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Pinto C, Guerra J, Pinheiro M, Escudeiro C, Santos C, Pinto P, Porto M, Bartosch C, Silva J, Peixoto A, Teixeira MR. Combined germline and tumor mutation signature testing identifies new families with NTHL1 tumor syndrome. Front Genet 2023; 14:1254908. [PMID: 37727376 PMCID: PMC10505957 DOI: 10.3389/fgene.2023.1254908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 08/14/2023] [Indexed: 09/21/2023] Open
Abstract
NTHL1 tumor syndrome is an autosomal recessive rare disease caused by biallelic inactivating variants in the NTHL1 gene and which presents a broad tumor spectrum. To contribute to the characterization of the phenotype of this syndrome, we studied 467 index patients by KASP assay or next-generation sequencing, including 228 patients with colorectal polyposis and 239 patients with familial/personal history of multiple tumors (excluding multiple breast/ovarian/polyposis). Three NTHL1 tumor syndrome families were identified in the group of patients with polyposis and none in patients with familial/personal history of multiple tumors. Altogether, we identified nine affected patients with polyposis (two of them diagnosed after initiating colorectal cancer surveillance) with biallelic pathogenic or likely pathogenic NTHL1 variants, as well as two index patients with one pathogenic or likely pathogenic NTHL1 variant in concomitance with a missense variant of uncertain significance. Here we identified a novel inframe deletion classified as likely pathogenic using the ACMG criteria, supported also by tumor mutational signature analysis. Our findings indicate that the NTHL1 tumor syndrome is a multi-tumor syndrome strongly associated with polyposis and not with multiple tumors without polyposis.
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Affiliation(s)
- Carla Pinto
- Department of Laboratory Genetics, Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center, Porto, Portugal
- Cancer Genetics Group, IPO-Porto Research Center (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center, Porto, Portugal
- Department of Pathological, Cytological and Thanatological Anatomy, School of Health, Polytechnic Institute of Porto, Porto, Portugal
| | - Joana Guerra
- Cancer Genetics Group, IPO-Porto Research Center (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center, Porto, Portugal
- Doctoral Programme in Biomedical Sciences, School of Medicine and Biomedical Sciences (ICBAS), University of Porto, Porto, Portugal
| | - Manuela Pinheiro
- Cancer Genetics Group, IPO-Porto Research Center (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center, Porto, Portugal
| | - Carla Escudeiro
- Department of Laboratory Genetics, Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center, Porto, Portugal
- Cancer Genetics Group, IPO-Porto Research Center (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center, Porto, Portugal
| | - Catarina Santos
- Department of Laboratory Genetics, Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center, Porto, Portugal
- Cancer Genetics Group, IPO-Porto Research Center (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center, Porto, Portugal
| | - Pedro Pinto
- Cancer Genetics Group, IPO-Porto Research Center (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center, Porto, Portugal
| | - Miguel Porto
- Cancer Genetics Group, IPO-Porto Research Center (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center, Porto, Portugal
| | - Carla Bartosch
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center, Porto, Portugal
- Cancer Biology and Epigenetics Group, IPO-Porto Research Center (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center, Porto, Portugal
| | - João Silva
- Cancer Genetics Group, IPO-Porto Research Center (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center, Porto, Portugal
- Department of Medical Genetics, Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center, Porto, Portugal
| | - Ana Peixoto
- Department of Laboratory Genetics, Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center, Porto, Portugal
- Cancer Genetics Group, IPO-Porto Research Center (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center, Porto, Portugal
| | - Manuel R. Teixeira
- Department of Laboratory Genetics, Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center, Porto, Portugal
- Cancer Genetics Group, IPO-Porto Research Center (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center, Porto, Portugal
- School of Medicine and Biomedical Sciences (ICBAS), University of Porto, Porto, Portugal
