Development and validation of a variant detection workflow for BRCA1 and BRCA2 genes and its clinical application based on the Ion Torrent technology

Background Breast cancer is the most common among women worldwide, and ovarian cancer is the most difficult gynecological tumor to diagnose and with the lowest chance of cure. Mutations in BRCA1 and BRCA2 genes increase the risk of ovarian cancer by 60% and breast cancer by up to 80% in women. Molec...
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Gespeichert in:

Autor*in:	Buzolin, Ana Lígia [verfasserIn] Moreira, Caroline Mônaco [verfasserIn] Sacramento, Patricia Rossi [verfasserIn] Oku, Andre Yuji [verfasserIn] Fornari, Alexandre Ricardo dos Santos [verfasserIn] Antonio, David Santos Marco [verfasserIn] Quaio, Caio Robledo D Angioli Costa [verfasserIn] Baratela, Wagner Rosa [verfasserIn] Mitne-Neto, Miguel [verfasserIn]

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2017

Schlagwörter:	Cancer Breast Ovarian Ion Torrent BRCA

Übergeordnetes Werk:	Enthalten in: Human genomics - London [u.a.] : Henry Stewart Publ., 2003, 11(2017), 1 vom: 26. Juni
Übergeordnetes Werk:	volume:11 ; year:2017 ; number:1 ; day:26 ; month:06

Links:	Volltext

DOI / URN:	10.1186/s40246-017-0110-x

Katalog-ID:	SPR032929102

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520			\|a Background Breast cancer is the most common among women worldwide, and ovarian cancer is the most difficult gynecological tumor to diagnose and with the lowest chance of cure. Mutations in BRCA1 and BRCA2 genes increase the risk of ovarian cancer by 60% and breast cancer by up to 80% in women. Molecular tests allow a better orientation for patients carrying these mutations, affecting prophylaxis, treatment, and genetic counseling. Results Here, we evaluated the performance of a panel for BRCA1 and BRCA2, using the Ion Torrent PGM (Life Technologies) platform in a customized workflow and multiplex ligation-dependent probe amplification for detection of mutations, insertions, and deletions in these genes. We validated the panel with 26 samples previously analyzed by Myriad Genetics Laboratory, and our workflow showed 95.6% sensitivity and 100% agreement with Myriad reports, with 85% sensitivity on the positive control sample from NIST. We also screened 68 clinical samples and found 22 distinct mutations. Conclusions The selection of a robust methodology for sample preparation and sequencing, together with bioinformatics tools optimized for the data analysis, enabled the development of a very sensitive test with high reproducibility. We also highlight the need to explore the limitations of the NGS technique and the strategies to overcome them in a clinically confident manner.
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700	1		\|a Mitne-Neto, Miguel \|e verfasserin \|4 aut
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author_variant	a l b al alb c m m cm cmm p r s pr prs a y o ay ayo a r d s f ards ardsf d s m a dsm dsma c r d a c q crdac crdacq w r b wr wrb m m n mmn
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allfields	10.1186/s40246-017-0110-x doi (DE-627)SPR032929102 (SPR)s40246-017-0110-x-e DE-627 ger DE-627 rakwb eng 610 570 ASE Buzolin, Ana Lígia verfasserin aut Development and validation of a variant detection workflow for BRCA1 and BRCA2 genes and its clinical application based on the Ion Torrent technology 2017 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Background Breast cancer is the most common among women worldwide, and ovarian cancer is the most difficult gynecological tumor to diagnose and with the lowest chance of cure. Mutations in BRCA1 and BRCA2 genes increase the risk of ovarian cancer by 60% and breast cancer by up to 80% in women. Molecular tests allow a better orientation for patients carrying these mutations, affecting prophylaxis, treatment, and genetic counseling. Results Here, we evaluated the performance of a panel for BRCA1 and BRCA2, using the Ion Torrent PGM (Life Technologies) platform in a customized workflow and multiplex ligation-dependent probe amplification for