1
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Kechin A, Boyarskikh U, Borobova V, Khrapov E, Subbotin S, Filipenko M. BRACNAC: A BRCA1 and BRCA2 Copy Number Alteration Caller from Next-Generation Sequencing Data. Int J Mol Sci 2023; 24:16630. [PMID: 38068953 PMCID: PMC10706169 DOI: 10.3390/ijms242316630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/17/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
Detecting copy number variations (CNVs) and alterations (CNAs) in the BRCA1 and BRCA2 genes is essential for testing patients for targeted therapy applicability. However, the available bioinformatics tools were initially designed for identifying CNVs/CNAs in whole-genome or -exome (WES) NGS data or targeted NGS data without adaptation to the BRCA1/2 genes. Most of these tools were tested on sample cohorts of limited size, with their use restricted to specific library preparation kits or sequencing platforms. We developed BRACNAC, a new tool for detecting CNVs and CNAs in the BRCA1 and BRCA2 genes in NGS data of different origin. The underlying mechanism of this tool involves various coverage normalization steps complemented by CNV probability evaluation. We estimated the sensitivity and specificity of our tool to be 100% and 94%, respectively, with an area under the curve (AUC) of 94%. The estimation was performed using the NGS data obtained from 213 ovarian and prostate cancer samples tested with in-house and commercially available library preparation kits and additionally using multiplex ligation-dependent probe amplification (MLPA) (12 CNV-positive samples). Using freely available WES and targeted NGS data from other research groups, we demonstrated that BRACNAC could also be used for these two types of data, with an AUC of up to 99.9%. In addition, we determined the limitations of the tool in terms of the minimum number of samples per NGS run (≥20 samples) and the minimum expected percentage of CNV-negative samples (≥80%). We expect that our findings will improve the efficacy of BRCA1/2 diagnostics. BRACNAC is freely available at the GitHub server.
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Affiliation(s)
- Andrey Kechin
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
- Faculty of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Ulyana Boyarskikh
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
| | - Viktoriya Borobova
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
- Faculty of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Evgeniy Khrapov
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
| | - Sergey Subbotin
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
| | - Maxim Filipenko
- Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia
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2
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Sun Z, Bai C, Su M, Tang H, Wu X, Wang Y, Bao H, Liu X, Wu X, Shao Y, Xu B. Comprehensive profiling of pathogenic germline large genomic rearrangements in a pan-cancer analysis. Mol Oncol 2023; 17:1917-1929. [PMID: 37013911 PMCID: PMC10483597 DOI: 10.1002/1878-0261.13430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 03/07/2023] [Accepted: 04/03/2023] [Indexed: 04/05/2023] Open
Abstract
The presence of large genomic rearrangements (LGRs) has been heavily investigated in breast and ovarian cancer. However, correlations between LGRs and cancer types beyond these two have not been extensively profiled, likely due to the highly inefficient methods of detecting these types of alterations. This study utilized next-generation sequencing (NGS) to analyze and classify the germline LGR profile in 17 025 cancer patients across 22 cancer types. We characterized newly identified LGRs based on predicted pathogenicity and took a closer look at genes that acquire both germline and somatic mutations within our samples. The detection method for LGRs was validated using droplet digital polymerase chain reaction (ddPCR) assay of commonly investigated LGR genes. In total, 15 659 samples from across 22 cancer types were retained for analysis after filtering. We observed that, in our cohort, the cancer types with the highest proportion of germline LGRs were ovarian cancer (4.7%), renal cell carcinoma (2.5%), breast cancer (2%), glioma (1.8%) and thyroid carcinoma (1.8%). Annotation of detected germline variants revealed several genes-MSH2, FANCA and PMS2-that contain novel LGRs. We observed co-occurrences between germline LGRs in MSH2 and somatic single nucleotide variants/insertion and deletions (SNVs/InDels) in BRCA2, KTM2B, KDM5A, CHD8, and HNF1A. Furthermore, our analysis showed that samples with pathogenic and likely pathogenic germline LGRs tended to also have higher mutational burden, chromosomal instability, and microsatellite instability ratio compared to samples with pathogenic germline SNVs/InDels. In this study, we demonstrated the prevalence of pathogenic germline LGRs beyond breast and ovarian cancer. The profiles of these pathogenic or likely pathogenic alterations will fuel further investigations and highlight new understanding of LGRs across multiple cancer types.
