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Series GSE105092 Query DataSets for GSE105092
Status Public on Jun 26, 2018
Title Evaluation of copy number variation detection between high-resolution array CGH and low-coverage short-insert and mate-pair whole-genome sequencing
Organism Homo sapiens
Experiment type Genome variation profiling by array
Summary In principle, whole-genome sequencing (WGS) of the human genome even at low coverage offers higher resolution for genomic copy number variation (CNV) detection compared to array-based technologies, which is currently the first-tier approach in clinical cytogenetics. There are, however, obstacles in replacing array-based CNV detection with that of low-coverage WGS such as cost, turnaround time, and lack of systematic performance comparisons. With technological advances in WGS in terms of library preparation, instrument platforms, and data analysis algorithms, obstacles imposed by cost and turnaround time are fading. However, a systematic performance comparison between array and low-coverage WGS-based CNV detection has yet to be performed. Here, we compared the CNV detection capabilities between WGS (short-insert, 3kb-, and 5kb-mate-pair libraries) at 1X, 3X, and 5X coverages and standardly used high-resolution arrays in the genome of 1000-Genomes-Project CEU genome NA12878. CNV detection was performed using standard analysis methods, and the results were then compared to a list of Gold Standard NA12878 CNVs distilled from the 1000-Genomes Project. Overall, low-coverage WGS is able to detect drastically more (approximately 5 fold more on average) Gold Standard CNVs compared to arrays and is accompanied with fewer CNV calls without secondary validation. Furthermore, we also show that WGS (at ≥1X coverage) is able to detect all seven validated deletions larger than 100 kb in the NA12878 genome whereas only one of such deletions is detected in most arrays. Finally, we show that the much larger 15 Mbp Cri-du-chat deletion can be clearly seen at even 1X coverage from short-insert WGS.
 
Overall design To detection of Cri-du-chat deletion and other CNVs from NA16595 DNA (obtained from Coriell) using Illumina MEGA array
Web link https://doi.org/10.1101/192310
 
Contributor(s) Zhou B, Zhang X
Citation(s) 30061371
Submission date Oct 17, 2017
Last update date Jul 25, 2021
Contact name Bo Zhou
E-mail(s) bo.zhou@stanford.edu
Organization name Stanford University
Department Psychiatry
Street address 3165 Porter Drive, Rm 2260
City Palo Alto
State/province CA
ZIP/Postal code 94306
Country USA
 
Platforms (1)
GPL24127 Illumina Infinium Multi-Ethnic Global-8 v1.0 Array
Samples (2)
GSM2817863 NA16595_rep1
GSM2817864 NA16595_rep2
Relations
BioProject PRJNA414621

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
GSE105092_RAW.tar 237.9 Mb (http)(custom) TAR (of IDAT)
Processed data included within Sample table

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