detection of mutations, insertions, and deletions in these genes. We validated the panel with 26 samples previously analyzed by Myriad Genetics Laboratory, and our workflow showed 95.6% sensitivity and 100% agreement with Myriad reports, with 85% sensitivity on the positive control sample from NIST. We also screened 68 clinical samples and found 22 distinct mutations. Conclusions The selection of a robust methodology for sample preparation and sequencing, together with bioinformatics tools optimized for the data analysis, enabled the development of a very sensitive test with high reproducibility. We also highlight the need to explore the limitations of the NGS technique and the strategies to overcome them in a clinically confident manner. Cancer (dpeaa)DE-He213 Breast (dpeaa)DE-He213 Ovarian (dpeaa)DE-He213 Ion Torrent (dpeaa)DE-He213 BRCA (dpeaa)DE-He213 Moreira, Caroline Mônaco verfasserin aut Sacramento, Patricia Rossi verfasserin aut Oku, Andre Yuji verfasserin aut Fornari, Alexandre Ricardo dos Santos verfasserin aut Antonio, David Santos Marco verfasserin aut Quaio, Caio Robledo D Angioli Costa verfasserin aut Baratela, Wagner Rosa verfasserin aut Mitne-Neto, Miguel verfasserin aut Enthalten in Human genomics London [u.a.] : Henry Stewart Publ., 2003 11(2017), 1 vom: 26. Juni (DE-627)388549408 (DE-600)2147618-4 1479-7364 nnns volume:11 year:2017 number:1 day:26 month:06 https://dx.doi.org/10.1186/s40246-017-0110-x kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_2153 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 11 2017 1 26 06
spelling	10.1186/s40246-017-0110-x doi (DE-627)SPR032929102 (SPR)s40246-017-0110-x-e DE-627 ger DE-627 rakwb eng 610 570 ASE Buzolin, Ana Lígia verfasserin aut Development and validation of a variant detection workflow for BRCA1 and BRCA2 genes and its clinical application based on the Ion Torrent technology 2017 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Background Breast cancer is the most common among women worldwide, and ovarian cancer is the most difficult gynecological tumor to diagnose and with the lowest chance of cure. Mutations in BRCA1 and BRCA2 genes increase the risk of ovarian cancer by 60% and breast cancer by up to 80% in women. Molecular tests allow a better orientation for patients carrying these mutations, affecting prophylaxis, treatment, and genetic counseling. Results Here, we evaluated the performance of a panel for BRCA1 and BRCA2, using the Ion Torrent PGM (Life Technologies) platform in a customized workflow and multiplex ligation-dependent probe amplification for detection of mutations, insertions, and deletions in these genes. We validated the panel with 26 samples previously analyzed by Myriad Genetics Laboratory, and our workflow showed 95.6% sensitivity and 100% agreement with Myriad reports, with 85% sensitivity on the positive control sample from NIST. We also screened 68 clinical samples and found 22 distinct mutations. Conclusions The selection of a robust methodology for sample preparation and sequencing, together with bioinformatics tools optimized for the data analysis, enabled the development of a very sensitive test with high reproducibility. We also highlight the need to explore the limitations of the NGS technique and the strategies to overcome them in a clinically confident manner. Cancer (dpeaa)DE-He213 Breast (dpeaa)DE-He213 Ovarian (dpeaa)DE-He213 Ion Torrent (dpeaa)DE-He213 BRCA (dpeaa)DE-He213 Moreira, Caroline Mônaco verfasserin aut Sacramento, Patricia Rossi verfasserin aut Oku, Andre Yuji verfasserin aut Fornari, Alexandre Ricardo dos Santos verfasserin aut Antonio, David Santos Marco verfasserin aut Quaio, Caio Robledo D Angioli Costa verfasserin aut Baratela, Wagner Rosa verfasserin aut Mitne-Neto, Miguel verfasserin aut Enthalten in Human genomics London [u.a.] : Henry Stewart Publ., 2003 11(2017), 1 vom: 26. Juni (DE-627)388549408 (DE-600)2147618-4 1479-7364 nnns volume:11 year:2017 number:1 day:26 month:06 https://dx.doi.org/10.1186/s40246-017-0110-x kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_2153 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 11 2017 1 26 06