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Affiliation(s)
- Zhe Sun
- The First Clinical Medical CollegeGuangzhou University of Chinese MedicineGuangdongChina
| | - Chujie Bai
- Department of Bone and Soft Tissue Tumor, Key Laboratory of Carcinogenesis and Translational ResearchPeking University Cancer Hospital and InstituteBeijingChina
| | - Miaoyi Su
- Department of Radiation OncologyGuangqian HospitalQuanzhouChina
| | - Haimeng Tang
- Geneseeq Research InstituteNanjing Geneseeq Technology Inc.China
| | - Xiaoying Wu
- Geneseeq Research InstituteNanjing Geneseeq Technology Inc.China
| | - Yue Wang
- Geneseeq Research InstituteNanjing Geneseeq Technology Inc.China
| | - Hua Bao
- Geneseeq Research InstituteNanjing Geneseeq Technology Inc.China
| | - Xunbiao Liu
- Geneseeq Research InstituteNanjing Geneseeq Technology Inc.China
| | - Xue Wu
- Geneseeq Research InstituteNanjing Geneseeq Technology Inc.China
| | - Yang Shao
- Geneseeq Research InstituteNanjing Geneseeq Technology Inc.China
- School of Public HealthNanjing Medical UniversityChina
| | - Bei Xu
- Department of Medical OncologyZhongshan HospitalShanghaiChina
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3
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Tang Z, Zhao W, Sun Y, Deng Y, Bao J, Qiu C, Xiao X, Xu Y, Xie Z, Cai J, Chen X, Lin M, Xu G, Chen Z, Yu L. Spectrophotometric Detection of the BRCA1 Gene via Exponential Isothermal Amplification and Hybridization Chain Reaction of Surface-Bound Probes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:12050-12057. [PMID: 36153844 DOI: 10.1021/acs.langmuir.2c01903] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
In this work, we demonstrated an ultrasensitive approach with a dual-amplification strategy for DNA assay based on isothermal exponential amplification (EXPAR) and the hybridization chain reaction (HCR). In the presence of target DNA, the hairpin probe DNA (HP1) recognized and partially hybridized with the target DNA to form double-stranded structures containing the full recognition sequences for nicking endonuclease and then initiated EXPAR. Under the reaction of EXPAR, a large number of single-stranded DNA (ssDNA) was produced in the circle of nicking, polymerization, and strand displacement. The resulting ssDNA can bind to the surface-bound probe on the well of the microplate and trigger the hybridization chain reaction, resulting in the production of numerous double-stranded DNA concatamers with biotin labeling. In the presence of streptavidin-conjugated horseradish peroxidase (HRP), the amplified signal can be detected by a spectrophotometer via HRP-catalyzed substrate 3,3'5,5'-tetramethylbenzidine (TMB). This proposed dual-amplification method provides a detection limit of 74.48 aM, which also exhibits good linearity ranging from 0.1 fM to 100 pM.
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Affiliation(s)
- Zibin Tang
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523808, China
- School of Medical Technology, Guangdong Medical University, Dongguan 523808, China
| | - Wenyong Zhao
- Faculty of Forensic Medicine, School of Basic Medicine, Guangdong Medical University, Dongguan 523808, China
| | - Yuanzhong Sun
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523808, China
- School of Medical Technology, Guangdong Medical University, Dongguan 523808, China
| | - Yuling Deng
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523808, China
- School of Medical Technology, Guangdong Medical University, Dongguan 523808, China
| | - Juan Bao
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523808, China
- School of Medical Technology, Guangdong Medical University, Dongguan 523808, China
| | - Cailing Qiu
- Department of Medical Laboratory, Dalang Hospital of Dongguan, Dongguan 523770, China
| | - Xiang Xiao
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523808, China
| | - Yao Xu
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523808, China
| | - Zhaoyang Xie
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523808, China
- School of Medical Technology, Guangdong Medical University, Dongguan 523808, China
| | - Jingyi Cai
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523808, China
- School of Medical Technology, Guangdong Medical University, Dongguan 523808, China
| | - Xiaofang Chen
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523808, China
- School of Medical Technology, Guangdong Medical University, Dongguan 523808, China
| | - Manhua Lin
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523808, China
- School of Medical Technology, Guangdong Medical University, Dongguan 523808, China
| | - Guangxian Xu
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523808, China
- School of Medical Technology, Guangdong Medical University, Dongguan 523808, China
| | - Zhangquan Chen
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523808, China
- School of Medical Technology, Guangdong Medical University, Dongguan 523808, China
| | - Luxin Yu
- Guangdong Provincial Key Laboratory of Medical Molecular Diagnostics, The First Dongguan Affiliated Hospital, Guangdong Medical University, Dongguan 523808, China
- School of Medical Technology, Guangdong Medical University, Dongguan 523808, China
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4
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Wang H, Li Y, Chi Y, Wang C, Ma Q, Yang X. A novel Cu:Al nanocluster-based electrochemiluminescence system with CeO2 NPs/polydopamine biomimetic film for BRCA detection. Microchem J 2022. [DOI: 10.1016/j.microc.2022.107687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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5
