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Forkosh E, Bergel M, Hatchell KE, Nielsen SM, Heald B, Benson AA, Friedman E, Esplin ED, Katz LH. Ashkenazi Jewish and Other White APC I1307K Carriers Are at Higher Risk for Multiple Cancers. Cancers (Basel) 2022; 14. [PMID: 36497357 DOI: 10.3390/cancers14235875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/25/2022] [Accepted: 11/25/2022] [Indexed: 12/02/2022] Open
Abstract
Purpose: APC I1307K has a higher prevalence among Ashkenazi Jews (AJ), and a two-fold increased risk for colorectal cancer (CRC) compared to non-Jewish populations. We assessed CRC and extracolonic malignancies among I1307K carriers from AJ and non-AJ whites (NAW). Methods: We compared the rate of I1307K in cancer patients who underwent germline genetic testing via a multi-gene panel with healthy subjects retrieved from the gnomAD database. Cases undergoing testing were not selected and testing was undertaken through a commercial laboratory. Results: Overall, 586/7624 (7.6%) AJ with cancer carried I1307K compared to 342/4918 (6.9%) in the AJ control group (p = NS). In the NAW, 318/141,673 (0.2%) cancer patients and 73/58,918 (0.1%) controls carried the variant [OR = 1.8, (95% CI 1.41−2.35), p < 0.001]. I1307K in NAW was associated with an increased risk of CRC [OR = 1.95, (95% CI 1.39−2.73), p < 0.01], melanoma [OR = 2.54, (95% CI 1.57−3.98)], breast [females, OR = 1.73, (95% CI 1.18−2.65), p < 0.01], and prostate cancer [males, OR = 2.42, (95% CI 1.45−3.94), p < 0.01]. Among AJ, the variant increased the risk for CRC [OR = 1.67, (95% CI 1.36−2.05), p < 0.001] and renal cancer [OR = 1.64, (95% CI 1.04−2.47)]. AJ men had a higher risk for any cancer [OR = 1.32, (95% CI 1.05−1.66), p < 0.05] and melanoma [OR = 2.04, (95% CI 1.24−3.22); p < 0.05]. Conclusions: This is the most extensive study to date conducted on I1307K carriers, although it is amenable to selection bias. NAW carrying I1307K had a higher risk of any cancer and several specific cancer types, whereas AJ carrying the variant had a risk for only a few select cancers. Our data add to the research base on I1307 carriers concerning future risk management.
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Moledina M, Charteris DG, Chandra A. The Genetic Architecture of Non-Syndromic Rhegmatogenous Retinal Detachment. Genes (Basel) 2022; 13:genes13091675. [PMID: 36140841 PMCID: PMC9498391 DOI: 10.3390/genes13091675] [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] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/14/2022] [Accepted: 09/16/2022] [Indexed: 11/16/2022] Open
Abstract
Rhegmatogenous retinal detachment (RRD) is the most common form of retinal detachment (RD), affecting 1 in 10,000 patients per year. The condition has significant ocular morbidity, with a sizeable proportion of patients obtaining poor visual outcomes. Despite this, the genetics underpinning Idiopathic Retinal Detachment (IRD) remain poorly understood; this is likely due to small sample sizes in relevant studies. The majority of research pertains to the well-characterised Mende lian syndromes, such as Sticklers and Wagners, associated with RRD. Nevertheless, in recent years, there has been an increasing body of literature identifying the common genetic mutations and mechanisms associated with IRD. Several recent Genomic Wide Association Studies (GWAS) studies have identified a number of genetic loci related to the development of IRD. Our review aims to provide an up-to-date summary of the significant genetic mechanisms and associations of Idiopathic RRD.
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Affiliation(s)
- Malik Moledina
- Department of Ophthalmology, Southend University Hospital, Mid & South Essex NHS Foundation Trust, Southend-on-Sea SS0 0RY, UK
| | - David G. Charteris
- Institute of Ophthalmology, University College, London EC1V 9EL, UK
- Vitreoretinal Unit, Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK
| | - Aman Chandra
- Department of Ophthalmology, Southend University Hospital, Mid & South Essex NHS Foundation Trust, Southend-on-Sea SS0 0RY, UK
- School of Medicine, Anglia Ruskin University, Chelmsford CM1 1SQ, UK
- Correspondence: ; Tel.: +44-7914-817445
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Fujita M, Liu X, Iwasaki Y, Terao C, Mizukami K, Kawakami E, Takata S, Inai C, Aoi T, Mizukoshi M, Maejima K, Hirata M, Murakami Y, Kamatani Y, Kubo M, Akagi K, Matsuda K, Nakagawa H, Momozawa Y. Population-based Screening for Hereditary Colorectal Cancer Variants in Japan. Clin Gastroenterol Hepatol 2022; 20:2132-2141.e9. [PMID: 33309985 DOI: 10.1016/j.cgh.2020.12.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 12/01/2020] [Accepted: 12/06/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Colorectal cancer (CRC) is one of the most common cancers in the world. A small proportion of CRCs can be attributed to recognizable hereditary germline variants of known CRC susceptibility genes. To better understand cancer risk, it is necessary to explore the prevalence of hereditary CRC and pathogenic variants of multiple cancer-predisposing genes in non-European populations. METHODS We analyzed the coding regions of 27 cancer-predisposing genes in 12,503 unselected Japanese CRC patients and 23,705 controls by target sequencing and genome-wide SNP chip. Their clinical significance was assessed using ClinVar and the guidelines by ACMG/AMP. RESULTS We identified 4,804 variants in the 27 genes and annotated them as pathogenic in 397 and benign variants in 941, of which 43.6% were novel. In total, 3.3% of the unselected CRC patients and 1.5% of the controls had a pathogenic variant. The pathogenic variants of MSH2 (odds ratio (OR) = 18.1), MLH1 (OR = 8.6), MSH6 (OR = 4.9), APC (OR = 49.4), BRIP1 (OR=3.6), BRCA1 (OR = 2.6), BRCA2 (OR = 1.9), and TP53 (OR = 1.7) were significantly associated with CRC development in the Japanese population (P-values<0.01, FDR<0.05). These pathogenic variants were significantly associated with diagnosis age and personal/family history of cancer. In total, at least 3.5% of the Japanese CRC population had a pathogenic variant or CNV of the 27 cancer-predisposing genes, indicating hereditary cancers. CONCLUSIONS This largest study of CRC heredity in Asia can contribute to the development of guidelines for genetic testing and variant interpretation for heritable CRCs.
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Affiliation(s)
| | - Xiaoxi Liu
- RIKEN Center for Integrative Medical Sciences, Yokohama
| | | | | | | | - Eiryo Kawakami
- Medical Sciences Innovation Hub Program, RIKEN, Yokohama; Artificial intelligence Medicine, Graduate School of Medicine, Chiba University, Chiba
| | | | - Chihiro Inai
- RIKEN Center for Integrative Medical Sciences, Yokohama
| | - Tomomi Aoi
- RIKEN Center for Integrative Medical Sciences, Yokohama
| | | | | | - Makoto Hirata
- Institute of Medical Science, University of Tokyo, Tokyo
| | | | | | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama
| | - Kiwamu Akagi
- Division of Molecular Diagnosis and Cancer Prevention, Saitama Cancer Center, Saitama
| | - Koichi Matsuda
- Graduate School of Frontier Science, University of Tokyo, Tokyo, Japan
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Broggi G, Tirrò E, Alzoubi H, Arcella A, Gianno F, Antonelli M, Minasi S, Vigneri P, Certo F, Altieri R, Barbagallo GMV, Miele E, Caltabiano R, Giangaspero F. Cerebellar liponeurocytoma: clinical, histopathological and molecular features of a series of three cases, including one recurrent tumor. Neuropathology 2022; 42:169-180. [PMID: 35042275 DOI: 10.1111/neup.12799] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 11/10/2021] [Accepted: 11/21/2021] [Indexed: 12/11/2022]
Abstract
Cerebellar liponeurocytoma (CL) is an unusual tumor, histologically composed of a mixture of small to medium-sized, rounded neurocytic cells and a variable lipomatous component. Although CL was originally considered as a subtype of medulloblastoma, subsequent molecular studies demonstrated that this tumor was a distinct entity, exhibiting the tumor protein p53 gene (TP53) missense mutations in 20% of cases, chromosome 17 deletion, and the absence of mutations in the adenomatous polyposis coli gene (APC), the protein patched homolog gene (PTCH), the kinase insert domain receptor gene (KDR), and the β-catenin gene (CTNNB). Apart from these molecular features, little is known about the pathogenesis and the genetic landscape of CL to date. In order to characterize the mutational landscape of CL and identify alterations that are driving tumorigenesis, we report a series of three cases, including one recurrent tumor, analysed by next-generation sequencing (NGS), which identified a total of 22 variants, of which four were missense mutations, nine were synonymous variants, and nine were located on intronic regions. In particular, DNA sequencing identified missense mutations in APC, KDR, and TP53 that could be implicated in promoting tumor progression and angiogenesis of CL. Furthermore, the NGS analysis revealed that recurrent CL did not have additional genetic changes compared with the primary tumor. Moreover, the high frequencies of detected mutations suggested that the identified alterations are germline variants. Indeed, an additional NGS on the genomic DNA obtained from one of the three patients confirmed the presence of the variants in the germline DNA. In conclusion, the obtained data support the hypothesis that CL is a distinct pathological entity that does not show specific somatic alterations driving tumorigenesis.
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Affiliation(s)
- Giuseppe Broggi
- Department of Medical and Surgical Sciences and Advanced Technologies "G.F. Ingrassia", Anatomic Pathology, University of Catania, Catania, Italy
| | - Elena Tirrò
- Center of Experimental Oncology and Hematology, A.O.U. Policlinico "G. Rodolico - San Marco", Catania, Italy.,Department of Surgical, Oncological and Stomatological Sciences, University of Palermo, Palermo, Italy
| | - Hiba Alzoubi
- Department of Basic Medical Sciences, Faculty of Medicine, Yarmouk University, Irbid, Jordan
| | | | - Francesca Gianno
- IRCCS Neuromed, Pozzilli, Italy.,Department of Radiology, Oncology and Anatomic Pathology, University La Sapienza, Rome, Italy
| | - Manila Antonelli
- Department of Radiology, Oncology and Anatomic Pathology, University La Sapienza, Rome, Italy
| | - Simone Minasi
- Department of Radiology, Oncology and Anatomic Pathology, University La Sapienza, Rome, Italy
| | - Paolo Vigneri
- Center of Experimental Oncology and Hematology, A.O.U. Policlinico "G. Rodolico - San Marco", Catania, Italy
| | - Francesco Certo
- Department of Medical and Surgical Sciences and Advanced Technologies "G.F. Ingrassia", Neurological Surgery, Policlinico "G. Rodolico-San Marco" University Hospital, University of Catania, Catania, Italy
| | - Roberto Altieri
- Department of Medical and Surgical Sciences and Advanced Technologies "G.F. Ingrassia", Neurological Surgery, Policlinico "G. Rodolico-San Marco" University Hospital, University of Catania, Catania, Italy
| | - Giuseppe Maria Vincenzo Barbagallo
- Department of Medical and Surgical Sciences and Advanced Technologies "G.F. Ingrassia", Neurological Surgery, Policlinico "G. Rodolico-San Marco" University Hospital, University of Catania, Catania, Italy
| | - Evelina Miele
- Department of Pediatric Onco-Hematology and Cell and Gene Therapy, Ospedale Pediatrico Bambino Gesù, IRCCS, Rome, Italy
| | - Rosario Caltabiano
- Department of Medical and Surgical Sciences and Advanced Technologies "G.F. Ingrassia", Anatomic Pathology, University of Catania, Catania, Italy
| | - Felice Giangaspero
- IRCCS Neuromed, Pozzilli, Italy.,Department of Radiology, Oncology and Anatomic Pathology, University La Sapienza, Rome, Italy
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Crouch DJM, Bodmer WF. Polygenic inheritance, GWAS, polygenic risk scores, and the search for functional variants. Proc Natl Acad Sci U S A 2020; 117:18924-33. [PMID: 32753378 DOI: 10.1073/pnas.2005634117] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The reconciliation between Mendelian inheritance of discrete traits and the genetically based correlation between relatives for quantitative traits was Fisher's infinitesimal model of a large number of genetic variants, each with very small effects, whose causal effects could not be individually identified. The development of genome-wide genetic association studies (GWAS) raised the hope that it would be possible to identify single polymorphic variants with identifiable functional effects on complex traits. It soon became clear that, with larger and larger GWAS on more and more complex traits, most of the significant associations had such small effects, that identifying their individual functional effects was essentially hopeless. Polygenic risk scores that provide an overall estimate of the genetic propensity to a trait at the individual level have been developed using GWAS data. These provide useful identification of groups of individuals with substantially increased risks, which can lead to recommendations of medical treatments or behavioral modifications to reduce risks. However, each such claim will require extensive investigation to justify its practical application. The challenge now is to use limited genetic association studies to find individually identifiable variants of significant functional effect that can help to understand the molecular basis of complex diseases and traits, and so lead to improved disease prevention and treatment. This can best be achieved by 1) the study of rare variants, often chosen by careful candidate assessment, and 2) the careful choice of phenotypes, often extremes of a quantitative variable, or traits with relatively high heritability.
