1
|
Bozsik A, Butz H, Grolmusz VK, Polgár C, Patócs A, Papp J. Genome sequencing-based discovery of a novel deep intronic APC pathogenic variant causing exonization. Eur J Hum Genet 2023; 31:841-845. [PMID: 36828923 PMCID: PMC10326037 DOI: 10.1038/s41431-023-01322-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 02/09/2023] [Accepted: 02/13/2023] [Indexed: 02/26/2023] Open
Abstract
Familial adenomatous polyposis (FAP) is a hereditary cancer syndrome that occurs as a result of germline mutations in the APC gene. Despite a clear clinical diagnosis of FAP, a certain proportion of the APC variants are not readily detectable through conventional genotyping routines. We accomplished genome sequencing in duo of the disease-affected proband and non-affected sibling followed by in silico predictions and a series of RNA-based assays clarifying variant functionality. By prioritizing variants obtained by genome sequencing, we discovered the novel deep intronic alteration APC:c.531 + 1482 A > G that was demonstrated to cause out-of-frame exonization of 56 base pairs from intron 5 of the gene. Further cDNA assays confirmed, that the aberrant splicing event was complete and its splice product was subject to nonsense-mediated decay. Co-segregation was observed between the variant carrier status and the disease phenotype. Cumulative evidence confirmed that APC:c.531 + 1482 A > G is a pathogenic variant causative of the disease.
Collapse
Affiliation(s)
- Anikó Bozsik
- Department of Molecular Genetics, National Institute of Oncology, Ráth György út 7-9, Budapest, H-1122, Hungary.
- Hereditary Cancers Research Group, Hungarian Academy of Sciences - Semmelweis University, Nagyvárad tér 4, Budapest, H-1089, Hungary.
- National Tumorbiology Laboratory, National Institute of Oncology, Ráth György út 7-9, Budapest, H-1122, Hungary.
| | - Henriett Butz
- Department of Molecular Genetics, National Institute of Oncology, Ráth György út 7-9, Budapest, H-1122, Hungary
- Hereditary Cancers Research Group, Hungarian Academy of Sciences - Semmelweis University, Nagyvárad tér 4, Budapest, H-1089, Hungary
- National Tumorbiology Laboratory, National Institute of Oncology, Ráth György út 7-9, Budapest, H-1122, Hungary
| | - Vince Kornél Grolmusz
- Department of Molecular Genetics, National Institute of Oncology, Ráth György út 7-9, Budapest, H-1122, Hungary
- Hereditary Cancers Research Group, Hungarian Academy of Sciences - Semmelweis University, Nagyvárad tér 4, Budapest, H-1089, Hungary
- National Tumorbiology Laboratory, National Institute of Oncology, Ráth György út 7-9, Budapest, H-1122, Hungary
| | - Csaba Polgár
- National Tumorbiology Laboratory, National Institute of Oncology, Ráth György út 7-9, Budapest, H-1122, Hungary
- Center of Radiotherapy, National Institute of Oncology, Ráth György út 7-9, Budapest, H-1122, Hungary
- Department of Oncology, Semmelweis University, Ráth György út 7-9, Budapest, H-1122, Hungary
| | - Attila Patócs
- Department of Molecular Genetics, National Institute of Oncology, Ráth György út 7-9, Budapest, H-1122, Hungary
- Hereditary Cancers Research Group, Hungarian Academy of Sciences - Semmelweis University, Nagyvárad tér 4, Budapest, H-1089, Hungary
- National Tumorbiology Laboratory, National Institute of Oncology, Ráth György út 7-9, Budapest, H-1122, Hungary
| | - János Papp
- Department of Molecular Genetics, National Institute of Oncology, Ráth György út 7-9, Budapest, H-1122, Hungary
- Hereditary Cancers Research Group, Hungarian Academy of Sciences - Semmelweis University, Nagyvárad tér 4, Budapest, H-1089, Hungary
- National Tumorbiology Laboratory, National Institute of Oncology, Ráth György út 7-9, Budapest, H-1122, Hungary
| |
Collapse
|
2
|
Olkinuora AP, Mayordomo AC, Kauppinen AK, Cerliani MB, Coraglio M, Collia ÁK, Gutiérrez A, Alvarez K, Cassana A, Lopéz-Köstner F, Jauk F, García-Rivello H, Ristimäki A, Koskenvuo L, Lepistö A, Nieminen TT, Vaccaro CA, Pavicic WH, Peltomäki P. Mono- and biallelic germline variants of DNA glycosylase genes in colon adenomatous polyposis families from two continents. Front Oncol 2022; 12:870863. [DOI: 10.3389/fonc.2022.870863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 10/03/2022] [Indexed: 11/13/2022] Open
