Statistical Genetics Seminar

Winter Quarter 2010
Tuesday 4:00-5:00,F643 HSB


  • Jan 5:
    Greg Cooper (Genome Sciences)
    has kindly agreed to give us an introduction to statistical/quantitative issues in technology/biology of CNV.
  • Jan 12: Organizational meeting
    See HERE, for some thoughts and possible references. (posted Jan 8, 2010).
    Also a review paper Zhang F, Gu W, Hurles ME, Lupski JR. Copy number variation in human health, disease, and evolution. Annu Rev Genomics Hum Genet. 2009;10:451-81. -- contains many references.

  • Jan 19: Natalie Thompson, Kevin Rubenstein (with Vladimir Minin)
    Topic: CGH arrays for CNV detection
    Paper: Subharup GUHA, Yi LI, and Donna NEUBERG (2008)
    Bayesian Hidden Markov Modeling of Array CGH Data.
    JASA 103: 485--497.

  • Jan 26: Charles Cheung and Wei Zhou (with Elizabeth Thompson)
    SNP arrays on unrelateds for CNV detection-- SCIMM
    Gregory M Cooper, Troy Zerr, Jeffrey M Kidd, Evan E Eichler & Deborah A Nickerson (2008)
    Systematic assessment of copy number variant detection via genome-wide SNP genotyping
    Nat Genet. 40: 1199-2003. Supplementary information for this paper

    Note also: Thursday, January 21, GS Dissertation Defense: Troy Zerr
    Genotyping Human Genomic Structural Variation 3:30, Health Sciences T-625

    A more statistical paper (but too long):
    Robert B. Scharpf, Giovanni Parmigiani, Jonathan Pevsner, Ingo Ruczinski, (2008)
    Hidden Markov models for the assessment of chromosomal alterations using high-throughput SNP arrays,
    The Annals of Applied Statistics. 2: 687-713.

  • Feb 2: Marshall Brown, Rui Zhang, and Julia Palacios Roman (with Ellen Wijsman)
    Kai Wang, Zhen Chen, Mahlet G. Tadesse4, Joseph Glessner, Struan F. A. Grant, Hakon Hakonarson, Maja Bucan1 and Mingyao Li (2008)
    Modeling genetic inheritance of copy number variations
    Nucleic Acids Research (Methods Online), 36: e138.36: e138.36: e138.

    Here is a link to their earlier paper: Wang, K. et al. (2007)
    PennCNV: An integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data
    Genome Research 17: 1665-1674.

  • Feb 9: Sarah Ng and Zeinab Yazdi (with Bruce Weir)
    Alkan, Kidd, et al. et Eichler (2009) (PDF)
    Personalized copy number and segmental duplication maps using next-generation sequencing.
    Nat Genet 41; (Oct 2009); 1061-1068.

  • Feb 16: Liz Marchani and Sangsoon Woo (with Elizabeth Thompson)
    M. Jakobsson et al. et N. A. Rosenberg et A. B. Singleton (2008) Genotype, haplotype and copy-number variation in worldwide human populations. Nature 451(7181):998-1003. (see Figure 1)
    with a reanalysis in
    Itsara et al. et Nickerson et Cooper (2009) Population analysis of large copy number variants and hotspots of human genetic disease. AJHG 84(2):148-61. (see the section on Population Diversity in the Results)

  • Feb 23: Sulgi Kim, Peter Chi, and Yoonha Choi (with Elizabeth Thompson)
    Donald F Conrad, Matthew E Hurles (2007)
    The population genetics of structural variation
    Nature Genetics 39, S30-S36

  • Mar 2: Patrick Danaher, Leila Zelnick and Xiuwen Zheng (with Ellen Wijsman)
    Walsh et al. et MC King, J. Sebat (2008)
    Rare Structural Variants Disrupt Multiple Genes in Neurodevelopmental Pathways in Schizophrenia
    Science 320 (5875): 539--543.
    AC Need et al. et DB Goldstein (2009)
    A Genome-Wide Investigation of SNPs and CNVs in Schizophrenia.
    PLOS Genetics 5 (2): e1000373. (Feb 2009)

  • Mar 9: Matt Conomos, Tim O'Brien, and Ming Su (with Elizabeth Thompson)
    Chris Barnes, Vincent Plagnol, Tomas Fitzgerald, Richard Redon, Jonathan Marchini, David Clayton, Matthew E Hurles (2008)
    A robust statistical method for case-control association testing with copy number variation
    Nature Genetics 40, 1245-1252