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Emerging digital PCR technology in precision medicine. Biosens Bioelectron 2022; 211:114344. [DOI: 10.1016/j.bios.2022.114344] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 04/23/2022] [Accepted: 05/03/2022] [Indexed: 12/20/2022]
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6
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De Paolis E, Perrucci A, Marchetti C, Pietragalla A, Scambia G, Urbani A, Fagotti A, Minucci A. BRCA testing on buccal swab to improve access to healthcare and cancer prevention: a performance evaluation. Int J Gynecol Cancer 2022; 32:ijgc-2022-003718. [PMID: 36028233 DOI: 10.1136/ijgc-2022-003718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
OBJECTIVE BRCA1/2 (BRCA) genetic testing allows patients with high-grade serous ovarian cancer to receive appropriate medical management with molecular target therapy and prevention strategies. Most of the BRCA sequencing methods use blood as the primary source of germline DNA. Buccal swab emerged as an alternative collection device due to its convenient and non-invasive characteristics. This study assessed the suitability of buccal swabs as the DNA source in next-generation sequencing-based BRCA genotyping. METHODS Matched buccal swabs and blood samples were collected from 51 patients with high-grade serous ovarian cancer, including 29 BRCA-mutated patients, from June to December 2021. Buccal swabs were self-collected using COPAN FLOQSwabs hDNA Free. BRCA genes were amplified using Devyser's BRCA next-generation sequencing kit and sequenced on the Illumina MiSeq platform. We evaluated collection and extraction procedures, amplification and sequencing performances, coverage data, blood/swab variant calling concordance, and interpretation. RESULTS Comparable sequencing parameters were observed between the two sample types in term of mean total number of reads passing filter for indexed sample (p>0.05) and sequencing coverage distribution, with a widespread overlap of mean depth of coverage/target region between blood and swab samples. An overall concordance of 100% in both polymorphisms and pathogenic variants calling between the two DNA sources were observed, including the copy number variation prediction. CONCLUSIONS Data from this study support the use of buccal swabs as an alternative source of DNA for BRCA evaluation. The use of this alternative delivery mode of BRCA testing may facilitate access to care without compromising patient outcomes.
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Affiliation(s)
- Elisa De Paolis
- Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
- Departmental Unit of Molecular and Genomic Diagnostics, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Alessia Perrucci
- Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
- Departmental Unit of Molecular and Genomic Diagnostics, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
| | - Claudia Marchetti
- Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
- Università Cattolica del Sacro Cuore, Rome, Italy
| | | | - Giovanni Scambia
- Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
- Università Cattolica del Sacro Cuore, Rome, Italy
| | - Andrea Urbani
- Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
- Università Cattolica del Sacro Cuore, Rome, Italy
| | - Anna Fagotti
- Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
- Università Cattolica del Sacro Cuore, Rome, Italy
| | - Angelo Minucci
- Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
- Departmental Unit of Molecular and Genomic Diagnostics, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Rome, Italy
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7
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Dobre EG, Constantin C, Neagu M. Skin Cancer Research Goes Digital: Looking for Biomarkers within the Droplets. J Pers Med 2022; 12:jpm12071136. [PMID: 35887633 PMCID: PMC9323323 DOI: 10.3390/jpm12071136] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/12/2022] [Accepted: 07/12/2022] [Indexed: 12/24/2022] Open
Abstract
Skin cancer, which includes the most frequent malignant non-melanoma carcinomas (basal cell carcinoma, BCC, and squamous cell carcinoma, SCC), along with the difficult to treat cutaneous melanoma (CM), pose important worldwide issues for the health care system. Despite the improved anti-cancer armamentarium and the latest scientific achievements, many skin cancer patients fail to respond to therapies, due to the remarkable heterogeneity of cutaneous tumors, calling for even more sophisticated biomarker discovery and patient monitoring approaches. Droplet digital polymerase chain reaction (ddPCR), a robust method for detecting and quantifying low-abundance nucleic acids, has recently emerged as a powerful technology for skin cancer analysis in tissue and liquid biopsies (LBs). The ddPCR method, being capable of analyzing various biological samples, has proved to be efficient in studying variations in gene sequences, including copy number variations (CNVs) and point mutations, DNA methylation, circulatory miRNome, and transcriptome dynamics. Moreover, ddPCR can be designed as a dynamic platform for individualized cancer detection and monitoring therapy efficacy. Here, we present the latest scientific studies applying ddPCR in dermato-oncology, highlighting the potential of this technology for skin cancer biomarker discovery and validation in the context of personalized medicine. The benefits and challenges associated with ddPCR implementation in the clinical setting, mainly when analyzing LBs, are also discussed.
