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An optimized BRCA1/2 next-generation sequencing for different clinical sample types
OBJECTIVE: A simultaneous detection of germline and somatic mutations in ovarian cancer (OC) using tumor materials is considered to be cost-effective for BRCA1/2 testing. However, there are limited studies of the analytical performances according to various sample types. The aim of this study is to...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Asian Society of Gynecologic Oncology; Korean Society of Gynecologic Oncology
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6918881/ https://www.ncbi.nlm.nih.gov/pubmed/31788999 http://dx.doi.org/10.3802/jgo.2020.31.e9 |
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author | Kim, Yoonjung Cho, Chi-Heum Ha, Jung-Sook Kim, Do-Hoon Kwon, Sun Young Oh, Seoung Chul Lee, Kyung-A |
author_facet | Kim, Yoonjung Cho, Chi-Heum Ha, Jung-Sook Kim, Do-Hoon Kwon, Sun Young Oh, Seoung Chul Lee, Kyung-A |
author_sort | Kim, Yoonjung |
collection | PubMed |
description | OBJECTIVE: A simultaneous detection of germline and somatic mutations in ovarian cancer (OC) using tumor materials is considered to be cost-effective for BRCA1/2 testing. However, there are limited studies of the analytical performances according to various sample types. The aim of this study is to propose a strategy for routine BRCA1/2 next-generation sequencing (NGS) screening based on analytical performance according to different sample types. METHODS: We compared BRCA1/2 NGS screening assay using buffy coat, fresh-frozen (FF) and formalin-fixed paraffin-embedded (FFPE) from 130 samples. RESULTS: The rate of repeated tests in a total of buffy coat, FF and FFPE was 0%, 8%, and 34%, respectively. The accuracy of BRCA1/2 NGS testing was 100.0%, 99.9% and 99.9% in buffy coat, FFPE and FF, respectively. However, due to the presence of variant allele frequency (VAF) shifted heterozygous variants, tumor materials (FFPE and FF) showed lower sensitivity (95.5%–99.0%) than buffy coat (100%). Furthermore, FFPE showed 51.4% of the positive predictive value (PPV) on account of sequence artifacts. When performed in the post-filtration process, PPV was increased by approximately 20% in FFPE. Buffy coat showed 100% of sensitivity, specificity and accuracy in BRCA1/2 NGS test. CONCLUSIONS: On the comparison of the analytical performance according to different sample types, the buffy coat was not affected by sequencing artifacts and VAF shifted variants. Therefore, the blood test should be given priority in detecting germline BRCA1/2 mutation, and tumor materials could be suitable to detect somatic mutations in OC patients without identifying germline BRCA1/2 mutation. |
format | Online Article Text |
id | pubmed-6918881 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Asian Society of Gynecologic Oncology; Korean Society of Gynecologic Oncology |
record_format | MEDLINE/PubMed |
spelling | pubmed-69188812020-01-01 An optimized BRCA1/2 next-generation sequencing for different clinical sample types Kim, Yoonjung Cho, Chi-Heum Ha, Jung-Sook Kim, Do-Hoon Kwon, Sun Young Oh, Seoung Chul Lee, Kyung-A J Gynecol Oncol Original Article OBJECTIVE: A simultaneous detection of germline and somatic mutations in ovarian cancer (OC) using tumor materials is considered to be cost-effective for BRCA1/2 testing. However, there are limited studies of the analytical performances according to various sample types. The aim of this study is to propose a strategy for routine BRCA1/2 next-generation sequencing (NGS) screening based on analytical performance according to different sample types. METHODS: We compared BRCA1/2 NGS screening assay using buffy coat, fresh-frozen (FF) and formalin-fixed paraffin-embedded (FFPE) from 130 samples. RESULTS: The rate of repeated tests in a total of buffy coat, FF and FFPE was 0%, 8%, and 34%, respectively. The accuracy of BRCA1/2 NGS testing was 100.0%, 99.9% and 99.9% in buffy coat, FFPE and FF, respectively. However, due to the presence of variant allele frequency (VAF) shifted heterozygous variants, tumor materials (FFPE and FF) showed lower sensitivity (95.5%–99.0%) than buffy coat (100%). Furthermore, FFPE showed 51.4% of the positive predictive value (PPV) on account of sequence artifacts. When performed in the post-filtration process, PPV was increased by approximately 20% in FFPE. Buffy coat showed 100% of sensitivity, specificity and accuracy in BRCA1/2 NGS test. CONCLUSIONS: On the comparison of the analytical performance according to different sample types, the buffy coat was not affected by sequencing artifacts and VAF shifted variants. Therefore, the blood test should be given priority in detecting germline BRCA1/2 mutation, and tumor materials could be suitable to detect somatic mutations in OC patients without identifying germline BRCA1/2 mutation. Asian Society of Gynecologic Oncology; Korean Society of Gynecologic Oncology 2019-08-06 /pmc/articles/PMC6918881/ /pubmed/31788999 http://dx.doi.org/10.3802/jgo.2020.31.e9 Text en Copyright © 2020. Asian Society of Gynecologic Oncology, Korean Society of Gynecologic Oncology https://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (https://creativecommons.org/licenses/by-nc/4.0/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Original Article Kim, Yoonjung Cho, Chi-Heum Ha, Jung-Sook Kim, Do-Hoon Kwon, Sun Young Oh, Seoung Chul Lee, Kyung-A An optimized BRCA1/2 next-generation sequencing for different clinical sample types |
title | An optimized BRCA1/2 next-generation sequencing for different clinical sample types |
title_full | An optimized BRCA1/2 next-generation sequencing for different clinical sample types |
title_fullStr | An optimized BRCA1/2 next-generation sequencing for different clinical sample types |
title_full_unstemmed | An optimized BRCA1/2 next-generation sequencing for different clinical sample types |
title_short | An optimized BRCA1/2 next-generation sequencing for different clinical sample types |
title_sort | optimized brca1/2 next-generation sequencing for different clinical sample types |
topic | Original Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6918881/ https://www.ncbi.nlm.nih.gov/pubmed/31788999 http://dx.doi.org/10.3802/jgo.2020.31.e9 |
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