allfields_unstemmed	10.1186/s40246-017-0110-x doi (DE-627)SPR032929102 (SPR)s40246-017-0110-x-e DE-627 ger DE-627 rakwb eng 610 570 ASE Buzolin, Ana Lígia verfasserin aut Development and validation of a variant detection workflow for BRCA1 and BRCA2 genes and its clinical application based on the Ion Torrent technology 2017 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Background Breast cancer is the most common among women worldwide, and ovarian cancer is the most difficult gynecological tumor to diagnose and with the lowest chance of cure. Mutations in BRCA1 and BRCA2 genes increase the risk of ovarian cancer by 60% and breast cancer by up to 80% in women. Molecular tests allow a better orientation for patients carrying these mutations, affecting prophylaxis, treatment, and genetic counseling. Results Here, we evaluated the performance of a panel for BRCA1 and BRCA2, using the Ion Torrent PGM (Life Technologies) platform in a customized workflow and multiplex ligation-dependent probe amplification for detection of mutations, insertions, and deletions in these genes. We validated the panel with 26 samples previously analyzed by Myriad Genetics Laboratory, and our workflow showed 95.6% sensitivity and 100% agreement with Myriad reports, with 85% sensitivity on the positive control sample from NIST. We also screened 68 clinical samples and found 22 distinct mutations. Conclusions The selection of a robust methodology for sample preparation and sequencing, together with bioinformatics tools optimized for the data analysis, enabled the development of a very sensitive test with high reproducibility. We also highlight the need to explore the limitations of the NGS technique and the strategies to overcome them in a clinically confident manner. Cancer (dpeaa)DE-He213 Breast (dpeaa)DE-He213 Ovarian (dpeaa)DE-He213 Ion Torrent (dpeaa)DE-He213 BRCA (dpeaa)DE-He213 Moreira, Caroline Mônaco verfasserin aut Sacramento, Patricia Rossi verfasserin aut Oku, Andre Yuji verfasserin aut Fornari, Alexandre Ricardo dos Santos verfasserin aut Antonio, David Santos Marco verfasserin aut Quaio, Caio Robledo D Angioli Costa verfasserin aut Baratela, Wagner Rosa verfasserin aut Mitne-Neto, Miguel verfasserin aut Enthalten in Human genomics London [u.a.] : Henry Stewart Publ., 2003 11(2017), 1 vom: 26. Juni (DE-627)388549408 (DE-600)2147618-4 1479-7364 nnns volume:11 year:2017 number:1 day:26 month:06 https://dx.doi.org/10.1186/s40246-017-0110-x kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_2153 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 11 2017 1 26 06
allfieldsGer	10.1186/s40246-017-0110-x doi (DE-627)SPR032929102 (SPR)s40246-017-0110-x-e DE-627 ger DE-627 rakwb eng 610 570 ASE Buzolin, Ana Lígia verfasserin aut Development and validation of a variant detection workflow for BRCA1 and BRCA2 genes and its clinical application based on the Ion Torrent technology 2017 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Background Breast cancer is the most common among women worldwide, and ovarian cancer is the most difficult gynecological tumor to diagnose and with the lowest chance of cure. Mutations in BRCA1 and BRCA2 genes increase the risk of ovarian cancer by 60% and breast cancer by up to 80% in women. Molecular tests allow a better orientation for patients carrying these mutations, affecting prophylaxis, treatment, and genetic counseling. Results Here, we evaluated the performance of a panel for BRCA1 and BRCA2, using the Ion Torrent PGM (Life Technologies) platform in a customized workflow and multiplex ligation-dependent probe amplification for detection of mutations, insertions, and deletions in these genes. We validated the panel with 26 samples previously analyzed by Myriad Genetics Laboratory, and our workflow showed 95.6% sensitivity and 100% agreement with Myriad reports, with 85% sensitivity on the positive control sample from NIST. We also screened 68 clinical samples and found 22 distinct mutations. Conclusions The selection of a robust methodology for sample preparation and sequencing, together