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Affiliation(s)
- Elena-Georgiana Dobre
- Faculty of Biology, University of Bucharest, Splaiul Independentei 91–95, 050095 Bucharest, Romania;
- Correspondence:
| | - Carolina Constantin
- Immunology Department, “Victor Babes” National Institute of Pathology, 050096 Bucharest, Romania;
- Pathology Department, Colentina Clinical Hospital, 020125 Bucharest, Romania
| | - Monica Neagu
- Faculty of Biology, University of Bucharest, Splaiul Independentei 91–95, 050095 Bucharest, Romania;
- Immunology Department, “Victor Babes” National Institute of Pathology, 050096 Bucharest, Romania;
- Pathology Department, Colentina Clinical Hospital, 020125 Bucharest, Romania
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8
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Sagath L, Lehtokari VL, Wallgren-Pettersson C, Pelin K, Kiiski K. A custom ddPCR method for the detection of copy number variations in the nebulin triplicate region. PLoS One 2022; 17:e0267793. [PMID: 35576196 PMCID: PMC9109913 DOI: 10.1371/journal.pone.0267793] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 04/15/2022] [Indexed: 11/21/2022] Open
Abstract
The human genome contains repetitive regions, such as segmental duplications, known to be prone to copy number variation. Segmental duplications are highly identical and homologous sequences, posing a specific challenge for most mutation detection methods. The giant nebulin gene is expressed in skeletal muscle. It harbors a large segmental duplication region composed of eight exons repeated three times, the so-called triplicate region. Mutations in nebulin are known to cause nemaline myopathy and other congenital myopathies. Using our custom targeted Comparative Genomic Hybridization arrays, we have previously shown that copy number variations in the nebulin triplicate region are pathogenic when the copy number of the segmental duplication block deviates two or more copies from the normal number, which is three per allele. To complement our Comparative Genomic Hybridization arrays, we have established a custom Droplet Digital PCR method for the detection of copy number variations within the nebulin triplicate region. The custom Droplet Digital PCR assays allow sensitive, rapid, high-throughput, and cost-effective detection of copy number variations within this region and is ready for implementation a screening method for disease-causing copy number variations of the nebulin triplicate region. We suggest that Droplet Digital PCR may also be used in the study and diagnostics of other segmental duplication regions of the genome.
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Affiliation(s)
- Lydia Sagath
- Folkhälsan Research Center, Helsinki, Finland
- Department of Medical Genetics, Medicum, University of Helsinki, Helsinki, Finland
- * E-mail: , (LS); (KK)
| | - Vilma-Lotta Lehtokari
- Folkhälsan Research Center, Helsinki, Finland
- Department of Medical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Carina Wallgren-Pettersson
- Folkhälsan Research Center, Helsinki, Finland
- Department of Medical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Katarina Pelin
- Folkhälsan Research Center, Helsinki, Finland
- Department of Medical Genetics, Medicum, University of Helsinki, Helsinki, Finland
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Kirsi Kiiski
- Folkhälsan Research Center, Helsinki, Finland
- Department of Medical Genetics, Medicum, University of Helsinki, Helsinki, Finland
- * E-mail: , (LS); (KK)
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9
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Pirozzi F, Berkseth M, Shear R, Gonzalez L, Timms AE, Sulc J, Pao E, Oyama N, Forzano F, Conti V, Guerrini R, Doherty ES, Saitta SC, Lockwood CM, Pritchard CC, Dobyns WB, Novotny E, Wright JNN, Saneto RP, Friedman S, Hauptman J, Ojemann J, Kapur RP, Mirzaa GM. Profiling PI3K-AKT-MTOR variants in focal brain malformations reveals new insights for diagnostic care. Brain 2022; 145:925-938. [PMID: 35355055 PMCID: PMC9630661 DOI: 10.1093/brain/awab376] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 09/04/2021] [Accepted: 09/09/2021] [Indexed: 12/28/2022] Open
Abstract
Focal malformations of cortical development including focal cortical dysplasia, hemimegalencephaly and megalencephaly, are a spectrum of neurodevelopmental disorders associated with brain overgrowth, cellular and architectural dysplasia, intractable epilepsy, autism and intellectual disability. Importantly, focal cortical dysplasia is the most common cause of focal intractable paediatric epilepsy. Gain and loss of function variants in the PI3K-AKT-MTOR pathway have been identified in this spectrum, with variable levels of mosaicism and tissue distribution. In this study, we performed deep molecular profiling of common PI3K-AKT-MTOR pathway variants in surgically resected tissues using droplet digital polymerase chain reaction (ddPCR), combined with analysis of key phenotype data. A total of 159 samples, including 124 brain tissue samples, were collected from 58 children with focal malformations of cortical development. We designed an ultra-sensitive and highly targeted molecular diagnostic panel using ddPCR for six mutational hotspots in three PI3K-AKT-MTOR pathway genes, namely PIK3CA (p.E542K, p.E545K, p.H1047R), AKT3 (p.E17K) and MTOR (p.S2215F, p.S2215Y). We quantified the level of mosaicism across all samples and correlated genotypes with key clinical, neuroimaging and histopathological data. Pathogenic variants were identified in 17 individuals, with an overall molecular solve rate of 29.31%. Variant allele fractions ranged from 0.14 to 22.67% across all mutation-positive samples. Our data show that pathogenic MTOR variants are mostly associated with focal cortical dysplasia, whereas pathogenic PIK3CA variants are more frequent in hemimegalencephaly. Further, the presence of one of these hotspot mutations correlated with earlier onset of epilepsy. However, levels of mosaicism did not correlate with the severity of the cortical malformation by neuroimaging or histopathology. Importantly, we could not identify these mutational hotspots in other types of surgically resected epileptic lesions (e.g. polymicrogyria or mesial temporal sclerosis) suggesting that PI3K-AKT-MTOR mutations are specifically causal in the focal cortical dysplasia-hemimegalencephaly spectrum. Finally, our data suggest that ultra-sensitive molecular profiling of the most common PI3K-AKT-MTOR mutations by targeted sequencing droplet digital polymerase chain reaction is an effective molecular approach for these disorders with a good diagnostic yield when paired with neuroimaging and histopathology.