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6
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Sa R, Song H, Wei M, Su H, Hong Y, Zhou L, Bai Y. The impact of APC polymorphisms on the transition from polyps to colorectal cancer (CRC). Gene 2020; 740:144486. [PMID: 32087273 DOI: 10.1016/j.gene.2020.144486] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 02/17/2020] [Accepted: 02/18/2020] [Indexed: 11/24/2022]
Abstract
OBJECTIVE The purpose of this study was to investigate the function of APC polymorphisms (D1822V and E1317Q) on the transition from polyps to colorectal cancer (CRC). METHODS 259 patients with polyps were included in the study. APC polymorphisms were genotyped via polymerase chain reaction (PCR) and subsequent sequencing. χ2 test was performed to analyze the relationship of APC polymorphisms or CRC occurrence with clinical features. COX regression was used to find out risk factors for CRC. Hazard ratio (HR) and 95% confidence interval (CI) represented the risk of CRC. RESULTS Clinical information on sex, regular physical activity, smoking history, alcohol use and polyps types was recorded. Neither D1822V nor E1317Q polymorphism was associated with these factors. In following analysis, we found significant difference in the frequency of males between CRC and non-CRC patients (87.4% vs. 58.7%, P < 0.001). Distinct difference in the distribution of D1822V polymorphism was also observed between CRC and non-CRC patients (P = 0.001). In COX analysis, sex was identified as a risk factor for transition from polyps to CRC (HR = 2.442, 95%CI = 1.281-4.654). D1822V polymorphism tended to inhibit the transition process (HR = 0.286, 95%CI = 0.170-0.480). However, E1317Q seemed to have no significant effect on this process (HR = 1.042, 95%CI = 0.676-1.606). CONCLUSION In a word, APC D1822V polymorphism has strong effect on the transition from polyps to CRC.
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7
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Deng M, Chen Z, Tan J, Liu H. Down-regulation of SLC35C1 induces colon cancer through over-activating Wnt pathway. J Cell Mol Med 2020; 24:3079-3090. [PMID: 31961998 PMCID: PMC7077602 DOI: 10.1111/jcmm.14969] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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: 06/13/2019] [Revised: 12/18/2019] [Accepted: 12/22/2019] [Indexed: 01/20/2023] Open
Abstract
The canonical Wnt signalling pathway is a critical pathway involved in the proliferation of cells. It has been well-established that it plays the central role during colorectal carcinogenesis and development. Yet the exact molecular mechanism of how the canonical Wnt pathway is fine-tuned remains elusive. We found that SLC35C1, a GDP-fucose transporter, negatively regulates the Wnt signalling pathway. We show here that SLC35C1 is reduced in all colon cancer by both immunohistochemistry images and TCGA data, whereas β-catenin is increased. Down-regulation of SLC35C1 is also detected by real-time PCR in stage 3 and stage 4 colorectal cancer tissues. Moreover, analysing the TCGA database with cBioPortal reveals the negative correlation of SLC35C1 mRNA level to the expression of β-catenin. Reduced SLC35C1 significantly promotes cell proliferation and colony formation of HEK293 cells. Meanwhile, in HEK293 cells silencing SLC35C1 activates canonical Wnt pathway, whereas overexpressing SLC35C1 inhibits it. Consistently, the reduction of SLC35C1 in HEK293 cells also elevated the mRNA level of Wnt target genes C-myc, Axin2 and Cyclin D1, as well as the secretion of Wnt3a. In conclusion, we identified SLC35C1 as a negative regulator of the Wnt signalling pathway in colon cancer. Decreased SLC35C1 may cause over-activation of Wnt signalling in colorectal cancer.
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Affiliation(s)
- Minzi Deng
- Department of Gastroenterology, The Third Xiangya Hospital of Central South University, Changsha, China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Changsha, China
| | - Zhihong Chen
- Department of Pathology, The People's Hospital of Hunan Province, Changsha, China
| | - Jieqiong Tan
- Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, China
| | - Heli Liu
- Department of Gastrointestinal Surgery, Xiangya Hospital of Central South University, Changsha, China
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8
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Rego S, Dagan-Rosenfeld O, Zhou W, Sailani MR, Limcaoco P, Colbert E, Avina M, Wheeler J, Craig C, Salins D, Röst HL, Dunn J, McLaughlin T, Steinmetz LM, Bernstein JA, Snyder MP. High-frequency actionable pathogenic exome variants in an average-risk cohort. Cold Spring Harb Mol Case Stud 2018; 4:mcs.a003178. [PMID: 30487145 PMCID: PMC6318774 DOI: 10.1101/mcs.a003178] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [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: 05/12/2018] [Accepted: 09/10/2018] [Indexed: 12/19/2022] Open
Abstract
Exome sequencing is increasingly utilized in both clinical and nonclinical settings, but little is known about its utility in healthy individuals. Most previous studies on this topic have examined a small subset of genes known to be implicated in human disease and/or have used automated pipelines to assess pathogenicity of known variants. To determine the frequency of both medically actionable and nonactionable but medically relevant exome findings in the general population we assessed the exomes of 70 participants who have been extensively characterized over the past several years as part of a longitudinal integrated multiomics profiling study. We analyzed exomes by identifying rare likely pathogenic and pathogenic variants in genes associated with Mendelian disease in the Online Mendelian Inheritance in Man (OMIM) database. We then used American College of Medical Genetics (ACMG) guidelines for the classification of rare sequence variants. Additionally, we assessed pharmacogenetic variants. Twelve out of 70 (17%) participants had medically actionable findings in Mendelian disease genes. Five had phenotypes or family histories associated with their genetic variants. The frequency of actionable variants is higher than that reported in most previous studies and suggests added benefit from utilizing expanded gene lists and manual curation to assess actionable findings. A total of 63 participants (90%) had additional nonactionable findings, including 60 who were found to be carriers for recessive diseases and 21 who have increased Alzheimer's disease risk because of heterozygous or homozygous APOE e4 alleles (18 participants had both). Our results suggest that exome sequencing may have considerably more utility for health management in the general population than previously thought.
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Affiliation(s)
- Shannon Rego
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Orit Dagan-Rosenfeld
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Wenyu Zhou
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - M Reza Sailani
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Patricia Limcaoco
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Elizabeth Colbert
- Department of Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Monika Avina
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Jessica Wheeler
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Colleen Craig
- Department of Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Denis Salins
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Hannes L Röst
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Jessilyn Dunn
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA.,Mobilize Center, Stanford University, Stanford, California 94305, USA
| | - Tracey McLaughlin
- Department of Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Lars M Steinmetz
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA.,Stanford Genome Technology Center, Stanford University, Palo Alto, California 94304, USA.,European Molecular Biology Laboratory (EMBL), Genome Biology Unit, 69117 Heidelberg, Germany
| | - Jonathan A Bernstein
- Department of Pediatrics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Michael P Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
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Sonoda H, Shimizu T, Miyake T, Ohta H, Akabori H, Tani M. Severe Mental Retardation Patient With a De Novo Chromosomal Deletion 5q14-22 Can Be a Carrier of a Rectal And Duodenal Cancer Associated With Over 200 Colorectal Polyps: A Case Report. Int Surg 2021; 105:322-6. [DOI: 10.9738/intsurg-d-16-00114.1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Introduction
Familial adenomatous polyposis (FAP) caused by a de novo 5q chromosomal deletion is rare, and precise cytogenetic analysis using comparative genomic hybridization (CGH) arrays have been performed in a few cases.
Case presentation
We herein present the case of a 38-year-old man with advanced rectal and duodenal cancer, FAP, and severe mental retardation caused by a de novo chromosomal deletion at 5q14–22. He was referred to our outpatient clinic because of a positive fecal occult blood test result. He was found to have advanced rectal cancer, with over 200 colorectal polyps, and duodenal cancer. He underwent laparoscopic total proctocolectomy with definitive ileostomy followed by partial resection of the duodenum. Comparative genomic hybridization to characterize deleted genes identified a large 5q deletion expanding approximately 24.9 Mbp, including the APC gene.
Conclusion
Patients who harbor a chromosomal deletion involving 5q21 are at risk of developing rectal cancer and polyposis. Therefore, such patients need early cancer screening following the availability of genetic information.
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Ghatak S, Chakraborty P, Sarkar SR, Chowdhury B, Bhaumik A, Kumar NS. Novel APC gene mutations associated with protein alteration in diffuse type gastric cancer. BMC Med Genet 2017; 18:61. [PMID: 28576136 PMCID: PMC5457612 DOI: 10.1186/s12881-017-0427-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [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] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 05/24/2017] [Indexed: 12/13/2022]
Abstract
BACKGROUND The role of adenomatous polyposis coli (APC) gene in mitosis might be critical for regulation of genomic stability and chromosome segregation. APC gene mutations have been associated to have a role in colon cancer and since gastric and colon tumors share some common genetic lesions, it is relevant to investigate the role of APC tumor suppressor gene in gastric cancer. METHODS We investigated for somatic mutations in the Exons 14 and 15 of APC gene from 40 diffuse type gastric cancersamples. Rabbit polyclonal anti-APC antibody was used, which detects the wild-type APC protein and was recommended for detection of the respective protein in human tissues. Cell cycle analysis was done from tumor and adjacent normal tissue. RESULTS APC immunoreactivity showed positive expression of the protein in stages I, II, III and negative expression in Stages III and IV. Two novel deleterious variations (g.127576C > A, g.127583C > T) in exon 14 sequence were found to generate stop codon (Y622* and Q625*)in the tumor samples. Due to the generation of stop codon, the APC protein might be truncated and all the regulatory features could be lost which has led to the down-regulation of protein expression. Our results indicate that aneuploidy might occurdue to the codon 622 and 625 APC-driven gastric tumorigenesis, in agreement with our cell cycle analysis. The APC gene function in mitosis and chromosomal stability might be lost and G1 might be arrested with high quantity of DNA in the S phase. Six missense somatic mutations in tumor samples were detected in exon 15 A-B, twoof which showed pathological and disease causing effects based on SIFT, Polyphen2 and SNPs & GO score and were not previously reported in the literature or the public mutation databases. CONCLUSION The two novel pathological somatic mutations (g.127576C > A, g.127583C > T) in exon 14 might be altering the protein expression leading to development of gastric cancer in the study population. Our study showed that mutations in the APC gene alter the protein expression and cell cycle regulation in diffuse type gastric adenocarcinoma.
