Statistical Genetics Seminar
Winter Quarter 2010
Tuesday 4:00-5:00,F643 HSB
Greg Cooper (Genome Sciences)
has kindly agreed to give us an
introduction to statistical/quantitative issues in technology/biology
Jan 12: Organizational meeting
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.
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.
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
Nat Genet. 40: 1199-2003.
Supplementary information for this paper
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): Feb 2:
Marshall Brown, Rui Zhang, and Julia Palacios Roman (with Ellen Wijsman)
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.
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)
Sarah Ng and Zeinab Yazdi (with Bruce Weir)
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.
Alkan, Kidd, et al. et Eichler (2009)
Personalized copy number and segmental duplication maps using
Nat Genet 41; (Oct 2009); 1061-1068.
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