic and clinical risk stratification for coronary artery disease in China: a large-scale prospective cohort study. Eur Heart J. 2022;ehac093. doi: 10.1093/eurheartj/ehac093. (in press)

Jiang L, Jiang H, Dai S, Chen Y, Song YQ, Tang CS, Pang SYY, Ho SL, Wang B, Garcia-Barcelo MM, Tam PKH, Cherny SS, Li MJ, Sham PC*, Li MX*. Deviation from baseline mutation burden provides powerful and robust rare-variants association test for complex diseases. Nucleic Acids Res. 2021 Dec 20;gkab1234. doi: 10.1093/nar/gkab1234. (in press)

Ji Y, Tam PKH*, Tang CSM*. Roles of enteric neural stem cell niche and enteric nervous system development in Hirschsprung disease. International Journal of Molecular Sciences. 2021 Sep 7; 22(18):9659. doi: 10.3390/ijms22189659.

Lam WY, Tang CSM, So MT, Yue H, Hsu JS, Chung PH, Nicholls JM, Yeung F, Lee CD, Ngo DN, Nguyen PAH, Mitchison HM, Jenkins D, O'Callaghan C, Garcia-Barceló MM, Lee SL, Sham PC, Lui VC*, Tam PK*. Identification of a wide spectrum of ciliary gene mutations in nonsyndromic biliary atresia patients implicates ciliary dysfunction as a novel disease mechanism. EBioMedicine. 2021 Aug 26;71:103530. doi: 10.1016/j.ebiom.2021.103530. PMID: 34455394.

Kuil LE, MacKenzie KC, Tang CSM, Windster JD, Le TL, Karim A, de Graaf BM, van der Helm R, van Bever Y, Sloots CEJ, Meeussen C, Tibboel D, de Klein A, Wijnen RMH, Amiel J, Lyonnet S, Garcia-Barcelo MM, Tam PKH, Alves MM, Brooks AS, Hofstra RMW, Brosens E. Size matters: Large copy number losses in Hirschsprung disease patients reveal genes involved in enteric nervous system development. PLoS Genet. 2021 Aug 6;17(8):e1009698. doi: 10.1371/journal.pgen.1009698. PMID: 34358225.

Karim MA, Tang CSM*, Tam PKH*. The emerging genetic landscape of Hirschsprung disease and its potential clinical applications. Frontiers in Pediatrics. 2021 Aug 5;9:638093. doi: 10.3389/fped.2021.638093. PMID: 34422713.

Yu MHC, Mak CCY, Fung JLF, Lee M, Tsang MHY, Chau JFT, Chung PH, Yang W, Chan GCF, Lee SL, Lau YL, Tam PKH, Tang CSM*, Yeung KS*, Chung BHY*. Actionable secondary findings in 1116 Hong Kong Chinese based on exome sequencing data. J Hum Genet. 2021 Jun;66(6):637-641. doi: 10.1038/s10038-020-00875-w. Epub 2020 Nov 22. PMID: 33223521.

Sun P, Zhou W, Fu Y, Cheung YY, Dong Y, Yang ML, Zhang H, Jia J, Huo Y, Willer CJ, Chen YE, Tang CSM, Tse HF, Lam KSL, Gao W, Xu M, Yu H, Sham PC, Zhang Y, Ganesh SK. An Asian-specific MPL genetic variant alters JAK–STAT signaling and influences platelet count in the population. Human Molecular Genetics. 2021 May 28; 30(9):836-842. doi: 10.1093/hmg/ddab062. PMID: 33693786.

Yu MHC, Chan MCY, Chung CCY, Wang A, Li T, Yip CYW, Mak CCY, Chau JFT, Lee M, Fung JLF, Tsang MHY, Chan JCK, Wong WHS, Yang J, Chui WCM, Chung PHY, Yang W, Lee SL, Chan GCF, Tam PKH, Lau YL, Tang CS*, Yeung KS*, Chung BHY*. Actionable pharmacogenetic variants in 1116 Hong Kong Chinese exome sequencing data and its projected prescription impact in the Hong Kong population. PLoS Genet. 2021 Feb 18;17(2):e1009323. doi: 10.1371/journal.pgen.1009323. eCollection 2021 Feb.

