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Nancy Zhang Seminar

Stanford University, "Simultaneous Change-point Models with Applications to Cross-sample and Cross-platform Analysis of DNA Copy Number"

What
When	2009-10-22 14:00 2009-10-22 15:15 2009-10-22 from 14:00 to 15:15
Where	RRI 101
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Contents

1 abstract
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1 abstract

DNA copy number analysis involves the detection of chromosomal gains and losses using high-density microarray platforms. Change-point methods have been applied successfully to detecting signals in single data sequences derived from one biological sample. However, it is common to have data sets involving hundreds to thousands of biological samples. How should information be combined across samples to detect population level common polymorphisms?

Also, how should the samples be summarized to give a sparse signature of variation across the cohort? It is also now common to have the same biological sample assayed using multiple experimental platforms. For example, in the Cancer Genome Atlas project, each biological sample is processed using Illumina, Aﬀymetrix and Agilent chips. How should data be integrated across platforms to achieve higher accuracy?

I will discuss the statistical issues underlying these problems and formulate a class of simultaneous change-point models for cross-sample and cross-platform data integration. These models lead to interpretable scan statistics whose signiﬁcance level can be theoretically analyzed. I will also discuss model selection approaches for this class of models. The insights gained from this study can be applied to integrative analysis of data from other types of genome-wide proﬁling experiments, such as methylation or RNA expression.