Abstract
Recently, biallelic germline variants of the DNA glycosylase genes MUTYH and NTHL1 were linked to polyposis susceptibility. Significant fractions remain without a molecular explanation, warranting searches for underlying causes. We used exome sequencing to investigate clinically well-defined adenomatous polyposis cases and families from Finland (N=34), Chile (N=21), and Argentina (N=12), all with known susceptibility genes excluded. Nine index cases (13%) revealed germline variants with proven or possible pathogenicity in the DNA glycosylase genes, involving NEIL1 (mono- or biallelic) in 3 cases, MUTYH (monoallelic) in 3 cases, NTHL1 (biallelic) in 1 case, and OGG1 (monoallelic) in 2 cases. NTHL1 was affected with the well-established, pathogenic c.268C>T, p.(Gln90Ter) variant. A recurrent heterozygous NEIL1 c.506G>A, p.(Gly169Asp) variant was observed in two families. In a Finnish family, the variant occurred in trans with a truncating NEIL1 variant (c.821delT). In an Argentine family, the variant co-occurred with a genomic deletion of exons 2 – 11 of PMS2. Mutational signatures in tumor tissues complied with biological functions reported for NEIL1. Our results suggest that germline variants in DNA glycosylase genes may occur in a non-negligible proportion of unexplained colon polyposis cases and may predispose to tumor development.
Collapse
|
3
|
Wanitsuwan W, Vijasika S, Jirarattanasopa P, Horpaopan S. A distinct APC pathogenic germline variant identified in a southern Thai family with familial adenomatous polyposis. BMC Med Genomics 2021; 14:87. [PMID: 33740971 PMCID: PMC7980625 DOI: 10.1186/s12920-021-00933-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 03/08/2021] [Indexed: 11/28/2022] Open
Abstract
Background Familial adenomatous polyposis (FAP) is caused by pathogenic germline variants in the APC gene. To date, multiple pathogenic variants in coding regions, splice sites, and deep intronic regions have been revealed. However, there are still pathogenic variants that remain unidentified. Methods Twenty-nine primer pairs flanking exons 2–16 (i.e., coding exons 1–15) of APC and their exon–intron junctions were used for germline pathogenic variant screening in Southern Thai patients with familial adenomatous polyposis (FAP). Transcription analysis was performed to confirm the pathogenicity of a splice site deletion of intron 10. Family members were interviewed for clinical histories. Blood samples were collected from 18 family members for a segregation study. Subsequently, clinical data of affected members were collected from the hospital databases. Results We found a distinct heterozygous 16-bp deletion at the splice donor site of intron 10 leading to a skipping of exon 10 which was confirmed by transcript analysis (APC: c 1312 + 4_1312 + 19del, r.934_1312del). Predictive testing for the pathogenic APC variant in 18 of the proband’s family members (ten healthy and eight affected) from three generations showed the same heterozygous germline pathogenic variant in eight affected adult members (15–62 years old) and two children (7 and 10 years old). Seven of the ten carriers of the disease-causing variant had undergone colonoscopy, and colonic polyps were found in all cases, which confirmed the segregation of the inherited pathogenic variant. The phenotypic spectrum was found to vary within the family; and some affected family members exhibited extracolonic manifestations. Conclusions To our knowledge, the pathogenic APC variant, c.1312 + 4_1312 + 19del, r.934_1312del, has not previously been reported. This study is one of the few reports describing the phenotypic consequences of a pathogenic APC variant in a high number of affected family members. Supplementary Information The online version contains supplementary material available at 10.1186/s12920-021-00933-y.
