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Sierra-Díaz DC, Morel A, Fonseca-Mendoza DJ, Bravo NC, Molano-Gonzalez N, Borras M, Munevar I, Lema M, Idrobo H, Trujillo D, Serrano N, Orduz AI, Lopera D, González J, Rojas G, Londono-De Los Ríos P, Manneh R, Cabrera R, Rubiano W, de la Peña J, Quintero MC, Mantilla W, Restrepo CM. Germline mutations of breast cancer susceptibility genes through expanded genetic analysis in unselected Colombian patients. Hum Genomics 2024; 18:68. [PMID: 38890714 PMCID: PMC11184794 DOI: 10.1186/s40246-024-00623-7] [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: 02/05/2024] [Accepted: 05/15/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND In Colombia and worldwide, breast cancer (BC) is the most frequently diagnosed neoplasia and the leading cause of death from cancer among women. Studies predominantly involve hereditary and familial cases, demonstrating a gap in the literature regarding the identification of germline mutations in unselected patients from Latin-America. Identification of pathogenic/likely pathogenic (P/LP) variants is important for shaping national genetic analysis policies, genetic counseling, and early detection strategies. The present study included 400 women with unselected breast cancer (BC), in whom we analyzed ten genes, using Whole Exome Sequencing (WES), know to confer risk for BC, with the aim of determining the genomic profile of previously unreported P/LP variants in the affected population. Additionally, Multiplex Ligation-dependent Probe Amplification (MLPA) was performed to identify Large Genomic Rearrangements (LGRs) in the BRCA1/2 genes. To ascertain the functional impact of a recurrent intronic variant (ATM c.5496 + 2_5496 + 5delTAAG), a minigene assay was conducted. RESULTS We ascertained the frequency of P/LP germline variants in BRCA2 (2.5%), ATM (1.25%), BRCA1 (0.75%), PALB2 (0.50%), CHEK2 (0.50%), BARD1 (0.25%), and RAD51D (0.25%) genes in the population of study. P/LP variants account for 6% of the total population analyzed. No LGRs were detected in our study. We identified 1.75% of recurrent variants in BRCA2 and ATM genes. One of them corresponds to the ATM c.5496 + 2_5496 + 5delTAAG. Functional validation of this variant demonstrated a splicing alteration probably modifying the Pincer domain and subsequent protein structure. CONCLUSION This study described for the first time the genomic profile of ten risk genes in Colombian women with unselected BC. Our findings underscore the significance of population-based research, advocating the consideration of molecular testing in all women with cancer.
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Affiliation(s)
- Diana Carolina Sierra-Díaz
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá, Colombia
| | - Adrien Morel
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá, Colombia
| | - Dora Janeth Fonseca-Mendoza
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá, Colombia
| | - Nora Contreras Bravo
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá, Colombia
| | - Nicolas Molano-Gonzalez
- Clinical Research Group, School of Medicine and Health Science, Universidad del Rosario, Bogotá, Colombia
| | - Mariana Borras
- Fundación Cardioinfantil, Instituto de Cardiología, Bogotá, Colombia
| | - Isabel Munevar
- Fundación Cardioinfantil, Instituto de Cardiología, Bogotá, Colombia
| | | | | | | | - Norma Serrano
- Hospital Internacional de Colombia HIC, Piedecuesta, Colombia
| | | | - Diego Lopera
- Oncólogos del Occidente S.A.S, Manizales, Colombia
| | | | - Gustavo Rojas
- Oncólogos del Occidente S.A.S, Manizales, Colombia
- Oncologos del Occidente SAS, Pereira, Colombia
| | | | - Ray Manneh
- SOHEC, Sociedad de Oncología y Hematología del Cesar, Valledupar, Colombia
| | - Rodrigo Cabrera
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá, Colombia
- Laboratorio de Biología Molecular y Pruebas Diagnósticas de Alta Complejidad, Fundación Cardioinfantil-Instituto de Cardiología, Bogotá, Colombia
| | | | | | | | - William Mantilla
- Fundación Cardioinfantil, Instituto de Cardiología, Bogotá, Colombia
- Fundación CTIC-Fundación Cardioinfantil, Instituto de Cardiología, Bogotá, Colombia
| | - Carlos M Restrepo
- School of Medicine and Health Sciences, Center for Research in Genetics and Genomics (CIGGUR), Institute of Translational Medicine (IMT), Universidad Del Rosario, Bogotá, Colombia.
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Summey RM, Gornstein E, Decker B, Dougherty KC, Rader JS, Hopp E. Landscape of potential germline pathogenic variants in select cancer susceptibility genes in patients with adult-type ovarian granulosa cell tumors. Cancer Med 2024; 13:e7340. [PMID: 38898688 PMCID: PMC11187164 DOI: 10.1002/cam4.7340] [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: 10/22/2023] [Revised: 05/14/2024] [Accepted: 05/18/2024] [Indexed: 06/21/2024] Open
Abstract
OBJECTIVE The objective of this study was to assess the frequency of potential germline pathogenic variants that may contribute to risk of development of adult granulosa cell tumors (AGCT) given the paucity of germline testing guidelines for these patients. METHODS This was a retrospective cross-sectional study analyzing comprehensive genomic profiling (CGP) results of AGCT with the FOXL2 p.C134W mutation submitted to Foundation Medicine between 2012 and 2022. Cases with a potential germline pathogenic variant were identified by filtering single nucleotide variants and short indels by variant allele frequency (VAF) and presence in ClinVar for select cancer susceptibility genes. Odds ratios for AGCT risk were calculated compared to a healthy population. RESULTS Prior to analysis, 595 patients were screened and 516 with a somatic FOXL2 p.C134W mutation were included. Potential germline pathogenic variants in a DNA repair-related gene (ATM, BRCA1, BRCA2, CHEK2, PALB2, PMS2, RAD51C, or RAD51D) were found in 6.6% of FOXL2-mutated AGCT. Potential germline pathogenic CHEK2 variants were found in 3.5% (18/516) of AGCT patients, a rate that was 2.8-fold higher than Genome Aggregation Database non-cancer subjects (95% CI 1.8-4.6, p < 0.001). The founder variants p.I157T (38.9%, 7/18) and p.T367fs*15 (c.1100delC; 27.8%, 5/18) were most commonly observed. CHEK2 VAF indicated frequent loss of the wildtype copy of the gene. CONCLUSIONS These results support ongoing utilization of genomic tumor profiling and confirmatory germline testing for potential germline pathogenic variants. Further prospective investigation into the biology of germline variants in this population is warranted.
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Affiliation(s)
- Rebekah M. Summey
- Division of Gynecologic Oncology, Department of Obstetrics and GynecologyMedical College of WisconsinMilwaukeeWisconsinUSA
| | | | | | | | - Janet S. Rader
- Division of Gynecologic Oncology, Department of Obstetrics and GynecologyMedical College of WisconsinMilwaukeeWisconsinUSA
| | - Elizabeth Hopp
- Division of Gynecologic Oncology, Department of Obstetrics and GynecologyMedical College of WisconsinMilwaukeeWisconsinUSA
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Evans DGR, Howell A, Howell Sacha J. Metaplastic breast cancer and BRCA1: first strong evidence of a link. Eur J Hum Genet 2023; 31:1207-1208. [PMID: 37592173 PMCID: PMC10620387 DOI: 10.1038/s41431-023-01441-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 07/06/2023] [Indexed: 08/19/2023] Open
Affiliation(s)
- D Gareth R Evans
- Manchester for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, UK.
- Division of Evolution, Infection and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK.
- Prevent Breast Cancer Centre, Wythenshawe Hospital Manchester Universities Foundation Trust, Wythenshawe, Manchester, UK.
- Manchester Breast Centre, The Christie NHS Foundation Trust, Wilmslow Road, Manchester, UK.
| | - Anthony Howell
- Prevent Breast Cancer Centre, Wythenshawe Hospital Manchester Universities Foundation Trust, Wythenshawe, Manchester, UK
- Manchester Breast Centre, The Christie NHS Foundation Trust, Wilmslow Road, Manchester, UK
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - J Howell Sacha
- Prevent Breast Cancer Centre, Wythenshawe Hospital Manchester Universities Foundation Trust, Wythenshawe, Manchester, UK
- Manchester Breast Centre, The Christie NHS Foundation Trust, Wilmslow Road, Manchester, UK
- Division of Cancer Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
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Kotnik U, Maver A, Peterlin B, Lovrecic L. Assessment of pathogenic variation in gynecologic cancer genes in a national cohort. Sci Rep 2023; 13:5307. [PMID: 37002323 PMCID: PMC10066348 DOI: 10.1038/s41598-023-32397-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
Population-based estimates of pathogenic variation burden in gynecologic cancer predisposition genes are a prerequisite for the development of effective precision public health strategies. This study aims to reveal the burden of pathogenic variants in a comprehensive set of clinically relevant breast, ovarian, and endometrial cancer genes in a large population-based study. We performed a rigorous manual classification procedure to identify pathogenic variants in a panel of 17 gynecologic cancer predisposition genes in a cohort of 7091 individuals, representing 0.35% of the general population. The population burden of pathogenic variants in hereditary gynecologic cancer-related genes in our study was 2.14%. Pathogenic variants in genes ATM, BRCA1, and CDH1 are significantly enriched and the burden of pathogenic variants in CHEK2 is decreased in our population compared to the control population. We have identified a high burden of pathogenic variants in several gynecologic cancer-related genes in the Slovenian population, most importantly in the BRCA1 gene.
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Affiliation(s)
- Urška Kotnik
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia.
- Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia.
| | - Aleš Maver
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Borut Peterlin
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Luca Lovrecic
- Clinical Institute of Genomic Medicine, University Medical Centre Ljubljana, Ljubljana, Slovenia
- Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
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Akin Duman T, Ozturk FN. Frequency and distribution of BRCA1/BRCA2 large genomic rearrangements in Turkish population with breast cancer. J Hum Genet 2023. [PMID: 36864289 DOI: 10.1038/s10038-023-01140-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/04/2023]
Abstract
Germline mutations in BRCA1 and BRCA2 genes are mainly responsible for breast and/or ovarian cancer patients. Most of the mutations in these genes are single nucleotide changes or deletions/insertions of small numbers of bases, while a minority of mutations in these genes are large genomic rearrangements (LGRs). The frequency of LGRs in the Turkish population is not clearly known. Also insufficient awareness of the importance of LGRs in breast and/or ovarian cancer development can lead to some disruptions in patient management. So, we aimed to determine the frequency and distribution of the LGRs in the BRCA1/2 genes in the Turkish population. We investigated rearrangements of BRCA genes using multiplex ligation-dependent probe amplification (MLPA) analysis in 1540 patients with a personal and/or family history of breast and/or ovarian cancer or who had familial known large deletion/duplication and applied for segregation. The estimated overall frequency of LGRs in our group was 3,4% (52/1540) with 91% in BRCA1 gene and 9% in BRCA2 gene. 13 different rearrangements were detected (10 BRCA1, 3 BRCA2). To the best our knowledge, BRCA1 exon 1-16 duplication and BRCA2 exon 6 deletion have not been previously reported before. Our study results supported that the detection of rearrangements in BRCA genes is of great importance and it should be planned routinely in patients whose mutations cannot be detected by sequence analysis in screening programs.
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Affiliation(s)
- Tugba Akin Duman
- Department of Medical Genetics, Istanbul Haseki Education and Training Hospital, Istanbul, Turkey.
| | - Fatma Nihal Ozturk
- Department of Medical Genetics, Istanbul Haseki Education and Training Hospital, Istanbul, Turkey
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Evans DG, Woodward ER. RE: Heterozygous BRCA1/BRCA2 and mismatch repair gene pathogenic variants in children and adolescents with cancer. J Natl Cancer Inst 2023; 115:224-225. [PMID: 36495190 PMCID: PMC9905954 DOI: 10.1093/jnci/djac223] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022] Open
Affiliation(s)
- D Gareth Evans
- North west Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, UK
- Genomic Medicine, Division of Evolution and Genomic Sciences, The University of Manchester, St Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Emma R Woodward
- North west Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, UK
- Genomic Medicine, Division of Evolution and Genomic Sciences, The University of Manchester, St Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester, UK
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Alesi V, Lepri FR, Dentici ML, Genovese S, Sallicandro E, Bejo K, Dallapiccola B, Capolino R, Novelli A, Digilio MC. Intragenic inversions in NF1 gene as pathogenic mechanism in neurofibromatosis type 1. Eur J Hum Genet 2022; 30:1239-1243. [PMID: 35879407 PMCID: PMC9626576 DOI: 10.1038/s41431-022-01153-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 06/28/2022] [Accepted: 07/05/2022] [Indexed: 02/04/2023] Open
Abstract
Neurofibromatosis type 1 (NF1), an autosomal dominant disorder characterized by skin pigmentary lesions and multiple cutaneous neurofibromas, is caused by neurofibromin 1 (NF1) loss of function variants. Currently, a molecular diagnosis is frequently established using a multistep protocol based on cDNA and gDNA sequence analysis and/or Multiplex Ligation-dependent Probe Amplification (MLPA) assay on genomic DNA, providing an overall detection rate of about 95-97%. The small proportion of clinically diagnosed patients, which at present do not obtain a molecular confirmation likely are mosaic, as their pathogenic variant may remain undetected due to low sensitivity of low coverage NGS approaches, or they may carry a type of pathogenic variant refractory to currently used technologies. Here, we report two unrelated patients presenting with two different inversions that disrupt the NF1 coding sequence, resulting in an NF1 phenotype. In one subject, the inversion was associated with microdeletions spanning a few NF1 exons at both breakpoints, while in the other the rearrangement did not cause exon loss, thus testing negative by MLPA assay. Considering the high proportion of repeated regions within the NF1 sequence, we propose that intragenic structural rearrangements should be considered as possible pathogenic mechanisms in patients fulfilling the NIH diagnostic criteria of NF1 but lacking of molecular confirmation and in patients with NF1 intragenic microdeletions.
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Affiliation(s)
- Viola Alesi
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, Rome, Italy.
| | - Francesca Romana Lepri
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
| | - Maria Lisa Dentici
- Medical Genetics Unit, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
- Genetics and Rare Disease Research Division, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
| | - Silvia Genovese
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
| | - Ester Sallicandro
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
| | - Kristel Bejo
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
| | - Bruno Dallapiccola
- Genetics and Rare Disease Research Division, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
| | - Rossella Capolino
- Medical Genetics Unit, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
- Genetics and Rare Disease Research Division, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
| | - Antonio Novelli
- Laboratory of Medical Genetics, Translational Cytogenomics Research Unit, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
| | - Maria Cristina Digilio
- Medical Genetics Unit, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
- Genetics and Rare Disease Research Division, Bambino Gesù Children Hospital, IRCCS, Rome, Italy
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Tritto V, Eoli M, Paterra R, Redaelli S, Moscatelli M, Rusconi F, Riva P. Characterization of 22q12 Microdeletions Causing Position Effect in Rare NF2 Patients with Complex Phenotypes. Int J Mol Sci 2022; 23:ijms231710017. [PMID: 36077416 PMCID: PMC9456353 DOI: 10.3390/ijms231710017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/11/2022] [Accepted: 08/25/2022] [Indexed: 11/18/2022] Open
Abstract
Neurofibromatosis type 2 is an autosomal dominant tumor-prone disorder mainly caused by NF2 point mutations or intragenic deletions. Few individuals with a complex phenotype and 22q12 microdeletions have been described. The 22q12 microdeletions’ pathogenic effects at the genetic and epigenetic levels are currently unknown. We here report on 22q12 microdeletions’ characterization in three NF2 patients with different phenotype complexities. A possible effect of the position was investigated by in silico analysis of 22q12 topologically associated domains (TADs) and regulatory elements, and by expression analysis of 12 genes flanking patients’ deletions. A 147 Kb microdeletion was identified in the patient with the mildest phenotype, while two large deletions of 561 Kb and 1.8 Mb were found in the other two patients, showing a more severe symptomatology. The last two patients displayed intellectual disability, possibly related to AP1B1 gene deletion. The microdeletions change from one to five TADs, and the 22q12 chromatin regulatory landscape, according to the altered expression levels of four deletion-flanking genes, including PIK3IP1, are likely associated with an early ischemic event occurring in the patient with the largest deletion. Our results suggest that the identification of the deletion extent can provide prognostic markers, predictive of NF2 phenotypes, and potential therapeutic targets, thus overall improving patient management.