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Guerra J, Pinto C, Pinto P, Pinheiro M, Santos C, Peixoto A, Escudeiro C, Barbosa A, Porto M, Francisco I, Lopes P, Isidoro AR, Cunha AL, Albuquerque C, Claro I, Oliveira C, Silva J, Teixeira MR. Frequency of CDH1, CTNNA1 and CTNND1 Germline Variants in Families with Diffuse and Mixed Gastric Cancer. Cancers (Basel) 2023; 15:4313. [PMID: 37686589 PMCID: PMC10486404 DOI: 10.3390/cancers15174313] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/23/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
The most well-characterized hereditary form of gastric cancer is hereditary diffuse gastric cancer (HDGC), an autosomal dominant syndrome characterized by an increased risk of diffuse gastric and lobular breast cancer. HDGC is predominantly caused by germline pathogenic variants in the CDH1 gene, and more rarely in the CTNNA1 gene. Furthermore, the International Gastric Cancer Linkage Consortium (IGCLC) guidelines do not clarify whether or not mixed gastric cancer (with a diffuse component) should be considered in the HDGC genetic testing criteria. We aimed to evaluate the contribution of CTNNA1 and CTNND1 germline variants to HDGC. Additionally, we also intended to compare the frequencies of CDH1 and CTNNA1 (and eventually CTNND1) germline variants between patients with diffuse and mixed gastric carcinomas to evaluate if genetic testing for these genes should or should not be considered in patients with the latter. We analyzed the CDH1 gene in 67 cases affected with early-onset/familial mixed gastric carcinomas and the CTNNA1 and CTNND1 genes in 208 cases with diffuse or mixed gastric cancer who had tested negative for CDH1 pathogenic germline variants. A deleterious CTNNA1 germline variant was found in 0.7% (1/141) of diffuse gastric cancer patients meeting the 2020 IGCLC criteria, as compared to the rate of 2.8% of CDH1 deleterious variants found by us in this setting. No deleterious variants were found in CTNND1, but six variants of uncertain significance were identified in this gene. We did not find any pathogenic CDH1, CTNNA1 or CTNND1 variant in index patients with early-onset/familial mixed gastric cancer, so there is no evidence that supports including this tumor type in the testing criteria for germline variants in these genes. The role of the CTNND1 gene in inherited gastric cancer predisposition is still unclear.
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Affiliation(s)
- Joana Guerra
- Cancer Genetics Group, IPO-Porto Research Center (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center, 4200-072 Porto, Portugal; (J.G.); (C.P.); (P.P.); (M.P.); (C.S.); (A.P.); (C.E.); (A.B.); (M.P.); (J.S.)
- Doctoral Programme in Biomedical Sciences, School Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), 4050-313 Porto, Portugal
| | - Carla Pinto
- Cancer Genetics Group, IPO-Porto Research Center (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center, 4200-072 Porto, Portugal; (J.G.); (C.P.); (P.P.); (M.P.); (C.S.); (A.P.); (C.E.); (A.B.); (M.P.); (J.S.)
- Department of Laboratory Genetics, Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center, 4200-072 Porto, Portugal
- Department of Pathological, Cytological and Thanatological Anatomy, School of Health, Polytechnic Institute of Porto, 4200-072 Porto, Portugal
| | - Pedro Pinto
- Cancer Genetics Group, IPO-Porto Research Center (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center, 4200-072 Porto, Portugal; (J.G.); (C.P.); (P.P.); (M.P.); (C.S.); (A.P.); (C.E.); (A.B.); (M.P.); (J.S.)
| | - Manuela Pinheiro
- Cancer Genetics Group, IPO-Porto Research Center (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center, 4200-072 Porto, Portugal; (J.G.); (C.P.); (P.P.); (M.P.); (C.S.); (A.P.); (C.E.); (A.B.); (M.P.); (J.S.)
| | - Catarina Santos
- Cancer Genetics Group, IPO-Porto Research Center (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center, 4200-072 Porto, Portugal; (J.G.); (C.P.); (P.P.); (M.P.); (C.S.); (A.P.); (C.E.); (A.B.); (M.P.); (J.S.)
- Department of Laboratory Genetics, Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center, 4200-072 Porto, Portugal
| | - Ana Peixoto
- Cancer Genetics Group, IPO-Porto Research Center (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center, 4200-072 Porto, Portugal; (J.G.); (C.P.); (P.P.); (M.P.); (C.S.); (A.P.); (C.E.); (A.B.); (M.P.); (J.S.)
- Department of Laboratory Genetics, Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center, 4200-072 Porto, Portugal
| | - Carla Escudeiro
- Cancer Genetics Group, IPO-Porto Research Center (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center, 4200-072 Porto, Portugal; (J.G.); (C.P.); (P.P.); (M.P.); (C.S.); (A.P.); (C.E.); (A.B.); (M.P.); (J.S.)
- Department of Laboratory Genetics, Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center, 4200-072 Porto, Portugal
| | - Ana Barbosa
- Cancer Genetics Group, IPO-Porto Research Center (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center, 4200-072 Porto, Portugal; (J.G.); (C.P.); (P.P.); (M.P.); (C.S.); (A.P.); (C.E.); (A.B.); (M.P.); (J.S.)