Mederer T, Schmitteckert S, Volz J, Martinez C, Röth R, Thumberger T, Eckstein V, Scheuerer J, Thöni C, Lasitschka F, Carstensen L, Günther P, Holland-Cunz S, Hofstra R, Brosens E, Schriemer D, Ceccherini I, Rusmini M, Tilghman J, Chakravati A, Borrego-Lopez S, Tang CS, Garcia-Barcelo MM, Tam PKH, Paramasivam N, Bewerunge-Hudler M, de la Torre C, Gretz N, Rappold G, Romero P, Niesler B. A complementary study approach unravels novel players in the pathoetiology of Hirschsprung disease. PLoS Genet. 2020 Nov 5;16(11):e1009106. doi: 10.1371/journal.pgen.1009106.

Fu AX, Lui KNC, Tang CS, Ng RK, Lai FPL, Lau ST, Li X, Garcia-Barcelo MM, Sham PC, Tam PKH, Ngan ESW, Yip KY. Whole-genome analysis of noncoding genetic variations identifies multi-scale regulatory element perturbations associated with Hirschsprung disease. Genome Research. 2020 Nov; 30(11):1618-1632. doi: 10.1101/gr.264473.120. Epub 2020 Sep 18. PMID: 32948616.

Zhuang X, Ye R, So MT, L WY, Karim A, Yu M, Ngo ND, Cherny SS, Tam PKH, Garcia-Barcelo MM, Tang CS, Sham PC. A random forest-based framework for genotyping and accuracy assessment of copy number variations. NAR Genomics and Bioinformatics. 2020 Sep 22;2(3):lqaa071. doi: 10.1093/nargab/lqaa071. eCollection 2020 Sep.

Wong YK, Cheung YY, Tang CSM, Hai SHJJ, Lee CHP, Lau GKK, Au KW, Cheung BMY, Sham PC, Xu A, Lam KSL, Tse HF. High sensitivity troponin I and B-type natriuretic peptide biomarkers for prediction of cardiovascular events in patients with coronary artery disease with and without diabetes mellitus. Cardiovascular Diabetology. 2019 Dec 17; 18(1):171. doi: 10.1186/s12933-019-0974-2.

Tang CS, Li P, Lai FPK, Fu AX, Lau ST, So MT, Lui KN, Li Z, Zhuang X, Yu M, Liu X, Ngo ND, Miao X, Zhang X, Yi B, Tang S, Sun X, Zhang F, Liu H, Liu Q, Zhang R, Wang H, Huang L, Dong X, Tou J, Cheah KSE, Yang W, Yuan Z, Yip KY, Sham PC, Tam PKH, Garcia-Barcelo MM, Ngan ESW. Identification of genes associated with Hirschsprung disease, based on whole genome sequence analysis, and potential effects on enteric nervous system development. Gastroenterology. 2018 Dec;155(6):1908-1922.e5. doi: 10.1053/j.gastro.2018.09.012. Epub 2018 Sep 12. PMID: 30217742.

Karim A, Akter M, Aziz TT, Hoque M, Chowdhury TK, Imam MS, Walid A, Kabir M, So MT, Lam WY, Tang CS, Wong KK, Tam PKH, Garcia-Barcelo MM, Banu T. Epidemiological characteristics of Hirschsprung’s disease (HSCR): Results of a case series of fifty patients from Bangladesh. J Pediatr Surg. 2018;53(10):1955-1959.

Mak TSH, Lee YK, Tang CS, Hai JSH, Ran X, Sham PC, Tse HF. Coverage and diagnostic yield of Whole Exome Sequencing for the Evaluation of Cases with Dilated and Hypertrophic Cardiomyopathy. Sci Rep. 2018;18;8(1):10846.

Tang CS†, Zhuang X†, Lam WY, Ngan ES, Hsu JS, Yu M, So MT, Cherny SS, Ngo ND, Sham PC, Tam PK, Garcia-Barcelo MM. Uncovering the genetic lesions underlying the most severe form of Hirschsprung disease by whole-genome sequencing. Eur J Hum Genet. 2018 Jun;26(6):818-826. doi: 10.1038/s41431-018-0129-z. Epub 2018 Feb 26. PMID: 29483666.