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Affiliation(s)
- Viviana Tritto
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, 20054 Segrate, Italy
| | - Marica Eoli
- Unità di Neuro-Oncologia Molecolare, Fondazione IRCCS, Istituto Neurologico Carlo Besta, 20133 Milan, Italy
- Correspondence: (M.E.); (P.R.)
| | - Rosina Paterra
- Unità di Neuro-Oncologia Molecolare, Fondazione IRCCS, Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Serena Redaelli
- Dipartimento di Medicina e Chirurgia, University of Milano-Bicocca, 20900 Monza, Italy
| | - Marco Moscatelli
- Unità di Neuroradiologia, Fondazione IRCCS, Istituto Neurologico Carlo Besta, 20133 Milan, Italy
| | - Francesco Rusconi
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, 20054 Segrate, Italy
| | - Paola Riva
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, 20054 Segrate, Italy
- Correspondence: (M.E.); (P.R.)
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Multidisciplinary approach to Gorlin-Goltz syndrome: from diagnosis to surgical treatment of jawbones. Maxillofac Plast Reconstr Surg 2022; 44:25. [PMID: 35843976 PMCID: PMC9288940 DOI: 10.1186/s40902-022-00355-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 07/06/2022] [Indexed: 12/03/2022] Open
Abstract
Background Gorlin syndrome, also known as Gorlin-Goltz syndrome (GGS) or basal cell nevus syndrome (BCNS) or nevoid basal cell carcinoma syndrome (NBCCS), is an autosomal dominant familial cancer syndrome. It is characterized by the presence of numerous basal cell carcinomas (BCCs), along with skeletal, ophthalmic, and neurological abnormalities. It is essential to anticipate the diagnosis by identifying the pathology through the available diagnostic tests, clinical signs, and radiological manifestations, setting up an adequate treatment plan. Main body In the first part, we searched recent databases including MEDLINE (PubMed), Embase, and the Cochrane Library by analyzing the etiopathogenesis of the disease, identifying the genetic alterations underlying them. Subsequently, we defined what are, to date, the major and minor clinical diagnostic criteria, the possible genetic tests to be performed, and the pathologies with which to perform differential diagnosis. The radiological investigations were reviewed based on the most recent literature, and in the second part, we performed a review regarding the existing jawbone protocols, treating simple enucleation, enucleation with bone curettage in association or not with topical use of cytotoxic chemicals, and “en bloc” resection followed by possible bone reconstruction, marsupialization, decompression, and cryotherapy. Conclusion To promote the most efficient and accurate management of GGS, this article summarizes the clinical features of the disease, pathogenesis, diagnostic criteria, differential diagnosis, and surgical protocols. To arrive at an early diagnosis of the syndrome, it would be advisable to perform radiographic and clinical examinations from the young age of the patient. The management of the patient with GGS requires a multidisciplinary approach ensuring an adequate quality of life and effective treatment of symptoms.
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Evans DGR, van Veen EM, Harkness EF, Brentnall AR, Astley SM, Byers H, Woodward ER, Sampson S, Southworth J, Howell SJ, Maxwell AJ, Newman WG, Cuzick J, Howell A. Breast cancer risk stratification in women of screening age: Incremental effects of adding mammographic density, polygenic risk, and a gene panel. Genet Med 2022; 24:1485-1494. [PMID: 35426792 DOI: 10.1016/j.gim.2022.03.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 03/14/2022] [Accepted: 03/15/2022] [Indexed: 12/17/2022] Open
Abstract
PURPOSE There is great promise in breast cancer risk stratification to target screening and prevention. It is unclear whether adding gene panels to other risk tools improves breast cancer risk stratification and adds discriminatory benefit on a population basis. METHODS In total, 10,025 of 57,902 women aged 46 to 73 years in the Predicting Risk of Cancer at Screening study provided DNA samples. A case-control study was used to evaluate breast cancer risk assessment using polygenic risk scores (PRSs), cancer gene panel (n = 33), mammographic density (density residual [DR]), and risk factors collected using a self-completed 2-page questionnaire (Tyrer-Cuzick [TC] model version 8). In total, 525 cases and 1410 controls underwent gene panel testing and PRS calculation (18, 143, and/or 313 single-nucleotide polymorphisms [SNPs]). RESULTS Actionable pathogenic variants (PGVs) in BRCA1/2 were found in 1.7% of cases and 0.55% of controls, and overall PGVs were found in 6.1% of cases and 1.3% of controls. A combined assessment of TC8-DR-SNP313 and gene panel provided the best risk stratification with 26.1% of controls and 9.7% of cases identified at <1.4% 10-year risk and 9.01% of controls and 23.3% of cases at ≥8% 10-year risk. Because actionable PGVs were uncommon, discrimination was identical with/without gene panel (with/without: area under the curve = 0.67, 95% CI = 0.64-0.70). Only 7 of 17 PGVs in cases resulted in actionable risk category change. Extended case (n = 644)-control (n = 1779) series with TC8-DR-SNP143 identified 18.9% of controls and only 6.4% of stage 2+ cases at <1.4% 10-year risk and 20.7% of controls and 47.9% of stage 2+ cases at ≥5% 10-year risk. CONCLUSION Further studies and economic analysis will determine whether adding panels to PRS is a cost-effective strategy for risk stratification.
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Affiliation(s)
- D Gareth R Evans
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom; Prevention Breast Cancer Unit and Nightingale Breast Screening Centre, Manchester University NHS Foundation Trust (South), Manchester, United Kingdom; The Christie NHS Foundation Trust, Manchester, United Kingdom; Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust (Central), Manchester, United Kingdom; Manchester Breast Centre, Manchester Cancer Research Centre, The University of Manchester, Manchester, United Kingdom; Cancer Prevention Early Detection Theme, NIHR Manchester Biomedical Research Centre, The Christie NHS Foundation Trust, Manchester, United Kingdom.
| | - Elke M van Veen
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Elaine F Harkness
- Prevention Breast Cancer Unit and Nightingale Breast Screening Centre, Manchester University NHS Foundation Trust (South), Manchester, United Kingdom; Cancer Prevention Early Detection Theme, NIHR Manchester Biomedical Research Centre, The Christie NHS Foundation Trust, Manchester, United Kingdom; Division of Informatics, Imaging and Data Sciences, School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom; Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom
| | - Adam R Brentnall
- Centre for Cancer Prevention, Wolfson Institute of Preventive Medicine, Charterhouse Square, Barts and The London, Queen Mary University of London, London, United Kingdom
| | - Susan M Astley
- Prevention Breast Cancer Unit and Nightingale Breast Screening Centre, Manchester University NHS Foundation Trust (South), Manchester, United Kingdom; Manchester Breast Centre, Manchester Cancer Research Centre, The University of Manchester, Manchester, United Kingdom; Cancer Prevention Early Detection Theme, NIHR Manchester Biomedical Research Centre, The Christie NHS Foundation Trust, Manchester, United Kingdom; Division of Informatics, Imaging and Data Sciences, School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom; Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom
| | - Helen Byers
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom; Cancer Prevention Early Detection Theme, NIHR Manchester Biomedical Research Centre, The Christie NHS Foundation Trust, Manchester, United Kingdom
| | - Emma R Woodward
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom; Cancer Prevention Early Detection Theme, NIHR Manchester Biomedical Research Centre, The Christie NHS Foundation Trust, Manchester, United Kingdom
| | - Sarah Sampson
- Prevention Breast Cancer Unit and Nightingale Breast Screening Centre, Manchester University NHS Foundation Trust (South), Manchester, United Kingdom
| | - Jake Southworth
- Prevention Breast Cancer Unit and Nightingale Breast Screening Centre, Manchester University NHS Foundation Trust (South), Manchester, United Kingdom
| | - Sacha J Howell
- Prevention Breast Cancer Unit and Nightingale Breast Screening Centre, Manchester University NHS Foundation Trust (South), Manchester, United Kingdom; The Christie NHS Foundation Trust, Manchester, United Kingdom; Manchester Breast Centre, Manchester Cancer Research Centre, The University of Manchester, Manchester, United Kingdom; Cancer Prevention Early Detection Theme, NIHR Manchester Biomedical Research Centre, The Christie NHS Foundation Trust, Manchester, United Kingdom
| | - Anthony J Maxwell
- Prevention Breast Cancer Unit and Nightingale Breast Screening Centre, Manchester University NHS Foundation Trust (South), Manchester, United Kingdom; Manchester Breast Centre, Manchester Cancer Research Centre, The University of Manchester, Manchester, United Kingdom; Cancer Prevention Early Detection Theme, NIHR Manchester Biomedical Research Centre, The Christie NHS Foundation Trust, Manchester, United Kingdom; Division of Informatics, Imaging and Data Sciences, School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom; Manchester Academic Health Science Centre, The University of Manchester, Manchester, United Kingdom
| | - William G Newman
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom; Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust (Central), Manchester, United Kingdom; Manchester Breast Centre, Manchester Cancer Research Centre, The University of Manchester, Manchester, United Kingdom
| | - Jack Cuzick
- Centre for Cancer Prevention, Wolfson Institute of Preventive Medicine, Charterhouse Square, Barts and The London, Queen Mary University of London, London, United Kingdom
| | - Anthony Howell
- Prevention Breast Cancer Unit and Nightingale Breast Screening Centre, Manchester University NHS Foundation Trust (South), Manchester, United Kingdom; The Christie NHS Foundation Trust, Manchester, United Kingdom; Manchester Breast Centre, Manchester Cancer Research Centre, The University of Manchester, Manchester, United Kingdom; Cancer Prevention Early Detection Theme, NIHR Manchester Biomedical Research Centre, The Christie NHS Foundation Trust, Manchester, United Kingdom
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11
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Woodward ER, Green K, Burghel GJ, Bulman M, Clancy T, Lalloo F, Schlecht H, Wallace AJ, Evans DG. 30 year experience of index case identification and outcomes of cascade testing in high-risk breast and colorectal cancer predisposition genes. Eur J Hum Genet 2022; 30:413-419. [PMID: 34866136 PMCID: PMC8645350 DOI: 10.1038/s41431-021-01011-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 09/27/2021] [Accepted: 11/15/2021] [Indexed: 11/19/2022] Open
Abstract
It is 30 years since the first diagnostic cancer predisposition gene (CPG) test in the Manchester Centre for Genomic Medicine (MCGM), providing opportunities for cancer prevention, early detection and targeted treatments in index cases and at-risk family members. Here, we present time trends (1990-2020) of identification of index cases with a germline CPG variant and numbers of subsequent cascade tests, for 15 high-risk breast and gastro-intestinal tract cancer-associated CPGs: BRCA1, BRCA2, PALB2, PTEN, TP53, APC, BMPR1a, CDH1, MLH1, MSH2, MSH6, PMS2, SMAD4, STK11 and MUTYH. We recorded 2082 positive index case diagnostic screening tests, generating 3216 positive and 3140 negative family cascade (non-index) tests. This is equivalent to an average of 3.05 subsequent cascade tests per positive diagnostic index test, with 1.54 positive and 1.51 negative non-index tests per family. The CPGs with the highest numbers of non-index positive cases identified on cascade testing were BRCA1/2 (n = 1999) and the mismatch repair CPGs associated with Lynch Syndrome (n = 731). These data are important for service provision and health economic assessment of CPG diagnostic testing, in terms of cancer prevention and early detection strategies, and identifying those likely to benefit from targeted treatment strategies.
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Affiliation(s)
- Emma R Woodward
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, M13 9WL, UK
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PL, UK
| | - Kate Green
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, M13 9WL, UK
| | - George J Burghel
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Michael Bulman
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Tara Clancy
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PL, UK
| | - Fiona Lalloo
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Helene Schlecht
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, M13 9WL, UK
| | - Andrew J Wallace
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, M13 9WL, UK
| | - D Gareth Evans
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, M13 9WL, UK.
- Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PL, UK.
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12
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Leite Rocha D, Ashton-Prolla P, Rosset C. Reviewing the occurrence of large genomic rearrangements in patients with inherited cancer predisposing syndromes: importance of a comprehensive molecular diagnosis. Expert Rev Mol Diagn 2022; 22:319-346. [PMID: 35234551 DOI: 10.1080/14737159.2022.2049247] [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: 11/04/2022]
Abstract
INTRODUCTION Hereditary cancer predisposition syndromes are caused by germline pathogenic or likely pathogenic variants in cancer predisposition genes (CPG). The majority of pathogenic variants in CPGs are point mutations, but large gene rearrangements (LGRs) are present in several CPGs. LGRs can be much more difficult to characterize and perhaps they may have been neglected in molecular diagnoses. AREAS COVERED We aimed to evaluate the frequencies of germline LGRs in studies conducted in different populations worldwide through a qualitative systematic review based on an online literature research in PubMed. Two reviewers independently extracted data from published studies between 2009 and 2020. In total, 126 studies from 37 countries and 5 continents were included in the analysis. The number of studies in different continents ranged from 3 to 48 and for several countries there was an absolute lack of information. Asia and Europe represented most of the studies, and LGR frequencies varied from 3.04 to 15.06% in different continents. MLPA was one of the methods of choice in most studies (93%). EXPERT OPINION The LGR frequencies found in this review reinforce the need for comprehensive molecular testing regardless of the population of origin and should be considered by genetic counseling providers.
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Affiliation(s)
- Débora Leite Rocha
- Laboratório de Medicina Genômica, Serviço de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Rua Ramiro Barcelos, 2350, CEP: 90035-930, Porto Alegre, Rio Grande do Sul, Brazil
| | - Patrícia Ashton-Prolla
- Laboratório de Medicina Genômica, Serviço de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Rua Ramiro Barcelos, 2350, CEP: 90035-930, Porto Alegre, Rio Grande do Sul, Brazil.,Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil. Av. Bento Gonçalves, 9500 - Prédio 43312 M, CEP: 91501-970, Caixa Postal 1505, Porto Alegre, Rio Grande do Sul, Brazil.,Serviço de Genética Médica, HCPA, Rio Grande do Sul, Brazil. Rua Ramiro Barcelos, 2350, CEP: 90035-930, Porto Alegre, Rio Grande do Sul, Brazil
| | - Clévia Rosset
- Laboratório de Medicina Genômica, Serviço de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Rua Ramiro Barcelos, 2350, CEP: 90035-930, Porto Alegre, Rio Grande do Sul, Brazil
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13
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SavvyCNV: Genome-wide CNV calling from off-target reads. PLoS Comput Biol 2022; 18:e1009940. [PMID: 35294448 PMCID: PMC8959187 DOI: 10.1371/journal.pcbi.1009940] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 03/28/2022] [Accepted: 02/19/2022] [Indexed: 12/04/2022] Open
Abstract
Identifying copy number variants (CNVs) can provide diagnoses to patients and provide important biological insights into human health and disease. Current exome and targeted sequencing approaches cannot detect clinically and biologically-relevant CNVs outside their target area. We present SavvyCNV, a tool which uses off-target read data from exome and targeted sequencing data to call germline CNVs genome-wide. Up to 70% of sequencing reads from exome and targeted sequencing fall outside the targeted regions. We have developed a new tool, SavvyCNV, to exploit this ‘free data’ to call CNVs across the genome. We benchmarked SavvyCNV against five state-of-the-art CNV callers using truth sets generated from genome sequencing data and Multiplex Ligation-dependent Probe Amplification assays. SavvyCNV called CNVs with high precision and recall, outperforming the five other tools at calling CNVs genome-wide, using off-target or on-target reads from targeted panel and exome sequencing. We then applied SavvyCNV to clinical samples sequenced using a targeted panel and were able to call previously undetected clinically-relevant CNVs, highlighting the utility of this tool within the diagnostic setting. SavvyCNV outperforms existing tools for calling CNVs from off-target reads. It can call CNVs genome-wide from targeted panel and exome data, increasing the utility and diagnostic yield of these tests. SavvyCNV is freely available at https://github.com/rdemolgen/SavvySuite. We have created SavvyCNV, a new tool for calling genetic variants. Large regions of the genome can be deleted or duplicated–these variants can have important consequences, for example causing a patient’s genetic disease. However, many standard genetic tests only target a small fraction of the genome and will miss variants outside of these regions. Therefore, we developed a tool to exploit sequencing data which falls outside of these regions (due to flaws in the targeting process) to call large deletions and duplications. This allows large deletions and duplications to be detected anywhere in the genome. Researchers and diagnostic laboratories can use this tool to discover more genetic variants by re-analysing their sequencing data.