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Affiliation(s)
- Filomena Pirozzi
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Matthew Berkseth
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Rylee Shear
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | | | - Andrew E Timms
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Josef Sulc
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Emily Pao
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Nora Oyama
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Francesca Forzano
- Department of Clinical Genetics, Guy's and St Thomas NHS Foundation Trust and King's College London, London, UK
| | - Valerio Conti
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Children's Hospital A. Meyer-University of Florence, Italy
| | - Renzo Guerrini
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Children's Hospital A. Meyer-University of Florence, Italy
| | - Emily S Doherty
- Section of Clinical Genetics, Carilion Clinic Children's Hospital, Roanoke, VA, USA
| | - Sulagna C Saitta
- Division of Medical Genetics, Department of Obstetrics and Gynecology, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, CA, USA
| | - Christina M Lockwood
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.,Brotman-Baty Institute for Precision Medicine, University of Minnesota, Seattle, WA, USA
| | - Colin C Pritchard
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.,Brotman-Baty Institute for Precision Medicine, University of Minnesota, Seattle, WA, USA
| | - William B Dobyns
- Division of Genetics and Metabolism, Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
| | - Edward Novotny
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA.,Division of Pediatric Neurology, Department of Neurology, Seattle Children's Hospital, Seattle, WA, USA.,Department of Neurology, University of Washington, Seattle, WA, USA
| | - Jason N N Wright
- Department of Radiology, Seattle Children's Hospital, Seattle, WA, USA
| | - Russell P Saneto
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA.,Division of Pediatric Neurology, Department of Neurology, Seattle Children's Hospital, Seattle, WA, USA
| | - Seth Friedman
- Center for Clinical and Translational Research, Seattle Children's Hospital, Seattle, WA, USA
| | - Jason Hauptman
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - Jeffrey Ojemann
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - Raj P Kapur
- Department of Laboratories, Seattle Children's Hospital, Seattle, WA, USA
| | - Ghayda M Mirzaa
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA.,Brotman-Baty Institute for Precision Medicine, University of Minnesota, Seattle, WA, USA.,Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA.,Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
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10
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Role of Homologous Recombination Repair (HRR) Genes in Uterine Leiomyosarcomas: A Retrospective Analysis. Cancers (Basel) 2022; 14:cancers14081934. [PMID: 35454841 PMCID: PMC9024785 DOI: 10.3390/cancers14081934] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 04/06/2022] [Accepted: 04/10/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary A more in-depth molecular characterization of uterine leiomyosarcomas (uLMS), a rare disease characterized with dismal prognosis, could provide data suitable for the identification of potential target-based drugs. We aimed to define frequencies of gene alterations in uLMS, especially regarding the somatic mutations of BRCA and HRR gene alterations, and identify the impact of these molecular alterations on clinical outcomes. This retrospective analysis of the mutational profile of uLMS showed that the most frequent alterations involved the TP53 gene, and that patients with TP53 alterations experienced a worse prognosis compared to patients with wild-type TP53 genes. Conversely, patient clinical outcomes were similar within patients with BRCA- and HRR-related genes versus non-HRR-related genes. However, although the frequency of patients with BRCA- and HRR-related alterations and mutations was relatively small, this setting could deserve an investigation into drug actionability, and potentially benefit from PARP inhibitors. Abstract Uterine leiomyosarcomas (uLMS) is a very rare disease, and patients experience a dismal prognosis even when treated with chemotherapy. Therefore, a more in-depth molecular characterization of this disease could provide suitable data for the identification of potential target-based drugs. This retrospective, single institutional study aimed to define the frequencies of gene alterations in uLMS, especially regarding the somatic mutations of BRCA and Homologous Recombination Repair (HRR) genes, and the impact of molecular alterations on clinical outcomes. The 16-genes Next-Generation Sequencing (NGS) panel, Homologous Recombination Solution TM (HRS, Sophia Genetics, Saint Sulpice, Switzerland), was used for the molecular evaluation of samples. The majority of patients (66/105, 63%) carried at least one sequence alteration, with a prevalence of TP53 involvement followed by RAD51B, BRCA1/2, and FANCL. Patients with TP53 gene alterations experienced a significantly worse prognosis for progression free survival (PFS) and overall survival (OS) versus wild-type patients. Given the number of patients with the BRCA1/2 mutation (N = 12), we included them in the HRR patient group; there was no difference in clinical outcomes with HRR versus non-HRR. The Cox’s multivariate analysis showed that stage and TP53 gene alterations resulted in a significantly worse OS. The integration of gene networking data, such as tumor mutation burdens and cancer driver gene identification, could show a clearer discrimination of gene distribution patterns, and lead to the implementation of therapeutic targets.