Hsu JSJ, So M, Tang CSM, Karim A, Porsch RM, Wong C, Yu M, Yeung F, Xia H, Zhang R, Cherny SS, Chung PHY, Wong KKY, Sham PC, Ngo ND, Li M, Tam PKH, Lui VCH, Garcia-Barcelo MM. De novo mutations in Caudal Type Homeo Box transcription Factor 2 (CDX2) in patients with persistent cloaca. Hum Mol Genet. 2018 Jan 15;27(2):351-358. doi: 10.1093/hmg/ddx406.

Tang CS*, Dattani S, So MT, Cherny SS, Tam PKH, Sham PC, Garcia-Barceló MM. Actionable secondary findings from whole-genome sequencing of 954 East Asians: ethnic similarities and differences. Hum Genet. 2018 Jan;137(1):31-37. doi: 10.1007/s00439-017-1852-1. Epub 2017 Nov 11. PMID: 29128982.

Lu X, Peloso GM, Liu DJ, Wu Y, Zhang H, Zhou W, Li J, Tang CS, Dorajoo R, Li H, Long J, Guo X, Xu M, Spracklen CN, Chen Y, Liu X, Zhang Y, Khor CC, Liu J, Sun L, Wang L, Gao YT, Hu Y, Yu K, Wang Y, Cheung CYY, Wang F, Huang J, Fan Q, Cai Q, Chen S, Shi J, Yang X, Zhao W, Sheu WH, Cherny SS, He M, Feranil AB, Adair LS, Gordon-Larsen P, Du S, Varma R, Chen YI, Shu XO, Lam KSL, Wong TY, Ganesh SK, Mo Z, Hveem K, Fritsche LG, Nielsen JB, Tse HF, Huo Y, Cheng CY, Chen YE, Zheng W, Tai ES, Gao W, Lin X, Huang W, Abecasis G; GLGC Consortium, Kathiresan S, Mohlke KL, Wu T, Sham PC, Gu D, Willer CJ. Exome chip meta-analysis identifies novel loci and East Asian-specific coding variants contributing to lipid levels and coronary artery disease. Nat Genet. 2017 Dec;49(12):1722-1730. doi: 10.1038/ng.3978. Epub 2017 Oct 30. PMID: 29083407.

Gui H, Schriemer D, Cheng WW, Chauhan RK, Antiňolo G, Berrios C, Bleda M, Brooks AS, Brouwer RW, Burns AJ, Cherny SS, Dopazo J, Eggen BJ, Griseri P, Jalloh B, Le TL, Lui VC, Luzón-Toro B, Matera I, Ngan ES, Pelet A, Ruiz-Ferrer M, Sham PC, Shepherd IT, So MT, Sribudiani Y, Tang CS, van den Hout MC, van der Linde HC, van Ham TJ, van IJcken WF, Verheij JB, Amiel J, Borrego S, Ceccherini I, Chakravarti A, Lyonnet S, Tam PK, Garcia-Barceló MM, Hofstra RM. Whole exome sequencing coupled with unbiased functional analysis reveals new Hirschsprung disease genes. Genome Biology. 2017;18(1):48. doi: 10.1186/s13059-017-1174-6.

Tang CS, Gui H, Kapoor A, Kim J, Luzón-Toro B, Pelet A, Burzynski G, Lantieri F, So MT, Berrios C, Shin HD, Fernández RM, Le TL, Verheij JBGM, Matera I, Cherny SS, Nandakumar P, Cheong HS, Antiñolo G, Amiel J, Seo JM, Kim DY, Oh JT, Lyonnet S, Borrego S, Ceccherini I, Hofstra RMW, Chakravarti A, Kim HY, Sham PC, Tam PKH, Garcia-Barceló MM. Trans-ethnic meta-analysis of genome-wide association studies for Hirschsprung disease. Hum Mol Genet. 2016 Dec 1;25(23):5265-5275. doi: 10.1093/hmg/ddw333. PMID: 27702942.