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Series GSE96846 Query DataSets for GSE96846
Status Public on Mar 22, 2017
Title Comprehensive performance comparison of high-resolution array platforms for genome-wide Copy Number Variation (CNV) analysis in humans [IlluminaHumanOmni2.5Exome]
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
Summary Background High-resolution microarray technology is routinely used in basic research and clinical practice to efficiently detect copy number variants (CNVs) across the entire human genome. A new generation of arrays combining high probe densities with optimized designs will comprise essential tools for genome analysis in the coming years. We systematically compared the genome-wide CNV detection power of all 17 available array designs from the Affymetrix, Agilent, and Illumina platforms by hybridizing the well-characterized genome of 1000 Genomes Project subject NA12878 to all arrays, and performing data analysis using both manufacturer-recommended and platform-independent software. We benchmarked the resulting CNV call sets from each array using a gold standard set of CNVs for this genome derived from 1000 Genomes Project whole genome sequencing data. Results The arrays tested comprise both SNP and aCGH platforms with varying designs and contain between ~0.5 to ~4.6 million probes. Across the arrays CNV detection varied widely in number of CNV calls (4 - 489), CNV size range (~40 bp to ~8 Mbp), and percentage of non-validated CNVs (0 - 86 %). We discovered strikingly strong effects of specific array design principles on performance. For example, some SNP array designs with the largest numbers of probes and extensive exonic coverage produced a considerable number of CNV calls that could not be validated, compared to designs with probe numbers that are sometimes an order of magnitude smaller. This effect was only partially ameliorated using different analysis software and optimizing data analysis parameters. Conclusions High-resolution microarrays will continue to be used as reliable, cost- and time-efficient tools for CNV analysis. However, different applications tolerate different limitations in CNV detection. Our study quantified how these arrays differ in total number and size range of detected CNVs as well as sensitivity, and determined how each array balances these attributes. This analysis will inform appropriate array selection for future CNV studies, and allow better assessment of the CNV-analytical power of both published and ongoing array-based genomics studies. Furthermore, our findings emphasize the importance of concurrent use of multiple analysis algorithms and independent experimental validation in array-based CNV detection studies.
 
Overall design We systematically compared the genome-wide CNV detection power of all 17 available array designs from the Affymetrix, Agilent, and Illumina platforms by hybridizing the well-characterized genome of 1000 Genomes Project subject NA12878 to all arrays in two technical replicates, and performing data analysis using both manufacturer-recommended and platform-independent software. We benchmarked the resulting CNV call sets from each array using a gold standard set of CNVs for this genome derived from 1000 Genomes Project whole genome sequencing data.
 
Contributor(s) Haraksingh RR
Citation(s) 28438122
Submission date Mar 21, 2017
Last update date Jun 16, 2017
Contact name Rajini Haraksingh
E-mail(s) rharaksingh@gmail.com
Phone 2035358367
Organization name The University of the West Indies
Department Life Sciences
Street address The University of the West Indies
City St. Augustine
ZIP/Postal code -
Country Trinidad and Tobago
 
Platforms (1)
GPL23200 IlluminaHumanOmni2.5Exome-8 v1.0 B
Samples (2)
GSM2544975 NA12878 Genomic DNA Replicate 1 (HumanOmni2.5Exome)
GSM2544976 NA12878 Genomic DNA Replicate 2 (HumanOmni2.5Exome)
This SubSeries is part of SuperSeries:
GSE96909 Comprehensive performance comparison of high-resolution array platforms for genome-wide Copy Number Variation (CNV) analysis in humans
Relations
BioProject PRJNA379916

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
GSE96846_RAW.tar 417.4 Mb (http)(custom) TAR (of IDAT, TXT)
Processed data provided as supplementary file

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