with bioinformatics tools optimized for the data analysis, enabled the development of a very sensitive test with high reproducibility. We also highlight the need to explore the limitations of the NGS technique and the strategies to overcome them in a clinically confident manner. Cancer (dpeaa)DE-He213 Breast (dpeaa)DE-He213 Ovarian (dpeaa)DE-He213 Ion Torrent (dpeaa)DE-He213 BRCA (dpeaa)DE-He213 Moreira, Caroline Mônaco verfasserin aut Sacramento, Patricia Rossi verfasserin aut Oku, Andre Yuji verfasserin aut Fornari, Alexandre Ricardo dos Santos verfasserin aut Antonio, David Santos Marco verfasserin aut Quaio, Caio Robledo D Angioli Costa verfasserin aut Baratela, Wagner Rosa verfasserin aut Mitne-Neto, Miguel verfasserin aut Enthalten in Human genomics London [u.a.] : Henry Stewart Publ., 2003 11(2017), 1 vom: 26. Juni (DE-627)388549408 (DE-600)2147618-4 1479-7364 nnns volume:11 year:2017 number:1 day:26 month:06 https://dx.doi.org/10.1186/s40246-017-0110-x kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_2153 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 11 2017 1 26 06
allfieldsSound	10.1186/s40246-017-0110-x doi (DE-627)SPR032929102 (SPR)s40246-017-0110-x-e DE-627 ger DE-627 rakwb eng 610 570 ASE Buzolin, Ana Lígia verfasserin aut Development and validation of a variant detection workflow for BRCA1 and BRCA2 genes and its clinical application based on the Ion Torrent technology 2017 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier Background Breast cancer is the most common among women worldwide, and ovarian cancer is the most difficult gynecological tumor to diagnose and with the lowest chance of cure. Mutations in BRCA1 and BRCA2 genes increase the risk of ovarian cancer by 60% and breast cancer by up to 80% in women. Molecular tests allow a better orientation for patients carrying these mutations, affecting prophylaxis, treatment, and genetic counseling. Results Here, we evaluated the performance of a panel for BRCA1 and BRCA2, using the Ion Torrent PGM (Life Technologies) platform in a customized workflow and multiplex ligation-dependent probe amplification for detection of mutations, insertions, and deletions in these genes. We validated the panel with 26 samples previously analyzed by Myriad Genetics Laboratory, and our workflow showed 95.6% sensitivity and 100% agreement with Myriad reports, with 85% sensitivity on the positive control sample from NIST. We also screened 68 clinical samples and found 22 distinct mutations. Conclusions The selection of a robust methodology for sample preparation and sequencing, together with bioinformatics tools optimized for the data analysis, enabled the development of a very sensitive test with high reproducibility. We also highlight the need to explore the limitations of the NGS technique and the strategies to overcome them in a clinically confident manner. Cancer (dpeaa)DE-He213 Breast (dpeaa)DE-He213 Ovarian (dpeaa)DE-He213 Ion Torrent (dpeaa)DE-He213 BRCA (dpeaa)DE-He213 Moreira, Caroline Mônaco verfasserin aut Sacramento, Patricia Rossi verfasserin aut Oku, Andre Yuji verfasserin aut Fornari, Alexandre Ricardo dos Santos verfasserin aut Antonio, David Santos Marco verfasserin aut Quaio, Caio Robledo D Angioli Costa verfasserin aut Baratela, Wagner Rosa verfasserin aut Mitne-Neto, Miguel verfasserin aut Enthalten in Human genomics London [u.a.] : Henry Stewart Publ., 2003 11(2017), 1 vom: 26. Juni (DE-627)388549408 (DE-600)2147618-4 1479-7364 nnns volume:11 year:2017 number:1 day:26 month:06 https://dx.doi.org/10.1186/s40246-017-0110-x kostenfrei Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_206 GBV_ILN_213 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_2153 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 11 2017 1 26 06
language	English
source	Enthalten in Human genomics 11(2017), 1 vom: 26. Juni volume:11 year:2017 number:1 day:26 month:06
sourceStr	Enthalten in Human genomics 11(2017), 1 vom: 26. Juni volume:11 year:2017 number:1 day:26 month:06
format_phy_str_mv	Article
institution	findex.gbv.de
topic_facet	Cancer Breast Ovarian Ion Torrent BRCA