Collapse
Affiliation(s)
- Worrawit Wanitsuwan
- Department of Surgery, Faculty of Medicine, Prince of Songkla University, Songkhla, 90110, Thailand
| | - Sukanya Vijasika
- Department of Surgery, Faculty of Medicine, Prince of Songkla University, Songkhla, 90110, Thailand
| | - Pichai Jirarattanasopa
- Department of Ophthalmology, Faculty of Medicine, Prince of Songkla University, Songkhla, 90110, Thailand
| | - Sukanya Horpaopan
- Department of Anatomy, Faculty of Medical Science, Naresuan University, Phitsanulok, 65000, Thailand.
| |
Collapse
|
4
|
van den Akker J, Hon L, Ondov A, Mahkovec Z, O'Connor R, Chan RC, Lock J, Zimmer AD, Rostamianfar A, Ginsberg J, Leon A, Topper S. Intronic Breakpoint Signatures Enhance Detection and Characterization of Clinically Relevant Germline Structural Variants. J Mol Diagn 2021; 23:612-629. [PMID: 33621668 DOI: 10.1016/j.jmoldx.2021.01.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 12/14/2020] [Accepted: 01/27/2021] [Indexed: 12/16/2022] Open
Abstract
The relevance of large copy number variants (CNVs) to hereditary disorders has been long recognized, and population sequencing efforts have chronicled many common structural variants (SVs). However, limited data are available on the clinical contribution of rare germline SVs. Here, a detailed characterization of SVs identified using targeted next-generation sequencing was performed. Across 50 genes associated with hereditary cancer and cardiovascular disorders, a minimum of 828 unique SVs were reported, including 584 fully characterized SVs. Almost 40% of CNVs were <5 kb, with one in three deletions impacting a single exon. Additionally, 36 mid-range deletions/duplications (50 to 250 bp), 21 mobile element insertions, 6 inversions, and 27 complex rearrangements were detected. This data set was used to model SV detection in a bioinformatics pipeline solely relying on read depth, which revealed that genome sequencing (30×) allows detection of 71%, a 500× panel only targeting coding regions 53%, and exome sequencing (100×) <20% of characterized SVs. SVs accounted for 14.1% of all unique pathogenic variants, supporting the importance of SVs in hereditary disorders. Robust SV detection requires an ensemble of variant-calling algorithms that utilize sequencing of intronic regions. These algorithms should use distinct data features representative of each class of mutational mechanism, including recombination between two sequences sharing high similarity, covariants inserted between CNV breakpoints, and complex rearrangements containing inverted sequences.
Collapse
|
5
|
Lorca V, Garre P. Current status of the genetic susceptibility in attenuated adenomatous polyposis. World J Gastrointest Oncol 2019; 11:1101-1114. [PMID: 31908716 PMCID: PMC6937445 DOI: 10.4251/wjgo.v11.i12.1101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 08/18/2019] [Accepted: 10/14/2019] [Indexed: 02/05/2023] Open
Abstract
Adenomatous polyposis (AP) is classified according to cumulative adenoma number in classical AP (CAP) and attenuated AP (AAP). Genetic susceptibility is the major risk factor in CAP due to mutations in the known high predisposition genes APC and MUTYH. However, the contribution of genetic susceptibility to AAP is lower and less understood. New predisposition genes have been recently proposed, and some of them have been validated, but their scarcity hinders accurate risk estimations and prevalence calculations. AAP is a heterogeneous condition in terms of severity, clinical features and heritability. Therefore, clinicians do not have strong discriminating criteria for the recommendation of the genetic study of known predisposition genes, and the detection rate is low. Elucidation and knowledge of new AAP high predisposition genes are of great importance to offer accurate genetic counseling to the patient and family members. This review aims to update the genetic knowledge of AAP, and to expound the difficulties involved in the genetic analysis of a highly heterogeneous condition such as AAP.
