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Series GSE203509 Query DataSets for GSE203509
Status Public on Feb 21, 2023
Title A comprehensive assessment of a newly designed non-exonic SNP-based NGS panel for HRD detection
Organism Homo sapiens
Experiment type Genome variation profiling by SNP array
Summary Ovarian cancer is a global problem, is typically diagnosed at a late stage and has no effective screening strategy. Platinum-based chemotherapy or Poly(ADP-ribose) polymerase inhibitors (PARPis) treatment are most frequently applied for ovarian cancer patients who are inoperable and in the advanced stage. The recognition of homologous recombination deficiency (HRD) as a biomarker to predict the effect of Platinum-based or PARPis treatment. WGS and WES can detect tumor HRD status but have several disadvantages which restrict their clinical application. My choice HRD CDx and Foundation Focus CDx are approved by FDA for HRD detection, however, whether they are applicable to the Chinese population or not is unknown. In this study, we created an SNP-based Tg-NGS panel to fill in gaps in Chinese patients’ HRD screening. Our results showed that the panel is cost and time-saving compared with WGS, but equivalent with SNP microarray on CNV and HRD detection. In summary, this newly developed kit is promising in clinical application to guide ovarian cancer and even other cancer types therapy.
 
Overall design 27 Ovarian cancer samples were tested by OncoScan® CNV FFPE Arrays to detect whole genome copy number variation.
 
Contributor(s) Zheng J, Wei B, Jiang C, Zhang H, Zhang M, Cheng T, Li J, Wang Z, Deng L, Wang L, Xia Q, Ma J
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Submission date May 21, 2022
Last update date Feb 24, 2023
Contact name Cai Jiang
E-mail(s) jchnsdu@hotmail.com
Phone 86-18949660176
Organization name Nanodigmbio (Nanjing) Biotechnology Co., Ltd.
Street address Room 910, Tower D6, 9 Weidi Road, Qixia District(R&D Center)
City Nanjing
State/province Jiangsu
ZIP/Postal code 210046
Country China
 
Platforms (1)
GPL21558 [OncoScan_CNV] Affymetrix OncoScan CNV FFPE Assay
Samples (27)
GSM6175191 sample1
GSM6175192 sample2
GSM6175193 sample3
Relations
BioProject PRJNA841172

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
GSE203509_RAW.tar 643.3 Mb (http)(custom) TAR (of CEL, OSCHP)
Processed data provided as supplementary file

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