Identification of a Splice Variant (c.5074+3A>C) of <i>BRCA1</i> by RNA Sequencing and TOPO Cloning
Grading the pathogenicity of <i>BRCA</i>1/2 variants has great clinical importance in patient treatment as well as in the prevention and screening of hereditary breast and ovarian cancer (HBOC). For accurate evaluation, confirming the splicing effect of a possible splice site variant is...
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MDPI AG
2021-05-01
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| Online Access: | https://www.mdpi.com/2073-4425/12/6/810 |
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| author | Jinyoung Hong Ji Hyun Kim Se Hee Ahn Hyunjung Gu Suhwan Chang Woochang Lee Dae-Yeon Kim Sail Chun Won-Ki Min |
| author_facet | Jinyoung Hong Ji Hyun Kim Se Hee Ahn Hyunjung Gu Suhwan Chang Woochang Lee Dae-Yeon Kim Sail Chun Won-Ki Min |
| author_sort | Jinyoung Hong |
| collection | DOAJ |
| description | Grading the pathogenicity of <i>BRCA</i>1/2 variants has great clinical importance in patient treatment as well as in the prevention and screening of hereditary breast and ovarian cancer (HBOC). For accurate evaluation, confirming the splicing effect of a possible splice site variant is crucial. We report a significant splicing variant (c.5074+3A>C) in <i>BRCA1</i> in a patient with recurrent ovarian cancer. Next-generation sequencing (NGS) of <i>BRCA1/2</i> from patient’s peripheral blood identified the variant, which was strongly suspected of being a splicing mutation based on in silico predictions. Direct RNA analysis yielded multiple transcripts, and TOPO cloning of the complementary DNA (cDNA) and Sanger sequencing revealed an aberrant transcript with an insertion of the first 153 bp of intron 17, and another transcript with the 153 bp insertion along with an exon 18 deletion. A premature termination codon was presumed to be formed by the 153 bp partial intron retention common to the two transcripts. Therefore, <i>BRCA1</i> c.5074+3A>C was classified as a likely pathogenic variant. Our findings show that active use of functional studies of variants suspected of altered splicing are of great help in classifying them. |
| first_indexed | 2024-03-10T11:01:45Z |
| format | Article |
| id | doaj.art-b43eb83962ea4bbd8a46af603f7f012a |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-10T11:01:45Z |
| publishDate | 2021-05-01 |
| publisher | MDPI AG |
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| series | Genes |
| spelling | doaj.art-b43eb83962ea4bbd8a46af603f7f012a2023-11-21T21:27:52ZengMDPI AGGenes2073-44252021-05-0112681010.3390/genes12060810Identification of a Splice Variant (c.5074+3A>C) of <i>BRCA1</i> by RNA Sequencing and TOPO CloningJinyoung Hong0Ji Hyun Kim1Se Hee Ahn2Hyunjung Gu3Suhwan Chang4Woochang Lee5Dae-Yeon Kim6Sail Chun7Won-Ki Min8Department of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, KoreaDepartment of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, KoreaDepartment of Biomedical Sciences, University of Ulsan College of Medicine, Seoul 05505, KoreaDepartment of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, KoreaDepartment of Biomedical Sciences, University of Ulsan College of Medicine, Seoul 05505, KoreaDepartment of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, KoreaDepartment of Obstetrics and Gynecology, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, KoreaDepartment of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, KoreaDepartment of Laboratory Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, KoreaGrading the pathogenicity of <i>BRCA</i>1/2 variants has great clinical importance in patient treatment as well as in the prevention and screening of hereditary breast and ovarian cancer (HBOC). For accurate evaluation, confirming the splicing effect of a possible splice site variant is crucial. We report a significant splicing variant (c.5074+3A>C) in <i>BRCA1</i> in a patient with recurrent ovarian cancer. Next-generation sequencing (NGS) of <i>BRCA1/2</i> from patient’s peripheral blood identified the variant, which was strongly suspected of being a splicing mutation based on in silico predictions. Direct RNA analysis yielded multiple transcripts, and TOPO cloning of the complementary DNA (cDNA) and Sanger sequencing revealed an aberrant transcript with an insertion of the first 153 bp of intron 17, and another transcript with the 153 bp insertion along with an exon 18 deletion. A premature termination codon was presumed to be formed by the 153 bp partial intron retention common to the two transcripts. Therefore, <i>BRCA1</i> c.5074+3A>C was classified as a likely pathogenic variant. Our findings show that active use of functional studies of variants suspected of altered splicing are of great help in classifying them.https://www.mdpi.com/2073-4425/12/6/810hereditary breast and ovarian cancer syndrome<i>BRCA1</i> geneRNA sequence analysiscloning |
| spellingShingle | Jinyoung Hong Ji Hyun Kim Se Hee Ahn Hyunjung Gu Suhwan Chang Woochang Lee Dae-Yeon Kim Sail Chun Won-Ki Min Identification of a Splice Variant (c.5074+3A>C) of <i>BRCA1</i> by RNA Sequencing and TOPO Cloning Genes hereditary breast and ovarian cancer syndrome <i>BRCA1</i> gene RNA sequence analysis cloning |
| title | Identification of a Splice Variant (c.5074+3A>C) of <i>BRCA1</i> by RNA Sequencing and TOPO Cloning |
| title_full | Identification of a Splice Variant (c.5074+3A>C) of <i>BRCA1</i> by RNA Sequencing and TOPO Cloning |
| title_fullStr | Identification of a Splice Variant (c.5074+3A>C) of <i>BRCA1</i> by RNA Sequencing and TOPO Cloning |
| title_full_unstemmed | Identification of a Splice Variant (c.5074+3A>C) of <i>BRCA1</i> by RNA Sequencing and TOPO Cloning |
| title_short | Identification of a Splice Variant (c.5074+3A>C) of <i>BRCA1</i> by RNA Sequencing and TOPO Cloning |
| title_sort | identification of a splice variant c 5074 3a c of i brca1 i by rna sequencing and topo cloning |
| topic | hereditary breast and ovarian cancer syndrome <i>BRCA1</i> gene RNA sequence analysis cloning |
| url | https://www.mdpi.com/2073-4425/12/6/810 |
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