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Affiliation(s)
- Souvik Ghatak
- Department of Biotechnology, Mizoram University, Aizawl, 796004 Mizoram India
| | - Payel Chakraborty
- Department of Biotechnology, Mizoram University, Aizawl, 796004 Mizoram India
| | - Sandeep Roy Sarkar
- Department of Pathology, Agartala Government Medical College, Tripura, India
| | - Biswajit Chowdhury
- Department of Pathology, Agartala Government Medical College, Tripura, India
| | - Arup Bhaumik
- Department of Pathology, Agartala Government Medical College, Tripura, India
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11
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Zhu Q, Shepherd L, Lunetta KL, Yao S, Liu Q, Hu Q, Haddad SA, Sucheston-Campbell L, Bensen JT, Bandera EV, Rosenberg L, Liu S, Haiman CA, Olshan AF, Palmer JR, Ambrosone CB. Trans-ethnic follow-up of breast cancer GWAS hits using the preferential linkage disequilibrium approach. Oncotarget 2016; 7:83160-83176. [PMID: 27825120 PMCID: PMC5341253 DOI: 10.18632/oncotarget.13075] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 10/12/2016] [Indexed: 12/22/2022] Open
Abstract
Leveraging population-distinct linkage equilibrium (LD) patterns, trans-ethnic follow-up of variants discovered from genome-wide association studies (GWAS) has proved to be useful in facilitating the identification of bona fide causal variants. We previously developed the preferential LD approach, a novel method that successfully identified causal variants driving the GWAS signals within European-descent populations even when the causal variants were only weakly linked with the GWAS-discovered variants. To evaluate the performance of our approach in a trans-ethnic setting, we applied it to follow up breast cancer GWAS hits identified mostly from populations of European ancestry in African Americans (AA). We evaluated 74 breast cancer GWAS variants in 8,315 AA women from the African American Breast Cancer Epidemiology and Risk (AMBER) consortium. Only 27% of them were associated with breast cancer risk at significance level α=0.05, suggesting race-specificity of the identified breast cancer risk loci. We followed up on those replicated GWAS hits in the AMBER consortium utilizing the preferential LD approach, to search for causal variants or better breast cancer markers from the 1000 Genomes variant catalog. Our approach identified stronger breast cancer markers for 80% of the GWAS hits with at least nominal breast cancer association, and in 81% of these cases, the marker identified was among the top 10 of all 1000 Genomes variants in the corresponding locus. The results support trans-ethnic application of the preferential LD approach in search for candidate causal variants, and may have implications for future genetic research of breast cancer in AA women.
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Affiliation(s)
- Qianqian Zhu
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Lori Shepherd
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Kathryn L. Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Song Yao
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Qian Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Qiang Hu
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY, USA
| | | | - Lara Sucheston-Campbell
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Jeannette T. Bensen
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Elisa V. Bandera
- Cancer Prevention and Control, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Lynn Rosenberg
- Slone Epidemiology Center, Boston University, Boston, MA, USA
| | - Song Liu
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Christopher A. Haiman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Andrew F. Olshan
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Julie R. Palmer
- Slone Epidemiology Center, Boston University, Boston, MA, USA
| | - Christine B. Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY, USA
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Abdel-Malak C, Darwish H, Elsaid A, El-Tarapely F, Elshazli R. Association of APC I1307K and E1317Q polymorphisms with colorectal cancer among Egyptian subjects. Fam Cancer 2016; 15:49-56. [PMID: 26314409 DOI: 10.1007/s10689-015-9834-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Colorectal cancer is a multifactorial disease that involves both environmental and genetic factors. The gene encoding adenomatous polyposis coli (APC) has been reported to be associated with colorectal cancer (CRC) risk in several ethnic populations. The aim of this work is to assess the association of the APC I1307K and E1317Q polymorphisms with CRC risk among Egyptian subjects. This study included 120 unrelated CRC Egyptian patients who were compared to 100 healthy controls from the same locality. For all subjects, DNA was genotyped for APC I1307K and E1317Q polymorphisms using the PCR-ARMS technique. The frequency of APC I1307K carrier (TA+AA genotypes) was noted to be significantly higher among cases with CRC compared to controls (18.3 vs. 9.0 %, OR 2.58, 95 % CI 1.09-6.09, p = 0.03). Also the frequency of the APC I1307K A allele was significantly higher among cases compared to controls (10.4 vs. 4.5 %, OR 2.47; 95 % CI 1.12-5.42, p = 0.03). On the contrast, the frequencies of APC E1317Q GC genotype and C allele showed no significant difference among CRC patients compared to controls (3.3 vs. 2.0 %, OR 1.69; 95 % CI 0.30-9.42, p = 0.69 and 2.1 vs. 1.0 %, OR 2.11; 95 % CI 0.40-10.97, p = 0.46, respectively). Cases of the APC I1307K and E1317Q carriers (TA+AA and GC) showed no significant difference compared to those with I1307K and E1317Q non-carriers (TT and GG) regarding their clinical and laboratory markers. APC I1307K variant was associated with an increased risk of CRC among Egyptian subjects.
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Feldman M, Hershkovitz I, Sklan EH, Kahila Bar-Gal G, Pap I, Szikossy I, Rosin-Arbesfeld R. Detection of a Tumor Suppressor Gene Variant Predisposing to Colorectal Cancer in an 18th Century Hungarian Mummy. PLoS One 2016; 11:e0147217. [PMID: 26863316 PMCID: PMC4749341 DOI: 10.1371/journal.pone.0147217] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [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: 09/30/2015] [Accepted: 12/30/2015] [Indexed: 01/23/2023] Open
Abstract
Mutations of the Adenomatous polyposis coli (APC) gene are common and strongly associated with the development of colorectal adenomas and carcinomas. While extensively studied in modern populations, reports on visceral tumors in ancient populations are scarce. To the best of our knowledge, genetic characterization of mutations associated with colorectal cancer in ancient specimens has not yet been described. In this study we have sequenced hotspots for mutations in the APC gene isolated from 18th century naturally preserved human Hungarian mummies. While wild type APC sequences were found in two mummies, we discovered the E1317Q missense mutation, known to be a colorectal cancer predisposing mutation, in a large intestine tissue of an 18th century mummy. Our data suggests that this genetic predisposition to cancer already existed in the pre-industrialization era. This study calls for similar investigations of ancient specimens from different periods and geographical locations to be conducted and shared for the purpose of obtaining a larger scale analysis that will shed light on past cancer epidemiology and on cancer evolution.
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Affiliation(s)
- Michal Feldman
- Department of Anatomy and Anthropology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
- * E-mail:
| | - Israel Hershkovitz
- Department of Anatomy and Anthropology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Ella H. Sklan
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Gila Kahila Bar-Gal
- Koret School of Veterinary Medicine, The Robert H. Smith faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Ildikó Pap
- Department of Anthropology, Hungarian Natural History Museum, Budapest, Hungary
| | - Ildikó Szikossy
- Department of Anthropology, Hungarian Natural History Museum, Budapest, Hungary
| | - Rina Rosin-Arbesfeld
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
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Leshno A, Shapira S, Liberman E, Kraus S, Sror M, Harlap-Gat A, Avivi D, Galazan L, David M, Maharshak N, Moanis S, Arber N, Moshkowitz M. The APC I1307K allele conveys a significant increased risk for cancer. Int J Cancer 2015; 138:1361-7. [PMID: 26421687 DOI: 10.1002/ijc.29876] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Revised: 09/05/2015] [Accepted: 09/22/2015] [Indexed: 01/07/2023]
Abstract
This study is the first attempt to evaluate the association between the APC I1307K variant and overall cancer risk. It is unique in both its large sample size and in the reliability of data in the control group. The findings described in this article have major implications in terms of identifying asymptomatic individuals who are at increased risk to harbor cancer and therefore targeted to be enrolled in specific early detection and prevention programs. The prevalence of the APC I1307K missense mutation among Ashkenazi Jews is ∼ 6%. Carriers are at an increased risk for colorectal neoplasia. In this study, we examined the association of this variant with non-colorectal cancers. Consecutive 13,013 healthy subjects who underwent screening at the Integrated Cancer Prevention Center between 2006 and 2014 were enrolled. This population was supplemented with 1,611 cancer patients from the same institution. Demographics, medical history, and pathological data were recorded. Mortality data were obtained from the Ministry of Health's registry. The prevalence of APC I1307K in cancer patients and healthy subjects was compared. The APC I1307K variant was detected in 189 (11.8%) cancer patients compared to 614 (4.7%) healthy subjects, reflecting an adjusted age and sex odds ratio (OR) of 2.53 (p < 0.0001). History of two or more cancer types was associated with a positive carrier prevalence (OR = 4.38 p < 0.0001). Males had significantly increased carrier prevalence in lung, urologic, pancreatic, and skin cancers. The carrier prevalence among females was significantly higher only in breast and skin cancers. Female carriers developed cancer at a significantly older age compared to non-carriers (average 62.7 years vs. 57.8, respectively, p = 0.027), had better survival rates (HR = 0.58, p = 0.022) and overall increased longevity (average age of death 78.8 vs. 70.4 years, respectively, p = 0.003). In conclusion, the APC I1307K variant is a reliable marker for overall cancer risk (OR 2.53). Further studies are needed to evaluate its use for specific cancer types-particularly in males. Female carriers have better prognosis and increased lifespan.
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Affiliation(s)
- Ari Leshno
- Integrated Cancer Prevention Center, Tel- Aviv Sourasky Medical Center, Affiliated to the Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Shiran Shapira
- Integrated Cancer Prevention Center, Tel- Aviv Sourasky Medical Center, Affiliated to the Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Eliezer Liberman
- Integrated Cancer Prevention Center, Tel- Aviv Sourasky Medical Center, Affiliated to the Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Sarah Kraus
- Integrated Cancer Prevention Center, Tel- Aviv Sourasky Medical Center, Affiliated to the Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Miri Sror
- Integrated Cancer Prevention Center, Tel- Aviv Sourasky Medical Center, Affiliated to the Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Amira Harlap-Gat
- Integrated Cancer Prevention Center, Tel- Aviv Sourasky Medical Center, Affiliated to the Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Doran Avivi
- Integrated Cancer Prevention Center, Tel- Aviv Sourasky Medical Center, Affiliated to the Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Lior Galazan
- Integrated Cancer Prevention Center, Tel- Aviv Sourasky Medical Center, Affiliated to the Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Maayan David
- Integrated Cancer Prevention Center, Tel- Aviv Sourasky Medical Center, Affiliated to the Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Nitsan Maharshak
- Integrated Cancer Prevention Center, Tel- Aviv Sourasky Medical Center, Affiliated to the Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,Department of Gastroenterology, Tel- Aviv Sourasky Medical Center, Affiliated to the Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Serhan Moanis
- Integrated Cancer Prevention Center, Tel- Aviv Sourasky Medical Center, Affiliated to the Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Nadir Arber
- Integrated Cancer Prevention Center, Tel- Aviv Sourasky Medical Center, Affiliated to the Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,Department of Gastroenterology, Tel- Aviv Sourasky Medical Center, Affiliated to the Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Menachem Moshkowitz
- Integrated Cancer Prevention Center, Tel- Aviv Sourasky Medical Center, Affiliated to the Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel.,Department of Gastroenterology, Tel- Aviv Sourasky Medical Center, Affiliated to the Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
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Abstract
In this overview of my research, I have aimed to give the background as to how I came to be involved in my various areas of interest, with an emphasis on the early phases of my career, which largely determined my future directions. I had the enormous good fortune to have worked under two of the most outstanding scientists of the twentieth century, R.A. Fisher and Joshua Lederberg. From mathematics and statistics, I went to population genetics and the early use of computers for modeling and simulation. Molecular biology took me into the laboratory and eventually to somatic cell genetics and human gene mapping. One chance encounter led me into the HLA field and another led me into research on cancer, especially colorectal cancer. On the way, I became a champion of the Human Genome Project and of the need for scientists to help promote the public understanding of science.