- Department of Laboratory Genetics, Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center, 4200-072 Porto, Portugal
| | - Miguel Porto
- Cancer Genetics Group, IPO-Porto Research Center (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center, 4200-072 Porto, Portugal; (J.G.); (C.P.); (P.P.); (M.P.); (C.S.); (A.P.); (C.E.); (A.B.); (M.P.); (J.S.)
| | - Inês Francisco
- Molecular Pathobiology Research Unit, Portuguese Oncology Institute of Lisbon, 1099-023 Lisbon, Portugal; (I.F.); (C.A.)
| | - Paula Lopes
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center, 4200-072 Porto, Portugal; (P.L.); (A.R.I.); (A.L.C.)
| | - Ana Raquel Isidoro
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center, 4200-072 Porto, Portugal; (P.L.); (A.R.I.); (A.L.C.)
| | - Ana Luísa Cunha
- Department of Pathology, Portuguese Oncology Institute of Porto (IPO Porto)/Porto Comprehensive Cancer Center, 4200-072 Porto, Portugal; (P.L.); (A.R.I.); (A.L.C.)
| | - Cristina Albuquerque
- Molecular Pathobiology Research Unit, Portuguese Oncology Institute of Lisbon, 1099-023 Lisbon, Portugal; (I.F.); (C.A.)
| | - Isabel Claro
- Gastroenterology Department, Portuguese Oncology Institute of Lisbon, 1099-023 Lisbon, Portugal;
- Familiar Cancer Risk Clinic, Portuguese Oncology Institute of Lisbon, 1099-023 Lisbon, Portugal
| | - Carla Oliveira
- i3S-Instituto de Investigação e Inovação em Saúde, 4200-135 Porto, Portugal;
- IPATIMUP-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, 4200-135 Porto, Portugal
- FMUP-Faculty of Medicine of the University of Porto, 4100-179 Porto, Portugal
| | - João Silva
- Cancer Genetics Group, IPO-Porto Research Center (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center, 4200-072 Porto, Portugal; (J.G.); (C.P.); (P.P.); (M.P.); (C.S.); (A.P.); (C.E.); (A.B.); (M.P.); (J.S.)
- Medical Genetics Department, Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center, 4200-072 Porto, Portugal
| | - Manuel R. Teixeira
- Cancer Genetics Group, IPO-Porto Research Center (CI-IPOP)/RISE@CI-IPOP (Health Research Network), Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center, 4200-072 Porto, Portugal; (J.G.); (C.P.); (P.P.); (M.P.); (C.S.); (A.P.); (C.E.); (A.B.); (M.P.); (J.S.)
- Department of Laboratory Genetics, Portuguese Oncology Institute of Porto (IPO-Porto)/Porto Comprehensive Cancer Center, 4200-072 Porto, Portugal
- School of Medicine and Biomedical Sciences (ICBAS), University of Porto, 4050-313 Porto, Portugal
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Spolia A, Angural A, Sharma V, Razdan S, Dhar MK, Mahajan A, Verma V, Pandita KK, Sharma S, Rai E. Cost-effective Whole Exome Sequencing discovers pathogenic variant causing Neurofibromatosis type 1 in a family from Jammu and Kashmir, India. Sci Rep 2023; 13:7852. [PMID: 37188759 DOI: 10.1038/s41598-023-34941-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 05/10/2023] [Indexed: 05/17/2023] Open
Abstract
Neurofibromatosis type 1 (NF1) is a multisystemic hereditary disorder associated with an increased risk of benign and malignant tumor formation predominantly on the skin, bone, and peripheral nervous system. It has been reported that out of all the NF1 cases, more than 95% cases develop the disease due to heterozygous loss-of-function variants in Neurofibromin (NF1) gene. However, identification of NF1 causative variants by presently recommended method of gene-targeted Sanger sequencing is challenging and cost-intensive due to the large size of the NF1gene with 60 exons spanning about 350 kb. Further, conducting the genetic studies is difficult in low resource regions and among families with the limited financial capabilities, restricting them from availing diagnostic as well as proper disease management measures. Here, we studied a three-generation family from Jammu and Kashmir state in India, with multiple affected family members showing clinical indications of NF1. We combinedly used two applications, Whole Exome Sequencing (WES) and Sanger sequencing, for this study and discovered a nonsense variant NM_000267.3:c.2041C>T (NP_000258.1:p.Arg681Ter*) in exon 18 of NF1 gene in a cost effective manner. In silico analyses further substantiated the pathogenicity of this novel variant. The study also emphasized on the role of Next Generation Sequencing (NGS) as a cost-effective method for the discovery of pathogenic variants in disorders with known phenotypes found in large sized candidate genes. The current study is the first study based on the genetic characterization of NF1 from Jammu and Kashmir-India, highlighting the importance of the described methodology adopted for the identification and understanding of the disease in low resource region. The early diagnosis of genetic disorders would open the door to appropriate genetic counseling, reducing the disease burden in the affected families and the general population at large.