dewey-raw	610
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container_title	Human genomics
authorswithroles_txt_mv	Buzolin, Ana Lígia @@aut@@ Moreira, Caroline Mônaco @@aut@@ Sacramento, Patricia Rossi @@aut@@ Oku, Andre Yuji @@aut@@ Fornari, Alexandre Ricardo dos Santos @@aut@@ Antonio, David Santos Marco @@aut@@ Quaio, Caio Robledo D Angioli Costa @@aut@@ Baratela, Wagner Rosa @@aut@@ Mitne-Neto, Miguel @@aut@@
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Mutations in BRCA1 and BRCA2 genes increase the risk of ovarian cancer by 60% and breast cancer by up to 80% in women. Molecular tests allow a better orientation for patients carrying these mutations, affecting prophylaxis, treatment, and genetic counseling. Results Here, we evaluated the performance of a panel for BRCA1 and BRCA2, using the Ion Torrent PGM (Life Technologies) platform in a customized workflow and multiplex ligation-dependent probe amplification for detection of mutations, insertions, and deletions in these genes. We validated the panel with 26 samples previously analyzed by Myriad Genetics Laboratory, and our workflow showed 95.6% sensitivity and 100% agreement with Myriad reports, with 85% sensitivity on the positive control sample from NIST. We also screened 68 clinical samples and found 22 distinct mutations. Conclusions The selection of a robust methodology for sample preparation and sequencing, together with bioinformatics tools optimized for the data analysis, enabled the development of a very sensitive test with high reproducibility. 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author	Buzolin, Ana Lígia
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title	Development and validation of a variant detection workflow for BRCA1 and BRCA2 genes and its clinical application based on the Ion Torrent technology
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title_full	Development and validation of a variant detection workflow for BRCA1 and BRCA2 genes and its clinical application based on the Ion Torrent technology
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author_browse	Buzolin, Ana Lígia Moreira, Caroline Mônaco Sacramento, Patricia Rossi Oku, Andre Yuji Fornari, Alexandre Ricardo dos Santos Antonio, David Santos Marco Quaio, Caio Robledo D Angioli Costa Baratela, Wagner Rosa Mitne-Neto, Miguel
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title_sort	development and validation of a variant detection workflow for brca1 and brca2 genes and its clinical application based on the ion torrent technology
title_auth	Development and validation of a variant detection workflow for BRCA1 and BRCA2 genes and its clinical application based on the Ion Torrent technology
abstract	Background Breast cancer is the most common among women worldwide, and ovarian cancer is the most difficult gynecological tumor to diagnose and with the lowest chance of cure. Mutations in BRCA1 and BRCA2 genes increase the risk of ovarian cancer by 60% and breast cancer by up to 80% in women. Molecular tests allow a better orientation for patients carrying these mutations, affecting prophylaxis, treatment, and genetic counseling. Results Here, we evaluated the performance of a panel for BRCA1 and BRCA2, using the Ion Torrent PGM (Life Technologies) platform in a customized workflow and multiplex ligation-dependent probe amplification for detection of mutations, insertions, and deletions in these genes. We validated the panel with 26 samples previously analyzed by Myriad Genetics Laboratory, and our workflow showed 95.6% sensitivity and 100% agreement with Myriad reports, with 85% sensitivity on the positive control sample from NIST. We also screened 68 clinical samples and found 22 distinct mutations. Conclusions The selection of a robust methodology for sample preparation and sequencing, together with bioinformatics tools optimized for the data analysis, enabled the development of a very sensitive test with high reproducibility. We also highlight the need to explore the limitations of the NGS technique and the strategies to overcome them in a clinically confident manner.