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14
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Salmi F, Maachi F, Tazzite A, Aboutaib R, Fekkak J, Azeddoug H, Jouhadi H. Next-generation sequencing of BRCA1 and BRCA2 genes in Moroccan prostate cancer patients with positive family history. PLoS One 2021; 16:e0254101. [PMID: 34242281 PMCID: PMC8270444 DOI: 10.1371/journal.pone.0254101] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 06/18/2021] [Indexed: 12/14/2022] Open
Abstract
Prostate cancer is the most common male cancer in Morocco. Although sporadic forms account for a large proportion of patients, familial forms of prostate cancer are observed in 20% of cases and about 5% are due to hereditary transmission. Indeed, germline mutations in BRCA1/2 genes have been associated with prostate cancer risk. However, the spectrum of these mutations was not investigated in Moroccan Prostate cancer patients. Thereby, the aim of this study was to characterize and to estimate the prevalence of germline BRCA1/2 mutations and large rearrangements in Moroccan patients with familial prostate cancer. The entire coding regions and intron/exon boundaries of BRCA1 and BRCA2 genes have been analyzed by next generation sequencing (NGS) in a total of 30 familial prostate cancer patients. Three pathogenic mutations were detected in four unrelated patients (13.3%). One BRCA1 mutation (c.1953_1956delGAAA) and two BRCA2 mutations (c.7234_7235insG and BRCA2ΔE12). In addition, sixty-three distinct polymorphisms and unclassified variants have been found. Early identification of germline BRCA1/2 mutations may be relevant for the management of Moroccan prostate cancer patients.
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Affiliation(s)
- Fatiha Salmi
- Laboratory of Genetics and Molecular Pathology, Faculty of Medicine and Pharmacy, Hassan II University of Casablanca, Casablanca, Morocco
- * E-mail:
| | - Fatima Maachi
- Helicobacter Pylori and Gastric Pathologies Laboratory, Pasteur Institute of Morocco, Casablanca, Morocco
| | - Amal Tazzite
- Laboratory of Genetics and Molecular Pathology, Faculty of Medicine and Pharmacy, Hassan II University of Casablanca, Casablanca, Morocco
| | - Rachid Aboutaib
- Department of Urology, Ibn Rochd University Hospital Center, Casablanca, Morocco
| | - Jamal Fekkak
- Molecular Biology Department, Anoual Laboratory, Casablanca, Morocco
| | - Houssine Azeddoug
- Faculty of Sciences-Biochemistry and Molecular Biology Laboratory, University Hassan II Casablanca, Casablanca, Morocco
| | - Hassan Jouhadi
- Laboratory of Genetics and Molecular Pathology, Faculty of Medicine and Pharmacy, Hassan II University of Casablanca, Casablanca, Morocco
- Mohammed VI Center for Cancer Treatment, Ibn Rochd University Hospital Center, Casablanca, Morocco
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15
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Sahin I, Saat H. A novel BRCA1 duplication and new insights on the spectrum and frequency of germline large genomic rearrangements in BRCA1/BRCA2. Mol Biol Rep 2021; 48:5057-5062. [PMID: 34146199 DOI: 10.1007/s11033-021-06499-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 06/15/2021] [Indexed: 10/21/2022]
Abstract
Heritable breast cancers account for 5% to 10% of all breast cancers, and monogenic, highly penetrant genes cause them. Around 90% of pathogenic variants in BRCA1 and BRCA2 are observed using gene sequencing, with another 10% identified through gene duplication/deletion analysis, which differs across various communities. In this study, we performed a next-generation sequencing panel and MLPA on 1484 patients to explain the importance of recurrent germline duplications/deletions of BRCA1-2 and their clinical results and determine how often BRCA gene LGRs were seen in people suspected of hereditary breast and ovarian cancer syndrome. The large genomic rearrangements (LGRs) frequency was approximately 1% (14/1484). All 14 mutations were heterozygous and detected in patients with breast cancer. BRCA1 mutations were more predominant (n = 8, 57.1%) than BRCA2 mutations (6, 42.9%). The most common recurrent mutations were BRCA2 exon three and BRCA1 exon 24 (23) deletions. To the best of our knowledge, BRCA1 5'UTR-exon11 duplication has never been reported before. Testing with MLPA is essential to identify patients at high risk. Our data demonstrate that BRCA1-2 LGRs should be considered when ordering genetic testing for individuals with a personal or family history of cancer, particularly breast cancer. Further research could shed light on BRCA1-2 LGRs' unique carcinogenesis roles.
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Affiliation(s)
- Ibrahim Sahin
- Department of Medical Genetics, University of Health Sciences, Dışkapı Yıldırım Beyazıt Training and Research Hospital, Ankara, Turkey.
| | - Hanife Saat
- Department of Medical Genetics, University of Health Sciences, Dışkapı Yıldırım Beyazıt Training and Research Hospital, Ankara, Turkey
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16
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Bennett S, Alexander E, Fraser H, Bowers N, Wallace A, Woodward ER, Lalloo F, Quinn AM, Huang S, Schlecht H, Evans DG. Germline FFPE inherited cancer panel testing in deceased family members: implications for clinical management of unaffected relatives. Eur J Hum Genet 2021; 29:861-871. [PMID: 33654310 PMCID: PMC8110779 DOI: 10.1038/s41431-021-00817-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 01/07/2021] [Accepted: 01/23/2021] [Indexed: 01/29/2023] Open
Abstract
Where previously, germline genetic testing in deceased affected relatives was not possible due to the absence of lymphocytic DNA, the North-West-Genomic-Laboratory Hub (NWGLH) has developed and validated next-generation sequencing based gene panels utilising formalin-fixed-paraffin-embedded (FFPE) tissue DNA from deceased individuals. This technology has been utilised in the clinical setting for the management of unaffected relatives seen in the Clinical Genetics Service (CGS). Here we assess the clinical impact. At the time of data collection, the NWGLH had analysed 180 FFPE tissue samples from deceased affected individuals: 134 from breast and/or ovarian cancer cases for germline variants in the BRCA1/BRCA2 genes and 46 from colorectal, gastric, ovarian and endometrial cancer cases for germline variants in a panel of 13 genes implicated in inherited colorectal cancer and gastric cancer conditions. Successful analysis was achieved in 140/180 cases (78%). In total, 29 germline pathogenic/likely pathogenic variants were identified in autosomal dominant cancer predisposition genes where the gene was pertinent to the cancer family history (including BRCA1/BRCA2, the mismatch-repair genes and APC). Of the 180 cases, the impact of the result on clinical management of unaffected relatives was known in 143 cases. Of these, the results in 54 cases (38%) directly impacted the clinical management of relatives seen by the CGS. This included changes to risk assessments, screening recommendations and the availability of predictive genetic testing to unaffected relatives. Our data demonstrate how FFPE testing in deceased relatives is an accurate and informative tool in the clinical management of patients referred to the CGS.
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Affiliation(s)
- Sarah Bennett
- Clinical Genetics Service, Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Elizabeth Alexander
- Clinical Genetics Service, Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Harry Fraser
- Northern Regional Genetic Service, Genetics Health Service New Zealand, Auckland City Hospital, Auckland, New Zealand
| | - Naomi Bowers
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Andrew Wallace
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Emma R. Woodward
- Clinical Genetics Service, Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester, UK ,Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Health innovation Manchester, Manchester, UK
| | - Fiona Lalloo
- Clinical Genetics Service, Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester, UK
| | - Anne Marie Quinn
- Department of Anatomic Pathology, University Hospital Galway, Galway, Ireland
| | - Shuwen Huang
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Helene Schlecht
- North West Genomic Laboratory Hub, Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - D. Gareth Evans
- Clinical Genetics Service, Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Manchester, UK ,Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Health innovation Manchester, Manchester, UK
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17
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Typical 22q11.2 deletion syndrome appears to confer a reduced risk of schwannoma. Genet Med 2021; 23:1779-1782. [PMID: 33879870 PMCID: PMC8460436 DOI: 10.1038/s41436-021-01175-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 03/28/2021] [Accepted: 03/30/2021] [Indexed: 11/17/2022] Open
Abstract
Purpose The LZTR1 gene has been associated with schwannomatosis tumor predisposition and is located in a region that is deleted in the great majority (89%) of patients with 22q11.2 deletion syndrome (22q11.2DS). Since it is known that approximately 1 in 500 people in the general population will develop a sporadic schwannoma and there are no reports of the occurrence of schwannoma in 22q11.2DS, we investigated whether whole-gene deletion of LZTR1 occurs in schwannomatosis and assessed the risk of schwannoma in 22q11.2DS. Methods We assessed the genetic testing results for LZTR1-associated schwannomatosis and the clinical phenotypes of patients with 22q11.2DS. Results There were no reports of schwannoma in over 1,500 patients with 22q11.2DS. In addition, no patients meeting clinical diagnostic criteria for schwannomatosis had a whole-gene deletion in LZTR1. Only 1 patient in 110 with an apparently sporadic vestibular schwannoma had a constitutional whole-gene deletion of LZTR1. Conclusion People with a large 22q11.2 deletion may have a reduced risk of developing a schwannoma compared to the general population. ![]()
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18
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Pócza T, Grolmusz VK, Papp J, Butz H, Patócs A, Bozsik A. Germline Structural Variations in Cancer Predisposition Genes. Front Genet 2021; 12:634217. [PMID: 33936164 PMCID: PMC8081352 DOI: 10.3389/fgene.2021.634217] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 03/08/2021] [Indexed: 12/14/2022] Open
Abstract
In addition to single nucleotide variations and small-scale indels, structural variations (SVs) also contribute to the genetic diversity of the genome. SVs, such as deletions, duplications, amplifications, or inversions may also affect coding regions of cancer-predisposing genes. These rearrangements may abrogate the open reading frame of these genes or adversely affect their expression and may thus act as germline mutations in hereditary cancer syndromes. With the capacity of disrupting the function of tumor suppressors, structural variations confer an increased risk of cancer and account for a remarkable fraction of heritability. The development of sequencing techniques enables the discovery of a constantly growing number of SVs of various types in cancer predisposition genes (CPGs). Here, we provide a comprehensive review of the landscape of germline SV types, detection methods, pathomechanisms, and frequency in CPGs, focusing on the two most common cancer syndromes: hereditary breast- and ovarian cancer and gastrointestinal cancers. Current knowledge about the possible molecular mechanisms driving to SVs is also summarized.
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Affiliation(s)
- Tímea Pócza
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary
| | - Vince Kornél Grolmusz
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary.,Hereditary Cancers Research Group, Hungarian Academy of Sciences, Semmelweis University, Budapest, Hungary
| | - János Papp
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary.,Hereditary Cancers Research Group, Hungarian Academy of Sciences, Semmelweis University, Budapest, Hungary
| | - Henriett Butz
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary.,Hereditary Cancers Research Group, Hungarian Academy of Sciences, Semmelweis University, Budapest, Hungary.,Department of Laboratory Medicine, Semmelweis University, Budapest, Hungary
| | - Attila Patócs
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary.,Hereditary Cancers Research Group, Hungarian Academy of Sciences, Semmelweis University, Budapest, Hungary.,Department of Laboratory Medicine, Semmelweis University, Budapest, Hungary
| | - Anikó Bozsik
- Department of Molecular Genetics, National Institute of Oncology, Budapest, Hungary.,Hereditary Cancers Research Group, Hungarian Academy of Sciences, Semmelweis University, Budapest, Hungary
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19
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Woodward ER, van Veen EM, Evans DG. From BRCA1 to Polygenic Risk Scores: Mutation-Associated Risks in Breast Cancer-Related Genes. Breast Care (Basel) 2021; 16:202-213. [PMID: 34248461 DOI: 10.1159/000515319] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 02/16/2021] [Indexed: 12/12/2022] Open
Abstract
Background There has been huge progress over the last 30 years in identifying the familial component of breast cancer. Summary Currently around 20% is explained by the high-risk genes BRCA1 and BRCA2, a further 2% by other high-penetrance genes, and around 5% by the moderate risk genes ATM and CHEK2. In contrast, the more than 300 low-penetrance single-nucleotide polymorphisms (SNP) now account for around 28% and they are predicted to account for most of the remaining 45% yet to be found. Even for high-risk genes which confer a 40-90% risk of breast cancer, these SNP can substantially affect the level of breast cancer risk. Indeed, the strength of family history and hormonal and reproductive factors is very important in assessing risk even for a BRCA carrier. The risks of contralateral breast cancer are also affected by SNP as well as by the presence of high or moderate risk genes. Genetic testing using gene panels is now commonplace. Key-Messages There is a need for a more parsimonious approach to panels only testing those genes with a definite 2-fold increased risk and only testing those genes with challenging management implications, such as CDH1 and TP53, when there is strong clinical indication to do so. Testing of SNP alongside genes is likely to provide a more accurate risk assessment.
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Affiliation(s)
- Emma R Woodward
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, United Kingdom.,Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Elke M van Veen
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, United Kingdom.,Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - D Gareth Evans
- Manchester Centre for Genomic Medicine, Manchester University Hospitals NHS Foundation Trust, Manchester, United Kingdom.,Division of Evolution and Genomic Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom.,PREVENT Breast Cancer Prevention Centre, Nightingale Centre, Manchester Universities Foundation Trust, Wythenshawe Hospital, Manchester, United Kingdom.,Manchester Breast Centre, Manchester Cancer Research Centre, The Christie, University of Manchester, Manchester, United Kingdom
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20
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Cushman-Vokoun A, Lauring J, Pfeifer J, Olson DR, Berry A, Thorson J, Voelkerding K, Myles J, Barbeau J, Chandra P, Li M, Vance GH, Jensen BW, Hansen MY, Yohe S. Laboratory and Clinical Implications of Incidental and Secondary Germline Findings During Tumor Testing. Arch Pathol Lab Med 2021; 146:70-77. [PMID: 33769456 DOI: 10.5858/arpa.2020-0025-cp] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/13/2021] [Indexed: 11/06/2022]
Abstract
CONTEXT.— Next-generation sequencing is a powerful clinical tool for cancer management but can produce incidental/secondary findings that require special consideration. OBJECTIVE.— To discuss clinical and laboratory issues related to incidental or secondary germline findings in the clinical setting of tumor testing and inform future guidelines in this area. DESIGN.— A College of American Pathologists workgroup including representation from the American Society of Clinical Oncology, the Association for Molecular Pathology, and the American College of Medical Genetics and Genomics created a review of items that should be considered when developing guidelines for incidental or secondary findings when performing clinical tumor testing. RESULTS.— Testing recommendations should be cognizant of the differences among anticipated incidental, unanticipated incidental, and secondary findings, and whether normal tissue is also tested. In addition to defining which variants will be reported, robust recommendations must also take into account test design and validation, reimbursement, cost, infrastructure, impact on reflex testing, and maintenance of proficiency. Care providers need to consider the potential of a test to uncover incidental or secondary findings, the recommendation of upfront counseling, the need for consent, the timing of testing and counseling, and that the exact significance of a finding may not be clear. CONCLUSIONS.— As clinical oncology testing panels have become a mainstay of clinical cancer care, guidelines addressing the unique aspects of incidental and secondary findings in oncology testing are needed. This paper highlights clinical and laboratory considerations with regard to incidental/secondary findings and is a clarion call to create recommendations.
