Research


Genetics and Genomics

You-Qiang Song, PhD

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

BS (Sichuan Agri); PhD (Reading)

Contact
Email: songy@hkucc.hku.hk
Tel: (852) 2819 9245
Office: L3-63, Laboratory Block, 21 Sassoon Road, Hong Kong

Research Description:

Human genetics
QTLThe main research at 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 most 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 improve the study of human complex diseases, we are also developing bioinformatic tools such as the cartilage gene database (iCartiGD) http://smpserve.hku.hk/iCartiGD/main; tools for the interrogation of genome-wide association data (IGG3: http://bioinfo.hku.hk:13080/iggweb/home.htm, Li et al., 2007; 2009) and tools that incorporate biological function with statistical analysis (KGG: http://bioinfo.hku.hk:13080/kggweb/home.htm, Li et al., 2010).

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

 

Research Team:

  • Dr. Yan Li – Post-doctoral Research Associate
  • Patrick Kao – PhD Student
  • Yalun Zhang – PhD Student
  • Luhua Chen – PhD Student
  • Yanhui Fan – PhD Student
  • Suying Bao – PhD Student
  • Yizhen Jia – PhD Student
  • Janice Lam – PhD Student

YQ lab members

Previously Graduated Students:

  • Dr. Li Yan - PhD (graduated 2007)
  • Dr. Daniel Ho - PhD (graduated 2008)
  • Dr. Miaoxin Li  - PhD (graduated 2009)
  • Dr. Paul Tung - PhD (graduated 2010)
  • Lam To Kam Cherry – MPhil (graduated 2008)

Major Grants:

  • 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)

Publications, Achievements, and Grants:

  • 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 (HAM) in Mice leads to an Identification of a Genetic Variant in CER1 Associated with Bone Mineral Density in Premenopausal Women. The Journal of Bone and Mineral Research 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, Yee AFY, Leong JCY, Luk KDK, Yip SP, Cheah KSE, Sham P, Ikegawa S and Chan D (2008) Asporin D14 allele increases the risk of lumbar disc degeneration in Chinese and Japanese populations. Am J Hum Genet 82(3):744-7.
  • So J, Song YQ, Tsang S, Tang LF, Chan A, Ma E, Chan LC (2008) The HBS1L-MYB intergenic region on chromosome 6q23 is a quantitative trait locus controlling foetal haemoglobin level in beta thalassaemia carriers. J Med Genet. 45(11):745-51.
  • 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.
  • 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.
  • Li Y, Leung WC, Chen YQ, Cheung BMY, Liang RYH, Yik PY, Ng KM, Mak W, Jin DY, st. George-Hyslop P, Song YQ (2006) Intron 2 (T/C) CYP46 polymorphism is associated with Alzheimer's disease in Chinese. Dement Geriatr Cogn Disord 22:399-404.
  • 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.