abstractGer	Background Breast cancer is the most common among women worldwide, and ovarian cancer is the most difficult gynecological tumor to diagnose and with the lowest chance of cure. Mutations in BRCA1 and BRCA2 genes increase the risk of ovarian cancer by 60% and breast cancer by up to 80% in women. Molecular tests allow a better orientation for patients carrying these mutations, affecting prophylaxis, treatment, and genetic counseling. Results Here, we evaluated the performance of a panel for BRCA1 and BRCA2, using the Ion Torrent PGM (Life Technologies) platform in a customized workflow and multiplex ligation-dependent probe amplification for detection of mutations, insertions, and deletions in these genes. We validated the panel with 26 samples previously analyzed by Myriad Genetics Laboratory, and our workflow showed 95.6% sensitivity and 100% agreement with Myriad reports, with 85% sensitivity on the positive control sample from NIST. We also screened 68 clinical samples and found 22 distinct mutations. Conclusions The selection of a robust methodology for sample preparation and sequencing, together with bioinformatics tools optimized for the data analysis, enabled the development of a very sensitive test with high reproducibility. We also highlight the need to explore the limitations of the NGS technique and the strategies to overcome them in a clinically confident manner.
abstract_unstemmed	Background Breast cancer is the most common among women worldwide, and ovarian cancer is the most difficult gynecological tumor to diagnose and with the lowest chance of cure. Mutations in BRCA1 and BRCA2 genes increase the risk of ovarian cancer by 60% and breast cancer by up to 80% in women. Molecular tests allow a better orientation for patients carrying these mutations, affecting prophylaxis, treatment, and genetic counseling. Results Here, we evaluated the performance of a panel for BRCA1 and BRCA2, using the Ion Torrent PGM (Life Technologies) platform in a customized workflow and multiplex ligation-dependent probe amplification for detection of mutations, insertions, and deletions in these genes. We validated the panel with 26 samples previously analyzed by Myriad Genetics Laboratory, and our workflow showed 95.6% sensitivity and 100% agreement with Myriad reports, with 85% sensitivity on the positive control sample from NIST. We also screened 68 clinical samples and found 22 distinct mutations. Conclusions The selection of a robust methodology for sample preparation and sequencing, together with bioinformatics tools optimized for the data analysis, enabled the development of a very sensitive test with high reproducibility. We also highlight the need to explore the limitations of the NGS technique and the strategies to overcome them in a clinically confident manner.
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title_short	Development and validation of a variant detection workflow for BRCA1 and BRCA2 genes and its clinical application based on the Ion Torrent technology
url	https://dx.doi.org/10.1186/s40246-017-0110-x
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author2	Moreira, Caroline Mônaco Sacramento, Patricia Rossi Oku, Andre Yuji Fornari, Alexandre Ricardo dos Santos Antonio, David Santos Marco Quaio, Caio Robledo D Angioli Costa Baratela, Wagner Rosa Mitne-Neto, Miguel
author2Str	Moreira, Caroline Mônaco Sacramento, Patricia Rossi Oku, Andre Yuji Fornari, Alexandre Ricardo dos Santos Antonio, David Santos Marco Quaio, Caio Robledo D Angioli Costa Baratela, Wagner Rosa Mitne-Neto, Miguel
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up_date	2024-07-03T15:30:35.894Z
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Mutations in BRCA1 and BRCA2 genes increase the risk of ovarian cancer by 60% and breast cancer by up to 80% in women. Molecular tests allow a better orientation for patients carrying these mutations, affecting prophylaxis, treatment, and genetic counseling. Results Here, we evaluated the performance of a panel for BRCA1 and BRCA2, using the Ion Torrent PGM (Life Technologies) platform in a customized workflow and multiplex ligation-dependent probe amplification for detection of mutations, insertions, and deletions in these genes. We validated the panel with 26 samples previously analyzed by Myriad Genetics Laboratory, and our workflow showed 95.6% sensitivity and 100% agreement with Myriad reports, with 85% sensitivity on the positive control sample from NIST. We also screened 68 clinical samples and found 22 distinct mutations. Conclusions The selection of a robust methodology for sample preparation and sequencing, together with bioinformatics tools optimized for the data analysis, enabled the development of a very sensitive test with high reproducibility. 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Development and validation of a variant detection workflow for BRCA1 and BRCA2 genes and its clinical application based on the Ion Torrent technology

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