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Affiliation(s)
- Allison Cushman-Vokoun
- From the Department of Pathology and Microbiology, University of Nebraska Medical Center Nebraska Medicine, Omaha (Cushman-Vokoun)
| | - Josh Lauring
- the Breast and Ovarian Cancer Program, The Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, Maryland (Lauring)
| | - John Pfeifer
- the Department of Pathology, Washington University School of Medicine, Saint Louis, Missouri (Pfeifer)
| | - Damon R Olson
- the Department of Pathology, Children's Hospitals and Clinics of Minnesota, Minneapolis (Olson)
| | - Anna Berry
- Molecular Pathology Genomics, Swedish Cancer Institute Lab, Seattle, Washington (Berry)
| | - John Thorson
- the Department of Pathology, University of California, San Diego (Thorson)
| | - Karl Voelkerding
- the Department of Pathology, University of Utah, ARUP Laboratories Institute for Clinical and Experimental Pathology, Salt Lake City (Voelkerding)
| | - Jonathan Myles
- the Department of Anatomic Pathology, Cleveland Clinic, Cleveland, Ohio (Myles)
| | - James Barbeau
- the Department of Pathology and Laboratory Medicine, Brown University Alpert Medical School, Lifespan Academic Medical Center, Providence, Rhode Island (Barbeau)
| | - Pranil Chandra
- the Department of Molecular and Clinical Pathology, PathGroup Lab LLC, Nashville, Tennessee (Chandra)
| | - Marilyn Li
- the Department of Genomic Diagnostics, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia (Li)
| | - Gail H Vance
- the Department of Medical and Molecular Genetics, Indiana University, Indianapolis (Vance)
| | - Brad W Jensen
- the Department of Anatomic and Clinical Pathology, PeaceHealth Medical Center, Vancouver, Washington (Jensen)
| | - Molly Y Hansen
- Proficiency Testing, College of American Pathologists, Northfield, Illinois (Hansen)
| | - Sophia Yohe
- the Department of Laboratory Medicine and Pathology, University of Minnesota Medical Center, Minneapolis (Yohe)
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21
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Abstract
Purpose: Lobular breast cancer (LBC) accounts for ~ 15% of breast cancer. Here, we studied the frequency of pathogenic germline variants (PGVs) in an extended panel of genes in women affected with LBC. Methods: 302 women with LBC and 1567 without breast cancer were tested for BRCA1/2 PGVs. A subset of 134 LBC affected women who tested negative for BRCA1/2 PGVs underwent extended screening, including: ATM, CDH1, CHEK2, NBN, PALB2, PTEN, RAD50, RAD51D, and TP53.Results: 35 PGVs were identified in the group with LBC, of which 22 were in BRCA1/2. Ten actionable PGVs were identified in additional genes (ATM(4), CDH1(1), CHEK2(1), PALB2(2) and TP53(2)). Overall, PGVs in three genes conferred a significant increased risk for LBC. Odds ratios (ORs) were: BRCA1: OR = 13.17 (95%CI 2.83–66.38; P = 0.0017), BRCA2: OR = 10.33 (95%CI 4.58–23.95; P < 0.0001); and ATM: OR = 8.01 (95%CI 2.52–29.92; P = 0.0053). We did not detect an increased risk of LBC for PALB2, CDH1 or CHEK2. Conclusion: The overall PGV detection rate was 11.59%, with similar rates of BRCA1/2 (7.28%) PGVs as for other actionable PGVs (7.46%), indicating a benefit for extended panel genetic testing in LBC. We also report a previously unrecognised association of pathogenic variants in ATM with LBC.
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22
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E2F1 copy number variations in germline and breast cancer: a retrospective study of 222 Italian women. Mol Med 2021; 27:26. [PMID: 33691613 PMCID: PMC7948349 DOI: 10.1186/s10020-021-00287-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 03/04/2021] [Indexed: 11/29/2022] Open
Abstract
Background Breast cancer is the most common neoplasia among women in developed countries. The risk factors of breast cancer can be distinguished in modifiable and unmodifiable factors and, among the latter, genetic factors play a key role. Copy number variations (CNVs) are genetic variants that are classified as rare when present in less than 1% of the healthy population. Since rare CNVs are often cause of diseases, over the last years, their contribution in carcinogenesis has become a relevant matter of study. E2F1 is a transcriptional factor that plays an important role in regulating cell cycle and apoptosis. Its double and conflicting role is the reason why it acts both as oncogene and as tumour suppressor, depending on cell context. Since anomalies in expression or in number of copies of E2F1 have been related to several cancers, we aimed to study number of germline copies of E2F1 in women with breast cancer in order to better elucidate their contribution as predisposing factor to this tumour. Methods We performed, hence, a retrospective study on 222 Italian women with breast cancer recruited from October 2002 to December 2007. TaqMan CNV assay and Real-Time PCR were carried out to analyse, respectively, E2F1 CNV and E2F1 expression in the subjects of the study. Chi square test or Fisher’s exact test and Student's t‐test were used to calculate the frequency of CNVs and differences in continuous variables between groups, respectively. Results Intriguingly, we found that 10/222 (4.5%) women with breast cancer had more copies than controls (0/200, 0%), furthermore, the number of copies positively correlated with E2F1 gene expression in breast cancer tissue, suggesting that the constitutive gain of the gene could translate into an increased risk of genomic instability. Additionally, we found that altered E2F1 copies were present prevalently in the patients with contralateral breast cancer (20%) and all of them had a positive family history, both typically associated with hereditary cancer. Conclusions Our findings suggest that copy number variations of E2F1 might be a susceptibility factor for breast cancer, however, further studies on large cohorts are to be performed in order to better delineate the phenotype linked to the gain of E2F1 copies.
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23
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Evans DG, Lalloo F, Ryan NA, Bowers N, Green K, Woodward ER, Clancy T, Bolton J, McVey RJ, Wallace AJ, Newton K, Hill J, McMahon R, Crosbie EJ. Advances in genetic technologies result in improved diagnosis of mismatch repair deficiency in colorectal and endometrial cancers. J Med Genet 2021; 59:328-334. [PMID: 33452216 PMCID: PMC8961751 DOI: 10.1136/jmedgenet-2020-107542] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 12/17/2020] [Accepted: 12/23/2020] [Indexed: 11/04/2022]
Abstract
Background Testing cancers for mismatch repair deficiency (dMMR) by immunohistochemistry (IHC) is a quick and inexpensive means of triaging individuals for germline Lynch syndrome testing. The aim of this study was to evaluate tumour dMMR and the prevalence of Lynch syndrome in patients referred to the Manchester Centre for Genomic Medicine, which serves a population of 5.6 million. Methods Tumour testing used IHC for MMR proteins with targeted BRAF and MLH1 promotor methylation testing followed by germline mutation and somatic testing as appropriate. Results In total, 3694 index tumours were tested by IHC (2204 colorectal cancers (CRCs), 739 endometrial cancers (ECs) and 761 other), of which 672/3694 (18.2%) had protein loss, including 348 (9.4%) with MLH1 loss. MLH1 loss was significantly higher for 739 ECs (15%) vs 2204 CRCs (10%) (p=0.0003) and was explained entirely by higher rates of somatic MLH1 promoter hypermethylation (87% vs 41%, p<0.0001). Overall, 65/134 (48.5%) patients with MLH1 loss and no MLH1 hypermethylation or BRAF c.1799T>A had constitutional MLH1 pathogenic variants. Of 456 patients with tumours showing loss of MSH2/MSH6, 216 (47.3%) had germline pathogenic variants in either gene. Isolated PMS2 loss was most suggestive of a germline MMR variant in 19/26 (73%). Of those with no germline pathogenic variant, somatic testing identified likely causal variants in 34/48 (71%) with MLH1 loss and in MSH2/MSH6 in 40/47 (85%) with MSH2/MSH6 loss. Conclusions Reflex testing of EC/CRC leads to uncertain diagnoses in many individuals with dMMR following IHC but without germline pathogenic variants or MLH1 hypermethylation. Tumour mutation testing is effective at decreasing this by identifying somatic dMMR in >75% of cases.
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Affiliation(s)
- D Gareth Evans
- Division of Evolution and Genomic Medicine, The University of Manchester, Manchester, UK.,Clinical Genetics Service, Manchester Centre for Genomic Medicine, North-West Genomics Laboratory Hub, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Fiona Lalloo
- Clinical Genetics Service, Manchester Centre for Genomic Medicine, North-West Genomics Laboratory Hub, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Neil Aj Ryan
- Division of Cancer Sciences, The University of Manchester, Manchester, UK.,Department of Obstetrics and Gynaecology, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Naomi Bowers
- Clinical Genetics Service, Manchester Centre for Genomic Medicine, North-West Genomics Laboratory Hub, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Kate Green
- Clinical Genetics Service, Manchester Centre for Genomic Medicine, North-West Genomics Laboratory Hub, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Emma R Woodward
- Division of Evolution and Genomic Medicine, The University of Manchester, Manchester, UK.,Clinical Genetics Service, Manchester Centre for Genomic Medicine, North-West Genomics Laboratory Hub, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Tara Clancy
- Clinical Genetics Service, Manchester Centre for Genomic Medicine, North-West Genomics Laboratory Hub, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - James Bolton
- Department of Pathology, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Rhona J McVey
- Department of Pathology, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Andrew J Wallace
- Clinical Genetics Service, Manchester Centre for Genomic Medicine, North-West Genomics Laboratory Hub, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Katy Newton
- Department of Surgery, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - James Hill
- Department of Surgery, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Raymond McMahon
- Department of Pathology, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Emma J Crosbie
- Division of Cancer Sciences, The University of Manchester, Manchester, UK .,Department of Obstetrics and Gynaecology, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
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24
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Malik SS, Mubarik S, Aftab A, Khan R, Masood N, Asif M, Bano R. Correlation of MSH2 exonic deletions and protein downregulation with breast cancer biomarkers and outcome in Pakistani women/patients. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:3066-3077. [PMID: 32902747 DOI: 10.1007/s11356-020-10717-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 09/02/2020] [Indexed: 06/11/2023]
Abstract
Mismatch repair (MMR) pathway is one of the underlying mechanisms of predisposition to breast cancer (BC). The present study explored the association of MSH2 exonic deletions, respective survival analysis, protein structure prediction, transcription profiling, and expression analysis with BC risk. Genotyping analysis of 493 BC cases and 387 controls confirmed the association of two MSH2 exonic deletions, i.e., exon 3 (OR:6.4, CI = 3.4-12.1) and 9 (OR:7.8, CI = 4.1-14.8) with BC risk. In order to confirm the phenotypic-genotypic relationship, we have performed MSH2 transcriptomic (p < 0.05) and protein expression analysis (OR:30, CI = 4-230) which further confirmed its downregulation/loss in BC biopsy samples highlighting potential role in the onset of breast carcinogenesis. Additionally, we have presented that MSH2 mutations can alter the expression profile of other BC associated biomarkers like ER, PR, CK-7, GATA-3, and E-cadherin. Subsequently, the effect of exonic deletions on secondary structure of protein has shown missing of beta and alpha helices in their protein products via in-silico analysis. However, loss of exon 3 results in the altered core protein structure leading to dysfunction protein, possible cause of BC development. No association of MSH2 exonic deletions with survival statistics was observed conceivably due to the shorter follow-up time. Thus, our results at genetic, transcriptomic, and proteomic levels confirmed the downregulated MSH2, emphasizing its potential contribution in MMR mechanisms for breast tumorigenesis. In conclusion, MSH2 deficiency may cause breast cancer development and progression.
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Affiliation(s)
- Saima Shakil Malik
- Department of Zoology, University of Gujrat, Gujrat, Pakistan.
- Microbiology & Biotechnology Research Lab., Fatima Jinnah Women University, The Mall Rawalpindi, Rawalpindi, Punjab, Pakistan.
| | - Sumaira Mubarik
- Department of Epidemiology and Biostatistics, School of Health Sciences, Wuhan University, Wuhan, 430071, Hubei, China
| | - Ayesha Aftab
- Department of Biological Sciences, International Islamic University, Sector H10, Islamabad, Pakistan
| | - Ranjha Khan
- The CAS Key Laboratory of Innate Immunity and Chronic Diseases, School of Life Sciences, University of Science and Technology of China, Huangshan Road, Hefei, 230027, Anhui, China
| | - Nosheen Masood
- Microbiology & Biotechnology Research Lab., Fatima Jinnah Women University, The Mall Rawalpindi, Rawalpindi, Punjab, Pakistan
| | - Muhammad Asif
- Department of Histopathology, Armed Forces Institute of Pathology, Rawalpindi, Pakistan
| | - Razia Bano
- Breast Clinic, Combined Military Hospital, Rawalpindi, Pakistan
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25
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Rosenblum RE, Ang C, Suckiel SA, Soper ER, Sigireddi MR, Cullina S, Belbin GM, Lucas AL, Kenny EE, Abul-Husn NS. Lynch Syndrome-Associated Variants and Cancer Rates in an Ancestrally Diverse Biobank. JCO Precis Oncol 2020; 4:PO.20.00290. [PMID: 33283134 PMCID: PMC7713527 DOI: 10.1200/po.20.00290] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/16/2020] [Indexed: 12/22/2022] Open
Abstract
PURPOSE Limited data are available on the prevalence and clinical impact of Lynch syndrome (LS)-associated genomic variants in non-European ancestry populations. We identified and characterized individuals harboring LS-associated variants in the ancestrally diverse BioMe Biobank in New York City. PATIENTS AND METHODS Exome sequence data from 30,223 adult BioMe participants were evaluated for pathogenic, likely pathogenic, and predicted loss-of-function variants in MLH1, MSH2, MSH6, and PMS2. Survey and electronic health record data from variant-positive individuals were reviewed for personal and family cancer histories. RESULTS We identified 70 individuals (0.2%) harboring LS-associated variants in MLH1 (n = 12; 17%), MSH2 (n = 13; 19%), MSH6 (n = 16; 23%), and PMS2 (n = 29; 41%). The overall prevalence was 1 in 432, with higher prevalence among individuals of self-reported African ancestry (1 in 299) than among Hispanic/Latinx (1 in 654) or European (1 in 518) ancestries. Thirteen variant-positive individuals (19%) had a personal history, and 19 (27%) had a family history of an LS-related cancer. LS-related cancer rates were highest in individuals with MSH6 variants (31%) and lowest in those with PMS2 variants (7%). LS-associated variants were associated with increased risk of colorectal (odds ratio [OR], 5.0; P = .02) and endometrial (OR, 30.1; P = 8.5 × 10-9) cancers in BioMe. Only 2 variant-positive individuals (3%) had a documented diagnosis of LS. CONCLUSION We found a higher prevalence of LS-associated variants among individuals of African ancestry in New York City. Although cancer risk is significantly increased among variant-positive individuals, the majority do not harbor a clinical diagnosis of LS, suggesting underrecognition of this disease.
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Affiliation(s)
- Rachel E. Rosenblum
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Celina Ang
- Division of Hematology and Medical Oncology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Sabrina A. Suckiel
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
- Division of Genomic Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Emily R. Soper
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
- Division of Genomic Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Meenakshi R. Sigireddi
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Sinead Cullina
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Gillian M. Belbin
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
- Division of General Internal Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Aimee L. Lucas
- Henry D. Janowitz Division of Gastroenterology, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Eimear E. Kenny
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
- Division of General Internal Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Noura S. Abul-Husn
- The Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, NY
- Division of Genomic Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY
- Division of General Internal Medicine, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY
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26
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Hyder Z, Fairclough A, Groom M, Getty J, Alexander E, van Veen EM, Makin G, Sethuraman C, Tang V, Evans DG, Maher ER, Woodward ER. Constitutional de novo deletion CNV encompassing REST predisposes to diffuse hyperplastic perilobar nephroblastomatosis (HPLN). J Med Genet 2020; 58:581-585. [PMID: 32917767 DOI: 10.1136/jmedgenet-2020-107087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 07/04/2020] [Accepted: 07/06/2020] [Indexed: 11/04/2022]
Abstract
BACKGROUND Nephroblastomatosis is a recognised precursor for the development of Wilms tumour (WT), the most common childhood renal tumour. While the majority of WT is sporadic in origin, germline intragenic mutations of predisposition genes such as WT1, REST and TRIM28 have been described in apparently isolated (non-familial) WT.Despite constitutional CNVs being a well-studied cause of developmental disorders, their role in cancer predisposition is less well defined, so that the interpretation of cancer risks associated with specific CNVs can be complex. OBJECTIVE To highlight the role of a constitutional deletion CNV (delCNV) encompassing the REST tumour suppressor gene in diffuse hyperplastic perilobar nephroblastomatosis (HPLN). METHODS/RESULTS Array comparative genomic hybridisation in an infant presenting with apparently sporadic diffuse HPLN revealed a de novo germline CNV, arr[GRCh37] 4q12(57,385,330-57,947,405)x1. The REST tumour suppressor gene is located at GRCh37 chr4:57,774,042-57,802,010. CONCLUSION This delCNV encompassing REST is associated with nephroblastomatosis. Deletion studies should be included in the molecular work-up of inherited predisposition to WT/nephroblastomatosis. Detection of delCNVs involving known cancer predisposition genes can yield insights into the relationship between underlying genomic architecture and associated tumour risk.
