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Series GSE10511 Query DataSets for GSE10511
Status Public on Mar 12, 2008
Title wuHMM: a robust algorithm to detect DNA copy number variation using long oligonucleotide microarray data
Organism Mus musculus
Experiment type Genome variation profiling by genome tiling array
Summary Copy number variants (CNVs) are currently defined as genomic sequences that are polymorphic in copy number and range in length from 1,000 to several million base pairs. Among current array-based CNV detection platforms, long-oligonucleotide arrays promise the highest resolution. However, the performance of currently available analytical tools suffers when applied to these data because of the lower signal:noise ratio inherent in oligonucleotide-based hybridization assays. We have developed wuHMM, an algorithm for mapping CNVs from array comparative genomic hybridization (aCGH) platforms comprised of 385,000 to more than 3 million probes. wuHMM is unique in that it can utilize sequence divergence information to reduce the false positive rate (FPR). We apply wuHMM to 385K-aCGH, 2.1M-aCGH, and 3.1M-aCGH experiments comparing the 129X1/SvJ and C57BL/6J inbred mouse genomes. We assess wuHMM’s performance on the 385K platform by comparison to the higher resolution platforms and we independently validate 10 CNVs. The method requires no training data and is robust with respect to changes in algorithm parameters. At a FPR of less than 10%, the algorithm can detect CNVs with five probes on the 385K platform and three on the 2.1M and 3.1M platforms, resulting in effective resolutions of 24 kb, 2-5 kb, and 1 kb, respectively.
Keywords: CNV detection algorithm development and assessment
 
Overall design All four samples in this series are hybridizations of genomic DNA from inbred mouse strains 129X1/SvJ versus C57BL6/J. The experiments were performed at increasing resolutions (one 385K, two 2.1M, and one 3.1M).
 
Contributor(s) Cahan P, Godfrey LE, Eis PS, Richmond TA, Selzer RR, Brent M, McLeod HL, Ley TJ, Graubert TA
Citation(s) 18334530
Submission date Feb 13, 2008
Last update date Mar 19, 2012
Contact name Patrick Cahan
E-mail patrick.cahan@jhmi.edu
Organization name Johns Hopkins University School of Medicine
Department ICE and Biomedical Engineering
Lab Cahan Lab
Street address 733 North Broadway, MRB 653
City Baltimore
State/province MD
ZIP/Postal code 21205
Country USA
 
Platforms (3)
GPL4276 NimbleGen Mouse 388K NCBI34
GPL6363 NimbleGen Mouse 3.1M NCBI36
GPL6436 NimbleGen Mouse 2.1M NCBI36
Samples (4)
GSM135508 129X1/SvJ
GSM265444 129X1/SvJ
GSM265502 129X1/SvJ 119905_SOM01GFG
Relations
BioProject PRJNA107973

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE10511_RAW.tar 145.4 Mb (http)(custom) TAR (of PAIR)
Raw data provided as supplementary file
Processed data included within Sample table
Raw data included within Sample table

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