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Lavoro A, Scalisi A, Candido S, Zanghì GN, Rizzo R, Gattuso G, Caruso G, Libra M, Falzone L. Identification of the most common BRCA alterations through analysis of germline mutation databases: Is droplet digital PCR an additional strategy for the assessment of such alterations in breast and ovarian cancer families? Int J Oncol 2022; 60:58. [PMID: 35383859 PMCID: PMC8997337 DOI: 10.3892/ijo.2022.5349] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/24/2022] [Indexed: 11/06/2022] Open
Abstract
Breast and ovarian cancer represent two of the most common tumor types in females worldwide. Over the years, several non‑modifiable and modifiable risk factors have been associated with the onset and progression of these tumors, including age, reproductive factors, ethnicity, socioeconomic status and lifestyle factors, as well as family history and genetic factors. Of note, BRCA1 and BRCA2 are two tumor suppressor genes with a key role in DNA repair processes, whose mutations may induce genomic instability and increase the risk of cancer development. Specifically, females with a family history of breast or ovarian cancer harboring BRCA1/2 germline mutations have a 60‑70% increased risk of developing breast cancer and a 15‑40% increased risk for ovarian cancer. Different databases have collected the most frequent germline mutations affecting BRCA1/2. Through the analysis of such databases, it is possible to identify frequent hotspot mutations that may be analyzed with next‑generation sequencing (NGS) and novel innovative strategies. In this context, NGS remains the gold standard method for the assessment of BRCA1/2 mutations, while novel techniques, including droplet digital PCR (ddPCR), may improve the sensitivity to identify such mutations in the hereditary forms of breast and ovarian cancer. On these bases, the present study aimed to provide an update of the current knowledge on the frequency of BRCA1/2 mutations and cancer susceptibility, focusing on the diagnostic potential of the most recent methods, such as ddPCR.
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Affiliation(s)
- Alessandro Lavoro
- Department of Biomedical and Biotechnological Sciences, University of Catania, I‑95123 Catania, Italy
| | - Aurora Scalisi
- Italian League Against Cancer, Section of Catania, I‑95122 Catania, Italy
| | - Saverio Candido
- Department of Biomedical and Biotechnological Sciences, University of Catania, I‑95123 Catania, Italy
| | - Guido Nicola Zanghì
- Department of General Surgery and Medical‑Surgical Specialties, Policlinico‑Vittorio Emanuele Hospital, University of Catania, I‑95123 Catania, Italy
| | - Roberta Rizzo
- Department of Biomedical and Biotechnological Sciences, University of Catania, I‑95123 Catania, Italy
| | - Giuseppe Gattuso
- Department of Biomedical and Biotechnological Sciences, University of Catania, I‑95123 Catania, Italy
| | - Giuseppe Caruso
- Department of Biomedical and Biotechnological Sciences, University of Catania, I‑95123 Catania, Italy
| | - Massimo Libra
- Department of Biomedical and Biotechnological Sciences, University of Catania, I‑95123 Catania, Italy
| | - Luca Falzone
- Epidemiology and Biostatistics Unit, National Cancer Institute IRCCS Fondazione 'G. Pascale', I‑80131 Naples, Italy
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De Paolis E, Marchetti C, Concolino P, Scambia G, Urbani A, Fagotti A, Minucci A. A commentary on the discrepancy between blood and tumour BRCA testing: An open question. BJOG 2022; 129:1422-1426. [PMID: 35319826 PMCID: PMC9543799 DOI: 10.1111/1471-0528.17158] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 03/08/2022] [Accepted: 03/20/2022] [Indexed: 11/26/2022]
Affiliation(s)
- Elisa De Paolis
- Departmental Unit of Molecular and Genomic Diagnostics, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Claudia Marchetti
- Division of Oncological Gynaecology, Department of Women's and Children's Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy.,Catholic University of the Sacred Heart, Rome, Italy
| | - Paola Concolino
- Departmental Unit of Molecular and Genomic Diagnostics, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Giovanni Scambia
- Division of Oncological Gynaecology, Department of Women's and Children's Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy.,Catholic University of the Sacred Heart, Rome, Italy
| | - Andrea Urbani
- Departmental Unit of Molecular and Genomic Diagnostics, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy.,Catholic University of the Sacred Heart, Rome, Italy
| | - Anna Fagotti
- Division of Oncological Gynaecology, Department of Women's and Children's Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy.,Catholic University of the Sacred Heart, Rome, Italy
| | - Angelo Minucci
- Departmental Unit of Molecular and Genomic Diagnostics, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
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Cheng YH, Wang CH, Hsu KF, Lee GB. Integrated Microfluidic System for Cell-Free DNA Extraction from Plasma for Mutant Gene Detection and Quantification. Anal Chem 2022; 94:4311-4318. [PMID: 35235296 DOI: 10.1021/acs.analchem.1c04988] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ovarian cancer (OvCa) is among the most severe gynecologic cancers, yet individuals may be asymptomatic during its early stages. Routine, early screening for genetic abnormalities associated with OvCa could improve prognoses, and this can be achieved by detecting mutant genes in cell-free DNA (cfDNA). Herein, we developed an integrated microfluidic chip (IMC) that could extract cfDNA from plasma and automatically detect and quantify mutations in the OvCa biomarker BRCA1. The cfDNA extraction module relied on a vortex-type micromixer to mix cfDNA with magnetic beads surface-coated with cfDNA probes and could isolate 76% of molecules from a 200 μL plasma sample in 45 min. The cfDNA quantification module, which comprised a micropump that evenly distributed 4.5 μL of purified cfDNA into the on-chip, allele-specific quantitative polymerase chain reaction (qPCR) zones, was capable of quantifying mutant genes within 90 min. By automating the cfDNA extraction and qPCR processes, this IMC could be used for clinical screening for OvCa-associated mutations.