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Affiliation(s)
- Zerin Hyder
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Adele Fairclough
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK.,NW Genomic Laboratory Hub, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Mike Groom
- NW Genomic Laboratory Hub, Liverpool Women's Hospital, Liverpool, UK
| | - Joan Getty
- NW Genomic Laboratory Hub, Liverpool Women's Hospital, Liverpool, UK
| | - Elizabeth Alexander
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Elke M van Veen
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Guy Makin
- Department of Paediatric Oncology, Royal Manchester Children's Hospital, Manchester, UK.,Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
| | - Chitra Sethuraman
- Department of Paediatric Histopathology, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Vivian Tang
- Department of Radiology, Royal Manchester Children's Hospital, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - D Gareth Evans
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
| | - Eamonn R Maher
- Department of Medical Genetics, University of Cambridge, Cambridge, Cambridgeshire, UK.,Department of Clinical Genetics, Cambridge University Hospitals NHS Foundation Trust, Cambridge, Cambridgeshire, UK
| | - Emma R Woodward
- Manchester Centre for Genomic Medicine, Manchester University NHS Foundation Trust, Manchester, Greater Manchester, UK
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27
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Rogoża-Janiszewska E, Malińska K, Górski B, Scott RJ, Cybulski C, Kluźniak W, Lener M, Jakubowska A, Gronwald J, Huzarski T, Lubiński J, Dębniak T. Prevalence of germline TP53 variants among early-onset breast cancer patients from Polish population. Breast Cancer 2020; 28:226-235. [PMID: 32888145 PMCID: PMC7796867 DOI: 10.1007/s12282-020-01151-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 08/20/2020] [Indexed: 11/28/2022]
Abstract
Background The objective of this study was to determine spectrum and prevalence of germline mutations in TP53 gene among Polish women with early-onset breast cancer (BC), which has not been determined until now. Methods A cohort of 100 females with BC diagnosed ≤ 30 years of age and with a positive family history of cancer was used as a discovery cohort. 1880 women with BC ≤ 45 years old and a control group of 2000 healthy women were genotyped as a replication phase of this study. Results Four heterozygous pathogenic missense mutations were detected in a group of 100 patients with early-onset breast cancer. On the basis of software prediction and available literature data, all these variants were defined as pathogenic. None of these TP53 variants were detected among 1880 breast cancer patients and 2000 healthy controls. No large mutations were found among early-onset cases using MLPA reaction. Conclusion Germline pathogenic TP53 variants were found in 4% early-onset Polish BC patients. No founder mutations were identified in Polish population. To improve the treatment and surveillance screening, the search for germline TP53 pathogenic variants is recommended for all female BC cases diagnosed ≤ 30 years old. Electronic supplementary material The online version of this article (10.1007/s12282-020-01151-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Emilia Rogoża-Janiszewska
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland.
| | - Karolina Malińska
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - Bohdan Górski
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - Rodney J Scott
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, NSW, Australia.,Department of Molecular Medicine, NSW Health Pathology-Hunter, Newcastle, NSW, Australia
| | - Cezary Cybulski
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - Wojciech Kluźniak
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - Marcin Lener
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - Anna Jakubowska
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - Jacek Gronwald
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - Tomasz Huzarski
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - Jan Lubiński
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
| | - Tadeusz Dębniak
- Department of Genetics and Pathology, International Hereditary Cancer Center, Pomeranian Medical University, Szczecin, Poland
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28
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Hu ZY, Liu L, Xie N, Lu J, Liu Z, Tang Y, Wang Y, Yang J, Ouyang Q. Germline PALB2 Mutations in Cancers and Its Distinction From Somatic PALB2 Mutations in Breast Cancers. Front Genet 2020; 11:829. [PMID: 33193564 PMCID: PMC7482549 DOI: 10.3389/fgene.2020.00829] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 07/09/2020] [Indexed: 12/27/2022] Open
Abstract
PALB2 is an important BRCAx candidate for familial breast cancers (FBC). PALB2 pathogenic variants (PVs) may not to conform to "two hit" paradigm. However, a recent study demonstrates that in the majority PALB2 germline mutant breast cancers, the loss of heterozygosity (LOH) and somatic point mutations are the "second hit." This study aimed to investigate the second hits in germline PALB2 mutations in breast cancers. We screened out 28 germline PALB2-mutation carriers among 480 familial cancer patients (including 143 FBC patients) in Geneplus database pool. Of the 143 patients with FBC, 10 had mono-allelic PALB2 germline mutations. All these germline PALB2 mutations were high-risk stop-gain, frameshift, or splicing mutations that concentrated in EX5-EX9 and might led to truncated proteins, severe functional defects and malignant phenotype. The hotspots were c.1057A[3 > 2] and c.3114-1G > A. Other mutations included c.389delA, c.2068C > T, c.2167_2168delAT, c.2629delT and c.2968G > T. Only one FBC patient has PALB2 somatic mutation and two patients had LOH of PALB2. All germline PALB2 mutations were high-risk mutations, whereas the somatic PALB2 mutations were moderate-risk missense mutations. We also distinguished PALB2 "novel mutations" from "reported mutations." In conclusion, germline PALB2 mutation should be put into the context of future screening.
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Affiliation(s)
- Zhe-Yu Hu
- Affiliated Cancer Hospital of Xiangya Medical School, Central South University/Hunan Cancer Hospital, Changsha, China.,Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, Changsha, China
| | - Liping Liu
- Affiliated Cancer Hospital of Xiangya Medical School, Central South University/Hunan Cancer Hospital, Changsha, China.,Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, Changsha, China
| | - Ning Xie
- Affiliated Cancer Hospital of Xiangya Medical School, Central South University/Hunan Cancer Hospital, Changsha, China.,Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, Changsha, China
| | - Jun Lu
- Affiliated Cancer Hospital of Xiangya Medical School, Central South University/Hunan Cancer Hospital, Changsha, China.,Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, Changsha, China
| | | | - Yu Tang
- Affiliated Cancer Hospital of Xiangya Medical School, Central South University/Hunan Cancer Hospital, Changsha, China.,Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, Changsha, China
| | - Yikai Wang
- Department of Biostatistics and Bioinformatics, Emory University Rollins School of Public Health, Atlanta, GA, United States
| | - Jianbo Yang
- Affiliated Cancer Hospital of Xiangya Medical School, Central South University/Hunan Cancer Hospital, Changsha, China.,Fujian Medical University Union Hospital, Fuzhou, China.,Department of Otolaryngology, Medical School, University of Minnesota, Minneapolis, MN, United States
| | - Quchang Ouyang
- Affiliated Cancer Hospital of Xiangya Medical School, Central South University/Hunan Cancer Hospital, Changsha, China.,Department of Breast Cancer Medical Oncology, Hunan Cancer Hospital, Changsha, China
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29
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Complex Characterization of Germline Large Genomic Rearrangements of the BRCA1 and BRCA2 Genes in High-Risk Breast Cancer Patients-Novel Variants from a Large National Center. Int J Mol Sci 2020; 21:ijms21134650. [PMID: 32629901 PMCID: PMC7370166 DOI: 10.3390/ijms21134650] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 06/19/2020] [Accepted: 06/27/2020] [Indexed: 12/23/2022] Open
Abstract
Large genomic rearrangements (LGRs) affecting one or more exons of BRCA1 and BRCA2 constitute a significant part of the mutation spectrum of these genes. Since 2004, the National Institute of Oncology, Hungary, has been involved in screening for LGRs of breast or ovarian cancer families enrolled for genetic testing. LGRs were detected by multiplex ligation probe amplification method, or next-generation sequencing. Where it was possible, transcript-level characterization of LGRs was performed. Phenotype data were collected and analyzed too. Altogether 28 different types of LGRs in 51 probands were detected. Sixteen LGRs were novel. Forty-nine cases were deletions or duplications in BRCA1 and two affected BRCA2. Rearrangements accounted for 10% of the BRCA1 mutations. Three exon copy gains, two complex rearrangements, and 23 exon losses were characterized by exact breakpoint determinations. The inferred mechanisms for LGR formation were mainly end-joining repairs utilizing short direct homologies. Comparing phenotype features of the LGR-carriers to that of the non-LGR BRCA1 mutation carriers, revealed no significant differences. Our study is the largest comprehensive report of LGRs of BRCA1/2 in familial breast and ovarian cancer patients in the Middle and Eastern European region. Our data add novel insights to genetic interpretation associated to the LGRs.
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30
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van der Merwe NC, Oosthuizen J, Theron M, Chong G, Foulkes WD. The contribution of large genomic rearrangements in BRCA1 and BRCA2 to South African familial breast cancer. BMC Cancer 2020; 20:391. [PMID: 32375709 PMCID: PMC7203887 DOI: 10.1186/s12885-020-06917-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 04/30/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Pathogenic variants that occur in the familial breast cancer genes (BRCA1/2) lead to truncated ineffective proteins in the majority of cases. These variants are mostly represented by small deletions/insertions, nonsense- and splice-site variants, although some larger pathogenic rearrangements occur. Currently, their contribution to familial breast cancer (BC) and ovarian cancer (OVC) in South Africa (SA) is unknown. METHODS Seven hundred and forty-four patients affected with BC or OVC were screened for larger genomic rearrangements (LGRs) by means of multiplex ligation-dependent probe amplification or Next Generation Sequencing using the Oncomine™ BRCA research assay. RESULTS The patients represented mostly medium to high-risk families, but also included lower risk patients without a family history of the disease, diagnosed at an early age of onset (< 40 years). Eight LGRs were detected (1.1%); seven in BRCA1 with a single whole gene deletion (WGD) detected for BRCA2. These eight LGRs accounted for 8.7% of the 92 BRCA1/2 pathogenic variants identified in the 744 cases. The pathogenic LGRs ranged from WGDs to the duplication of a single exon. CONCLUSIONS Larger rearrangements in BRCA1/2 contributed to the overall mutational burden of familial BC and OVC in SA. Almost a quarter of all pathogenic variants in BRCA1 were LGRs (7/30, 23%). The spectrum observed included two WGDs, one each for BRCA1 and BRCA2.
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Affiliation(s)
- Nerina C. van der Merwe
- Division of Human Genetics, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
- Division of Human Genetics, National Health Laboratory Services, Universitas Academic Hospital, Bloemfontein, South Africa
| | - Jaco Oosthuizen
- Division of Human Genetics, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
- Division of Human Genetics, National Health Laboratory Services, Universitas Academic Hospital, Bloemfontein, South Africa
| | - Magdalena Theron
- Division of Human Genetics, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
- Division of Human Genetics, National Health Laboratory Services, Universitas Academic Hospital, Bloemfontein, South Africa
| | - George Chong
- Lady Davis Institute and Segal Cancer Centre, Jewish General Hospital, Montréal, QC Canada
| | - William D. Foulkes
- Lady Davis Institute and Segal Cancer Centre, Jewish General Hospital, Montréal, QC Canada
- Research Institute of the McGill University Health Centre, Montréal, QC Canada
- Program in Cancer Genetics, Departments of Oncology and Human Genetics, McGill University, Montréal, QC Canada
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31
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Cerretelli G, Ager A, Arends MJ, Frayling IM. Molecular pathology of Lynch syndrome. J Pathol 2020; 250:518-531. [PMID: 32141610 DOI: 10.1002/path.5422] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 03/02/2020] [Accepted: 03/03/2020] [Indexed: 12/18/2022]
Abstract
Lynch syndrome (LS) is characterised by predisposition to colorectal, endometrial, and other cancers and is caused by inherited pathogenic variants affecting the DNA mismatch repair (MMR) genes MLH1, MSH2, MSH6, and PMS2. It is probably the most common predisposition to cancer, having an estimated prevalence of between 1/100 and 1/180. Resources such as the International Society for Gastrointestinal Hereditary Cancer's MMR gene variant database, the Prospective Lynch Syndrome Database (PLSD), and the Colon Cancer Family Register (CCFR), as well as pathological and immunological studies, are enabling advances in the understanding of LS. These include defined criteria by which to interpret gene variants, the function of MMR in the normal control of apoptosis, definition of the risks of the various cancers, and the mechanisms and pathways by which the colorectal and endometrial tumours develop, including the critical role of the immune system. Colorectal cancers in LS can develop along three pathways, including flat intramucosal lesions, which depend on the underlying affected MMR gene. This gives insights into the limitations of colonoscopic surveillance and highlights the need for other forms of anti-cancer prophylaxis in LS. Finally, it shows that the processes of autoimmunisation and immunoediting fundamentally constrain the development of tumours in LS and explain the efficacy of immune checkpoint blockade therapy in MMR-deficient tumours. © 2020 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Guia Cerretelli
- Division of Pathology, Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh, UK
| | - Ann Ager
- Division of Infection and Immunity, School of Medicine and Systems Immunity Research Institute, Cardiff University, Cardiff, UK
| | - Mark J Arends
- Division of Pathology, Cancer Research UK Edinburgh Centre, University of Edinburgh, Edinburgh, UK
| | - Ian M Frayling
- Inherited Tumour Syndromes Research Group, Institute of Cancer & Genetics, School of Medicine, Cardiff University, Cardiff, UK
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32
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Repo P, Järvinen RS, Jäntti JE, Markkinen S, Täll M, Raivio V, Turunen JA, Kivelä TT. Population-based analysis of BAP1 germline variations in patients with uveal melanoma. Hum Mol Genet 2020; 28:2415-2426. [PMID: 31058963 DOI: 10.1093/hmg/ddz076] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 04/03/2019] [Accepted: 04/03/2019] [Indexed: 02/06/2023] Open
Abstract
Pathogenic germline variants in the BRCA1-associated protein 1 (BAP1) gene cause the BAP1 tumor predisposition syndrome (BAP1-TPDS) with increased risk of several cancers, the most frequent of which is uveal melanoma (UM). Pathogenicity of loss-of-function (LOF) BAP1 variants is clear, as opposed to that of missense and regulatory region variants. We sequenced the coding, promoter, untranslated region (UTR) and intronic regions of BAP1 and analyzed copy number variations (CNVs). In this nationwide study, the cohort comprised UM patients diagnosed between 2010 and 2017. These included 432 of 520 consecutive Finnish UM patients, 16 of whom were familial, and one additional patient from a Finnish-Swedish family. Twenty-one different rare variants were found: seven exonic, seven intronic, four 3' UTR and three promoter. We considered five variants likely to be pathogenic by effect on splicing, nuclear localization or deubiquitination activity. Intron 2 (c.67+1G>T) and exon 14 (c.1780_1781insT) LOF variants were presumed founder mutations, occurring in two and four families, respectively; both abolished nuclear localization in vitro. Intron 2, exons 5 (c.281A>G) and 9 (c.680G>A) missense variants markedly reduced deubiquitinating activity. A deep intronic 25 base pair deletion in intron 1 caused aberrant splicing in vitro. On the basis of functional studies and family cancer history, we classified four exon 13 missense variants as benign. No CNVs were found. The prevalence of pathogenic variants was 9/433 (2%) and 4/16 (25%) in Finnish UM families. Family cancer history and functional assays are indispensable when establishing the pathogenicity of BAP1 variants. Deep intronic variants can cause BAP1-TPDS.
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Affiliation(s)
- Pauliina Repo
- Folkhälsan Research Center, Biomedicum Helsinki, Haartmaninkatu, FI Helsinki, Finland.,Department of Ophthalmology, University of Helsinki and Helsinki University Hospital, Haartmaninkatu C, FI Helsinki, Finland
| | - Reetta-Stiina Järvinen
- Folkhälsan Research Center, Biomedicum Helsinki, Haartmaninkatu, FI Helsinki, Finland.,Department of Ophthalmology, University of Helsinki and Helsinki University Hospital, Haartmaninkatu C, FI Helsinki, Finland
| | - Johannes E Jäntti
- Folkhälsan Research Center, Biomedicum Helsinki, Haartmaninkatu, FI Helsinki, Finland
| | - Salla Markkinen
- Folkhälsan Research Center, Biomedicum Helsinki, Haartmaninkatu, FI Helsinki, Finland
| | - Martin Täll
- Department of Ophthalmology, University of Helsinki and Helsinki University Hospital, Haartmaninkatu C, FI Helsinki, Finland
| | - Virpi Raivio
- Department of Ophthalmology, University of Helsinki and Helsinki University Hospital, Haartmaninkatu C, FI Helsinki, Finland
| | - Joni A Turunen
- Folkhälsan Research Center, Biomedicum Helsinki, Haartmaninkatu, FI Helsinki, Finland.,Department of Ophthalmology, University of Helsinki and Helsinki University Hospital, Haartmaninkatu C, FI Helsinki, Finland
| | - Tero T Kivelä
- Department of Ophthalmology, University of Helsinki and Helsinki University Hospital, Haartmaninkatu C, FI Helsinki, Finland
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33
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Boru G, Grosel TW, Pilarski R, Stautberg M, Massengill JB, Jeter J, Singh A, Marino MJ, McElroy JP, Davidorf FH, Cebulla CM, Abdel-Rahman MH. Germline large deletion of BAP1 and decreased expression in non-tumor choroid in uveal melanoma patients with high risk for inherited cancer. Genes Chromosomes Cancer 2019; 58:650-656. [PMID: 30883995 PMCID: PMC6612571 DOI: 10.1002/gcc.22752] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2018] [Revised: 03/09/2019] [Accepted: 03/12/2019] [Indexed: 12/12/2022] Open
Abstract
Uveal melanoma (UM) is the most common phenotype in patients with germline BAP1 mutation. This study aimed to identify selection criteria for BAP1 germline testing and assessed the role of large deletion/duplication and epigenetic inactivation. One hundred seventy-two UM patients with high risk of hereditary cancer were included. Germline variants in BAP1 were assessed by direct sequencing and large deletion/duplication by multiplex ligation-dependent probe amplification. BAP1 expression in unaffected choroid tissue from a patient with UM was assessed by quantitative RT-PCR and methylation by pyrosequencing. Twenty-eight patients had one or more germline sequence variants in BAP1; seven of these were pathogenic. One hundred forty patients were assessed for large deletion/duplication and in one BAP1 whole gene deletion was detected. In total, eight patients (4.7%) had pathogenic alterations in BAP1 with the highest frequencies of in patients with a personal/family history of ≥2 BAP1-related cancers 6/16 (38%), age of onset <35 years 4/21 (19%) and familial UM 6/34 (18%). One of 19 non-tumor choroid tissues tested showed uncharacteristically low expression as compared to the controls decrease in BAP1 RNA expression but no evidence of constitutional promotor hypermethylation was detected. UM patients with a strong personal or family history of cancers associated with BAP1, early age of onset and familial UM should be assessed for germline variants in BAP1, including large deletions.
