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Ryu JS, Lee HY, Cho EH, Yoon KA, Kim MK, Joo J, Lee ES, Kang HS, Lee S, Lee DO, Lim MC, Kong SY. Exon splicing analysis of intronic variants in multigene cancer panel testing for hereditary breast/ovarian cancer. Cancer Sci 2020; 111:3912-3925. [PMID: 32761968 PMCID: PMC7540976 DOI: 10.1111/cas.14600] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 07/29/2020] [Accepted: 08/01/2020] [Indexed: 12/14/2022] Open
Abstract
The use of multigene panel testing for patients with a predisposition to breast/ovarian cancer is increasing as the identification of variants is useful for diagnosis and disease management. We identified pathogenic and likely pathogenic (P/LP) variants of high-and moderate-risk genes using a 23-gene germline cancer panel in 518 patients with hereditary breast and ovarian cancers (HBOC). The frequency of P/LP variants was 12.4% (64/518) for high- and moderate-penetrant genes, namely, BRCA2 (5.6%), BRCA1 (3.3%), CHEK2 (1.2%), MUTYH (0.8%), PALB2 (0.8%), MLH1 (0.4%), ATM (0.4%), BRIP1 (0.4%), TP53 (0.2%), and PMS2 (0.2%). Five patients possessed two P/LP variants in BRCA1/2 and other genes. We also compared the results from in silico splicing predictive tools and exon splicing patterns from patient samples by analyzing RT-PCR product sequences in six P/LP intronic variants and two intronic variants of unknown significance (VUS). Altered transcriptional fragments were detected for P/LP intronic variants in BRCA1, BRIP1, CHEK2, PARB2, and PMS2. Notably, we identified an in-frame deletion of the BRCA1 C-terminal (BRCT) domain by exon skipping in BRCA1 c.5152+6T>C-as known VUS-indicating a risk for HBOC. Thus, exon splicing analysis can improve the identification of veiled intronic variants that would aid decision making and determination of hereditary cancer risk.
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Affiliation(s)
- Jin-Sun Ryu
- Division of Translational Science, Research Institute, National Cancer Center, Goyang, Korea
| | - Hye-Young Lee
- Department of Laboratory Medicine, Hospital, National Cancer Center, Goyang, Korea
| | - Eun Hae Cho
- Genomic research center, Green Cross Genome, Yongin, Korea
| | - Kyong-Ah Yoon
- College of Veterinary Medicine, Konkuk University, Seoul, Korea
| | - Min-Kyeong Kim
- Division of Translational Science, Research Institute, National Cancer Center, Goyang, Korea
| | - Jungnam Joo
- Division of Cancer Epidemiology and Management, Research Institute, National Cancer Center, Goyang, Korea
| | - Eun-Sook Lee
- Center for Breast Cancer, Hospital, National Cancer Center, Goyang, Korea
| | - Han-Sung Kang
- Center for Breast Cancer, Hospital, National Cancer Center, Goyang, Korea
| | - Seeyoun Lee
- Center for Breast Cancer, Hospital, National Cancer Center, Goyang, Korea
| | - Dong Ock Lee
- Center for Gynecologic Cancer, Hospital, National Cancer Center, Goyang, Korea
| | - Myong Cheol Lim
- Center for Gynecologic Cancer, Hospital, National Cancer Center, Goyang, Korea.,Division of Tumor Immunology and Center for Clinical Trial, Research Institute, National Cancer Center, Goyang, Korea
| | - Sun-Young Kong
- Division of Translational Science, Research Institute, National Cancer Center, Goyang, Korea.,Department of Laboratory Medicine, Hospital, National Cancer Center, Goyang, Korea.,Department of Cancer Biomedical Science, National Cancer Center Graduate School of Cancer Science and Policy, Goyang, Korea
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Gabrieli T, Sharim H, Fridman D, Arbib N, Michaeli Y, Ebenstein Y. Selective nanopore sequencing of human BRCA1 by Cas9-assisted targeting of chromosome segments (CATCH). Nucleic Acids Res 2019; 46:e87. [PMID: 29788371 PMCID: PMC6101500 DOI: 10.1093/nar/gky411] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Accepted: 05/04/2018] [Indexed: 12/15/2022] Open
Abstract
Next generation sequencing (NGS) is challenged by structural and copy number variations larger than the typical read length of several hundred bases. Third-generation sequencing platforms such as single-molecule real-time (SMRT) and nanopore sequencing provide longer reads and are able to characterize variations that are undetected in NGS data. Nevertheless, these technologies suffer from inherent low throughput which prohibits deep sequencing at reasonable cost without target enrichment. Here, we optimized Cas9-Assisted Targeting of CHromosome segments (CATCH) for nanopore sequencing of the breast cancer gene BRCA1. A 200 kb target containing the 80 kb BRCA1 gene body and its flanking regions was isolated intact from primary human peripheral blood cells, allowing long-range amplification and long-read nanopore sequencing. The target was enriched 237-fold and sequenced at up to 70× coverage on a single flow-cell. Overall performance and single-nucleotide polymorphism (SNP) calling were directly compared to Illumina sequencing of the same enriched sample, highlighting the benefits of CATCH for targeted sequencing. The CATCH enrichment scheme only requires knowledge of the target flanking sequence for Cas9 cleavage while providing contiguous data across both coding and non-coding sequence and holds promise for characterization of complex disease-related or highly variable genomic regions.