Collapse
Affiliation(s)
- Víctor Lorca
- Laboratorio de Oncología Molecular, Grupo de Investigación Clínica y Traslacional en Oncología, Hospital Clínico San Carlos, Madrid 28040, Spain
| | - Pilar Garre
- Laboratorio de Oncología Molecular, Servicio de Oncología, Hospital Clínico San Carlos, Madrid 28040, Spain
| |
Collapse
|
6
|
González-Del Pozo M, Martín-Sánchez M, Bravo-Gil N, Méndez-Vidal C, Chimenea Á, Rodríguez-de la Rúa E, Borrego S, Antiñolo G. Searching the second hit in patients with inherited retinal dystrophies and monoallelic variants in ABCA4, USH2A and CEP290 by whole-gene targeted sequencing. Sci Rep 2018; 8:13312. [PMID: 30190494 PMCID: PMC6127285 DOI: 10.1038/s41598-018-31511-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 08/20/2018] [Indexed: 12/19/2022] Open
Abstract
Inherited Retinal Dystrophies are clinically and genetically heterogeneous disorders affecting the photoreceptors. Although NGS has shown to be helpful for the molecular diagnosis of these conditions, some cases remain unsolved. Among these, several individuals harboured monoallelic variants in a recessive gene, suggesting that a comprehensive screening could improve the overall diagnosis. In order to assess the contribution of non-coding variations in a cohort of 29 patients, 25 of them with monoallelic mutations, we performed targeted NGS. The design comprised the entire genomic sequence of three genes (USH2A, ABCA4 and CEP290), the coding exons of 76 genes and two disease-associated intronic regions in OFD1 and PRPF31. As a result, likely causative mutations (8 novel) were identified in 17 probands (diagnostic rate: 58.62%), including two copy-number variations in USH2A (one deletion of exons 22-55 and one duplication of exons 46-47). Possibly damaging deep-intronic mutations were identified in one family, and another with a monoallelic variant harboured causal mutations in a different locus. In conclusion, due to the high prevalence of carriers of IRD mutations and the results obtained here, sequencing entire genes do not seem to be the approach of choice for detecting the second hit in IRD patients with monoallelic variants.
Collapse
Affiliation(s)
- María González-Del Pozo
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Seville, Spain
| | - Marta Martín-Sánchez
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain
| | - Nereida Bravo-Gil
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Seville, Spain
| | - Cristina Méndez-Vidal
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Seville, Spain
| | - Ángel Chimenea
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain
| | - Enrique Rodríguez-de la Rúa
- Department of Ophthalmology, University Hospital Virgen Macarena, Seville, Spain
- Retics Patologia Ocular. OFTARED. Instituto de Salud Carlos III, Madrid, Spain
| | - Salud Borrego
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Seville, Spain
| | - Guillermo Antiñolo
- Department of Maternofetal Medicine, Genetics and Reproduction, Institute of Biomedicine of Seville, University Hospital Virgen del Rocío/CSIC/University of Seville, Seville, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Seville, Spain.
| |
Collapse
|
7
|
Nieminen TT, Pavicic W, Porkka N, Kankainen M, Järvinen HJ, Lepistö A, Peltomäki P. Pseudoexons provide a mechanism for allele-specific expression of APC in familial adenomatous polyposis. Oncotarget 2016; 7:70685-98. [PMID: 27683109 DOI: 10.18632/oncotarget.12206] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 09/12/2016] [Indexed: 12/11/2022] Open
Abstract
Allele-specific expression (ASE) of the Adenomatous Polyposis Coli (APC) gene occurs in up to one-third of families with adenomatous polyposis (FAP) that have screened mutation-negative by conventional techniques. To advance our understanding of the genomic basis of this phenomenon, 54 APC mutation-negative families (21 with classical FAP and 33 with attenuated FAP, AFAP) were investigated. We focused on four families with validated ASE and scrutinized these families by sequencing of the blood transcriptomes (RNA-seq) and genomes (WGS). Three families, two with classical FAP and one with AFAP, revealed deep intronic mutations associated with pseudoexons. In all three families, intronic mutations (c.646-1806T>G in intron 6, c.1408+729A>G in intron 11, and c.1408+731C>T in intron 11) created new splice donor sites resulting in the insertion of intronic sequences (of 127 bp, 83 bp, and 83 bp, respectively) in the APC transcript. The respective intronic mutations were absent in the remaining polyposis families and the general population. Premature stop of translation as the predicted consequence as well as co-segregation with polyposis supported the pathogenicity of the pseudoexons. We conclude that next generation sequencing on RNA and genomic DNA is an effective strategy to reveal and validate pseudoexons that are regularly missed by traditional screening methods and is worth considering in apparent mutation-negative polyposis families.
