Joint estimation of DNA copy number from multiple platforms.

Bioinformatics
Nancy R ZhangJun Z Li

Abstract

DNA copy number variants (CNVs) are gains and losses of segments of chromosomes, and comprise an important class of genetic variation. Recently, various microarray hybridization-based techniques have been developed for high-throughput measurement of DNA copy number. In many studies, multiple technical platforms or different versions of the same platform were used to interrogate the same samples; and it became necessary to pool information across these multiple sources to derive a consensus molecular profile for each sample. An integrated analysis is expected to maximize resolution and accuracy, yet currently there is no well-formulated statistical method to address the between-platform differences in probe coverage, assay methods, sensitivity and analytical complexity. The conventional approach is to apply one of the CNV detection ('segmentation') algorithms to search for DNA segments of altered signal intensity. The results from multiple platforms are combined after segmentation. Here we propose a new method, Multi-Platform Circular Binary Segmentation (MPCBS), which pools statistical evidence across platforms during segmentation, and does not require pre-standardization of different data sources. It involves a weighted sum of...Continue Reading

References

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Oct 12, 2004·Biostatistics·Adam B OlshenMichael Wigler
Sep 15, 2005·Bioinformatics·Hanni Willenbrock, Jane Fridlyand
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Oct 9, 2009·Nature·Donald F ConradMatthew E Hurles

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Citations

Apr 8, 2011·Bioinformatics·Shu Mei TeoAgus Salim
Aug 30, 2011·Bioinformatics·Sandro MorganellaMichele Ceccarelli
Jan 7, 2011·Biostatistics·Franck PicardStéphane Robin
Aug 18, 2012·BMC Bioinformatics·Zhongyang ZhangChiara Sabatti
Feb 28, 2013·BMC Genomics·Gro NilsenOle Christian Lingjaerde
Jan 11, 2014·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Ayshwarya SubramanianRussell Schwartz

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