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Affiliation(s)
- Tslil Gabrieli
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Hila Sharim
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Dena Fridman
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Nissim Arbib
- Department of Obstetrics and Gynecology, Meir Hospital, Kfar Saba, Israel & Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yael Michaeli
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Yuval Ebenstein
- School of Chemistry, Center for Nanoscience and Nanotechnology, Center for Light-Matter Interaction, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel
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Liu W, Xu Y, Guan H, Meng H. Clinical potential of miR-940 as a diagnostic and prognostic biomarker in breast cancer patients. Cancer Biomark 2018; 22:487-493. [PMID: 29843213 DOI: 10.3233/cbm-171124] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Wenjun Liu
- Department of Breast and Thyroid Surgery, Shanxian Central Hospital, Heze 274300, Shandong, China
- Department of Breast and Thyroid Surgery, Shanxian Central Hospital, Heze 274300, Shandong, China
| | - Yongmei Xu
- Department of Breast and Thyroid Surgery, Shanxian Central Hospital, Heze 274300, Shandong, China
- Department of Breast and Thyroid Surgery, Shanxian Central Hospital, Heze 274300, Shandong, China
| | - Hongliang Guan
- Department of Breast and Thyroid Surgery, Shanxian Central Hospital, Heze 274300, Shandong, China
- Department of Breast and Thyroid Surgery, Shanxian Central Hospital, Heze 274300, Shandong, China
| | - Hongwei Meng
- Department of Internal Medicine, Shanxian Central Hospital, Heze 274300, Shandong, China
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Yang C, Jairam S, Amoroso KA, Robson ME, Walsh MF, Zhang L. Characterization of a novel germline BRCA1 splice variant, c.5332+4delA. Breast Cancer Res Treat 2017; 168:543-550. [PMID: 29185120 DOI: 10.1007/s10549-017-4595-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Accepted: 11/22/2017] [Indexed: 12/16/2022]
Abstract
PURPOSE Germline mutations in BRCA1 and BRCA2 confer a significant increase in risk for cancer, and determining pathogenicity of a BRCA variant can guide the clinical management of the disease. About 1/3 of BRCA1 variants reported in the public databases have uncertain clinical significance due to lack of conclusive evidence. This study aims to characterize a novel BRCA1 deletion affecting the + 4 splice donor site identified in an individual with early-onset breast cancer. METHODS The effect of BRCA1 c.5332+4delA variant on RNA splicing was evaluated by amplifying regions of BRCA1 from cDNA derived from the patient. The proportion of abnormal transcript in the total transcripts was quantified. Loss of heterozygosity (LOH) in tumor tissue was investigated using Sanger sequencing and fragment analysis. RESULTS BRCA1 c.5332+4delA caused skipping of exon 21 in patient-derived samples. Semi-quantitative analysis indicated that this aberrant RT-PCR product accounts for about 40% of the total transcript levels. Loss of heterozygosity (LOH) was observed in patient's tumor tissue. CONCLUSIONS Our results indicate that the BRCA1 c.5332+4delA variant contributes to cancer predisposition through disruption of normal mRNA splicing. We classify this variant as likely pathogenic.
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Affiliation(s)
- Ciyu Yang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, Box 36, New York, NY, 10065, USA
| | - Sowmya Jairam
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, Box 36, New York, NY, 10065, USA
| | - Kimberly A Amoroso
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Mark E Robson
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Michael F Walsh
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Liying Zhang
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, Box 36, New York, NY, 10065, USA.
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