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Affiliation(s)
- Akshi Spolia
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Kakryal, Jammu and Kashmir, 182320, India
| | - Arshia Angural
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Kakryal, Jammu and Kashmir, 182320, India
- Department of Medical Genetics, JSS Medical College and JSS Hospital, JSS Academy of Higher Education and Research, Mysuru, Karnataka, 570015, India
| | - Varun Sharma
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Kakryal, Jammu and Kashmir, 182320, India
- NMC Genetics India Pvt Ltd, Gurugram, 122002, Haryana, India
| | - Sushil Razdan
- Bhagwati Nagar, House No.:7, 180016, Jammu and Kashmir, India
| | - Manoj K Dhar
- School of Biotechnology, University of Jammu, Jammu and Kashmir, 180006, India
| | - Ankit Mahajan
- School of Biotechnology, University of Jammu, Jammu and Kashmir, 180006, India
| | - Vijeshwar Verma
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Kakryal, Jammu and Kashmir, 182320, India
| | - Kamal K Pandita
- Health Clinic, Swarn Vihar, Muthi, 181205, Jammu and Kashmir, India
| | - Swarkar Sharma
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Kakryal, Jammu and Kashmir, 182320, India.
- Centre for Molecular Biology, Central University of Jammu, Jammu and Kashmir, 181143, India.
| | - Ekta Rai
- Human Genetics Research Group, School of Biotechnology, Shri Mata Vaishno Devi University, Kakryal, Jammu and Kashmir, 182320, India.
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Increased Risk of Hereditary Prostate Cancer in Italian Families with Hereditary Breast and Ovarian Cancer Syndrome Harboring Mutations in BRCA and in Other Susceptibility Genes. Genes (Basel) 2022; 13:genes13101692. [PMID: 36292577 PMCID: PMC9601514 DOI: 10.3390/genes13101692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/14/2022] [Accepted: 09/16/2022] [Indexed: 11/29/2022] Open
Abstract
Hereditary prostate cancer (HPCa) has the highest heritability of any cancer in men. Interestingly, it occurs in several hereditary syndromes, including breast and ovarian cancer (HBOC) and Lynch syndrome (LS). Several gene mutations related to these syndromes have been identified as biomarkers in HPCa. The goal of this study was to screen for germline mutations in susceptibility genes by using a multigene panel, and to subsequently correlate the results with clinical and laboratory parameters. This was undertaken in 180 HBOC families, which included 217 males with prostate cancer (PCa). Mutational analysis was further extended to 104 family members of mutated patients. Screening of HBOC families revealed that 30.5% harbored germline mutations in susceptibility genes, with 21.6% harboring pathogenic variants (PVs) and 8.9% having variants of uncertain significance (VUS). We found PVs at similar frequency in BRCA1 and BRCA2 genes (8.8% and 9.4%, respectively), while 0.56% of PVs were present in well-established susceptibility genes PALB2, TP53 and RAD51C. Moreover, 0.56% of monoallelic PVs were present in MUTYH, a gene whose function in tumorigenesis in the context of PCa is still unclear. Finally, we reported double heterozygosity (DH) in BRCA1/2 genes in a single family, and found double mutation (DM) present in BRCA2 in a separate family. There was no significant difference between the mean age of onset of PCa in HBOC families with or without germline mutations in susceptibility genes, while the mean survival was highest in mutated patients compared to wild type. Furthermore, PCa is the second most recurrent cancer in our cohort, resulting in 18% of cases in both mutated and non-mutated families. Our investigation shows that PVs were located mostly in the 3′ of BRCA1 and BRCA2 genes, and in BRCA2, most PVs fell in exon 11, suggesting a mutation cluster region relating to risk of HPCa. A total of 65 family members inherited the proband’s mutation; of these, 24 developed cancer, with 41 remaining unaffected.