Collapse
|
8
|
Shirts BH, Pritchard CC, Walsh T. Family-Specific Variants and the Limits of Human Genetics. Trends Mol Med 2016; 22:925-34. [PMID: 27742414 DOI: 10.1016/j.molmed.2016.09.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 09/10/2016] [Accepted: 09/13/2016] [Indexed: 01/28/2023]
Abstract
Every single-nucleotide change compatible with life is present in the human population today. Understanding these rare human variants defines an extraordinary challenge for genetics and medicine. The new clinical practice of sequencing many genes for hereditary cancer risk has illustrated the utility of clinical next-generation sequencing in adults, identifying more medically actionable variants than single-gene testing. However, it has also revealed a linear relationship between the length of DNA evaluated and the number of rare 'variants of uncertain significance' reported. We propose that careful approaches to phenotype-genotype inference, distinguishing between diagnostic and screening intent, in conjunction with expanded use of family-scale genetics studies as a source of information on family-specific variants, will reduce variants of uncertain significance reported to patients.
Collapse
|
9
|
Papp J, Kovacs ME, Matrai Z, Orosz E, Kásler M, Børresen-Dale AL, Olah E. Contribution of APC and MUTYH mutations to familial adenomatous polyposis susceptibility in Hungary. Fam Cancer 2016; 15:85-97. [PMID: 26446593 DOI: 10.1007/s10689-015-9845-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Familial adenomatous polyposis (FAP) is a colorectal cancer predisposition syndrome with considerable genetic and phenotypic heterogeneity, defined by the development of multiple adenomas throughout the colorectum. FAP is caused either by monoallelic mutations in the adenomatous polyposis coli gene APC, or by biallelic germline mutations of MUTYH, this latter usually presenting with milder phenotype. The aim of the present study was to characterize the genotype and phenotype of Hungarian FAP patients. Mutation screening of 87 unrelated probands from FAP families (21 of them presented as the attenuated variant of the disease, showing <100 polyps) was performed using DNA sequencing and multiplex ligation-dependent probe amplification. Twenty-four different pathogenic mutations in APC were identified in 65 patients (75 %), including nine cases (37.5 %) with large genomic alterations. Twelve of the point mutations were novel. In addition, APC-negative samples were also tested for MUTYH mutations and we were able to identify biallelic pathogenic mutations in 23 % of these cases (5/22). Correlations between the localization of APC mutations and the clinical manifestations of the disease were observed, cases with a mutation in the codon 1200-1400 region showing earlier age of disease onset (p < 0.003). There were only a few, but definitive dissimilarities between APC- and MUTYH-associated FAP in our cohort: the age at onset of polyposis was significantly delayed for biallelic MUTYH mutation carriers as compared to patients with an APC mutation. Our data represent the first comprehensive study delineating the mutation spectra of both APC and MUTYH in Hungarian FAP families, and underscore the overlap between the clinical characteristics of APC- and MUTYH-associated phenotypes, necessitating a more appropriate clinical characterization of FAP families.
Collapse
|
10
|
Liu Q, Li X, Li S, Qu S, Wang Y, Tang Q, Ma H, Luo Y. Three novel mutations of APC gene in Chinese patients with familial adenomatous polyposis. Tumour Biol 2016; 37:11421-7. [PMID: 27000756 PMCID: PMC4999466 DOI: 10.1007/s13277-016-4986-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 02/10/2016] [Indexed: 12/30/2022] Open
Abstract
Familial adenomatous polyposis (FAP) is an autosomal dominant disorder characterized by the development of hundreds to thousands of colonic adenomas and an increased risk of colorectal cancer. Adenomatous polyposis coli (APC), encoding a large multidomain protein involved in antagonizing the Wnt signaling pathway, has been identified as the main causative gene responsible for FAP. In this study, we identified three novel mutations as well as two recurrent mutations in the APC in five Chinese FAP families by sequencing. Immunohistochemical analysis revealed that among these mutations, a nonsense mutation (c.2510C>G) and two small deletions (c.2016_2047del, c.3180_3184del) led to the truncation of the APC protein and the cytoplasmic and nuclear accumulation of β-catenin in the colorectal samples from affected individuals, respectively. Our study expands the database on mutations of APC and provides evidence to understand the function of APC in FAP.