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Affiliation(s)
- Walter Bodmer
- Cancer and Immunogenetics Laboratory, Weatherall Institute of Molecular Medicine, Oxford OX3 9DS, United Kingdom
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Sudhakar N. Whether molecular genetic analysis is sufficient enough in prediction of an amino acid substitution in a protein as a variant or deleterious mutation? Appl Immunohistochem Mol Morphol 2015; 23:236-7. [PMID: 25153501 DOI: 10.1097/PAI.0000000000000038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Amado NG, Predes D, Moreno MM, Carvalho IO, Mendes FA, Abreu JG. Flavonoids and Wnt/β-catenin signaling: potential role in colorectal cancer therapies. Int J Mol Sci. 2014;15:12094-12106. [PMID: 25007066 PMCID: PMC4139831 DOI: 10.3390/ijms150712094] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 06/20/2014] [Accepted: 06/23/2014] [Indexed: 12/22/2022] Open
Abstract
It is now well documented that natural products have played an important role in anticancer therapy. Many studies focus on the ability of these natural compounds to modulate tumor-related signaling pathways and the relationship of these properties to an anticancer effect. According to the World Health Organization (WHO), colorectal cancer (CRC) is the third most common cancer and the fourth leading cause of cancer death among men and women. Therefore, finding strategies to fight against CRC is an emergent health problem. CRC has a strong association with deregulation of Wnt/β-catenin signaling pathway. As some types of natural compounds are capable of modulating the Wnt/β-catenin signaling, one important question is whether they could counteract CRC. In this review, we discuss the role of flavonoids, a class of natural compounds, on Wnt/β-catenin regulation and its possible potential for therapeutic usage on colorectal cancer.
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Zauber P, Bishop T, Taylor C, Sabbath-Solitare M, Marotta S, Tomlinson I. Colorectal tumors from APC*I1307K carriers principally harbor somatic APC mutations outside the A8 tract. PLoS One 2014; 9:e84498. [PMID: 24416237 PMCID: PMC3886998 DOI: 10.1371/journal.pone.0084498] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Accepted: 11/15/2013] [Indexed: 01/13/2023] Open
Abstract
Purpose APC*I1307K (c.3920T>A) is an inherited variant associated with colorectal tumour risk found almost exclusively in those of Ashkenazi Jewish ancestry. A single nucleotide substitution creates an oligo-adenine tract (A8) that appears to be inherently prone to further mis-pairing and slippage. The reported multiple tumor phenotype of carriers is not easily reconciled with molecular and population genetics data. We postulated that some c.3920T>A carriers with multiple adenomas have other unidentified APC germ line or somatic mutations. Methods DNA from 82 colonic tumours and accompanying normal tissue collected from 29 carriers with multiple colorectal tumors was directly sequenced between codons 716 and 1604. We also assessed APC gene loss of heterozygosity. Results One patient (3.4%) was found to have an additional APC germ line mutation. Twenty-five of the tumours showed no significant somatic molecular change, 36 showed one change, 20 showed two, and one tumour showed more than 2 changes. Our data suggest a correlation between advancing histology and fewer beta-catenin binding sites remaining in the mutant proteins. Conclusions There were no other common germ line variants identified within the region of the APC gene examined, suggesting that any effect from this region on tumour production is attributable to the c.3920T>A allele. Our findings further suggest the only somatic genetic change clearly attributable to the c.3920T>A mutation is the c.3924_3925insA.
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Affiliation(s)
- Peter Zauber
- Department of Medicine, Saint Barnabas Medical Center, Livingston, New Jersey, United States of America
- * E-mail:
| | - Timothy Bishop
- Section of Epidemiology and Biostatistics, Leeds Institute of Molecular Medicine, University of Leeds, Leeds, United Kingdom
| | - Claire Taylor
- Cancer Research UK Genomics Facility, Leeds Institute of Molecular Medicine, University of Leeds, Leeds, United Kingdom
| | - Marlene Sabbath-Solitare
- Department of Pathology, Saint Barnabas Medical Center, Livingston, New Jersey, United States of America
| | - Stephen Marotta
- Department of Pathology, Saint Barnabas Medical Center, Livingston, New Jersey, United States of America
| | - Ian Tomlinson
- Molecular and Population Genetics, Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
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Daneshjou R, Zappala Z, Kukurba K, Boyle SM, Ormond KE, Klein TE, Snyder M, Bustamante CD, Altman RB, Montgomery SB. PATH-SCAN: a reporting tool for identifying clinically actionable variants. Pac Symp Biocomput 2014:229-240. [PMID: 24297550 PMCID: PMC4008882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The American College of Medical Genetics and Genomics (ACMG) recently released guidelines regarding the reporting of incidental findings in sequencing data. Given the availability of Direct to Consumer (DTC) genetic testing and the falling cost of whole exome and genome sequencing, individuals will increasingly have the opportunity to analyze their own genomic data. We have developed a web-based tool, PATH-SCAN, which annotates individual genomes and exomes for ClinVar designated pathogenic variants found within the genes from the ACMG guidelines. Because mutations in these genes predispose individuals to conditions with actionable outcomes, our tool will allow individuals or researchers to identify potential risk variants in order to consult physicians or genetic counselors for further evaluation. Moreover, our tool allows individuals to anonymously submit their pathogenic burden, so that we can crowd source the collection of quantitative information regarding the frequency of these variants. We tested our tool on 1092 publicly available genomes from the 1000 Genomes project, 163 genomes from the Personal Genome Project, and 15 genomes from a clinical genome sequencing research project. Excluding the most commonly seen variant in 1000 Genomes, about 20% of all genomes analyzed had a ClinVar designated pathogenic variant that required further evaluation.
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Affiliation(s)
- Roxana Daneshjou
- Department of Genetics, Stanford University, Stanford, CA 94061, United States
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Fan R, Lo SH. A robust model-free approach for rare variants association studies incorporating gene-gene and gene-environmental interactions. PLoS One 2013; 8:e83057. [PMID: 24358248 PMCID: PMC3866272 DOI: 10.1371/journal.pone.0083057] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [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: 05/24/2013] [Accepted: 10/30/2013] [Indexed: 11/19/2022] Open
Abstract
Recently more and more evidence suggest that rare variants with much lower minor allele frequencies play significant roles in disease etiology. Advances in next-generation sequencing technologies will lead to many more rare variants association studies. Several statistical methods have been proposed to assess the effect of rare variants by aggregating information from multiple loci across a genetic region and testing the association between the phenotype and aggregated genotype. One limitation of existing methods is that they only look into the marginal effects of rare variants but do not systematically take into account effects due to interactions among rare variants and between rare variants and environmental factors. In this article, we propose the summation of partition approach (SPA), a robust model-free method that is designed specifically for detecting both marginal effects and effects due to gene-gene (G×G) and gene-environmental (G×E) interactions for rare variants association studies. SPA has three advantages. First, it accounts for the interaction information and gains considerable power in the presence of unknown and complicated G×G or G×E interactions. Secondly, it does not sacrifice the marginal detection power; in the situation when rare variants only have marginal effects it is comparable with the most competitive method in current literature. Thirdly, it is easy to extend and can incorporate more complex interactions; other practitioners and scientists can tailor the procedure to fit their own study friendly. Our simulation studies show that SPA is considerably more powerful than many existing methods in the presence of G×G and G×E interactions.
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Affiliation(s)
- Ruixue Fan
- Department of Statistics, Columbia University, New York, New York, United States of America
| | - Shaw-Hwa Lo
- Department of Statistics, Columbia University, New York, New York, United States of America
- * E-mail: (SHL)
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De Queiroz Rossanese LB, De Lima Marson FA, Ribeiro JD, Coy CSR, Bertuzzo CS. APC germline mutations in families with familial adenomatous polyposis. Oncol Rep 2013; 30:2081-8. [PMID: 23970361 DOI: 10.3892/or.2013.2681] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 06/26/2013] [Indexed: 12/28/2022] Open
Abstract
Adenomatous polyposis coli (APC) germline mutations are responsible for the occurrence of familial adenomatous polyposis (FAP). Somatic mutations lead to malignant transformation of adenomas. In this context, considering the significance of APC germline mutations in FAP, we aimed to identify APC germline mutations. In the present study, 20 FAP patients were enrolled. The determination of APC germline mutations was performed using sequencing, and the mutations were compared with clinical markers (gender, age at diagnosis, smoking habits, TNM stage, Astler‑Coller stage, degree of differentiation of adenocarcinoma). The data were compared using the SPSS program, with the Fisher's exact test and χ2 test, considering α=0.05. According to the main results in our sample, 16 alleles with deleterious mutations (80% of the patients) were identified while 7 (35%) patients had no deleterious mutations. There was a predominance of nonsense (45% of the patients) and frameshift (20% of the patients) mutations. There was no statistical significance between the APC germline mutations identified and the clinical variables considered in our study. Only TNM stage was associated with the presence of deleterious mutations. Patients with deleterious mutations had an OR, 0.086 (IC=0.001-0.984); TNM stage I+II in comparison with III+IV, when compared with the patients with no deleterious mutations identified. In this context, as a conclusion, we demonstrated the molecular heterogeneity of APC germline mutations in FAP and the difficulty to perform molecular diagnostics in a Brazilian population, considering the admixed population analyzed.
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Boursi B, Sella T, Liberman E, Shapira S, David M, Kazanov D, Arber N, Kraus S. The APC p.I1307K polymorphism is a significant risk factor for CRC in average risk Ashkenazi Jews. Eur J Cancer 2013; 49:3680-5. [PMID: 23896379 DOI: 10.1016/j.ejca.2013.06.040] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Revised: 06/27/2013] [Accepted: 06/28/2013] [Indexed: 12/25/2022]
Abstract
BACKGROUND The p.I1307K adenomatous polyposis coli (APC) gene variant, prevalent among Ashkenazi Jews, may increase the risk for colorectal neoplasia. We studied the clinical importance of screening for this polymorphism in 3305 Israelis undergoing colonoscopy. PATIENTS AND METHODS Clinical data regarding potential risk factors for colorectal cancer (CRC) were collected from individuals undergoing colonoscopic examination at the Tel-Aviv medical center. The APC p.I1307K was detected using real-time PCR (polymerase chain reaction) from DNA extracted from peripheral mononuclear cells. RESULTS The overall prevalence of the p.I1307K polymorphism was 8.0% (10.1% among Ashkenazi and 2.7% among Sephardic Jews, p<0.001). The overall adjusted odds ratio (OR) for colorectal neoplasia among carriers was 1.51 (95% confidence intervals (CI), 1.16-1.98). Among average risk Ashkenazi Jews, the adjusted OR was 1.75 (95% CI 1.26-2.45). A multiplicative interaction was identified between Ashkenazi ethnicity and APC p.I1307K carrier status (P(INTERACTION) = 0.055). The histopathological features of adenomas and carcinomas did not differ between carriers and non-carriers. CONCLUSIONS The APC p.I1307K gene variant is an important risk factor for colorectal neoplasia in average risk Ashkenazi Jews. Carriers in this group should be considered for screening colonoscopy at the age of 40, to be repeated every 5 years, similar to recommendations in individuals with family history of colorectal cancer.