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Zanti M, Michailidou K, Loizidou MA, Machattou C, Pirpa P, Christodoulou K, Spyrou GM, Kyriacou K, Hadjisavvas A. Performance evaluation of pipelines for mapping, variant calling and interval padding, for the analysis of NGS germline panels. BMC Bioinformatics 2021; 22:218. [PMID: 33910496 PMCID: PMC8080428 DOI: 10.1186/s12859-021-04144-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 04/15/2021] [Indexed: 11/10/2022] Open
Abstract
Background Next-generation sequencing (NGS) represents a significant advancement in clinical genetics. However, its use creates several technical, data interpretation and management challenges. It is essential to follow a consistent data analysis pipeline to achieve the highest possible accuracy and avoid false variant calls. Herein, we aimed to compare the performance of twenty-eight combinations of NGS data analysis pipeline compartments, including short-read mapping (BWA-MEM, Bowtie2, Stampy), variant calling (GATK-HaplotypeCaller, GATK-UnifiedGenotyper, SAMtools) and interval padding (null, 50 bp, 100 bp) methods, along with a commercially available pipeline (BWA Enrichment, Illumina®). Fourteen germline DNA samples from breast cancer patients were sequenced using a targeted NGS panel approach and subjected to data analysis. Results We highlight that interval padding is required for the accurate detection of intronic variants including spliceogenic pathogenic variants (PVs). In addition, using nearly default parameters, the BWA Enrichment algorithm, failed to detect these spliceogenic PVs and a missense PV in the TP53 gene. We also recommend the BWA-MEM algorithm for sequence alignment, whereas variant calling should be performed using a combination of variant calling algorithms; GATK-HaplotypeCaller and SAMtools for the accurate detection of insertions/deletions and GATK-UnifiedGenotyper for the efficient detection of single nucleotide variant calls. Conclusions These findings have important implications towards the identification of clinically actionable variants through panel testing in a clinical laboratory setting, when dedicated bioinformatics personnel might not always be available. The results also reveal the necessity of improving the existing tools and/or at the same time developing new pipelines to generate more reliable and more consistent data. Supplementary Information The online version contains supplementary material available at 10.1186/s12859-021-04144-1.
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Affiliation(s)
- Maria Zanti
- Department of Electron Microscopy/Molecular Pathology, The Cyprus Institute of Neurology and Genetics, 2371, Nicosia, Cyprus.,Cyprus School of Molecular Medicine, 2371, Nicosia, Cyprus.,Bioinformatics Department, The Cyprus Institute of Neurology and Genetics, 2371, Nicosia, Cyprus
| | - Kyriaki Michailidou
- Cyprus School of Molecular Medicine, 2371, Nicosia, Cyprus.,Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, 2371, Nicosia, Cyprus
| | - Maria A Loizidou
- Department of Electron Microscopy/Molecular Pathology, The Cyprus Institute of Neurology and Genetics, 2371, Nicosia, Cyprus.,Cyprus School of Molecular Medicine, 2371, Nicosia, Cyprus
| | - Christina Machattou
- Department of Electron Microscopy/Molecular Pathology, The Cyprus Institute of Neurology and Genetics, 2371, Nicosia, Cyprus
| | - Panagiota Pirpa
- Department of Electron Microscopy/Molecular Pathology, The Cyprus Institute of Neurology and Genetics, 2371, Nicosia, Cyprus
| | - Kyproula Christodoulou
- Cyprus School of Molecular Medicine, 2371, Nicosia, Cyprus.,Neurogenetics Department, The Cyprus Institute of Neurology and Genetics, 2371, Nicosia, Cyprus
| | - George M Spyrou
- Cyprus School of Molecular Medicine, 2371, Nicosia, Cyprus.,Bioinformatics Department, The Cyprus Institute of Neurology and Genetics, 2371, Nicosia, Cyprus
| | - Kyriacos Kyriacou
- Department of Electron Microscopy/Molecular Pathology, The Cyprus Institute of Neurology and Genetics, 2371, Nicosia, Cyprus.,Cyprus School of Molecular Medicine, 2371, Nicosia, Cyprus
| | - Andreas Hadjisavvas
- Department of Electron Microscopy/Molecular Pathology, The Cyprus Institute of Neurology and Genetics, 2371, Nicosia, Cyprus. .,Cyprus School of Molecular Medicine, 2371, Nicosia, Cyprus.