Collapse
Affiliation(s)
- Qi Liu
- The Research Center for Medical Genomics, MOH Key Laboratory of Cell Biology and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang, 110122, China
| | - Xiaoxia Li
- Department of Gastrointestinal Surgery, Fourth Affiliated Hospital of China Medical University, Shenyang, 110032, China
| | - Sen Li
- The Research Center for Medical Genomics, MOH Key Laboratory of Cell Biology and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang, 110122, China
| | - Shengqiang Qu
- The Research Center for Medical Genomics, MOH Key Laboratory of Cell Biology and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang, 110122, China
| | - Yu Wang
- The Research Center for Medical Genomics, MOH Key Laboratory of Cell Biology and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang, 110122, China
| | - Qingzhu Tang
- The Research Center for Medical Genomics, MOH Key Laboratory of Cell Biology and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang, 110122, China
| | - Hongwei Ma
- Department of Developing Pediatrics, Shengjing Hospital, China Medical University, Shenyang, 110004, China
| | - Yang Luo
- The Research Center for Medical Genomics, MOH Key Laboratory of Cell Biology and Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang, 110122, China.
| |
Collapse
|
11
|
Paratala BS, Dolfi SC, Khiabanian H, Rodriguez-Rodriguez L, Ganesan S, Hirshfield KM. Emerging Role of Genomic Rearrangements in Breast Cancer: Applying Knowledge from Other Cancers. Biomark Cancer 2016; 8:1-14. [PMID: 26917980 PMCID: PMC4756769 DOI: 10.4137/bic.s34417] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 12/28/2015] [Accepted: 12/31/2015] [Indexed: 12/16/2022]
Abstract
Significant advances in our knowledge of cancer genomes are rapidly changing the way we think about tumor biology and the heterogeneity of cancer. Recent successes in genomically-guided treatment approaches accompanied by more sophisticated sequencing techniques have paved the way for deeper investigation into the landscape of genomic rearrangements in cancer. While considerable research on solid tumors has focused on point mutations that directly alter the coding sequence of key genes, far less is known about the role of somatic rearrangements. With many recurring alterations observed across tumor types, there is an obvious need for functional characterization of these genomic biomarkers in order to understand their relevance to tumor biology, therapy, and prognosis. As personalized therapy approaches are turning toward genomic alterations for answers, these biomarkers will become increasingly relevant to the practice of precision medicine. This review discusses the emerging role of genomic rearrangements in breast cancer, with a particular focus on fusion genes. In addition, it raises several key questions on the therapeutic value of such rearrangements and provides a framework to evaluate their significance as predictive and prognostic biomarkers.
Collapse
Affiliation(s)
- Bhavna S Paratala
- Department of Medicine, Division of Medical Oncology, Rutgers Cancer Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA.; Department of Cellular and Molecular Pharmacology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ, USA
| | - Sonia C Dolfi
- Department of Medicine, Division of Medical Oncology, Rutgers Cancer Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Hossein Khiabanian
- Department of Pathology, Division of Medical Informatics, Rutgers Cancer Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Lorna Rodriguez-Rodriguez
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, Rutgers Cancer Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Shridar Ganesan
- Department of Medicine, Division of Medical Oncology, Rutgers Cancer Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Kim M Hirshfield
- Department of Medicine, Division of Medical Oncology, Rutgers Cancer Institute of New Jersey, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| |
Collapse
|
12
|
Shirts BH, Casadei S, Jacobson AL, Lee MK, Gulsuner S, Bennett RL, Miller M, Hall SA, Hampel H, Hisama FM, Naylor LV, Goetsch C, Leppig K, Tait JF, Scroggins SM, Turner EH, Livingston R, Salipante SJ, King MC, Walsh T, Pritchard CC. Improving performance of multigene panels for genomic analysis of cancer predisposition. Genet Med 2016; 18:974-81. [PMID: 26845104 DOI: 10.1038/gim.2015.212] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 12/11/2015] [Indexed: 11/09/2022] Open
Abstract
PURPOSE Screening multiple genes for inherited cancer predisposition expands opportunities for cancer prevention; however, reports of variants of uncertain significance (VUS) may limit clinical usefulness. We used an expert-driven approach, exploiting all available information, to evaluate multigene panels for inherited cancer predisposition in a clinical series that included multiple cancer types and complex family histories. METHODS For 1,462 sequential patients referred for testing by BROCA or ColoSeq multigene panels, genomic DNA was sequenced and variants were interpreted by multiple experts using International Agency for Research on Cancer guidelines and incorporating evolutionary conservation, known and predicted variant consequences, and personal and family cancer history. Diagnostic yield was evaluated for various presenting conditions and family-history profiles. RESULTS Of 1,462 patients, 12% carried damaging mutations in established cancer genes. Diagnostic yield varied by clinical presentation. Actionable results were identified for 13% of breast and colorectal cancer patients and for 4% of cancer-free subjects, based on their family histories of cancer. Incidental findings explaining cancer in neither the patient nor the family were present in 1.7% of subjects. Less than 1% of patients carried VUS in BRCA1 or BRCA2. For all genes combined, initial reports contained VUS for 10.5% of patients, which declined to 7.5% of patients after reclassification based on additional information. CONCLUSIONS Individualized interpretation of gene panels is a complex medical activity. Interpretation by multiple experts in the context of personal and family histories maximizes actionable results and minimizes reports of VUS.Genet Med 18 10, 974-981.