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Affiliation(s)
- Yu-Hung Cheng
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Chih-Hung Wang
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Keng-Fu Hsu
- Department of Obstetrics and Gynecology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 70403, Taiwan
| | - Gwo-Bin Lee
- Department of Power Mechanical Engineering, National Tsing Hua University, Hsinchu 30013, Taiwan.,Institute of NanoEngineering and MicroSystems, National Tsing Hua University, Hsinchu 30013, Taiwan
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14
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De Paolis E, Concolino P, Onori ME, Santonocito C, Marchetti C, Fagotti A, Scambia G, Urbani A, Minucci A. Tumor BRCA testing in ovarian cancer and EQA scheme: our experience of a critical evaluation. Mol Biol Rep 2021; 48:8203-8209. [PMID: 34643925 PMCID: PMC8604882 DOI: 10.1007/s11033-021-06812-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 10/05/2021] [Indexed: 11/16/2022]
Abstract
Next generation sequencing (NGS) is a widespread molecular biology method integrated into clinical practice to detect genetic variants, for diagnostic and prognostic purposes. The scheduled external quality assessments (EQA) is integral part of clinical molecular laboratory quality assurance. The EQA provides an efficient system to compare analytic test performances among different laboratories, which is essential to evaluate consistency of molecular test. EQA failures demands targeted corrective action plans. In this context, the complexity of the NGS techniques requires careful and continuous quality control procedures. We report a tumor BRCA1/2 (tBRCA) testing benchmark discrepancy provided by the European Molecular Genetics Quality Network in our laboratory during a round of EQA for somatic mutation testing of BRCA genes in relation to ovarian cancer. The critical analysis emerging from the tBRCA EQA is presented. We underline that harmonization processes are still required for the EQA in the molecular biology field, especially if applied to the evaluation of methods characterized by high complexity.
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Affiliation(s)
- Elisa De Paolis
- Molecular and Genomic Diagnostics Unit (MGDUnit), Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Paola Concolino
- Molecular and Genomic Diagnostics Unit (MGDUnit), Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Maria Elisabetta Onori
- Molecular and Genomic Diagnostics Unit (MGDUnit), Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Concetta Santonocito
- Molecular and Genomic Diagnostics Unit (MGDUnit), Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Claudia Marchetti
- Division of Oncological Gynecology, Department of Women's and Children's Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
- Università Cattolica del Sacro Cuore, Rome, Italy
| | - Anna Fagotti
- Division of Oncological Gynecology, Department of Women's and Children's Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
- Università Cattolica del Sacro Cuore, Rome, Italy
| | - Giovanni Scambia
- Division of Oncological Gynecology, Department of Women's and Children's Health, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
- Università Cattolica del Sacro Cuore, Rome, Italy
| | - Andrea Urbani
- Molecular and Genomic Diagnostics Unit (MGDUnit), Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
- Università Cattolica del Sacro Cuore, Rome, Italy
| | - Angelo Minucci
- Molecular and Genomic Diagnostics Unit (MGDUnit), Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy.
- Molecular and Genomic Diagnostics Unit (MGDUnit), Fondazione Policlinico Universitario Agostino Gemelli IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy.