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Vietri MT, D’Elia G, Caliendo G, Resse M, Casamassimi A, Passariello L, Albanese L, Cioffi M, Molinari AM. Hereditary Prostate Cancer: Genes Related, Target Therapy and Prevention. Int J Mol Sci 2021; 22:ijms22073753. [PMID: 33916521 PMCID: PMC8038462 DOI: 10.3390/ijms22073753] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 03/27/2021] [Accepted: 04/02/2021] [Indexed: 02/07/2023] Open
Abstract
Prostate cancer (PCa) is globally the second most diagnosed cancer type and the most common cause of cancer-related deaths in men. Family history of PCa, hereditary breast and ovarian cancer (HBOC) and Lynch syndromes (LS), are among the most important risk factors compared to age, race, ethnicity and environmental factors for PCa development. Hereditary prostate cancer (HPCa) has the highest heritability of any major cancer in men. The proportion of PCa attributable to hereditary factors has been estimated in the range of 5–15%. To date, the genes more consistently associated to HPCa susceptibility include mismatch repair (MMR) genes (MLH1, MSH2, MSH6, and PMS2) and homologous recombination genes (BRCA1/2, ATM, PALB2, CHEK2). Additional genes are also recommended to be integrated into specific research, including HOXB13, BRP1 and NSB1. Importantly, BRCA1/BRCA2 and ATM mutated patients potentially benefit from Poly (ADP-ribose) polymerase PARP inhibitors, through a mechanism of synthetic lethality, causing selective tumor cell cytotoxicity in cell lines. Moreover, the detection of germline alterations in MMR genes has therapeutic implications, as it may help to predict immunotherapy benefits. Here, we discuss the current knowledge of the genetic basis for inherited predisposition to PCa, the potential target therapy, and the role of active surveillance as a management strategy for patients with low-risk PCa. Finally, the current PCa guideline recommendations are reviewed.
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Affiliation(s)
- Maria Teresa Vietri
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Via L. De Crecchio, 80138 Naples, Italy; (A.C.); (A.M.M.)
- U.O.C. Clinical and Molecular Pathology, A.O.U. University of Campania “Luigi Vanvitelli”, 80138 Naple, Italy; (G.D.); (G.C.); (M.R.); (L.P.); (L.A.); (M.C.)
- Correspondence: ; Tel.: +39-081-566-7639; Fax: +39-081-450-169
| | - Giovanna D’Elia
- U.O.C. Clinical and Molecular Pathology, A.O.U. University of Campania “Luigi Vanvitelli”, 80138 Naple, Italy; (G.D.); (G.C.); (M.R.); (L.P.); (L.A.); (M.C.)
| | - Gemma Caliendo
- U.O.C. Clinical and Molecular Pathology, A.O.U. University of Campania “Luigi Vanvitelli”, 80138 Naple, Italy; (G.D.); (G.C.); (M.R.); (L.P.); (L.A.); (M.C.)
| | - Marianna Resse
- U.O.C. Clinical and Molecular Pathology, A.O.U. University of Campania “Luigi Vanvitelli”, 80138 Naple, Italy; (G.D.); (G.C.); (M.R.); (L.P.); (L.A.); (M.C.)
| | - Amelia Casamassimi
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Via L. De Crecchio, 80138 Naples, Italy; (A.C.); (A.M.M.)
| | - Luana Passariello
- U.O.C. Clinical and Molecular Pathology, A.O.U. University of Campania “Luigi Vanvitelli”, 80138 Naple, Italy; (G.D.); (G.C.); (M.R.); (L.P.); (L.A.); (M.C.)
| | - Luisa Albanese
- U.O.C. Clinical and Molecular Pathology, A.O.U. University of Campania “Luigi Vanvitelli”, 80138 Naple, Italy; (G.D.); (G.C.); (M.R.); (L.P.); (L.A.); (M.C.)
| | - Michele Cioffi
- U.O.C. Clinical and Molecular Pathology, A.O.U. University of Campania “Luigi Vanvitelli”, 80138 Naple, Italy; (G.D.); (G.C.); (M.R.); (L.P.); (L.A.); (M.C.)
| | - Anna Maria Molinari
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, Via L. De Crecchio, 80138 Naples, Italy; (A.C.); (A.M.M.)
- U.O.C. Clinical and Molecular Pathology, A.O.U. University of Campania “Luigi Vanvitelli”, 80138 Naple, Italy; (G.D.); (G.C.); (M.R.); (L.P.); (L.A.); (M.C.)
