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Series GSE39332 Query DataSets for GSE39332
Status Public on Jul 13, 2015
Title Chromosomal analysis of products of conception
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
SNP genotyping by SNP array
Summary Results of an unbiased series of 2833 fresh products of conception samples (in conjunction with maternal blood samples for comparison) that were tested using a 300K Illumina SNP array. we report on the rate and type of whole aneuploidies, UPD, partial aneuploidies, copy number variants found in our series as well as the rate of maternal cell contamination vs. true fetal results.
2833 consecutive fresh products of conception samples and corresponding maternal and/or paternal blood samples were analyzed using a SNP array plus informatics algorithms for the purpose of detecting causal chromosome abnormalities. Hypothesized advantages of using SNP microarray with Parental SupportTM informatics over the traditional standard G-banded karyotyping include: direct testing without need for cell culture, faster turn-around time, low failure rate, the ability to detect or rule out maternal cell contamination (MCC), and the detection of small segmental changes, uniparental disomy (UPD) and parent of origin of any aneuploidies. Results showed a 22% MCC rate. In the 78% of samples with true fetal results, 60% had abnormalities with single aneuploidy being the most common. Separate evaluation of the samples to determine the resolution of the SNP array with informatics showed the ability to detect copy number variations (CNVs) as small as 1 MB or less, with 1.4% of samples revealing a clinically relevant microdeletion or duplication.
 
Overall design 2833 fresh products of conception samples were analyze using no controls, no replicates, and no reference samples.
 
Contributor(s) Levy B, Sigurjonsson S, Pettersen BJ, Maisenbacher MK, Demko ZP, Lathi RB, Tao R, Aggarwal V, Rabinowitz M
Citation missing Has this study been published? Please login to update or notify GEO.
Submission date Jul 13, 2012
Last update date Dec 18, 2017
Contact name Jennifer Dikan
E-mail(s) jdikan@natera.com
Organization name Natera
Street address 201 Industrial Road, Suite 410
City San Carlos
State/province California
ZIP/Postal code 94070
Country USA
 
Platforms (2)
GPL8856 Illumina HumanCytoSnp-12 Beadchip version 1.0
GPL13829 Illumina HumanCytoSNP-12 v2.1 BeadChip
Samples (5062)
GSM961049 Case 2297 poc child cyto12 5497204006_R03C01
GSM961050 Case 2992 blood mother cyto12 5580649028_R03C01
GSM961051 Case 8189 poc child cyto12b 6186408075_R05C01
Relations
BioProject PRJNA170660

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
GSE39332_297481_intensities1_GPL13829.txt.gz 656.2 Mb (ftp)(http) TXT
GSE39332_297481_intensities2_GPL13829.txt.gz 662.2 Mb (ftp)(http) TXT
GSE39332_297481_intensities3_GPL13829.txt.gz 663.7 Mb (ftp)(http) TXT
GSE39332_297481_intensities4_GPL13829.txt.gz 656.0 Mb (ftp)(http) TXT
GSE39332_299671_intensities1_GPL8856.txt.gz 672.8 Mb (ftp)(http) TXT
GSE39332_299671_intensities2_GPL8856.txt.gz 665.5 Mb (ftp)(http) TXT
GSE39332_299671_intensities3_GPL8856.txt.gz 664.7 Mb (ftp)(http) TXT
GSE39332_299671_intensities4_GPL8856.txt.gz 670.3 Mb (ftp)(http) TXT
GSE39332_299671_intensities5_GPL8856.txt.gz 668.6 Mb (ftp)(http) TXT
GSE39332_299671_intensities6_GPL8856.txt.gz 671.0 Mb (ftp)(http) TXT
Processed data not provided for this record

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