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Affiliation(s)
- Ben Boursi
- The Integrated Cancer Prevention Center, Tel-Aviv Sourasky Medical Center, Tel-Aviv, Israel; Department of Medical Oncology, Sheba Medical Center, Tel-Aviv, Israel
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Liang J, Lin C, Hu F, Wang F, Zhu L, Yao X, Wang Y, Zhao Y. APC polymorphisms and the risk of colorectal neoplasia: a HuGE review and meta-analysis. Am J Epidemiol 2013; 177:1169-79. [PMID: 23576677 DOI: 10.1093/aje/kws382] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Adenomatous polyposis coli gene (APC) polymorphisms may influence the risk for colorectal neoplasia. However, results thus far have been inconclusive. We performed a systematic literature search of the Medline, Embase, Cochrane Collaboration, and HuGE databases and reviewed the references of pertinent articles through May 2012. Odds ratios with 95% confidence intervals were used to estimate the association between 3 APC polymorphisms (D1822V, E1317Q, and I1307K) and colorectal neoplasia. In total, 40 studies from 1997 to 2010 were included in this meta-analysis, and individuals with the D1822V variant homozygote VV genotype had a slight decrease in the risk for colorectal neoplasia compared with the wild-type homozygote DD genotype (pooled odds ratio = 0.87, 95% confidence interval: 0.77, 0.99). There was a small association between the APC E1317Q polymorphism and a risk for colorectal neoplasia (variant vs. wild-type: pooled odds ratio = 1.41, 95% confidence interval: 1.14, 1.76), particularly for colorectal adenomas (variant vs. wild-type: odds ratio = 2.89, 95% confidence interval: 1.83, 4.56). Compared with those who carried the wild-type I1307K, Ashkenazi Jews who carried the I1307K variant were at a significantly increased risk for colorectal neoplasia, with a pooled odds ratio of 2.17 (95% confidence interval: 1.64, 2.86). Our study suggests that APC is a candidate gene for colorectal neoplasia susceptibility.
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Affiliation(s)
- Jing Liang
- Department of Epidemiology, Public Health College, Harbin Medical University, 157 Baojian Street, Nangang District, Harbin, Heilongjiang Province, China
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Lefevre JH, Bonilla C, Colas C, Winney B, Johnstone E, Tonks S, Day T, Hutnik K, Boumertit A, Soubrier F, Midgley R, Kerr D, Parc Y, Bodmer WF. Role of rare variants in undetermined multiple adenomatous polyposis and early-onset colorectal cancer. J Hum Genet 2012; 57:709-16. [PMID: 22875147 DOI: 10.1038/jhg.2012.99] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Some 15-20% of multiple adenomatous polyposis have no genetic explanation and 20-30% of colorectal cancer (CRC) cases are thought to be due to inherited multifactorial causes. Accumulation of deleterious effects of low-frequency dominant and independently acting variants may be a partial explanation for such patients. The aim of this study was to type a selection of rare and low-frequency variants (<5%) to elucidate their role in CRC susceptibility. A total of 1181 subjects were included (866 controls; 315 cases). Cases comprised UK (n=184) and French (n=131) patients with MAP (n=187) or early-onset CRC (n=128). Seventy variants in 17 genes were examined in cases and controls. The effect of the variant effect on protein function was investigated in silico. Out of the 70 variants typed, 36 (51%) were tested for association. Twenty-one variants were rare (minor allele frequency (MAF) <1%). Four rare variants were found to have a significantly higher MAF in cases (EXO1-12, MLH1-1, CTNNB1-1 and BRCA2-37, P<0.05) than in controls. Pooling all rare variants with a MAF <0.5% showed an excess risk in cases (odds ratio=3.2; 95% confidence interval=1.1-9.5; P=0.04). Rare variants are important risk factors in CRC and, as such, should be systematically assayed alongside common variation in the search for the genetic basis of complex diseases.
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25
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Li P, Zhu S, Wu X, Zhu X, Li J, Pan L, Xin Z, Niu F, Wu J, Liu Y. Association of polymorphisms in mitofusin-2 gene with type 2 diabetes in Han Chinese. J Biomed Biotechnol 2012; 2012:205752. [PMID: 22778543 PMCID: PMC3385923 DOI: 10.1155/2012/205752] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Revised: 04/13/2012] [Accepted: 04/20/2012] [Indexed: 01/22/2023] Open
Abstract
MFN2 and ESRRA are candidate genes involved in the pathogenesis of T2D. Five tag-SNPs in MFN2 gene and three in ESRRA gene were selected and genotyped with TaqMan or PCR-RFLP method in stage 1 populations (555 patients with T2D and 649 control subjects) and stage 2 populations (546 patients with T2D versus 419 control subjects) in Han Chinese. And combining our published data, we estimated the interactions between genetic variants in the MFN2, ESRRA, and PGC-1α genes on the T2D risk using MDR. rs873458 (G > A) and rs2878677 (C > T) in MFN2 gene were significantly associated with T2D (P = 0.005 and 0.01) in stage 1 populations, and the association of other SNPs with T2D was not found. In stage 2 populations, we further confirmed the association between rs2878677 and T2D (P = 0.01). Combining the two stage populations, the data supported more significant effect of rs873458 and rs2878677 on T2D risk (P = 0.003 and 0.0001). A-C-G-T-C and G-T-C-T-C in MFN2 had significant association with T2D (P = 0.007 and 0.009). The present study also provided the evidence that MFN2 had interactions with PGC-1α (P < 0.0001) or ESRRA (P < 0.0001). This study suggested a role of MFN2 polymorphism in the risk of T2D; however, further studies are needed.
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Affiliation(s)
- Pengtao Li
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, 5 Dongdan 3 Tiao, Beijing 100005, China
| | - Shuying Zhu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, 5 Dongdan 3 Tiao, Beijing 100005, China
| | - Xiaopan Wu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, 5 Dongdan 3 Tiao, Beijing 100005, China
| | - Xilin Zhu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, 5 Dongdan 3 Tiao, Beijing 100005, China
| | - Jingyun Li
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, 5 Dongdan 3 Tiao, Beijing 100005, China
| | - Liping Pan
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, 5 Dongdan 3 Tiao, Beijing 100005, China
| | - Zhenhui Xin
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, 5 Dongdan 3 Tiao, Beijing 100005, China
| | - Fenghe Niu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, 5 Dongdan 3 Tiao, Beijing 100005, China
| | - Jia Wu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, 5 Dongdan 3 Tiao, Beijing 100005, China
| | - Ying Liu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, 5 Dongdan 3 Tiao, Beijing 100005, China
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Abstract
MOTIVATION Next-generation sequencing greatly increases the capacity to detect rare-variant complex-trait associations. However, it is still expensive to sequence a large number of samples and therefore often small datasets are used. Given cost constraints, a potentially more powerful two-step strategy is to sequence a subset of the sample to discover variants, and genotype the identified variants in the remaining sample. If only cases are sequenced, directly combining sequence and genotype data will lead to inflated type-I errors in rare-variant association analysis. Although several methods have been developed to correct for the bias, they are either underpowered or theoretically invalid. We proposed a new method SEQCHIP to integrate genotype and sequence data, which can be used with most existing rare-variant tests. RESULTS It is demonstrated using both simulated and real datasets that the SEQCHIP method has controlled type-I errors, and is substantially more powerful than all other currently available methods. AVAILABILITY SEQCHIP is implemented in an R-Package and is available at http://linkage.rockefeller.edu/suzanne/seqchip/Seqchip.html.
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Affiliation(s)
- Dajiang J Liu
- Department of Biostatistics, Center of Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA.
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27
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Francisco I, Albuquerque C, Lage P, Belo H, Vitoriano I, Filipe B, Claro I, Ferreira S, Rodrigues P, Chaves P. Familial colorectal cancer type X syndrome: two distinct molecular entities? Fam Cancer. 2011;10:623-631. [PMID: 21837511 DOI: 10.1007/s10689-011-9473-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In a fraction of families fulfilling the Amsterdam criteria for hereditary non-polyposis colorectal cancer, colorectal cancers are microsatellite stable and DNA mismatch repair gene (MMR) mutations are not found. These families were designated as familial colorectal cancer type X (FCCTX). We aimed to characterise a group of FCCTX families defined by the Amsterdam criteria and MSS tumours at clinical and molecular level. Twenty-four tumours from 15 FCCTX families were analysed for loss of known tumour suppressor gene (TSG) loci (APC, TP53, SMAD4 and DCC), MGMT and MMR genes promoter methylation, and also APC and KRAS somatic mutations. FCCTX families presented specific clinical features: absence of endometrial tumours, high adenoma/carcinoma ratio (1.91) and prevalence of rectal cancers (13/27, 48%). New molecular features were found: the majority of FCCTX tumours (13/18; 72%) presented TSG loss. TSG loss positive tumours presented frequent APC and KRAS somatic mutations and MGMT methylation [10/13 (77%), 7/13 (54%) and 6/11 (54%), respectively]. In TSG loss negative tumours (5/18; 28%), the same molecular events were found in 2/5 (40%), 2/5 (40%) and 1/3 (33%) tumours, respectively. Transition mutations in KRAS were more frequent among MGMT methylated tumours than in unmethylated [5/8 (63%) vs. 1/10 (10%), P = 0.03]. Although sharing similar clinical features, at least two different molecular entities should exist among FCCTX families, one whose tumours present frequent TSG loss, APC and KRAS somatic mutations, and MGMT promoter methylation, and a second, lesser predominant, with no evidence of TSG loss and rarely presenting promoter methylation.
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28
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Ladouceur M, Dastani Z, Aulchenko YS, Greenwood CMT, Richards JB. The empirical power of rare variant association methods: results from sanger sequencing in 1,998 individuals. PLoS Genet 2012; 8:e1002496. [PMID: 22319458 PMCID: PMC3271058 DOI: 10.1371/journal.pgen.1002496] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Accepted: 12/08/2011] [Indexed: 01/09/2023] Open
Abstract
The role of rare genetic variation in the etiology of complex disease remains unclear. However, the development of next-generation sequencing technologies offers the experimental opportunity to address this question. Several novel statistical methodologies have been recently proposed to assess the contribution of rare variation to complex disease etiology. Nevertheless, no empirical estimates comparing their relative power are available. We therefore assessed the parameters that influence their statistical power in 1,998 individuals Sanger-sequenced at seven genes by modeling different distributions of effect, proportions of causal variants, and direction of the associations (deleterious, protective, or both) in simulated continuous trait and case/control phenotypes. Our results demonstrate that the power of recently proposed statistical methods depend strongly on the underlying hypotheses concerning the relationship of phenotypes with each of these three factors. No method demonstrates consistently acceptable power despite this large sample size, and the performance of each method depends upon the underlying assumption of the relationship between rare variants and complex traits. Sensitivity analyses are therefore recommended to compare the stability of the results arising from different methods, and promising results should be replicated using the same method in an independent sample. These findings provide guidance in the analysis and interpretation of the role of rare base-pair variation in the etiology of complex traits and diseases.