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Yang C, Zhang Z, Tang X, Zhang X, Chen Y, Hu T, Zhang H, Guan M, Zhang X, Wu Z. Pan-cancer analysis reveals homologous recombination deficiency score as a predictive marker for immunotherapy responders. Hum Cell 2021; 35:199-213. [PMID: 34628623 DOI: 10.1007/s13577-021-00630-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 10/02/2021] [Indexed: 02/07/2023]
Abstract
The immune context of the tumor microenvironment (TME) is critical for effective immunotherapy. Nonetheless, DNA-based biomarkers for the immune-sensitive TME and the identification of immune checkpoint inhibitor (ICI) responders are under-explored. This study aims to comprehensively landscape the homologous recombination deficiency (HRD) score, an emerging hallmark for tumor genome instability that triggers immune responsiveness across major cancer types, and to unveil their link to the TME and immunotherapeutic response. The HRD-associated genomic scars were characterized in 9088 tumor samples across 32 cancer types from TCGA. We evaluated the HRD score's performance in classifying ICI responders using an independent breast cancer cohort (GSE87049) and 11 in vivo murine mammary tumor models treated with anti-PD1/CTLA4 regimen (GSE124821). This study revealed a broad association between HRD-high genotype and neoantigenesis in the major cancer types including bladder cancer, breast cancer, head and neck squamous carcinoma, lung adenocarcinoma, lung squamous cell carcinoma, ovarian cancer, and sarcoma. Tumors with high HRD score bears increased leukocyte infiltration and lymphocyte fraction and demonstrated immune-sensitive microenvironment. The tumor immune dysfunction and exclusion (TIDE) model further confirmed HRD score-high genotype as a potential predictor for ICI immunotherapy responders in breast cancer. In conclusion, tumors with high HRD score exhibit an immune-sensitive TME. The HRD-high genotype is a promising marker for identifying ICI therapy responders among breast cancer patients.
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Affiliation(s)
- Can Yang
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Zijing Zhang
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Xuemei Tang
- Central Laboratory, Huashan Hospital North, Fudan University, Shanghai, 201907, China
| | - Xinju Zhang
- Central Laboratory, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Yuming Chen
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Tingting Hu
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Huating Zhang
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Ming Guan
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China.
- Central Laboratory, Huashan Hospital North, Fudan University, Shanghai, 201907, China.
- Central Laboratory, Huashan Hospital, Fudan University, Shanghai, 200040, China.
- Clinical Laboratory, Huashan Hospital North, Fudan University, Shanghai, 201907, China.
| | - Xiuming Zhang
- Medical Laboratory, Shenzhen Luohu People's Hospital, Shenzhen, 518002, China.
| | - Zhiyuan Wu
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China.
- Central Laboratory, Huashan Hospital North, Fudan University, Shanghai, 201907, China.
- Clinical Laboratory, Huashan Hospital North, Fudan University, Shanghai, 201907, China.
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Borkowska EM, Barańska M, Kowalczyk M, Pietruszewska W. Detection of PIK3CA Gene Mutation in Head and Neck Squamous Cell Carcinoma Using Droplet Digital PCR and RT-qPCR. Biomolecules 2021; 11:818. [PMID: 34072735 PMCID: PMC8227819 DOI: 10.3390/biom11060818] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/18/2021] [Accepted: 05/25/2021] [Indexed: 12/11/2022] Open
Abstract
Head and neck squamous cell carcinomas (HNSCC) are the seventh cause of human malignancy with low survival rate due to late diagnosis and treatment. Its etiology is diverse; however genetic factors are significant. The most common mutations in HNSCC were found in the genes: PIK3CA (10-12%), BRCA1 (6%), and BRCA2 (7-9%). In some cases, these biomarkers correlate with recurrences or survival showing a potential of prognostic and predictive value. A total of 113 formalin-fixed paraffin embedded (FFPE) tumor samples were collected from patients with HNSCC (oral cavity: 35 (31.0%); oropharynx: 30 (26.0%); larynx: 48 (43.0%)). We examined PIK3CA H1047R mutation by Real Time PCR (RT-qPCR) and droplet digital PCR (ddPCR). BRCA1 and BRCA2 mutations were analyzed by RT-qPCR while p16 protein expression was assessed by immunohistochemistry. Finally, we identified HPV infection by RT-qPCR. The relationships between genomic alterations and clinical parameters were assessed using the Yates' corrected Chi-squared test or Fisher's exact test for nominal variables. Kaplan Meier plots were applied for survival analysis. Our results revealed 9 PIK3CA H1047R mutations detected by ddPCR: 8 of them were negative in RT-qPCR. Due to the use of different methods to test the presence of the PIK3CA gene mutation, different treatment decisions might be made. That is why it is so important to use the most sensitive methods available. We confirmed the usefulness of ddPCR in the PIK3CA mutation assessment in FFPE samples.
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Affiliation(s)
- Edyta M. Borkowska
- Department of Clinical Genetics Chair of Laboratory and Clinical Genetics, Medical University of Lodz, 92-213 Lodz, Poland;
| | - Magda Barańska
- Department of Otolaryngology, Head and Neck Oncology, Medical University of Lodz, 93-143 Lodz, Poland; (M.B.); (M.K.)
| | - Magdalena Kowalczyk
- Department of Otolaryngology, Head and Neck Oncology, Medical University of Lodz, 93-143 Lodz, Poland; (M.B.); (M.K.)
| | - Wioletta Pietruszewska
- Department of Otolaryngology, Head and Neck Oncology, Medical University of Lodz, 93-143 Lodz, Poland; (M.B.); (M.K.)
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