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Affiliation(s)
- Getachew Boru
- Department of Ophthalmology and Visual Science, Havener Eye Institute, The Ohio State University Columbus, Ohio
| | - Timothy W. Grosel
- Department of Ophthalmology and Visual Science, Havener Eye Institute, The Ohio State University Columbus, Ohio
| | - Robert Pilarski
- Division of Human Genetics, Department of Internal Medicine, The Ohio State University Columbus, Ohio
| | - Meredith Stautberg
- Division of Human Genetics, Department of Internal Medicine, The Ohio State University Columbus, Ohio
| | - James B. Massengill
- Department of Ophthalmology and Visual Science, Havener Eye Institute, The Ohio State University Columbus, Ohio
| | - Joanne Jeter
- Division of Human Genetics, Department of Internal Medicine, The Ohio State University Columbus, Ohio
- Division of Medical Oncology, The Ohio State University Comprehensive Cancer Center, Columbus, Ohio
| | - Arun Singh
- Cole Eye Institute, Department of Ophthalmic Oncology, Cleveland Clinic, Cleveland, Ohio
| | - Meghan J. Marino
- Cole Eye Institute, Department of Ophthalmic Oncology, Cleveland Clinic, Cleveland, Ohio
| | - Joseph P. McElroy
- Center for Biostatistics, Department of Biomedical Informatics, The Ohio State University, Columbus, Ohio
| | - Frederick H. Davidorf
- Department of Ophthalmology and Visual Science, Havener Eye Institute, The Ohio State University Columbus, Ohio
| | - Colleen M. Cebulla
- Department of Ophthalmology and Visual Science, Havener Eye Institute, The Ohio State University Columbus, Ohio
| | - Mohamed H. Abdel-Rahman
- Department of Ophthalmology and Visual Science, Havener Eye Institute, The Ohio State University Columbus, Ohio
- Division of Human Genetics, Department of Internal Medicine, The Ohio State University Columbus, Ohio
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34
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Halliday D, Emmanouil B, Vassallo G, Lascelles K, Nicholson J, Chandratre S, Anand G, Wasik M, Pretorius P, Evans DG, Parry A, Axon P, Gair J, Smyth C, Afridi SK, Obholzer R, Everett V, Jarvis N, Henshaw K, Hanemann CO, Howard W, May A, Redman C, Rattihalli R, Tomkins H. Trends in phenotype in the English paediatric neurofibromatosis type 2 cohort stratified by genetic severity. Clin Genet 2019; 96:151-162. [DOI: 10.1111/cge.13551] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 04/03/2019] [Accepted: 04/07/2019] [Indexed: 11/27/2022]
Affiliation(s)
- Dorothy Halliday
- Oxford Centre for Genomic MedicineOxford University Hospitals NHS Trust Oxford UK
- Oxford NF2 Unit, Oxford University Hospitals NHS Trust Oxford UK
| | - Beatrice Emmanouil
- Oxford NF2 Unit, Oxford University Hospitals NHS Trust Oxford UK
- Oxford Brookes University, Faculty of Health and Life Sciences, Department of Psychology, Health and Professional Development Oxford UK
| | - Grace Vassallo
- Department of Paediatric NeurologyCentral Manchester University Hospitals NHS Foundation Trust Manchester UK
| | - Karine Lascelles
- Department of Paediatric NeurologyGuy's and St Thomas' NHS Foundation Trust London UK
| | - James Nicholson
- Department of Paediatric OncologyCambridge University Hospitals NHS Foundation Trust Cambridge UK
| | - Saleel Chandratre
- Department of Paediatric NeurologyOxford University Hospitals NHS Foundation Trust Oxford UK
| | - Geetha Anand
- Department of PaediatricsOxford University Hospitals NHS Foundation Trust Oxford UK
| | - Martin Wasik
- Department of OphthalmologyOxford University Hospitals NHS Foundation Trust Oxford UK
| | - Pieter Pretorius
- Depatment of NeuroradiologyOxford University Hospitals NHS Foundation Trust Oxford UK
| | - D. Gareth Evans
- Genomic Medicine, Division of Evolution and Genomic Sciences, MAHSCUniversity of Manchester, St Mary's Hospital Manchester UK
| | - Allyson Parry
- Oxford NF2 Unit, Oxford University Hospitals NHS Trust Oxford UK
- Department of NeurosciencesOxford University Hospitals NHS Foundation Trust Oxford UK
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35
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CNspector: a web-based tool for visualisation and clinical diagnosis of copy number variation from next generation sequencing. Sci Rep 2019; 9:6426. [PMID: 31015508 PMCID: PMC6478945 DOI: 10.1038/s41598-019-42858-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 04/08/2019] [Indexed: 11/23/2022] Open
Abstract
Next Generation Sequencing is now routinely used in the practice of diagnostic pathology to detect clinically relevant somatic and germline sequence variations in patient samples. However, clinical assessment of copy number variations (CNVs) and large-scale structural variations (SVs) is still challenging. While tools exist to estimate both, their results are typically presented separately in tables or static plots which can be difficult to read and are unable to show the context needed for clinical interpretation and reporting. We have addressed this problem with CNspector, a multi-scale interactive browser that shows CNVs in the context of other relevant genomic features to enable fast and effective clinical reporting. We illustrate the utility of CNspector at different genomic scales across a variety of sample types in a range of case studies. We show how CNspector can be used for diagnosis and reporting of exon-level deletions, focal gene-level amplifications, chromosome and chromosome arm level amplifications/deletions and in complex genomic rearrangements. CNspector is a web-based clinical variant browser tailored to the clinical application of next generation sequencing for CNV assessment. We have demonstrated the utility of this interactive software in typical applications across a range of tissue types and disease contexts encountered in the context of diagnostic pathology. CNspector is written in R and the source code is available for download under the GPL3 Licence from https://github.com/PapenfussLab/CNspector.
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36
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Suszynska M, Klonowska K, Jasinska AJ, Kozlowski P. Large-scale meta-analysis of mutations identified in panels of breast/ovarian cancer-related genes - Providing evidence of cancer predisposition genes. Gynecol Oncol 2019; 153:452-462. [PMID: 30733081 DOI: 10.1016/j.ygyno.2019.01.027] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 01/23/2019] [Accepted: 01/30/2019] [Indexed: 02/05/2023]
Abstract
OBJECTIVE Germline mutations occurring in the highly penetrant genes BRCA1 and BRCA2 are responsible for only certain cases of familial breast cancer (BC) and ovarian cancer (OC). Thus, the use of NGS multi-gene panel (MGP) testing has recently become very popular. METHODS To estimate a reliable BC and OC risk associated with pathogenic variants in the selected candidate BC/OC predisposition genes, a comprehensive meta-analysis of 48 MGP-based studies analyzing BC/OC patients was conducted. The role of 37 genes was evaluated, comparing, in total, the mutation frequency in ~120,000 BC/OC cases and ~120,000 controls, which guaranteed strong statistical support with high confidence for most analyzed genes. RESULTS We characterized the strategies of MGP analyses and the types and localizations of the identified mutations and showed that 13 and 11 of the analyzed genes were significantly associated with an increased BC and OC risk, respectively. The risk attributed to some of these genes (e.g., CDKN2A and PALB2 for BC) was similar to that observed for BRCA2. The analysis also showed a substantial difference in the profile of genes contributing to either BC or OC risk, including genes specifically associated with a high risk of OC but not BC (e.g., RAD51C, and RAD51D). CONCLUSIONS Our study provides strong statistical proof, defines the risk for many genes often considered candidates for BC/OC predisposition and excludes the role of other genes frequently analyzed in the MGPs. In the context of clinical diagnostics, the results support the knowledge-based interpretation of identified mutations.
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Affiliation(s)
- Malwina Suszynska
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Katarzyna Klonowska
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Anna J Jasinska
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland; Center for Neurobehavioral Genetics, Semel Institute for Neuroscience & Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA
| | - Piotr Kozlowski
- Department of Molecular Genetics, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.
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37
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Jansen S, van der Werf IM, Innes AM, Afenjar A, Agrawal PB, Anderson IJ, Atwal PS, van Binsbergen E, van den Boogaard MJ, Castiglia L, Coban-Akdemir ZH, van Dijck A, Doummar D, van Eerde AM, van Essen AJ, van Gassen KL, Guillen Sacoto MJ, van Haelst MM, Iossifov I, Jackson JL, Judd E, Kaiwar C, Keren B, Klee EW, Klein Wassink-Ruiter JS, Meuwissen ME, Monaghan KG, de Munnik SA, Nava C, Ockeloen CW, Pettinato R, Racher H, Rinne T, Romano C, Sanders VR, Schnur RE, Smeets EJ, Stegmann APA, Stray-Pedersen A, Sweetser DA, Terhal PA, Tveten K, VanNoy GE, de Vries PF, Waxler JL, Willing M, Pfundt R, Veltman JA, Kooy RF, Vissers LELM, de Vries BBA. De novo variants in FBXO11 cause a syndromic form of intellectual disability with behavioral problems and dysmorphisms. Eur J Hum Genet 2019; 27:738-746. [PMID: 30679813 DOI: 10.1038/s41431-018-0292-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 09/07/2018] [Accepted: 09/25/2018] [Indexed: 01/15/2023] Open
Abstract
Determining pathogenicity of genomic variation identified by next-generation sequencing techniques can be supported by recurrent disruptive variants in the same gene in phenotypically similar individuals. However, interpretation of novel variants in a specific gene in individuals with mild-moderate intellectual disability (ID) without recognizable syndromic features can be challenging and reverse phenotyping is often required. We describe 24 individuals with a de novo disease-causing variant in, or partial deletion of, the F-box only protein 11 gene (FBXO11, also known as VIT1 and PRMT9). FBXO11 is part of the SCF (SKP1-cullin-F-box) complex, a multi-protein E3 ubiquitin-ligase complex catalyzing the ubiquitination of proteins destined for proteasomal degradation. Twenty-two variants were identified by next-generation sequencing, comprising 2 in-frame deletions, 11 missense variants, 1 canonical splice site variant, and 8 nonsense or frameshift variants leading to a truncated protein or degraded transcript. The remaining two variants were identified by array-comparative genomic hybridization and consisted of a partial deletion of FBXO11. All individuals had borderline to severe ID and behavioral problems (autism spectrum disorder, attention-deficit/hyperactivity disorder, anxiety, aggression) were observed in most of them. The most relevant common facial features included a thin upper lip and a broad prominent space between the paramedian peaks of the upper lip. Other features were hypotonia and hyperlaxity of the joints. We show that de novo variants in FBXO11 cause a syndromic form of ID. The current series show the power of reverse phenotyping in the interpretation of novel genetic variances in individuals who initially did not appear to have a clear recognizable phenotype.
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Affiliation(s)
- Sandra Jansen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Ilse M van der Werf
- Department of Medical Genetics, University Hospital and University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium
| | - A Micheil Innes
- Alberta Children's Hospital Research Institute and Department of Medical Genetics, Cumming School of Medicine, University of Calgary, 2888 Shaganappi Trail NW, Calgary, AB, T3B 6A8, Canada
| | - Alexandra Afenjar
- Centre de Référence Déficiences Intellectuelles de Causes Rares, 75013, Paris, France.,APHP, GHUEP, Hôpital Armand Trousseau, Centre de Référence 'Malformations et maladies congénitales du cervelet', 75012, Paris, France
| | - Pankaj B Agrawal
- Divisions of Genetics and Genomics and Newborn Medicine, Manton Center for Orphan Disease Research, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Ilse J Anderson
- The University of Tennessee Genetics Center, Knoxville, TN, 37920, USA
| | - Paldeep S Atwal
- Department of Clinical Genomics, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Ellen van Binsbergen
- Department of Genetics, University Medical Centre Utrecht, P.O. Box 85500, 3508 GA, Utrecht, The Netherlands
| | - Marie-José van den Boogaard
- Department of Genetics, University Medical Centre Utrecht, P.O. Box 85500, 3508 GA, Utrecht, The Netherlands
| | - Lucia Castiglia
- Laboratory of Medical Genetics, Oasi Research Institute, 94018, Troina, Italy
| | - Zeynep H Coban-Akdemir
- Baylor-Hopkins Center for Mendelian Genomics, Baylor College of Medicine, Houston, TX, 77030, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Anke van Dijck
- Department of Medical Genetics, University Hospital and University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium
| | - Diane Doummar
- APHP, Service de Neurologie pédiatrique, Hôpital Armand Trousseau, Paris, France.,Sorbonne Université,GRC ConCer-LD, AP-HP, Hôpital Trousseau, Paris, France.,Service de neuropediatrie, Hôpital Trousseau, 26 avenue du dr Arnold Netter, 75012, Paris, France
| | - Albertien M van Eerde
- Department of Genetics, University Medical Centre Utrecht, P.O. Box 85500, 3508 GA, Utrecht, The Netherlands
| | - Anthonie J van Essen
- Department of Genetics, University of Groningen, University Medical Center Groningen (UMCG), 9700 RB, Groningen, The Netherlands
| | - Koen L van Gassen
- Department of Genetics, University Medical Centre Utrecht, P.O. Box 85500, 3508 GA, Utrecht, The Netherlands
| | | | - Mieke M van Haelst
- Department of Clinical Genetics, VU University Medical Center, 1081 HV, Amsterdam, The Netherlands
| | - Ivan Iossifov
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, 11724, USA.,New York Genome Center, New York, NY, 10013, USA
| | - Jessica L Jackson
- Department of Clinical Genomics, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Elizabeth Judd
- Department of Psychiatry, Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Charu Kaiwar
- Center for Individualized Medicine, Mayo Clinic, Scottsdale, AZ, 85259, USA.,Invitae, 1400 16th Street, San Francisco, CA, 94103, USA
| | - Boris Keren
- Département de Génétique, APHP, GH Pitié-Salpêtrière, Paris, 75013, France
| | - Eric W Klee
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Jolien S Klein Wassink-Ruiter
- Department of Genetics, University of Groningen, University Medical Center Groningen (UMCG), 9700 RB, Groningen, The Netherlands
| | - Marije E Meuwissen
- Department of Medical Genetics, University Hospital and University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium
| | | | - Sonja A de Munnik
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Caroline Nava
- Département de Génétique, APHP, GH Pitié-Salpêtrière, Paris, 75013, France.,INSERM, U 1127, CNRS UMR 7225, Institut du Cerveau et de la Moelle épinière, ICM, Sorbonne Universités, UPMC Université de Paris 06, 75013, Paris, France
| | - Charlotte W Ockeloen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Rosa Pettinato
- Pediatrics and Medical Genetics, Oasi Research Institute - IRCCS, 94018, Troina, Italy
| | - Hilary Racher
- Alberta Children's Hospital Research Institute and Department of Medical Genetics, Cumming School of Medicine, University of Calgary, 2888 Shaganappi Trail NW, Calgary, AB, T3B 6A8, Canada.,Impact Genetics, 1100 Bennett Road, Bowmanville, ON, L1C 3K5, Canada
| | - Tuula Rinne
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Corrado Romano
- Pediatrics and Medical Genetics, Oasi Research Institute - IRCCS, 94018, Troina, Italy
| | - Victoria R Sanders
- Department of Pediatrics, Division of Genetics, Birth Defects and Metabolism, Ann and Robert H Lurie Children's Hospital of Chicago, 225 East Chicago Avenue, Chicago, IL, 60611, USA
| | | | - Eric J Smeets
- Department of Clinical Genetics, Maastricht University Medical Centre, Universiteitssingel 50, 9229 ER, Maastricht, The Netherlands
| | - Alexander P A Stegmann
- Department of Clinical Genetics, Maastricht University Medical Centre, Universiteitssingel 50, 9229 ER, Maastricht, The Netherlands
| | - Asbjørg Stray-Pedersen
- Baylor-Hopkins Center for Mendelian Genomics, Baylor College of Medicine, Houston, TX, 77030, USA.,Norwegian National Unit for Newborn Screening, Department of Pediatric and Adolescent Medicine, Oslo University Hospital, Pb 4950 Nydalen, 0424, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, 0318, Oslo, Norway
| | - David A Sweetser
- Division of Medical Genetics, Massachusetts General Hospital for Children, Boston, MA, 02114, USA
| | - Paulien A Terhal
- Department of Genetics, University Medical Centre Utrecht, P.O. Box 85500, 3508 GA, Utrecht, The Netherlands
| | - Kristian Tveten
- Department of Medical Genetics, Telemark Hospital Trust, 3710, Skien, Norway
| | - Grace E VanNoy
- Divisions of Genetics and Genomics and Newborn Medicine, Manton Center for Orphan Disease Research, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Petra F de Vries
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Jessica L Waxler
- Division of Medical Genetics, Massachusetts General Hospital for Children, Boston, MA, 02114, USA
| | - Marcia Willing
- Department of Pediatrics, Washington University School of Medicine, St Louis, MO, 63110, USA
| | - Rolph Pfundt
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Joris A Veltman
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.,Institute of Genetic Medicine, International Centre for Life, Newcastle University, Central Parkway, Newcastle, NE1 3BZ, UK
| | - R Frank Kooy
- Department of Medical Genetics, University Hospital and University of Antwerp, Universiteitsplein 1, 2610, Antwerp, Belgium
| | - Lisenka E L M Vissers
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Bert B A de Vries
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.