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Affiliation(s)
- Martin Ladouceur
- Department of Human Genetics, McGill University, Montreal, Canada
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Canada
| | - Zari Dastani
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, Canada
| | - Yurii S. Aulchenko
- Department of Epidemiology, Erasmus MC, Rotterdam, The Netherlands
- Institute of Cytology and Genetics SD RAS, Novosibirsk, Russia
| | - Celia M. T. Greenwood
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Canada
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, Canada
- Department of Oncology, McGill University, Montreal, Canada
| | - J. Brent Richards
- Department of Human Genetics, McGill University, Montreal, Canada
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Canada
- Department of Medicine, Jewish General Hospital, McGill University, Montreal, Canada
- Twin Research and Genetic Epidemiology, King's College London, London, United Kingdom
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29
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Ehli EA, Hu Y, Lengyel-Nelson T, Hudziak JJ, Davies GE. Identification and functional characterization of three novel alleles for the serotonin transporter-linked polymorphic region. Mol Psychiatry 2012; 17:185-92. [PMID: 21200389 DOI: 10.1038/mp.2010.130] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A promoter polymorphism in the serotonin transporter gene (5-HTTLPR) has been reported to confer relative risk for phenotypes (depression/anxiety) and endophenotypes (amygdala reactivity). In this report, we identify and characterize three rare 5-HTTLPR alleles not previously described in the human literature. The three novel alleles were identified while genotyping 5-HTTLPR in a family-based attention deficit hyperactivity disorder clinical population. Two of the novel alleles are longer than the common 16-repeat long (L) allele (17 and 18 repeats) and the third is significantly smaller than the 14-repeat short (S) allele (11 repeats). The sequence and genetic architecture of each novel allele is described in detail. We report a significant decrease in the expression between the XL₁₇ (17r) allele and the L(A) (16r) allele. The XS₁₁ (11r) allele showed similar expression with the S (14r) allele. A 1.8-fold increase in expression was observed with the L(A)(16r) allele compared with the L(G) (16r) allele, which replicates results from earlier 5-HTTLPR expression experiments. In addition, transcription factor binding site (TFBS) analysis was performed using MatInspector (Genomatix) that showed the presence or absence of different putative TFBSs between the novel alleles and the common L (16r) and S (14r) alleles. The identification of rare variants and elucidation of their functional impact could potentially lead to understanding the contribution that the rare variant may have on the inheritance/susceptibility of multifactorial common diseases.
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30
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Yuan A, Chen G, Zhou Y, Bentley A, Rotimi C. A novel approach for the simultaneous analysis of common and rare variants in complex traits. Bioinform Biol Insights 2012; 6:1-9. [PMID: 22346348 PMCID: PMC3273305 DOI: 10.4137/bbi.s8852] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Genome-wide association studies (GWAS) have been successful in detecting common genetic variants underlying common traits and diseases. Despite the GWAS success stories, the percent trait variance explained by GWAS signals, the so called "missing heritability" has been, at best, modest. Also, the predictive power of common variants identified by GWAS has not been encouraging. Given these observations along with the fact that the effects of rare variants are often, by design, unaccounted for by GWAS and the availability of sequence data, there is a growing need for robust analytic approaches to evaluate the contribution of rare variants to common complex diseases. Here we propose a new method that enables the simultaneous analysis of the association between rare and common variants in disease etiology. We refer to this method as SCARVA (simultaneous common and rare variants analysis). SCARVA is simple to use and is efficient. We used SCARVA to analyze two independent real datasets to identify rare and common variants underlying variation in obesity among participants in the Africa America Diabetes Mellitus (AADM) study and plasma triglyceride levels in the Dallas Heart Study (DHS). We found common and rare variants associated with both traits, consistent with published results.
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Affiliation(s)
- Ao Yuan
- National Human Genome Center, Howard University, Washington DC, USA
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31
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Miladi-Abdennadher I, Amouri A, Ayadi L, Khabir A, Ellouze S, Tahri N, Frikha M, Sellami-Boudawara T, Mokdad-Gargouri R. A novel pathogenic germline mutation in the adenomatous polyposis coli gene in a Tunisian family with FAP. Fam Cancer 2011; 10:567-71. [PMID: 21598003 DOI: 10.1007/s10689-011-9451-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Familial adenomatous polyposis (FAP) is an autosomal dominant disorder which typically presents with colorectal cancer in early adult life, secondary to extensive adenomatous polyps of the colon. In addition to the colonic manifestations, the syndrome presents several extracolonic features including, congenital hypertrophy of the retinal pigment, osteomata and desmoid tumors. In this study, we aimed to investigate the clinical and genetic features in a Tunisian family with FAP. Sequence of the APC gene (Adenomatous Polyposis Coli) revealed a novel mutation (c.2016-2017 del TA) in exon 15, present in all affected individuals in an heterozygous state. The frameshift mutation generates a premature stop codon at amino acid 677 of the APC protein (p. H672Qfs X5). The unaffected family members did not harbor this mutation, however, a first degree relative of the patient aged of 32-year-old was phenotypically normal but carries the c.2016-2017 del TA mutation. This discrepancy can be explained by the effect of modifier gene which can affect the expressivity of the disease.
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32
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Curia MC, De Iure S, De Lellis L, Veschi S, Mammarella S, White MJ, Bartlett J, Di Iorio A, Amatetti C, Lombardo M, Di Gregorio P, Battista P, Mariani-Costantini R, Williams SM, Cama A. Increased variance in germline allele-specific expression of APC associates with colorectal cancer. Gastroenterology 2012; 142:71-77.e1. [PMID: 21995949 PMCID: PMC3246305 DOI: 10.1053/j.gastro.2011.09.048] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2011] [Revised: 09/07/2011] [Accepted: 09/26/2011] [Indexed: 12/16/2022]
Abstract
BACKGROUND & AIMS Germline variations in allele-specific expression (ASE) are associated with highly penetrant familial cancers, but their role in common sporadic cancers is unclear. ASE of adenomatous polyposis coli (APC) is associated with pathogenesis of familial adenomatous polyposis. We investigated whether moderate variations in ASE of APC contribute to common forms of colorectal cancer (CRC). METHODS Denaturing high-performance liquid chromatography was used to analyze germline ASE of APC in blood samples from patients with CRC (cases, n = 53) and controls (n = 68). Means, medians, and variances of ASE were compared. Variants in the APC gene region also were analyzed. RESULTS The distribution of ASE differed significantly between groups; cases had significantly larger amounts of variance than controls (P = .0004). Risk for CRC increased proportionally with the degree of deviation from the mean. The odds ratio for individuals with levels of ASE that deviated more than 1 standard deviation from the mean was 3.97 (95% confidence interval, 1.71-9.24; P = .001); for those with levels greater than 1.645 standard deviations, the odds ratio was 13.46 (95% confidence interval, 1.76-609.40; P = .005). Sequence analysis revealed that a patient with a high level of ASE who did not have a family history of CRC carried a nonsense mutation in APC (p.Arg216X). Genotype analysis of APC associated multiple single-nucleotide polymorphisms with ASE values and/or variance among cases, but not controls. Cis variants, therefore, might account for some of the variance in ASE of APC. CONCLUSIONS Patients with CRC have a larger variance in germline levels of ASE in APC than controls; large distances from the mean ASE were associated with risk for common forms of CRC.
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Affiliation(s)
- Maria Cristina Curia
- Department of Oncology and Experimental Medicine, “G. d’Annunzio” University, Chieti-Pescara, Chieti, Italy,Aging Research Center (Ce.S.I.) University “G. d’Annunzio” Foundation, Chieti, Italy
| | - Sabrina De Iure
- Department of Oncology and Experimental Medicine, “G. d’Annunzio” University, Chieti-Pescara, Chieti, Italy
| | - Laura De Lellis
- Department of Oncology and Experimental Medicine, “G. d’Annunzio” University, Chieti-Pescara, Chieti, Italy,Aging Research Center (Ce.S.I.) University “G. d’Annunzio” Foundation, Chieti, Italy
| | - Serena Veschi
- Aging Research Center (Ce.S.I.) University “G. d’Annunzio” Foundation, Chieti, Italy,Department of Human Movement Sciences, “G. d’Annunzio” University, Chieti-Pescara, Chieti, Italy
| | - Sandra Mammarella
- Department of Oncology and Experimental Medicine, “G. d’Annunzio” University, Chieti-Pescara, Chieti, Italy
| | - Marquitta J. White
- Department of Molecular Physiology and Biophysics, Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, USA
| | - Jacquelaine Bartlett
- Department of Molecular Physiology and Biophysics, Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, USA
| | - Angelo Di Iorio
- Department of Medicine and Sciences of Aging, University “G. d’Annunzio” Foundation, Chieti, Italy
| | | | - Marco Lombardo
- Division of Oncology, “S. Spirito” Hospital, Pescara, Italy
| | | | - Pasquale Battista
- Department of Human Movement Sciences, “G. d’Annunzio” University, Chieti-Pescara, Chieti, Italy
| | - Renato Mariani-Costantini
- Department of Oncology and Experimental Medicine, “G. d’Annunzio” University, Chieti-Pescara, Chieti, Italy,Aging Research Center (Ce.S.I.) University “G. d’Annunzio” Foundation, Chieti, Italy
| | - Scott M. Williams
- Department of Molecular Physiology and Biophysics, Center for Human Genetics Research, Vanderbilt University, Nashville, Tennessee, USA,Corresponding author: Department of Molecular Physiology and Biophysics, Center for Human Genetics Research, Vanderbilt University, 519 Light Hall, 37232 Nashville, Tennessee, USA. Telephone 615 322 8036;
| | - Alessandro Cama
- Department of Oncology and Experimental Medicine, “G. d’Annunzio” University, Chieti-Pescara, Chieti, Italy,Aging Research Center (Ce.S.I.) University “G. d’Annunzio” Foundation, Chieti, Italy
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33
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Abstract
Although progress in the treatment of patients with colorectal cancer (CRC) has resulted in improved median survival, most patients with metastatic CRC still die of their disease, and essentially all patients with early-stage disease must undergo surgical resection and subsequently face the possibility of adjuvant chemotherapy. As effective screening and prevention strategies for CRC have been developed, identification of individuals with a hereditary predisposition to developing CRC is especially important and provides the opportunity to reduce disease burden in this high-risk population. Increased awareness and improved diagnostic techniques for hereditary CRC syndromes have facilitated more frequent diagnosis and management of a small number of highly penetrant syndromes within families. However, known high-penetrance genetic predisposition syndromes account for a minority of all familial CRC, leaving much of the genetic basis of CRC unexplained. Recent advances in high-throughput genotyping have made possible genome-wide association studies, which have identified novel genetic variants associated with modest increases in CRC risk. While these associations have helped to identify potentially important pathways in CRC carcinogenesis, at the current time, the clinical use of such genetic risk variants in colon cancer risk stratification remains limited.
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Affiliation(s)
- David J Gallagher
- Department of Medicine, Clinical Genetics Service, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA.
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34
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Bonilla C, Lefèvre JH, Winney B, Johnstone E, Tonks S, Colas C, Day T, Hutnik K, Boumertit A, Midgley R, Kerr D, Parc Y, Bodmer WF. Cyclin D1 rare variants in UK multiple adenoma and early-onset colorectal cancer patients. J Hum Genet 2010; 56:58-63. [PMID: 21107342 DOI: 10.1038/jhg.2010.144] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We examined the influence that rare variants and low-frequency polymorphisms in the cancer candidate gene CCND1 have on the development of multiple intestinal adenomas and the early onset of colorectal cancer. Individuals with <100 multiple polyps and patients with colorectal cancer diagnosed before 50 years of age were recruited in UK, and screened for sequence changes in the coding and regulatory regions of CCND1. A set of about 800 UK control individuals was genotyped for the variants discovered in the cases. Variants in the promoter, intron-exon boundaries and untranslated regions of the CCND1 gene had higher frequencies in cases than in controls. Five of these variants were typed in a set of French multiple adenoma and early-onset patients, who also showed higher allele frequencies than UK controls. When pooled together, variants with frequencies lower than 1% conferred an increased risk of disease that was significant in the multiple adenoma group (odds ratio (OR) 2.2; 95% confidence interval, 1.1-4.4; P = 0.03). Most variants had a putative functional effect when assessed in silico. We conclude that rare variants of CCND1 are risk factors for colorectal cancer, with considerably larger effects than common polymorphisms, and as such should be systematically evaluated in susceptibility studies.