Collapse
Affiliation(s)
- Brian H Shirts
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Silvia Casadei
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Angela L Jacobson
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Ming K Lee
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Suleyman Gulsuner
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Robin L Bennett
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington, USA
| | | | - Sarah A Hall
- Kadlec Regional Medical Center, Richland, Washington, USA
| | - Heather Hampel
- Division of Human Genetics, Department of Internal Medicine, Ohio State University, Columbus, Ohio, USA
| | - Fuki M Hisama
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Lorraine V Naylor
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington, USA
| | | | - Kathleen Leppig
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington, USA.,Clinical Genetics, Group Health Cooperative, Seattle, Washington, USA
| | - Jonathan F Tait
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Sheena M Scroggins
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Emily H Turner
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Robert Livingston
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Stephen J Salipante
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Mary-Claire King
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington, USA.,Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Tom Walsh
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Colin C Pritchard
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| |
Collapse
|
13
|
Liu Q, Hesson LB, Nunez AC, Packham D, Williams R, Ward RL, Sloane MA. A cryptic paracentric inversion of MSH2 exons 2-6 causes Lynch syndrome. Carcinogenesis 2015; 37:10-17. [PMID: 26498247 DOI: 10.1093/carcin/bgv154] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 10/19/2015] [Indexed: 12/28/2022] Open
Abstract
Lynch syndrome is an autosomal dominant disorder that predisposes carriers of DNA mismatch repair (MMR) gene mutations to early-onset cancer. Germline testing screens exons and splice sites for mutations, but does not examine introns or RNA transcripts for alterations. Pathogenic mutations have not been detected in ~30% of suspected Lynch syndrome cases with standard screening practices. We present a 38-year-old male with a clinicopathological and family history consistent with Lynch syndrome, including loss of MSH2 expression in his tumor. Germline testing revealed normal MSH2 coding sequence, splice sites and exon copy number, however, cDNA sequencing identified an aberrant MSH2 transcript lacking exons 2-6. An inversion PCR on germline DNA identified an ~18kb unbalanced, paracentric inversion within MSH2, with breakpoints in a long terminal repeat in intron 1 and an Alu repeat in intron 6. The 3' end of the inversion had a 1.2 kb deletion and an 8 bp insertion at the junction with intron 6. Screening of 55 additional Australian patients presenting with MSH2-deficient tumors who were negative in germline genetic tests for MSH2 mutations identified another inversion-positive patient. We propose an Alu-mediated recombination model to explain the origin of the inversion. Our study illustrates the potential value of cDNA screening to identify patients with cryptic MMR gene rearrangements, clarifies why standard testing may not detect some pathogenic alterations, and provides a genetic test for screening individuals with suspected Lynch syndrome that present with unexplained MSH2-deficient tumors.
Collapse
Affiliation(s)
- Qing Liu
- Adult Cancer Program , Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia , Sydney New South Wales 2052 , Australia
| | - Luke B Hesson
- Adult Cancer Program , Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia , Sydney New South Wales 2052 , Australia
| | - Andrea C Nunez
- Adult Cancer Program , Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia , Sydney New South Wales 2052 , Australia
| | - Deborah Packham
- Adult Cancer Program , Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia , Sydney New South Wales 2052 , Australia
| | - Rachel Williams
- Hereditary Cancer Clinic , Prince of Wales Hospital , Randwick, New South Wales 2031 , Australia and
| | - Robyn L Ward
- Adult Cancer Program, Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia, Sydney New South Wales 2052, Australia.,Level 3 Brian Wilson Chancellery, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Mathew A Sloane
- Adult Cancer Program , Lowy Cancer Research Centre and Prince of Wales Clinical School, UNSW Australia , Sydney New South Wales 2052 , Australia
| |
Collapse
|