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Abstract
OBJECTIVE To introduce genetic testing as it relates to oncology and nursing. DATA SOURCES Peer-reviewed journals, government web sites and resources, published recommendations, and professional experience as a genetic counselor. CONCLUSION Genetic testing is a major component of oncology health care and with the continued expansion of the application of genetic testing, many patients will have genetic testing throughout their cancer journey. IMPLICATIONS FOR NURSING PRACTICE To provide supportive care for patients with cancer or at risk for cancer, oncology nurses need to appreciate the many and varied genetic testing platforms and testing strategies. Oncology nurses can be a resource for patients and family members regarding testing options, insurance coverage, and understanding medical management decisions.
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de Andrade KC, Frone MN, Wegman-Ostrosky T, Khincha PP, Kim J, Amadou A, Santiago KM, Fortes FP, Lemonnier N, Mirabello L, Stewart DR, Hainaut P, Kowalski LP, Savage SA, Achatz MI. Variable population prevalence estimates of germline TP53 variants: A gnomAD-based analysis. Hum Mutat 2018; 40:97-105. [PMID: 30352134 DOI: 10.1002/humu.23673] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 10/09/2018] [Accepted: 10/20/2018] [Indexed: 12/27/2022]
Abstract
Reports of variable cancer penetrance in Li-Fraumeni syndrome (LFS) have raised questions regarding the prevalence of pathogenic germline TP53 variants. We previously reported higher-than-expected population prevalence estimates in sequencing databases composed of individuals unselected for cancer history. This study aimed to expand and further evaluate the prevalence of pathogenic and likely pathogenic germline TP53 variants in the gnomAD dataset (version r2.0.2, n = 138,632). Variants were selected and classified based on our previously published algorithm and compared with alternative estimates based on three different classification databases: ClinVar, HGMD, and the UMD_TP53 database. Conservative prevalence estimates of pathogenic and likely pathogenic TP53 variants were within the range of one carrier in 3,555-5,476 individuals. Less stringent classification increased the approximate prevalence to one carrier in every 400-865 individuals, mainly due to the inclusion of the controvertible p.N235S, p.V31I, and p.R290H variants. This study shows a higher-than-expected population prevalence of pathogenic and likely pathogenic germline TP53 variants even with the most conservative estimates. However, these estimates may not necessarily reflect the prevalence of the classical LFS phenotype, which is based upon family history of cancer. Comprehensive approaches are needed to better understand the interplay of germline TP53 variant classification, prevalence estimates, cancer penetrance, and LFS-associated phenotype.
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Affiliation(s)
- Kelvin C de Andrade
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland.,International Research Center, A.C. Camargo Cancer Center, São Paulo, Brazil
| | - Megan N Frone
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland
| | - Talia Wegman-Ostrosky
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland.,Division of Research, National Cancer Institute, Mexico City, Mexico
| | - Payal P Khincha
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland
| | - Jung Kim
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland
| | - Amina Amadou
- Institute for Advanced Biosciences, Inserm U 1209 CNRS UMR 5309 Université Grenoble Alpes, Site Santé, Allée des Alpes, La Tronche, France
| | - Karina M Santiago
- International Research Center, A.C. Camargo Cancer Center, São Paulo, Brazil
| | - Fernanda P Fortes
- International Research Center, A.C. Camargo Cancer Center, São Paulo, Brazil
| | - Nathanaël Lemonnier
- Institute for Advanced Biosciences, Inserm U 1209 CNRS UMR 5309 Université Grenoble Alpes, Site Santé, Allée des Alpes, La Tronche, France
| | - Lisa Mirabello
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland
| | - Douglas R Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland
| | - Pierre Hainaut
- Institute for Advanced Biosciences, Inserm U 1209 CNRS UMR 5309 Université Grenoble Alpes, Site Santé, Allée des Alpes, La Tronche, France
| | - Luiz P Kowalski
- Department of Head and Neck Surgery and Otorhinolaryngology, AC Camargo Cancer Center, São Paulo, Brazil
| | - Sharon A Savage
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland
| | - Maria I Achatz
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland.,Centro de Oncologia, Sírio-Libanês Hospital, São Paulo, Brazil
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40
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Yost S, Münz M, Mahamdallie S, Renwick A, Ruark E, Rahman N. Clinical Annotation Reference Templates: a resource for consistent variant annotation. Wellcome Open Res 2018. [DOI: 10.12688/wellcomeopenres.14924.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Annotating the impact of a variant on a gene is a vital component of genetic medicine and genetic research. Different gene annotations for the same genomic variant are possible, because different structures and sequences for the same gene are available. The clinical community typically use RefSeq NMs to annotate gene variation, which do not always match the reference genome. The scientific community typically use Ensembl ENSTs to annotate gene variation. These match the reference genome, but often do not match the equivalent NM. Often the transcripts used to annotate gene variation are not provided, impeding interoperability and consistency. Here we introduce the concept of the Clinical Annotation Reference Template (CART). CARTs are analogous to the reference genome; they provide a universal standard template so reference genomic coordinates are consistently annotated at the protein level. Naturally, there are many situations where annotations using a specific transcript, or multiple transcripts are useful. The aim of the CARTs is not to impede this practice. Rather, the CART annotation serves as an anchor to ensure interoperability between different annotation systems and variant frequency accuracy. Annotations using other explicitly-named transcripts should also be provided, wherever useful. We have integrated transcript data to generate CARTs for over 18,000 genes, for both GRCh37 and GRCh38, based on the associated NM and ENST identified through the CART selection process. Each CART has a unique ID and can be used individually or as a stable set of templates; CART37A for GRCh37 and CART38A for GRCh38. We have made the CARTs available on the UCSC browser and in different file formats on the Open Science Framework: https://osf.io/tcvbq/. We have also made the CARTtools software we used to generate the CARTs available on GitHub. We hope the CARTs will be useful in helping to drive transparent, stable, consistent, interoperable variant annotation.
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Identification and Characterization of a New BRCA2 Rearrangement in an Italian Family with Hereditary Breast and Ovarian Cancer Syndrome. Mol Diagn Ther 2018. [PMID: 28620890 DOI: 10.1007/s40291-017-0288-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
INTRODUCTION Many studies document the involvement of BRCA1/2 gene rearrangements in genetic predisposition to breast and ovarian cancer. Large genomic rearrangements (LGRs) of BRCA1 account for 0-27% of all disease-causing mutations in various populations, while LGRs in BRCA2 are rarer. Here, we describe a novel BRCA2 LGR, involving the duplication of exons 4-26, in an Italian family with hereditary breast and ovarian cancer (HBOC) syndrome. OBJECTIVE Our purpose was to provide an effective characterization of this variant using a combination of different methods able to establish the exact breakpoints of the duplication. METHODS A multiplex amplicon quantification (MAQ) assay was used as the primary screening method in the detection of LGRs. Array comparative genomic hybridization (CGH), reverse transcriptase polymerase chain reaction (RT-PCR) and long-range PCR were used for the careful characterization of the rearrangement and breakpoint regions. The Repeat Masker program was employed to identify Alu sequences at breakpoint junctions. RESULTS Array CGH and long-range PCR strategies revealed that the BRCA2 exons 4-26 duplication (g.12016_87170dup) involved exactly 75,154 bp nucleotides between intron 3 and intron 26 of the gene. Given that no Alu repeats were found at the junction sites, we support the hypothesis that the new duplication could be the result of a microhomology-mediated event (MH) involving very short homologous sequences at an upstream breakpoint. DISCUSSION LGR investigation is mandatory in BRCA1/2 routine testing in order to provide a complete result for a targeted therapeutic decision. Nevertheless, the characterization and classification of novel BRCA1/2 variants represents a crucial step in the support of genetic counselling. Our results, including a comprehensive co-segregation analysis, indicate that the novel duplication identifed has a pathogenic role and would be considered a causing-disease variant in genetic and oncologic counselling.
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Concolino P, Rizza R, Mignone F, Costella A, Guarino D, Carboni I, Capoluongo E, Santonocito C, Urbani A, Minucci A. A comprehensive BRCA1/2 NGS pipeline for an immediate Copy Number Variation (CNV) detection in breast and ovarian cancer molecular diagnosis. Clin Chim Acta 2018; 480:173-179. [PMID: 29458049 DOI: 10.1016/j.cca.2018.02.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 02/10/2018] [Accepted: 02/13/2018] [Indexed: 02/07/2023]
Affiliation(s)
- Paola Concolino
- Laboratory of Molecular Biology, Institute of Biochemistry and Clinical Biochemistry, Catholic University of Sacred Heart, Largo A. Gemelli 8, 00168 Rome, Italy.
| | - Roberta Rizza
- Laboratory of Molecular Biology, Institute of Biochemistry and Clinical Biochemistry, Catholic University of Sacred Heart, Largo A. Gemelli 8, 00168 Rome, Italy
| | - Flavio Mignone
- Department of Science and Innovation Technology (DISIT), University of Piemonte Orientale, Alessandria, Italy
| | - Alessandra Costella
- Laboratory of Molecular Biology, Institute of Biochemistry and Clinical Biochemistry, Catholic University of Sacred Heart, Largo A. Gemelli 8, 00168 Rome, Italy
| | - Donatella Guarino
- Laboratory of Molecular Biology, Institute of Biochemistry and Clinical Biochemistry, Catholic University of Sacred Heart, Largo A. Gemelli 8, 00168 Rome, Italy
| | - Ilaria Carboni
- Institute of Legal Medicine, Catholic University of Sacred Heart, Largo A. Gemelli 8, 00168 Rome, Italy
| | - Ettore Capoluongo
- Laboratory of Molecular Biology, Institute of Biochemistry and Clinical Biochemistry, Catholic University of Sacred Heart, Largo A. Gemelli 8, 00168 Rome, Italy; Laboratory of Advanced Molecular Diagnostics (DIMA), Istituto Dermopatico dell'Immacolata, Fondazione Luigi Maria Monti, IRCCS, Rome, Italy
| | - Concetta Santonocito
- Laboratory of Molecular Biology, Institute of Biochemistry and Clinical Biochemistry, Catholic University of Sacred Heart, Largo A. Gemelli 8, 00168 Rome, Italy
| | - Andrea Urbani
- Laboratory of Molecular Biology, Institute of Biochemistry and Clinical Biochemistry, Catholic University of Sacred Heart, Largo A. Gemelli 8, 00168 Rome, Italy
| | - Angelo Minucci
- Laboratory of Molecular Biology, Institute of Biochemistry and Clinical Biochemistry, Catholic University of Sacred Heart, Largo A. Gemelli 8, 00168 Rome, Italy
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Dominguez-Valentin M, Evans DGR, Nakken S, Tubeuf H, Vodak D, Ekstrøm PO, Nissen AM, Morak M, Holinski-Feder E, Martins A, Møller P, Hovig E. Genetic variants of prospectively demonstrated phenocopies in BRCA1/2 kindreds. Hered Cancer Clin Pract 2018; 16:4. [PMID: 29371908 PMCID: PMC5769521 DOI: 10.1186/s13053-018-0086-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 01/10/2018] [Indexed: 01/03/2023] Open
Abstract
Background In kindreds carrying path_BRCA1/2 variants, some women in these families will develop cancer despite testing negative for the family’s pathogenic variant. These families may have additional genetic variants, which not only may increase the susceptibility of the families’ path_BRCA1/2, but also be capable of causing cancer in the absence of the path_BRCA1/2 variants. We aimed to identify novel genetic variants in prospectively detected breast cancer (BC) or gynecological cancer cases tested negative for their families’ pathogenic BRCA1/2 variant (path_BRCA1 or path_BRCA2). Methods Women with BC or gynecological cancer who had tested negative for path_BRCA1 or path_BRCA2 variants were included. Forty-four cancer susceptibility genes were screened for genetic variation through a targeted amplicon-based sequencing assay. Protein- and RNA splicing-dedicated in silico analyses were performed for all variants of unknown significance (VUS). Variants predicted as the ones most likely affecting pre-mRNA splicing were experimentally analyzed in a minigene assay. Results We identified 48 women who were tested negative for their family’s path_BRCA1 (n = 13) or path_BRCA2 (n = 35) variants. Pathogenic variants in the ATM, BRCA2, MSH6 and MUTYH genes were found in 10% (5/48) of the cases, of whom 15% (2/13) were from path_BRCA1 and 9% (3/35) from path_BRCA2 families. Out of the 26 unique VUS, 3 (12%) were predicted to affect RNA splicing (APC c.721G > A, MAP3K1 c.764A > G and MSH2 c.815C > T). However, by using a minigene, assay we here show that APC c.721G > A does not cause a splicing defect, similarly to what has been recently reported for the MAP3K1 c.764A > G. The MSH2 c.815C > T was previously described as causing partial exon skipping and it was identified in this work together with the path_BRCA2 c.9382C > T (p.R3128X). Conclusion All women in breast or breast/ovarian cancer kindreds would benefit from being offered genetic testing irrespective of which causative genetic variants have been demonstrated in their relatives. Electronic supplementary material The online version of this article (10.1186/s13053-018-0086-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mev Dominguez-Valentin
- 1Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - D Gareth R Evans
- 2Department of Genetic Medicine, The University of Manchester, Manchester Academic Health Science Centre, St. Mary's Hospital, Manchester, UK.,3Genesis Prevention Centre, University Hospital of South Manchester, Southmoor Road, Wythenshawe, UK
| | - Sigve Nakken
- 1Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Hélène Tubeuf
- 4Inserm-U1245, UNIROUEN, Normandie Univ, Normandy Centre for Genomic and Personalized Medicine, Rouen, France.,Interactive Biosoftware, Rouen, France
| | - Daniel Vodak
- 1Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Per Olaf Ekstrøm
- 1Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Anke M Nissen
- 6Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Ziemssenstr. 1, Munich, Germany.,MGZ-Medizinisch Genetisches Zentrum, Munich, Germany
| | - Monika Morak
- 6Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Ziemssenstr. 1, Munich, Germany.,MGZ-Medizinisch Genetisches Zentrum, Munich, Germany
| | - Elke Holinski-Feder
- 6Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Ziemssenstr. 1, Munich, Germany.,MGZ-Medizinisch Genetisches Zentrum, Munich, Germany
| | - Alexandra Martins
- 4Inserm-U1245, UNIROUEN, Normandie Univ, Normandy Centre for Genomic and Personalized Medicine, Rouen, France
| | - Pål Møller
- 1Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,8Department of Human Medicine, Universität Witten/Herdecke, Witten, Germany.,9Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Eivind Hovig
- 1Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,10Department of Informatics, University of Oslo, Oslo, Norway.,11Institute of Cancer Genetics and Informatics, Oslo University Hospital, Oslo, Norway
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44
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Innes J, Reali L, Clayton-Smith J, Hall G, Lim DHK, Burghel GJ, French K, Khan U, Walker D, Lalloo F, Evans DGR, McMullan D, Maher ER, Woodward ER. CNVs affecting cancer predisposing genes (CPGs) detected as incidental findings in routine germline diagnostic chromosomal microarray (CMA) testing. J Med Genet 2017; 55:89-96. [DOI: 10.1136/jmedgenet-2017-104892] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 08/23/2017] [Accepted: 08/28/2017] [Indexed: 11/03/2022]
Abstract
BackgroundIdentification of CNVs through chromosomal microarray (CMA) testing is the first-line investigation in individuals with learning difficulties/congenital abnormalities. Although recognised that CMA testing may identify CNVs encompassing a cancer predisposition gene (CPG), limited information is available on the frequency and nature of such results.MethodsWe investigated CNV gains and losses affecting 39 CPGs in 3366 pilot index case individuals undergoing CMA testing, and then studied an extended cohort (n=10 454) for CNV losses at 105 CPGs and CNV gains at 9 proto-oncogenes implicated in inherited cancer susceptibility.ResultsIn the pilot cohort, 31/3366 (0.92%) individuals had a CNV involving one or more of 16/39 CPGs. 30/31 CNVs involved a tumour suppressor gene (TSG), and 1/30 a proto-oncogene (gain of MET). BMPR1A, TSC2 and TMEM127 were affected in multiple cases. In the second stage analysis, 49/10 454 (0.47%) individuals in the extended cohort had 50 CNVs involving 24/105 CPGs. 43/50 CNVs involved a TSG and 7/50 a proto-oncogene (4 gains, 3 deletions). The most frequently involved genes, FLCN (n=10) and SDHA (n=7), map to the Smith-Magenis and cri-du-chat regions, respectively.ConclusionIncidental identification of a CNV involving a CPG is not rare and poses challenges for future cancer risk estimation. Prospective data collection from CPG-CNV cohorts ascertained incidentally and through syndromic presentations is required to determine the risks posed by specific CNVs. In particular, ascertainment and investigation of adults with CPG-CNVs and adults with learning disability and cancer, could provide important information to guide clinical management and surveillance.
