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Series GSE244578 Query DataSets for GSE244578
Status Public on Nov 20, 2023
Title Sequencing-based Functional Assays for Classification of BRCA2 Variants in Mouse ES Cells
Organism Mus musculus
Experiment type Genome variation profiling by high throughput sequencing
Summary Sequencing of genes, such as BRCA1 and BRCA2, is recommended for individuals with a personal or family history of early onset and/or bilateral breast and/or ovarian cancer, or a history of male breast cancer. Such sequencing efforts have resulted in the identification of more than 6000 BRCA2 variants. The functional significance of most variants remains unknown; consequently, they are called variants of uncertain clinical significance (VUS). We have previously developed mouse embryonic stem cell (mESC)-based assays for functional classification of BRCA2 variants. While the assays are reliable, the experimental process is time-consuming. This has impeded the number of variants that can be examined at a time. To overcome this, we have now developed a next-generation sequencing (NGS)-based approach for functional evaluation of BRCA2 variants. In this approach, instead of using clonogenic or XTT-based cell survival assays, pools of mESC expressing 25-30 BRCA2 variants from a given exon are analyzed by NGS. We have also developed a statistical model that utilizes the NGS data to determine the probability of impact on function (PIF) for these variants. While CRISPR/Cas9-based high throughput methods have resulted in the functional characterization of thousands of variants, only a fraction of the variants are included in ClinVar. In contrast, our targeted approach, which involves generating specific variants, resulted in the functional evaluation of 223 variants that are all listed in ClinVar. Our functional classification of BRCA2 variants is concordant with the classification reported in ClinVar or reported by other well-established assays.
 
Overall design Saturation genome editing (SGE) coupled with drug sensitivity assays of BRCA2
 
Contributor(s) Sounak S, Kajal B
Citation(s) 37922907
Submission date Oct 03, 2023
Last update date Dec 14, 2023
Contact name Shyam Sharan
E-mail(s) sharans@mail.nih.gov
Organization name Mouse Cancer Genetics Program
Street address Building 560, Room 32-33
City Frederick
State/province MD
ZIP/Postal code 21702
Country USA
 
Platforms (1)
GPL16417 Illumina MiSeq (Mus musculus)
Samples (176)
GSM7820736 Cell line Exon 11partc M15 Pool1 Replicate 1
GSM7820737 Cell line Exon 11partc M15 Pool1 Replicate 2
GSM7820738 Cell line Exon 11partc HAT Pool1 Replicate 1
Relations
BioProject PRJNA1023599

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
GSE244578_FS_for_variants_Geo_file.xlsx 103.2 Kb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA

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