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7
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The role of TP53 pathogenic variants in early-onset HER2-positive breast cancer. Fam Cancer 2020; 20:173-180. [PMID: 33051812 DOI: 10.1007/s10689-020-00212-2] [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: 05/25/2020] [Accepted: 10/08/2020] [Indexed: 12/21/2022]
Abstract
Breast cancer is the most frequent event in Li-Fraumeni syndrome associated with germline TP53 variants. Some studies have shown that breast cancers in women with Li-Fraumeni syndrome are commonly HER2-positive, suggesting that HER2 amplification or over-expression in a young woman may be a useful criterion to test for germline variants in the TP53 gene. We assessed the prevalence of germline TP53 variants by Sanger sequencing or next-generation sequencing in 149 women with HER2-positive breast cancer diagnosed until age 40. The pattern of HER2 amplification was evaluated with dual-probe FISH in a subset of breast carcinomas from patients with germline TP53 variants as compared with those of noncarriers. Among 149 women tested, three presented a deleterious TP53 germline variant (2%), with one patient diagnosed at age 31 and the other two with bilateral breast cancer at ages 29/33 and 28/32, respectively. Three of the 36 patients (8.3%) with the first breast cancer diagnosed at age 31 or younger presented a pathogenic TP53 variant. Additionally, all TP53 deleterious variant carriers had a first degree relative diagnosed with different early-onset cancers (frequently not belonging to the Li-Fraumeni syndrome tumor spectrum) diagnosed at age 45 or younger. Higher levels of HER2 amplification were found in breast carcinomas of TP53 pathogenic variant carriers than in those of noncarriers. Deleterious germline TP53 variants account for a small proportion of early-onset HER2-positive breast cancers, but these seem to have higher HER2 amplification ratios. All TP53 pathogenic variant carriers found in this study had the first breast carcinoma diagnosed at age 31 or younger and a first-degree relative with early-onset cancer. Further studies are needed to clarify if HER2 status in early-onset breast cancer patients, in combination with other personal and/or familial cancer history, is useful to update the TP53 testing criteria.
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8
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Brandão A, Paulo P, Teixeira MR. Hereditary Predisposition to Prostate Cancer: From Genetics to Clinical Implications. Int J Mol Sci 2020; 21:E5036. [PMID: 32708810 PMCID: PMC7404100 DOI: 10.3390/ijms21145036] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/10/2020] [Accepted: 07/13/2020] [Indexed: 02/07/2023] Open
Abstract
Prostate cancer (PrCa) ranks among the top five cancers for both incidence and mortality worldwide. A significant proportion of PrCa susceptibility has been attributed to inherited predisposition, with 10-20% of cases expected to occur in a hereditary/familial context. Advances in DNA sequencing technologies have uncovered several moderate- to high-penetrance PrCa susceptibility genes, most of which have previously been related to known hereditary cancer syndromes, namely the hereditary breast and ovarian cancer (BRCA1, BRCA2, ATM, CHEK2, and PALB2) and Lynch syndrome (MLH1, MSH2, MSH6, and PMS2) genes. Additional candidate genes have also been suggested, but further evidence is needed to include them in routine genetic testing. Recommendations based on clinical features, family history, and ethnicity have been established for more cost-efficient genetic testing of patients and families who may be at an increased risk of developing PrCa. The identification of alterations in PrCa predisposing genes may help to inform screening strategies, as well as treatment options, in the metastatic setting. This review provides an overview of the genetic basis underlying hereditary predisposition to PrCa, the current genetic screening recommendations, and the implications for clinical management of the disease.
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Affiliation(s)
- Andreia Brandão
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), 4200-072 Porto, Portugal; (A.B.); (P.P.)
| | - Paula Paulo
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), 4200-072 Porto, Portugal; (A.B.); (P.P.)
| | - Manuel R. Teixeira
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), 4200-072 Porto, Portugal; (A.B.); (P.P.)