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Mahamdallie S, Ruark E, Yost S, Ramsay E, Uddin I, Wylie H, Elliott A, Strydom A, Renwick A, Seal S, Rahman N. The ICR96 exon CNV validation series: a resource for orthogonal assessment of exon CNV calling in NGS data. Wellcome Open Res 2017. [PMID: 28630945 PMCID: PMC5473400 DOI: 10.12688/wellcomeopenres.11689.1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Detection of deletions and duplications of whole exons (exon CNVs) is a key requirement of genetic testing. Accurate detection of this variant type has proved very challenging in targeted next-generation sequencing (NGS) data, particularly if only a single exon is involved. Many different NGS exon CNV calling methods have been developed over the last five years. Such methods are usually evaluated using simulated and/or in-house data due to a lack of publicly-available datasets with orthogonally generated results. This hinders tool comparisons, transparency and reproducibility. To provide a community resource for assessment of exon CNV calling methods in targeted NGS data, we here present the ICR96 exon CNV validation series. The dataset includes high-quality sequencing data from a targeted NGS assay (the TruSight Cancer Panel) together with Multiplex Ligation-dependent Probe Amplification (MLPA) results for 96 independent samples. 66 samples contain at least one validated exon CNV and 30 samples have validated negative results for exon CNVs in 26 genes. The dataset includes 46 exon CNVs in
BRCA1,
BRCA2,
TP53,
MLH1,
MSH2,
MSH6,
PMS2,
EPCAM or
PTEN, giving excellent representation of the cancer predisposition genes most frequently tested in clinical practice. Moreover, the validated exon CNVs include 25 single exon CNVs, the most difficult type of exon CNV to detect. The FASTQ files for the ICR96 exon CNV validation series can be accessed through the European-Genome phenome Archive (EGA) under the accession number EGAS00001002428.
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Affiliation(s)
- Shazia Mahamdallie
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK.,TGLclinical, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Elise Ruark
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK.,TGLclinical, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Shawn Yost
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK.,TGLclinical, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Emma Ramsay
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK.,TGLclinical, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Imran Uddin
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK.,TGLclinical, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Harriett Wylie
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK.,TGLclinical, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Anna Elliott
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK.,TGLclinical, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Ann Strydom
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK.,TGLclinical, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Anthony Renwick
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Sheila Seal
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK.,TGLclinical, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Nazneen Rahman
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK.,TGLclinical, The Institute of Cancer Research, London, SM2 5NG, UK.,Cancer Genetics Unit, Royal Marsden NHS Foundation Trust, London, SM2 5PT, UK
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Rustad CF, Dahl HM, Bowers NL, Sitek JC, Heiberg A, Huson S, Prescott T, Evans DGR. Neurofibromatosis type 2: Multiple intra-dermal tumors in a toddler. Am J Med Genet A 2017; 173:1447-1449. [PMID: 28371307 DOI: 10.1002/ajmg.a.38177] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 01/22/2017] [Accepted: 01/23/2017] [Indexed: 11/05/2022]
Affiliation(s)
- Cecilie F Rustad
- Department of Medical Genetics, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Hilde M Dahl
- Department of Child Neurology, Oslo University Hospital Rikshospitalet, Nydalen, Oslo, Norway
| | - Naomi L Bowers
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Central Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Jan C Sitek
- Department of Dermatology, Oslo University Hospital Rikshospitalet, Nydalen, Oslo, Norway
| | - Arvid Heiberg
- Department of Medical Genetics, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | - Susan Huson
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre, Manchester, UK
| | - Trine Prescott
- Department of Laboratory Medicine, Telemark Hospital, Ulefossveien, Skien, Norway
| | - D Gareth R Evans
- University of Manchester, Division of Evolution and Genomic Science, St Mary's Hospital, Manchester Academic Health Science Centre, Central Manchester Foundation Trust, Manchester, UK
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McVeigh TP, Cody N, Carroll C, Duff M, Farrell M, Bradley L, Gallagher D, McDevitt T, Green AJ. Recurrent large genomic rearrangements in BRCA1 and BRCA2 in an Irish case series. Cancer Genet 2017; 214-215:1-8. [PMID: 28595730 DOI: 10.1016/j.cancergen.2017.02.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 02/24/2017] [Accepted: 02/25/2017] [Indexed: 12/12/2022]
Abstract
Mutations in BRCA1 and BRCA2 confer a highly increased risk of cancers, mainly of the breast and ovary. Most variants are point mutations or small insertions/deletions detectable by Sanger sequencing. Large genomic rearrangements, including deletions/duplications of multiple exons, are not routinely detectable by Sanger sequencing, but can be reliably identified by Multiplex Ligation-dependent Probe Amplification (MLPA), and account for 5-17% mutations in different populations. Comprehensive mutation testing using these two methods has been facilitated via our centre since 2005. The aim of this study was to investigate the incidence of and phenotype associated with large genomic rearrangements in BRCA1 and BRCA2 in an Irish cohort. An observational cohort study was undertaken. Patients with large genomic rearrangements in BRCA1/BRCA2 were identified from a prospectively maintained database of MLPA test results. Phenotypic and genotypic data were retrieved by chart review. Large genomic rearrangements in BRCA1 were identified in 49 families; and in BRCA2 in 7 families, representing ~11% of mutations in BRCA1/BRCA2 in Ireland. The most common large genomic rearrangement in BRCA1 was deletion of exons 1-23 (11 families, 7 from Co. Galway). Other common mutations included deletions of exon 3 (8 families) and exons 1-2 (6 families). Deletion of exons 19-20 in BRCA2 represented the familial mutation in five families, all from East Ireland (Wexford/Wicklow/Dublin). It is evident that a significant proportion of highly penetrant pathogenic variants in BRCA1 and BRCA2 will be missed if testing is limited to PCR-based Sanger sequencing alone. Screening for large genomic rearrangements in BRCA1 and BRCA2 in the routine diagnostic workflow is critical to avoid false negative results.
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Affiliation(s)
- Terri P McVeigh
- Department of Clinical Genetics, Our Lady's Children's Hospital, Crumlin, Ireland.
| | - Nuala Cody
- Department of Clinical Genetics, Our Lady's Children's Hospital, Crumlin, Ireland
| | - Cliona Carroll
- Department of Clinical Genetics, Our Lady's Children's Hospital, Crumlin, Ireland
| | - Marie Duff
- Department of Clinical Genetics, Our Lady's Children's Hospital, Crumlin, Ireland
| | - Michael Farrell
- Cancer Genetics Service, Mater Misericordiae University Hospital, Ireland
| | - Lisa Bradley
- Department of Clinical Genetics, Our Lady's Children's Hospital, Crumlin, Ireland
| | - David Gallagher
- Cancer Genetics Service, Mater Misericordiae University Hospital, Ireland; Cancer Genetics Service, St James' University Hospital, UK
| | - Trudi McDevitt
- Department of Clinical Genetics, Our Lady's Children's Hospital, Crumlin, Ireland
| | - Andrew J Green
- Department of Clinical Genetics, Our Lady's Children's Hospital, Crumlin, Ireland
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48
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Alternative outcomes of pathogenic complex somatic structural variations in the genomes of NF1 and NF2 patients. Neurogenetics 2017; 18:169-174. [PMID: 28285357 DOI: 10.1007/s10048-017-0512-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 02/27/2017] [Accepted: 03/02/2017] [Indexed: 10/20/2022]
Abstract
Multiplex ligation-dependent probe amplification (MLPA) has been widely used to identify copy-number variations (CNVs), but MLPA's sensitivity and specificity in mosaic CNV detection are largely unknown. Here, we present two mosaic deletions identified by MLPA as NF1 deletion of exons 17-21 and NF2 deletion of exons 9-10. Through cDNA analysis, genomic breakpoint-spanning PCR and Sanger sequencing, we found however both NF1 and NF2 deletions are each composed of two consecutive deletions, which cannot be differentiated by MLPA. Importantly, these consecutive deletions are most likely originating from a single genomic rearrangement and have been preserved independently in different populations of cells.
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49
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Fowler A, Mahamdallie S, Ruark E, Seal S, Ramsay E, Clarke M, Uddin I, Wylie H, Strydom A, Lunter G, Rahman N. Accurate clinical detection of exon copy number variants in a targeted NGS panel using DECoN. Wellcome Open Res 2016; 1:20. [PMID: 28459104 PMCID: PMC5409526 DOI: 10.12688/wellcomeopenres.10069.1] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background: Targeted next generation sequencing (NGS) panels are increasingly being used in clinical genomics to increase capacity, throughput and affordability of gene testing. Identifying whole exon deletions or duplications (termed exon copy number variants, ‘exon CNVs’) in exon-targeted NGS panels has proved challenging, particularly for single exon CNVs. Methods: We developed a tool for the
Detection of
Exon
Copy
Number variants (DECoN), which is optimised for analysis of exon-targeted NGS panels in the clinical setting. We evaluated DECoN performance using 96 samples with independently validated exon CNV data. We performed simulations to evaluate DECoN detection performance of single exon CNVs and to evaluate performance using different coverage levels and sample numbers. Finally, we implemented DECoN in a clinical laboratory that tests
BRCA1 and
BRCA2 with the TruSight Cancer Panel (TSCP). We used DECoN to analyse 1,919 samples, validating exon CNV detections by multiplex ligation-dependent probe amplification (MLPA). Results: In the evaluation set, DECoN achieved 100% sensitivity and 99% specificity for BRCA exon CNVs, including identification of 8 single exon CNVs. DECoN also identified 14/15 exon CNVs in 8 other genes. Simulations of all possible BRCA single exon CNVs gave a mean sensitivity of 98% for deletions and 95% for duplications. DECoN performance remained excellent with different levels of coverage and sample numbers; sensitivity and specificity was >98% with the typical NGS run parameters. In the clinical pipeline, DECoN automatically analyses pools of 48 samples at a time, taking 24 minutes per pool, on average. DECoN detected 24 BRCA exon CNVs, of which 23 were confirmed by MLPA, giving a false discovery rate of 4%. Specificity was 99.7%. Conclusions: DECoN is a fast, accurate, exon CNV detection tool readily implementable in research and clinical NGS pipelines. It has high sensitivity and specificity and acceptable false discovery rate. DECoN is freely available at
www.icr.ac.uk/decon.
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Affiliation(s)
- Anna Fowler
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Shazia Mahamdallie
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK.,TGLclinical, Institute of Cancer Research, London, UK
| | - Elise Ruark
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK.,TGLclinical, Institute of Cancer Research, London, UK
| | - Sheila Seal
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK.,TGLclinical, Institute of Cancer Research, London, UK
| | - Emma Ramsay
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK.,TGLclinical, Institute of Cancer Research, London, UK
| | - Matthew Clarke
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK
| | - Imran Uddin
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK.,TGLclinical, Institute of Cancer Research, London, UK
| | - Harriet Wylie
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK.,TGLclinical, Institute of Cancer Research, London, UK
| | - Ann Strydom
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK.,TGLclinical, Institute of Cancer Research, London, UK
| | - Gerton Lunter
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Nazneen Rahman
- Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK.,TGLclinical, Institute of Cancer Research, London, UK.,Cancer Genetics Unit, The Royal Marsden NHS Foundation Trust, Sutton, UK
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50
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Lagerstedt-Robinson K, Rohlin A, Aravidis C, Melin B, Nordling M, Stenmark-Askmalm M, Lindblom A, Nilbert M. Mismatch repair gene mutation spectrum in the Swedish Lynch syndrome population. Oncol Rep 2016; 36:2823-2835. [PMID: 27601186 DOI: 10.3892/or.2016.5060] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 05/31/2016] [Indexed: 12/21/2022] Open
Abstract
Lynch syndrome caused by constitutional mismatch‑repair defects is one of the most common hereditary cancer syndromes with a high risk for colorectal, endometrial, ovarian and urothelial cancer. Lynch syndrome is caused by mutations in the mismatch repair (MMR) genes i.e., MLH1, MSH2, MSH6 and PMS2. After 20 years of genetic counseling and genetic testing for Lynch syndrome, we have compiled the mutation spectrum in Sweden with the aim to provide a population-based perspective on the contribution from the different MMR genes, the various types of mutations and the influence from founder mutations. Mutation data were collected on a national basis from all laboratories involved in genetic testing. Mutation analyses were performed using mainly Sanger sequencing and multiplex ligation-dependent probe amplification. A total of 201 unique disease-predisposing MMR gene mutations were identified in 369 Lynch syndrome families. These mutations affected MLH1 in 40%, MSH2 in 36%, MSH6 in 18% and PMS2 in 6% of the families. A large variety of mutations were identified with splice site mutations being the most common mutation type in MLH1 and frameshift mutations predominating in MSH2 and MSH6. Large deletions of one or several exons accounted for 21% of the mutations in MLH1 and MSH2 and 22% in PMS2, but were rare (4%) in MSH6. In 66% of the Lynch syndrome families the variants identified were private and the effect from founder mutations was limited and predominantly related to a Finnish founder mutation that accounted for 15% of the families with mutations in MLH1. In conclusion, the Swedish Lynch syndrome mutation spectrum is diverse with private MMR gene mutations in two-thirds of the families, has a significant contribution from internationally recognized mutations and a limited effect from founder mutations.
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Affiliation(s)
- Kristina Lagerstedt-Robinson
- Department of Molecular Medicine and Surgery, Karolinska Institute and Department of Clinical Genetics, Karolinska University Hospital, Solna, SE-17176 Stockholm, Sweden
| | - Anna Rohlin
- Department of Clinical Pathology and Genetics, Sahlgrenska University Hospital, SE-41345 Gothenburg, Sweden
| | - Christos Aravidis
- Department of Immunology, Genetics and Pathology, Uppsala University, SE-75185 Uppsala, Sweden
| | - Beatrice Melin
- Department of Radiation Sciences, Division of Oncology, Umeå University, SE-90187 Umeå, Sweden
| | - Margareta Nordling
- Department of Clinical Pathology and Genetics, Sahlgrenska University Hospital, SE-41345 Gothenburg, Sweden
| | | | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institute and Department of Clinical Genetics, Karolinska University Hospital, Solna, SE-17176 Stockholm, Sweden
| | - Mef Nilbert
- Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, SE-22381 Lund, Sweden
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