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Affiliation(s)
- Carolina Bonilla
- Department of Clinical Pharmacology, University of Oxford, Headington, Oxford, UK
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35
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Heinen CD. Genotype to phenotype: analyzing the effects of inherited mutations in colorectal cancer families. Mutat Res 2010; 693:32-45. [PMID: 19766128 PMCID: PMC2891646 DOI: 10.1016/j.mrfmmm.2009.09.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2009] [Revised: 09/04/2009] [Accepted: 09/09/2009] [Indexed: 05/28/2023]
Abstract
With improvements to DNA sequencing technologies, including the advent of massively parallel sequencing to perform "deep sequencing" of tissue samples, the ability to determine all of the nucleotide variations in a tumor becomes a possibility. This information will allow us to more fully understand the heterogeneity within each tumor, as well as to identify novel genes involved in cancer development. However, the new challenge that arises will be to interpret the pathogenic significance of each genetic variant. The enormity and complexity of this challenge can be demonstrated by focusing on just the genes involved in the hereditary colon cancer syndromes, familial adenomatous polyposis (FAP) and hereditary non-polyposis coli (HNPCC). The genes responsible for each disease were identified almost two decades ago -APC for FAP and the MMR genes for HNPCC - and a large number of germline variations have been identified in these genes in hereditary cancer patients. However, relating the effect of an individual genotype to phenotype is not always straightforward. This review focuses on the roles of the APC and MMR genes in tumor development and the work that has been done to relate different variants in each gene to functional aberrations and ultimately tumorigenesis. By considering the work that has already been done on two well-defined diseases with clear genetic associations, one can begin to understand the challenges that lie ahead as new genes and gene mutations are discovered through tumor sequencing.
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Affiliation(s)
- Christopher D Heinen
- Neag Comprehensive Cancer Center and Center for Molecular Medicine, University of Connecticut Health Center, Farmington, CT 06030, USA.
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36
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Gaujoux S, Pinson S, Gimenez-Roqueplo AP, Amar L, Ragazzon B, Launay P, Meatchi T, Libé R, Bertagna X, Audebourg A, Zucman-Rossi J, Tissier F, Bertherat J. Inactivation of the APC gene is constant in adrenocortical tumors from patients with familial adenomatous polyposis but not frequent in sporadic adrenocortical cancers. Clin Cancer Res 2010; 16:5133-41. [PMID: 20978149 DOI: 10.1158/1078-0432.ccr-10-1497] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
PURPOSE In adrenocortical tumors (ACT), Wnt/β-catenin pathway activation can be explained by β-catenin somatic mutations only in a subset of tumors. ACT is observed in patients with familial adenomatous polyposis (FAP) with germline APC mutations, as well as in patients with Beckwith-Wiedemann syndrome with Wilms' tumors reported to have WTX somatic mutations. Both APC and WTX are involved in Wnt/β-catenin pathway regulation and may play a role in ACT tumorigenesis. The aim of this study was to report if APC and WTX may be associated with FAP-associated and sporadic ACT. EXPERIMENTAL DESIGN ACTs from patients with FAP and sporadic adrenocortical carcinomas (ACC) with abnormal β-catenin localization on immunohistochemistry but no somatic β-catenin mutations were studied. APC was analyzed by denaturing high-performance liquid chromatography followed by direct sequencing and by multiplex ligation-dependent probe amplification when allelic loss was suspected. WTX was studied by direct sequencing. RESULTS Four ACTs were observed in three patients with FAP and were ACC, adrenocortical adenoma, and bilateral macronodular adrenocortical hyperplasia, all with abnormal β-catenin localization. Biallelic inactivation of APC was strongly suggested by the simultaneous existence of somatic and germline alterations in all ACTs. In the 20 sporadic ACCs, a silent heterozygous somatic mutation as well as a rare heterozygous polymorphism in APC was found. No WTX mutations were observed. CONCLUSIONS ACT should be considered a FAP tumor. Biallelic APC inactivation mediates activation of the Wnt/β-catenin pathway in the ACTs of patients with FAP. In contrast, APC and WTX genetic alterations do not play a significant role in sporadic ACC.
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Affiliation(s)
- Sébastien Gaujoux
- Institut Cochin, Université Paris Descartes-Faculté de médecine, CNRS (UMR 8104), Paris, France
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Wong HL, Peters U, Hayes RB, Huang WY, Schatzkin A, Bresalier RS, Velie EM, Brody LC. Polymorphisms in the adenomatous polyposis coli (APC) gene and advanced colorectal adenoma risk. Eur J Cancer 2010; 46:2457-66. [PMID: 20510605 PMCID: PMC2924917 DOI: 10.1016/j.ejca.2010.04.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [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: 01/06/2010] [Revised: 04/14/2010] [Accepted: 04/20/2010] [Indexed: 02/07/2023]
Abstract
While germline mutations in the adenomatous polyposis coli (APC) gene cause the hereditary colon cancer syndrome (familial adenomatous polyposis (FAP)), the role of common germline APC variants in sporadic adenomatous polyposis remains unclear. We studied the association of eight APC single nucleotide polymorphisms (SNPs), possibly associated with functional consequences, and previously identified gene-environment (dietary fat intake and hormone replacement therapy (HRT) use) interactions, in relation to advanced colorectal adenoma in 758 cases and 767 sex- and race-matched controls, randomly selected from the screening arm of the Prostate, Lung, Colorectal and Ovarian Cancer Screening Trial. Cases had at least one verified advanced adenoma of the distal colon; controls, a negative sigmoidoscopy. We did not observe an association between genotypes for any of the eight APC SNPs and advanced distal adenoma risk (P(global gene-based)=0.92). Frequencies of identified common haplotypes did not differ between cases and controls (P(global haplotype test)=0.97). However, the risk for advanced distal adenoma was threefold higher for one rare haplotype (cases: 2.7%; controls: 1.6%) (odds ratio (OR)=3.27; 95% confidence interval (CI)=1.08-9.88). The genetic association between D1822V and advanced distal adenoma was confined to persons consuming a high-fat diet (P(interaction)=0.03). Similar interactions were not observed with HRT use. In our large, nested case-control study of advanced distal adenoma and clinically verified adenoma-free controls, we observed no association between specific APC SNPs and advanced adenoma. Fat intake modified the APC D1822V-adenoma association, but further studies are warranted.
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Affiliation(s)
- Hui-Lee Wong
- Department of Health and Human Services, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD
| | - Ulrike Peters
- Department of Health and Human Services, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD
- Cancer Prevention Research Program, Fred Hutchinson Cancer Research Center, Seattle, WA
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, WA
| | - Richard B. Hayes
- Department of Health and Human Services, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD
| | - Wen-Yi Huang
- Department of Health and Human Services, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD
| | - Arthur Schatzkin
- Department of Health and Human Services, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Rockville, MD
| | - Robert S. Bresalier
- Department of Gastrointestinal Medicine and Nutrition, M.D. Anderson Cancer Center, Houston, TX
| | - Ellen M. Velie
- Department of Epidemiology, Michigan State University, East Lansing, MI
| | - Lawrence C. Brody
- Department of Health and Human Services, Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, NIH, Bethesda MD
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Kuiper RP, Ligtenberg MJL, Hoogerbrugge N, Geurts van Kessel A. Germline copy number variation and cancer risk. Curr Opin Genet Dev 2010; 20:282-9. [PMID: 20381334 DOI: 10.1016/j.gde.2010.03.005] [Citation(s) in RCA: 92] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Revised: 03/05/2010] [Accepted: 03/15/2010] [Indexed: 01/13/2023]
Abstract
The human genome is subject to substantial structural variation, including copy number variation (CNV). Constitutional CNVs may either represent benign polymorphic variants or be associated with disease, including cancer predisposition. Rare nonpolymorphic CNVs, that is DNA lesions that result in gene deletions, inversions, and/or fusions, may be responsible for a high cancer risk. In addition, we previously elucidated a mechanism by which CNV-based transcriptional read-through mediates inactivation of a neighboring gene through in cis hypermethylation of its promoter. This novel mechanism explains the etiology of a recurrent and strongly inherited tissue-restricted epimutation. Recently, we obtained supporting evidence for such a CNV-associated scenario, suggesting that it may be more prevalent than previously thought. We expect that copy number profiling in unexplained high-risk families will lead to the discovery of additional cancer-predisposing genes and/or mechanisms.
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Affiliation(s)
- Roland P Kuiper
- Department of Human Genetics, Radboud University Nijmegen Medical Centre, Nijmegen Centre for Molecular Life Sciences, Nijmegen, The Netherlands.
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GARRE P, DE LA HOYA M, INIESTA P, ROMERA A, LLOVET P, GONZALEZ S, PEREZ-SEGURA P, CAPELLA G, DIAZ-RUBIO E, CALDES T. APC Yin-Yang haplotype associated with colorectal cancer risk. Exp Ther Med 2010; 1:879-883. [DOI: 10.3892/etm.2010.125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2010] [Accepted: 07/15/2010] [Indexed: 11/06/2022] Open
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Dallosso AR, Jones S, Azzopardi D, Moskvina V, Al-Tassan N, Williams GT, Idziaszczyk S, Davies DR, Milewski P, Williams S, Beynon J, Sampson JR, Cheadle JP. The APC Variant p.Glu1317Gln predisposes to colorectal adenomas by a novel mechanism of relaxing the target for tumorigenic somatic APC mutations. Hum Mutat 2009; 30:1412-8. [PMID: 19701947 DOI: 10.1002/humu.21089] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Multiple rare nonsynonymous variants in APC predispose to colorectal adenomas. The mechanisms through which such variants act have been unclear, but it has been proposed that a specific ("just-right") level of beta-catenin signaling is required for colorectal tumorigenesis. This appears to be mediated by selection for APC genotypes that retain one, or rarely two, 20 amino acid beta-catenin downregulating repeats (20AARs). We investigated the mechanism through which the variant p.Glu1317Gln (c.3949G>C) contributes to colorectal tumorigenesis. We compared the patterns of somatic APC mutations in tumors from patients with attenuated familial adenomatous polyposis (AFAP) who did, or did not, coinherit p.Glu1317Gln with their AFAP-causing APC mutations. Only 8.2% (4/49) of tumors carrying p.Glu1317Gln had somatic mutations predicted to result in mutant polypeptides retaining a single 20AAR, compared to 62.1% (36/58) of those which did not carry this variant (P=5.64 x 10(-9)). Furthermore, tumors with p.Glu1317Gln often carried somatic mutations that were unusually early or late (downstream of the second 20AAR) in the APC open reading frame. These data support a novel mechanism in which p.Glu1317Gln in combination with other weak mutant APC alleles (generating polypepetides with zero, two, or three 20AARs) can provide the necessary growth advantage for colorectal tumorigenesis.
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Affiliation(s)
- Anthony R Dallosso
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, United Kingdom
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Lin YM, Ko HC, Chang FM, Yeh TL, Sun HS. Population-specific functional variant of the TPH2 gene 2755C>A polymorphism contributes risk association to major depression and anxiety in Chinese peripartum women. Arch Womens Ment Health 2009; 12:401-8. [PMID: 19588223 DOI: 10.1007/s00737-009-0088-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2009] [Accepted: 06/19/2009] [Indexed: 12/19/2022]
Abstract
The rate-limiting enzyme of serotonin biosynthesis, tryptophan hydroxylase 2 (TPH2), is one of the most promising candidate genes for psychiatric disorders. Although evidence strongly suggests that the TPH2 is significant in the etiology of major depression and anxiety disorder, whether it also contributes to the etiology of peripartum major depression and anxiety disorder, a specific subtype influenced considerably by other environmental factors like hormones, is unclear. This study investigated the role of TPH2 in the etiology of peripartum major depression and anxiety disorder in a Han Chinese population in Taiwan. Six single nucleotide polymorphisms were selected from previously profiled genetic information of TPH2 in Han Chinese. A cohort of postpartum Chinese women that included 117 patients with major depression, anxiety disorder, or both and 83 healthy controls were genotyped with selected TPH2 markers. The TPH2 2755A allele was found only in women with peripartum major depression and anxiety disorder (p = 0.043) and exhibited a dominant gene action (p = 0.038) with an estimated disease risk of 1.73. Although the sample size is small, results from this study suggest that the TPH2 C2755A polymorphism may represent a population-specific risk factor for peripartum major depression and anxiety disorder, perhaps by interacting with hormones.