- Department of Genetics, Portuguese Oncology Institute of Porto (IPO Porto), 4200-072 Porto, Portugal
- Biomedical Sciences Institute Abel Salazar (ICBAS), University of Porto, 4200-072 Porto, Portugal
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9
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Pires-Luis A, Montezuma D, Vieira J, Ramalho-Carvalho J, Santos C, Teixeira M, Jerónimo C, Henrique R. Hybrid oncocytic/chromophobe renal cell tumor: An integrated genetic and epigenetic characterization of a case. Exp Mol Pathol 2018; 105:352-356. [DOI: 10.1016/j.yexmp.2018.10.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 08/09/2018] [Accepted: 10/17/2018] [Indexed: 10/28/2022]
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10
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Mahamdallie S, Ruark E, Holt E, Poyastro-Pearson E, Renwick A, Strydom A, Seal S, Rahman N. The ICR639 CPG NGS validation series: A resource to assess analytical sensitivity of cancer predisposition gene testing. Wellcome Open Res 2018; 3:68. [PMID: 30175241 PMCID: PMC6081973 DOI: 10.12688/wellcomeopenres.14594.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/06/2018] [Indexed: 11/20/2022] Open
Abstract
The analytical sensitivity of a next generation sequencing (NGS) test reflects the ability of the test to detect real sequence variation. The evaluation of analytical sensitivity relies on the availability of gold-standard, validated, benchmarking datasets. For NGS analysis the availability of suitable datasets has been limited. Most laboratories undertake small scale evaluations using in-house data, and/or rely on in silico generated datasets to evaluate the performance of NGS variant detection pipelines. Cancer predisposition genes (CPGs), such as BRCA1 and BRCA2, are amongst the most widely tested genes in clinical practice today. Hundreds of providers across the world are now offering CPG testing using NGS methods. Validating and comparing the analytical sensitivity of CPG tests has proved difficult, due to the absence of comprehensive, orthogonally validated, benchmarking datasets of CPG pathogenic variants. To address this we present the ICR639 CPG NGS validation series. This dataset comprises data from 639 individuals. Each individual has sequencing data generated using the TruSight Cancer Panel (TSCP), a targeted NGS assay for the analysis of CPGs, together with orthogonally generated data showing the presence of at least one CPG pathogenic variant per individual. The set consists of 645 pathogenic variants in total. There is strong representation of the most challenging types of variants to detect, with 339 indels, including 16 complex indels and 24 with length greater than five base pairs and 74 exon copy number variations (CNVs) including 23 single exon CNVs. The series includes pathogenic variants in 31 CPGs, including 502 pathogenic variants in BRCA1 or BRCA2, making this an important comprehensive validation dataset for providers of BRCA1 and BRCA2 NGS testing. We have deposited the TSCP FASTQ files of the ICR639 series in the European Genome-phenome Archive (EGA) under accession number EGAD00001004134.
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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
| | - Esty Holt
- Division of Genetics & Epidemiology, The Institute of Cancer Research, London, SM2 5NG, UK
| | - Emma Poyastro-Pearson
- 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
| | - 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
| | - 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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11
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Paulo P, Maia S, Pinto C, Pinto P, Monteiro A, Peixoto A, Teixeira MR. Targeted next generation sequencing identifies functionally deleterious germline mutations in novel genes in early-onset/familial prostate cancer. PLoS Genet 2018; 14:e1007355. [PMID: 29659569 PMCID: PMC5919682 DOI: 10.1371/journal.pgen.1007355] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 04/26/2018] [Accepted: 04/05/2018] [Indexed: 12/23/2022] Open
Abstract
Considering that mutations in known prostate cancer (PrCa) predisposition genes, including those responsible for hereditary breast/ovarian cancer and Lynch syndromes, explain less than 5% of early-onset/familial PrCa, we have sequenced 94 genes associated with cancer predisposition using next generation sequencing (NGS) in a series of 121 PrCa patients. We found monoallelic truncating/functionally deleterious mutations in seven genes, including ATM and CHEK2, which have previously been associated with PrCa predisposition, and five new candidate PrCa associated genes involved in cancer predisposing recessive disorders, namely RAD51C, FANCD2, FANCI, CEP57 and RECQL4. Furthermore, using in silico pathogenicity prediction of missense variants among 18 genes associated with breast/ovarian cancer and/or Lynch syndrome, followed by KASP genotyping in 710 healthy controls, we identified "likely pathogenic" missense variants in ATM, BRIP1, CHEK2 and TP53. In conclusion, this study has identified putative PrCa predisposing germline mutations in 14.9% of early-onset/familial PrCa patients. Further data will be necessary to confirm the genetic heterogeneity of inherited PrCa predisposition hinted in this study.
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Affiliation(s)
- Paula Paulo
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - Sofia Maia
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - Carla Pinto
- Department of Genetics, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - Pedro Pinto
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - Augusta Monteiro
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - Ana Peixoto
- Department of Genetics, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
| | - Manuel R. Teixeira
- Cancer Genetics Group, IPO Porto Research Center (CI-IPOP), Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
- Department of Genetics, Portuguese Oncology Institute of Porto (IPO Porto), Porto, Portugal
- Biomedical Sciences Institute Abel Salazar (ICBAS), University of Porto, Porto, Portugal
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