Statistical Genetics Seminar

Winter Quarter 2012
Tuesday 4:00-5:00, F643 HSB

CURRENT SCHEDULE

Sharon Browning will coordinate the seminar. The topic will be haplotype phase inference and imputation.

  • Jan 3: Organizational meeting.

  • Jan 10: Excoffier, L. & Slatkin, M. Maximum-likelihood estimation of molecular haplotype frequencies in a diploid population. Mol Biol Evol 12, 921-927 (1995). [Jan, Lisa, Bruce]

  • Jan 17: Stephens, M. & Scheet, P. Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation. Am J Hum Genet 76, 449-462 (2005). [Jean, Steven, Elizabeth]

  • Jan 24: Browning, S.R. & Browning, B.L. Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am J Hum Genet 81, 1084-1097 (2007). [Chaozhi, Sharon]

  • Jan 31: Browning, B.L. & Browning, S.R. A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals. Am J Hum Genet 84, 210-223 (2009). [Charles, Caitlin, Sharon]

  • Feb 7: Li, Y., Willer, C.J., Ding, J., Scheet, P. & Abecasis, G.R. MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes. Genet Epidemiol 34, 816-834 (2010). [Kevin, Matt, Vladimir]

  • Feb 14: Howie, B.N., Donnelly, P. & Marchini, J. A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet 5, e1000529 (2009). [Xiuwen, Bruce]

  • Feb 21: Delaneau, O., Marchini, J. & Zagury, J.-F. A linear complexity phasing method for thousands of genomes. Nat Meth advance online publication (2011). [Jerry, Peter, Vladimir]

  • Feb 28: Kong, A. et al. Detection of sharing by descent, long-range phasing and haplotype imputation. Nature Genetics 40, 1068-1075 (2008). [Serge, Chris, Elizabeth]

  • Mar 6: Jorge Duitama, et al. Fosmid-based whole genome haplotyping of a HapMap trio child: evaluation of Single Individual Haplotyping techniques. Nucl. Acids Res. advanced online publication (2011). [Sulgi, Adele, Ellen]

    • Optional additional reading:

  • Browning, S.R. & Browning, B.L. Haplotype phasing: existing methods and new developments. Nature Review Genetics 12, 703-714 (2011).
  • Tewhey, R., Bansal, V., Torkamani, A., Topol, E.J. & Schork, N.J. The importance of phase information for human genomics. Nat Rev Genet 12, 215-223 (2011).
  • Marchini, J. et al. A comparison of phasing algorithms for trios and unrelated individuals. Am J Hum Genet 78, 437-50 (2006).
  • Browning, S.R. Multilocus association mapping using variable-length Markov chains. Am J Hum Genet 78, 903-13 (2006). [Original description of the "BEAGLE" model.]