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Olschwang S, Vernerey D, Cottet V, Pariente A, Nalet B, Lafon J, Faivre J, Laurent-Puig P, Bonithon-Kopp C, Bonaiti-Pellié C. Analysis of candidate genes in occurrence and growth of colorectal adenomas. J Oncol 2009; 2009:306786. [PMID: 19888426 PMCID: PMC2771154 DOI: 10.1155/2009/306786] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/15/2009] [Accepted: 09/09/2009] [Indexed: 12/28/2022]
Abstract
Predisposition to sporadic colorectal tumours is influenced by genes with minor phenotypic effects. A case-control study was set up on 295 patients treated for a large adenoma matched with polyp-free individuals on gender, age, and geographic origin in a 1 : 2 proportion. A second group of 302 patients treated for a small adenoma was also characterized to distinguish effects on adenoma occurrence and growth. We focussed the study on 38 single nucleotide polymorphisms (SNPs) encompassing 14 genes involved in colorectal carcinogenesis. Effect of SNPs was tested using unconditional logistic regression. Comparisons were made for haplotypes within a given gene and for biologically relevant genes combinations using the combination test. The APC p.Glu1317Gly variant appeared to influence the adenoma growth (P = .04, exact test) but not its occurrence. This result needs to be replicated and genome-wide association studies may be necessary to fully identify low-penetrance alleles involved in early stages of colorectal tumorigenesis.
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Affiliation(s)
- Sylviane Olschwang
- Centre de Recherche en Cancérologie de Marseille, INSERM U891, 13009 Marseille, France
- Institut Paoli-Calmettes, Department of Biopathology, 13009 Marseille, France
| | - Déwi Vernerey
- INSERM, U535, 94800 Villejuif, France
- Université Paris-Sud, 94800 Villejuif, France
| | | | | | - Bernard Nalet
- Centre Hospitalier, Gastroenterology Unit, 26200 Montélimar, France
| | - Jacques Lafon
- Centre Hospitalier, Gastroenterology Unit, 13080 Aix-en-Provence, France
| | - Jean Faivre
- Centre Hospitalier Universitaire, 21000 Dijon, France
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Hall M, Liberman E, Dulkart O, Galazan L, Sagiv E, Shmueli E, Kazanov D, Hallak A, Moshkowitz M, Figer A, Kraus S, Inbar M, Neugut A, Arber N. Risk of colorectal neoplasia associated with the adenomatous polyposis coli E1317Q variant. Ann Oncol 2009; 20:1517-1521. [DOI: 10.1093/annonc/mdp023] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
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Filipe B, Baltazar C, Albuquerque C, Fragoso S, Lage P, Vitoriano I, Mão de Ferro S, Claro I, Rodrigues P, Fidalgo P, Chaves P, Cravo M, Nobre Leitão C. APCorMUTYHmutations account for the majority of clinically well-characterized families with FAP and AFAP phenotype and patients with more than 30 adenomas. Clin Genet 2009; 76:242-55. [DOI: 10.1111/j.1399-0004.2009.01241.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Lee CI, Hsu MY, Chou CH, Wang C, Lo YS, Loh JK, Howng SL, Hong YR. CTNNB1 (beta-catenin) mutation is rare in brain tumours but involved as a sporadic event in a brain metastasis. Acta Neurochir (Wien) 2009; 151:1107-11. [PMID: 19582367 DOI: 10.1007/s00701-009-0242-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2008] [Accepted: 10/13/2008] [Indexed: 10/20/2022]
Abstract
BACKGROUND The Wnt signaling pathway has been implicated in colon and other cancers. Nevertheless, few or no mutations of CTNNB1 (beta-catenin) have so far been described in brain cancer. We therefore examined the prevalence of constitutive activation of the Wnt signaling pathway in brain cancer specimens as well as cancer cell lines. METHOD We used polymerase chain reaction PCR and direct sequencing methods to investigate whether mutations in the CTNNB1 phosphorylation sites S33, S37, S41 and T45 were present in 68 brain tumours, including meningioma, astrocytoma, pituitary adenoma, neuroblastoma, metastasis to the brain, and cell lines. FINDINGS CTNNB1 gene mutations were not found in either the original brain tumour specimens or the cell lines. However, a missense mutation of CTNNB1 was identified at residue 33, TCT (Ser) --> TGT (Cys) in a patient with lung metastasis to brain. In addition, in vitro functional assay showed that the S33C mutant of beta-catenin did affect transcriptional activity in a TCF-4-luciferase reporter construct. CONCLUSIONS These results indicate that the mutation of exon 3 of the CTNNB1 gene in brain tumours may be a rare event and yet may be required for a small subset of human metastatic brain tumours.
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Marrakchi R, Bougatef K, Moussa A, Ouerhani S, Khodjet-el-Khil H, Messai Y, Mestiri O, Najar T, Benammar-Elgaaeid A. 3020insC insertion in NOD2/CARD15 gene, a prevalent variant associated with anti-Saccharomyces cerevisiae antibodies and ileal location of Crohn's disease in Tunisian population. Inflamm Res 2009; 57:e67-71. [PMID: 19184350 DOI: 10.1016/j.patbio.2008.01.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2007] [Accepted: 01/11/2008] [Indexed: 01/29/2023] Open
Abstract
OBJECTIVE Our aim is to investigate the relation between CARD15 3020insC mutation, anti-Saccharomyces cerevisiae antibodies (ASCA) and disease phenotype, in Tunisian inflammatory bowel disease (IBD) patients. MATERIALS A hundred Tunisian patients with IBD (75 Crohn's disease CD and 25 ulcerative colitis UC) and 60 matched healthy controls were studied. METHODS CARD15 mutation was analysed by using an allele-specific polymerase chain reaction and sequencing. Assessment of ASCA in serum was performed by ELISA. RESULTS The frequency of the mutation was significantly higher in Crohn's disease than in control (p = 0,0005; OR = 20.45; CI 95% = 2.86-413.85) and did not differ statistically in UC group (p = 0, 05) from control. ASCAs were present in 60% of CD and 20, 8% of UC. CONCLUSION This study suggests that in northern Tunisian population, 3020insC mutation in NOD2/CARD15 gene is a prevalent mutation leading to the typical Crohn's disease including ileal location, stricturing and penetrating clinical types and ASCA expression.
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Affiliation(s)
- R Marrakchi
- Laboratoire de Génétique, Immunologie et Pathologies Humaines, Faculté des Sciences de Tunis, Campus Universitaire 2092, Tunis, Tunisie.
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Abstract
Familial adenomatous polyposis (FAP) is a well-known hereditary condition characterised by alimentary system tumours. Tens to thousands of polyps occur in the colon and rectum of the patients. There is a high heterogeneity with regard to the number and time of the occurrence of polyps. The occurrence of FAP is associated with mutations in the APC tumour suppressor gene, which was described in 1991. Since then, many studies have been done to analyse the distribution of mutations in individual populations and to determine the function of the gene and a diagnostic approach to FAP. Here the APC gene was studied with respect to the occurrence of small mutations and large rearrangements in 300 unrelated Polish FAP families. Ninety-seven mutations were identified in 164 families. Out of these mutations, 80 were small mutations, including 58 small mutations that were first identified in the Polish population (42 novel and 16 described previously). An increased frequency of mutation c.3927_3931delAAAGA was observed in 10% of the Polish group. Seventeen large rearrangements were found in 29 families. Out of those rearrangements, 8 repeat rearrangements occurred in 20 families. A problem in fast molecular diagnostics of FAP is a high heterogeneity of mutations in the APC gene. It seems that a multiplex ligation-dependent probe amplification test and searching for small mutations by the use of screening methods at the 5' end of exon 15 and exons 14, 9, 11, 13, 5, and 3, help to improve the molecular diagnostics of FAP in Polish patients.
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Affiliation(s)
- Andrzej Plawski
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland.
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Cleary SP, Kim H, Croitoru ME, Redston M, Knight JA, Gallinger S, Gryfe R. Missense polymorphisms in the adenomatous polyposis coli gene and colorectal cancer risk. Dis Colon Rectum 2008; 51:1467-73; discussion 1473-4. [PMID: 18612690 DOI: 10.1007/s10350-008-9356-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2007] [Revised: 06/28/2007] [Accepted: 08/16/2007] [Indexed: 02/08/2023]
Abstract
PURPOSE Whereas truncating germline mutations of the adenomatous polyposis coli (APC) gene give rise to familial adenomatous polyposis, missense polymorphisms of APC may confer a weaker risk for colorectal cancer. METHODS We sequenced the entire open reading frame of the APC gene and tested for two common MYH mutations in a population-based series of patients with colorectal cancer and 5 to 99 adenomas. Missense adenomatous polyposis coli alterations identified in this colorectal cancer multiple-polyp population were analyzed in a population-based series of patients with colorectal cancer and healthy control subjects. RESULTS Germline APC or mutY human homologue (MYH) alterations were identified in 16 of 39 colorectal cancer-multiple polyp patients. Four missense APC gene alterations (S130G, E1317Q, D1822V, G2502S) were observed in 13 individuals and 3 additional patients carried presumed pathogenic (APC Y94X, biallelic MYH Y165C and heterozygous MYH G382D) mutations. When independently assessed in 971 patients with colorectal cancer and 954 healthy control subjects, none of the identified missense APC alterations conferred a significantly increased risk for colorectal cancer, odds ratio (95 percent confidence intervals): S130G = 3.1 (0.29-32.25), E1317Q = 1.08 (0.59-2.74), G2502S = 1 (0.65-1.63), D1822V (heterozygous) = 0.79 (0.64-0.98), D1822V (homozygous) = 0.82 (0.63-1.27). CONCLUSIONS Germline missense APC alterations observed in 33 percent of patients with multiple colorectal neoplasms seemed to play a limited role in colorectal cancer risk when independently assessed by a population-based, case-control analysis.
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Jaiswal AS, Narayan S. A novel function of adenomatous polyposis coli (APC) in regulating DNA repair. Cancer Lett 2008; 271:272-80. [PMID: 18662849 DOI: 10.1016/j.canlet.2008.06.024] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2008] [Revised: 04/07/2008] [Accepted: 06/11/2008] [Indexed: 11/22/2022]
Abstract
Prevailing literature suggests diversified cellular functions for the adenomatous polyposis coli (APC) gene. Among them a recently discovered unique role of APC is in DNA repair. The APC gene can modulate the base excision repair (BER) pathway through an interaction with DNA polymerase beta (Pol-beta) and flap endonuclease 1 (Fen-1). Taken together with the transcriptional activation of APC gene by alkylating agents and modulation of BER activity, APC may play an important role in carcinogenesis and chemotherapy by determining whether cells with DNA damage survive or undergo apoptosis. In this review, we summarize the evidence supporting this novel concept and suggest that these results will have implications for the development of more effective strategies for chemoprevention, prognosis and chemotherapy of certain types of tumors.
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Egan JB, Jacobs ET, Martínez ME, Gerner EW, Jurutka PW, Thompson PA. Presence of a TA Haplotype in the APC Gene Containing the Common 1822 Polymorphism and Colorectal Adenoma. Cancer Res 2008; 68:6006-13. [DOI: 10.1158/0008-5472.can-08-1084] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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