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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
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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.
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Overall design |
27 Ovarian cancer samples were tested by OncoScan® CNV FFPE Arrays to detect whole genome copy number variation.
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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 |
Citation missing |
Has this study been published? Please login to update or notify GEO. |
Submission date |
May 21, 2022 |
Last update date |
Feb 24, 2023 |
Contact name |
Cai Jiang |
E-mail(s) |
jchnsdu@hotmail.com
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Phone |
86-18949660176
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Organization name |
Nanodigmbio (Nanjing) Biotechnology Co., Ltd.
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Street address |
Room 910, Tower D6, 9 Weidi Road, Qixia District(R&D Center)
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City |
Nanjing |
State/province |
Jiangsu |
ZIP/Postal code |
210046 |
Country |
China |
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Platforms (1) |
GPL21558 |
[OncoScan_CNV] Affymetrix OncoScan CNV FFPE Assay |
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Samples (27)
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Relations |
BioProject |
PRJNA841172 |
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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