Research


Genetics and Genomics

Dr Song, You-qiang (宋又强)

Associate Professor, Department of Biochemistry and Centre for Reproduction, Development and Growth

BS (Sichuan Agri); PhD (Reading)

Contact
Email: songy@hku.hk
Tel: (852) 3917 9245
Office: L3-63, Laboratory Block, 21 Sassoon Road, Hong Kong

Research Description:

Human genetics
QTLThe main research in my laboratory is aimed at understanding the molecular basis of human complex diseases. These complex diseases are caused by the interaction between genes and environmental factors. We are mapping the disease gene's location in the genome and identifying novel genes through genomics screens and next-generation sequencing technologies. By pinpointing the responsible genes, we expect to acquire a better knowledge about the etiology of these so far poorly understood diseases, which in turn will allow more accurate diagnosis and more specific genetic counseling. We are more interested in the following diseases:

  • Neurodegenerative Diseases (Alzheimer disease)
  • Spine related disorders (Degenerative disc disease and scoliosis)
  • Nasopharyngeal carcinoma (NPC)


Developing bioinformatic tools for the study of human diseases
In order to speed up study of human complex diseases, we are also interested in developing bioinformatic tools such as cartilage gene database (iCartiGD) http://smpserve.hku.hk/iCartiGD/main; tools for interrogation of genome-wide association data (IGG3: http://bioinfo.hku.hk:13080/iggweb/home.htm, Li et al., 2007; 2009) and tools incorporate biological function with statistic analysis (KGG: http://bioinfo.hku.hk:13080/kggweb/home.htm, Li et al., 2010).

Systems Genetics
Except the above traditional mapping approaches to study human complex diseases, we are using a powerful method, Systems Genetics, to study complex traits and the underline relationships between genes. We have detected several important regulators in the important genetic pathways linking Alzheimer disease and cancers.

 

Research Team:

  • Yizhen Jia – PhD Student
  • Suying Bao – PhD Student
  • Jiang Li – PhD Student
  • Yu Zhe– PhD Student
  • Gordon Ng – MPhil Student
  • Yunyan Zhao – Visiting student
  • Zhigang Zhang – Research Assistant

YQ lab members

Previously Graduated Students:

  • Dr. Li Yan - PhD (graduated 2007)
  • Dr. Daniel Ho - PhD (graduated 2008)
  • Lam To Kam Cherry – MPhil (graduated 2008)
  • Dr. Miaoxin Li - PhD (graduated 2009)
  • Dr. Paul Tung - PhD (graduated 2010)
  • Dr. Patrich Kao – PhD (graduated 2010)
  • Dr. Yalun Zhang – PhD (graduated 2011)
  • Dr. Luhua Chen – PhD (graduated 2012)
  • Dr. Fanhiu Fan – PhD (graduated 2012)
  • Dr. Janice Lam – PhD (graduated 2013)

Major Grants:

  • Study of Population Specific Linkage Disequilibrium (LD) Patterns of Human Major Histocompatibility Complex (MHC) Region for Cancers, Infectious and Autoimmunity Diseases in Southern Chinese (HMRF 2014-2015)
  • Investigation on Pax6 regulation of neuronal apoptosis in Alzheimer’s disease (NSFC 2013-2016)
  • Identification of a genetic variant for heart defects (CHD) on chromosome 15 in mice (RGC 2013-2015)
  • In silico identification of genetic variations that affect resistance to influenza A virus infection (RFCID 2012-2013)
  • Detecting and functional analysis of a novel gene (Cer1) significantly associated with bone mineral density (BMD) in mice. (CERG 2008-2011)
  • Fine mapping candidate loci for nasopharyngeal carcinoma (NPC) in southern Chinese specifically linked to EBV aetiopathogenesis. (RFCID 2008-2010)
  • Mapping a genetic modifier for heart defects in Type IIA procollagen deficient mutant mice. (CERG 2006-2009)
  • Mapping and cloning a new gene for amyotrophic lateral sclerosis in a large Chinese family. (CERG 2004-2007)
  • Genetic linkage analysis of early onset degenerative disc disease in Southern Chinese. (CERG 2003-2006)

A key member in the following major program projects:

  • The HK HapMap team. UGC and ITF: 2004-2005.
  • The AoE on Developmental Genomics and Skeletal Research.  UGC, 2004-2009.
  • The National High Technology Research and Development Programme of China (国家高技术研究发展计划(863) 计划): 高效能计算机及网格服务环境---新药研发网格 (2006AA01A124)

Selected Publications:

  • Song YQ, Karasugi T (the two authors contributed equally), Cheung KMC, Chiba K,  Ho DWH, Miyake A, Kao PYP, Sze KL, Yee A, Takahashi A, Kawaguchi Y, Mikami Y, Matsumoto M, Togawa D, Kanayama D, Shi DQ, Dai J, Jiang Q, Wu CG, Tian W, Wang N, Leong JCY,  Luk KDK, Yip SP, Cherny SS, Wang JW, Mundlos S, Kelempisioti A, Eskola PJ, Männikkö M, Mäkelä P, Karppinen J, Järvelin MR, O'Reilly PF, Kubo M, Kimura T, Kubo T, Toyama Y, Mizuta Y, Cheah KSE, Tsunoda T, Sham P, Ikegawa S and Chan D (2013) Lumbar disc degeneration is linked to a carbohydrate sulfotransferase 3 variant. J Clin Invest 123(11):4909-4917. doi:10.1172/JCI69277. (Corresponding authors: SYQ, IS and CD)
  • Bao SY,  Zhou XY (the two authors contributed equally), Zhang LC, Zhou J, To KKW,  Wang B, Wang L, Zhang X, Song YQ (2013) Prioritizing genes affecting host resistance to influenza by network approaches. BMC Genomics 14(1):816.
  • Li MX, Kwan JS, Bao SY, Yang W, Ho SL, Song YQ, Sham PC. Predicting mendelian disease-causing non-synonymous single nucleotide variants in exome sequencing studies. PLoS Genet 2013 Jan;9(1):e1003143.
  • Chen LH, Kao PY, Fan YH, Ho DT, Chan CS, Yik PY, Ha JC, Chu LW, Song YQ. Polymorphisms of CR1, CLU and PICALM confer susceptibility of Alzheimer's disease in a southern Chinese population. Neurobiol Aging 2012 Jan, 33(1):210.e1-7.
  • Zhou XY, Bao SY (the two authors contributed equally), Wang BB, Zhang XG, and Song YQ: A Practical Guide for Mapping Short Reads. Shomron, Noam (eds.) Deep Sequencing Data Analysis. Methods in Molecular Biology, Springer (2012), pp93-112.
  • Bao S, Jiang R, Kwan W, Wang B, Ma X, Song YQ. Evaluation of next-generation sequencing software in mapping and assembly. J Hum Genet. 2011 56, 406–414.
  • Li Y, Chu LW, Wang B, Yik PY, Huriletemuer, Jin DY, Ma X, Song YQ. (2010)  CYP46A1 functional promoter haplotypes decipher genetic susceptibility to Alzheimer’s disease. J Alzheimers Dis 21(4):1311-23.
  • Li MX, Jiang L, Kao PY, Sham PC, Song YQ (2009) IGG3: A tool to rapidly integrate large genotype datasets for whole-genome imputation and individual-level meta-analysis. Bioinformatics 25(11):1449-50.
  • Tang PLF, Cheung CL, Sham PC,  McClurg P, Chan SY, Smith DK, Su AI,  Cheah KSE, Kung AWC and Song YQ (2009) Genome-wide haplotype association mapping in mice identifies a genetic variant in CER1 associated with BMD and fracture in southern Chinese women. J Bone Miner Res 24(6):1013-21.
  • Song YQ, Cheung KMC, Ho DWH (the first three authors contributed equally), Poon SCS, Chiba K, Kawaguchi Y, Hirose Y, Alini M, Grad S, Yee AFY, Leong JCY, Luk KDK, Yip SP, Karppinen J, Cheah KSE, Sham P, Ikegawa S and Chan D (2008) Association of the asporin D14 allele with lumbar-disc degeneration in Asians. Am J Hum Genet 82(3):744-7.
  • The International HapMap Consortium, including authors from the university of Hong Kong: Tsui LC, Mak W, Sham PC, Song YQ & Tam PKH (2007) A second generation human haplotype map of over 3.1 million SNPs. Nature 449, 851-861.
  • Sabeti PC, Varilly P, Fry B, Lohmueller J, Hostetter E, Cotsapas C, Xie XH, Byrne EH, McCarroll SA, Gaudet R, Schaffner SF, Lander ES, The International HapMap Consortium, including authors from the university of Hong Kong: Tsui LC, Mak W, Sham PC, Song YQ & Tam PKH (2007) Genome-wide detection and characterization of positive selection in human populations. Nature 449, 913-918. (Recommended by Faculty of 1000)
  • Li MX, Jiang L, Ho SL, Song YQ, Sham P (2007) IGG: A Tool to Integrate GeneChips for Genetic Studies. Bioinformatics 23(22):3105-7. (Corresponding author)
  • Chu LW, Li Y(the first two authors contributed equally), Li Z, Cheung BMY, Leung RYH, Yik PY, Jin DY, Song YQ  (2007) A Novel intronic polymorphism of ABCA1 gene reveals risk for sporadic Alzheimer's disease in Chinese. Am J Med Genet B 144(8):1007-13.
  • Virtanen IM, Song YQ, Cheung KMC (the first three authors contributed equally), Ala-Kokko L, Karppinen J, Ho DWH, Luk KDK, Yip SP, Leong JCY, Cheah KSE, Sham P, Chan D. (2007) Phenotypic and Population Differences in the Association between CILP and Lumbar Disc Disease. J Med Genet 44(4):285-8.
  • Cheung KMC, Chan D, Karppinen J, Chen YQ, Jim JJ, Yip SP, Ott J, Wong KK , Sham PC,  Luk KDK,   Cheah KSE,  Leong JCY and Song YQ (2006) Association of the Taq I allele in vitamin D receptor with degenerative disc disease and disc bulge in Chinese. Spine 31(10):1143-8.
  • The International HapMap Consortium, including authors from the university of Hong Kong: Tsui LC, Mak W, Sham PC, Song YQ & Tam PKH (2005) A Haplotype Map of the Human Genome. Nature 437:1299-320.
  • Nicolaou M, Song YQ (the first two authors contributed equally to the data), Sato C, Lang Y, Sorbi S, A Farrer L, St. George-Hyslop P, Rogaeva E (2001) Mutations in the open reading frame of the beta-site APP cleaving enzyme (BACE) locus are not a common cause of Alzheimer disease. Neurogenetics 3:203-206
  • Brindle N, Song Y, Rogaeva E (the first three authors contributed equally to the data), Premkumar S, Levesque G, Yu G, Ikeda M, Nishimura N, paterson A, Duara R, Farrer L, St. George-Hyslop P (1998) Analysis of the butyrycholinesterase gene and nearby chromosome 3 markers in Alzheimer Disease and ageing. Hum. Molec. Genet. 7:933-935.
  • Barker W, Harwood D, Rogaeva E, Duara R and St. George-Hyslop P, Song Y (1998) ApoE-e4 allele and the risk of Alzheimer's Disease among Hispanics. JAMA 280(19): 1661-1662.

Full List of Publications, Achievements, and Grants: