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Paneque M, O Shea R, Narravula A, Siglen E, Ciuca A, Abulí A, Serra-Juhé C. Correction to: Thirty-years of genetic counselling education in Europe: a growing professional area. Eur J Hum Genet 2024:10.1038/s41431-024-01571-5. [PMID: 38462655 DOI: 10.1038/s41431-024-01571-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2024] Open
Affiliation(s)
- M Paneque
- CGPP - Centro de Genética Preditiva e Preventiva, IBMC - Instituto de Biologia Molecular e Celular, i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.
- ICBAS - School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal.
| | - R O Shea
- Faculty of Medicine and Health, University of Sydney, Camperdown, Sydney, NSW, Australia
- Cancer Genetic Service, St. James Hospital, Dublin, Ireland
| | | | - E Siglen
- Western Norway Familial Cancer Center, Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - A Ciuca
- Department of Psychology, Babeș-Bolyai University, Cluj-Napoca, Romania
| | - A Abulí
- Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron, Barcelona, Spain
- Medicine Genetics Group Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - C Serra-Juhé
- Genetics Department, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, 08193, Barcelona, Spain
- U705 CIBERER, Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), 28029, Madrid, Spain
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Paneque M, O Shea R, Narravula A, Siglen E, Ciuca A, Abulí A, Serra-Juhé C. Thirty-years of genetic counselling education in Europe: a growing professional area. Eur J Hum Genet 2024:10.1038/s41431-024-01552-8. [PMID: 38355960 DOI: 10.1038/s41431-024-01552-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 01/18/2024] [Accepted: 01/24/2024] [Indexed: 02/16/2024] Open
Abstract
Genetic counselling education and training in Europe spans a continuum of 30 years. More master programs are opening due the demand for qualified genetic counselors. This report describes the evolution of training in Europe and the current state of genetic counselling training programs. Directors of master programs in Europe were invited to complete an online survey describing their program, including year of commencement, course duration, number of students and frequency of intake and number graduating. Results of the survey were presented at a closed meeting at the European Society of Human Genetics conference in 2022 along with a facilitated stakeholder engagement session in which 19 professionals participated to understand the challenges in delivering genetic counselling education in Europe. A total of 10 active programs exists in Europe with the first training program starting in 1992. The majority of training programs have a 2-year duration, with just over half of programs having an annual intake of students. Up to May 2022, 710 students have graduated from genetic counseling training programs across Europe. Of these, 670 students graduated from European Board of Medical Genetics-registered programs. Arranging clinical placements, clinical and counseling supervision of students, research collaboration for MSc research projects and incorporating genomics into the curriculum were identified as current challenges for genetic counseling education. Genetic counseling is still a developing profession in Europe and this historical and current view of the European genetic counselor pathways, allows for educational and professional standards to be examined as the profession evolves into the future.
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Affiliation(s)
- M Paneque
- CGPP - Centro de Genética Preditiva e Preventiva, IBMC - Instituto de Biologia Molecular e Celular, i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.
- ICBAS - School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal.
| | - R O Shea
- Faculty of Medicine and Health, University of Sydney, Camperdown, Sydney, NSW, Australia
- Cancer Genetic Service, St. James Hospital, Dublin, Ireland
| | | | - E Siglen
- Western Norway Familial Cancer Center, Department of Medical Genetics, Haukeland University Hospital, Bergen, Norway
| | - A Ciuca
- Department of Psychology, Babeș-Bolyai University, Cluj-Napoca, Romania
| | - A Abulí
- Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron, Barcelona, Spain
- Medicine Genetics Group Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - C Serra-Juhé
- Genetics Department, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, 08193, Barcelona, Spain
- U705 CIBERER, Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), 28029, Madrid, Spain
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3
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Stefanski A, Pérez-Palma E, Brünger T, Montanucci L, Gati C, Klöckner C, Johannesen KM, Goodspeed K, Macnee M, Deng AT, Aledo-Serrano Á, Borovikov A, Kava M, Bouman AM, Hajianpour MJ, Pal DK, Engelen M, Hagebeuk EEO, Shinawi M, Heidlebaugh AR, Oetjens K, Hoffman TL, Striano P, Freed AS, Futtrup L, Balslev T, Abulí A, Danvoye L, Lederer D, Balci T, Nouri MN, Butler E, Drewes S, van Engelen K, Howell KB, Khoury J, May P, Trinidad M, Froelich S, Lemke JR, Tiller J, Freed AN, Kang JQ, Wuster A, Møller RS, Lal D. SLC6A1 variant pathogenicity, molecular function and phenotype: a genetic and clinical analysis. Brain 2023; 146:5198-5208. [PMID: 37647852 PMCID: PMC10689929 DOI: 10.1093/brain/awad292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 06/05/2023] [Accepted: 07/08/2023] [Indexed: 09/01/2023] Open
Abstract
Genetic variants in the SLC6A1 gene can cause a broad phenotypic disease spectrum by altering the protein function. Thus, systematically curated clinically relevant genotype-phenotype associations are needed to understand the disease mechanism and improve therapeutic decision-making. We aggregated genetic and clinical data from 172 individuals with likely pathogenic/pathogenic (lp/p) SLC6A1 variants and functional data for 184 variants (14.1% lp/p). Clinical and functional data were available for a subset of 126 individuals. We explored the potential associations of variant positions on the GAT1 3D structure with variant pathogenicity, altered molecular function and phenotype severity using bioinformatic approaches. The GAT1 transmembrane domains 1, 6 and extracellular loop 4 (EL4) were enriched for patient over population variants. Across functionally tested missense variants (n = 156), the spatial proximity from the ligand was associated with loss-of-function in the GAT1 transporter activity. For variants with complete loss of in vitro GABA uptake, we found a 4.6-fold enrichment in patients having severe disease versus non-severe disease (P = 2.9 × 10-3, 95% confidence interval: 1.5-15.3). In summary, we delineated associations between the 3D structure and variant pathogenicity, variant function and phenotype in SLC6A1-related disorders. This knowledge supports biology-informed variant interpretation and research on GAT1 function. All our data can be interactively explored in the SLC6A1 portal (https://slc6a1-portal.broadinstitute.org/).
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Affiliation(s)
- Arthur Stefanski
- Genomic Medicine Institute and Epilepsy Center, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Eduardo Pérez-Palma
- Universidad del Desarrollo, Centro de Genética y Genómica, Facultad de Medicina Clínica Alemana, Santiago de Chile 7610658, Chile
| | - Tobias Brünger
- Cologne Center for Genomics (CCG), Medical Faculty of the University of Cologne, University Hospital of Cologne, Cologne 50931, Germany
| | - Ludovica Montanucci
- Genomic Medicine Institute and Epilepsy Center, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Cornelius Gati
- Department of Biological Sciences, Bridge Institute, USC Michelson Center for Convergent Bioscience, University of Southern California, Los Angeles, CA 90089, USA
| | - Chiara Klöckner
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig 04103, Germany
| | - Katrine M Johannesen
- Department of Epilepsy Genetics and Personalized Medicine, The Danish Epilepsy Centre, Dianalund 4293, Denmark
- Department of Genetics, University Hospital of Copenhagen, Rigshispitalet, Copenhagen 2100, Denmark
| | - Kimberly Goodspeed
- Children’s Health, Medical Center, Dallas, TX 75235, USA
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Marie Macnee
- Cologne Center for Genomics (CCG), Medical Faculty of the University of Cologne, University Hospital of Cologne, Cologne 50931, Germany
| | - Alexander T Deng
- Clinical Genetics, Guys and St Thomas NHS Trust, London SE19RT, UK
| | - Ángel Aledo-Serrano
- Epilepsy Program, Neurology Department, Hospital Ruber Internacional, Madrid 28034, Spain
| | - Artem Borovikov
- Research and Counseling Department, Research Centre for Medical Genetics, Moscow 115478, Russia
| | - Maina Kava
- Department of Neurology and Metabolic Medicine, Perth Children’s Hospital, Perth 6009, Australia
- School of Paediatrics and Child Health, UWA Medical School, University of Western Australia, Perth 6009, Australia
| | - Arjan M Bouman
- Department of Clinical Genetics, Erasmus MC, University Medical Center, Rotterdam 3015GD, The Netherlands
| | - M J Hajianpour
- Department of Pediatrics, Division of Medical Genetics and Genomics, Albany Medical College, Albany Med Health System, Albany, NY 12208, USA
| | - Deb K Pal
- Department of Basic and Clinical Neurosciences, Institute of Psychiatry, Psychology and Neuroscience, King’s College, London SE58AF, UK
- Department of Basic and Clinical Neurosciences, King’s College Hospital, London SE59RS, UK
| | - Marc Engelen
- Department of Pediatric Neurology, Amsterdam Public Health, Amsterdam University Medical Center, Amsterdam 1081HV, The Netherlands
| | - Eveline E O Hagebeuk
- Department of Pediatric Neurology, Stichting Epilepsie Instellingen Nederland (SEIN), Heemstede and Zwolle 2103SW, The Netherlands
| | - Marwan Shinawi
- Division of Genetics and Genomic Medicine, Department of Pediatrics, St.Louis Children’s Hospital, Washington University School of Medicine, St. Louis, MO 63110, USA
| | | | - Kathryn Oetjens
- Autism and Developmental Medicine Institute, Geisinger, Danville, PA 17837, USA
| | - Trevor L Hoffman
- Department of Regional Genetics, Anaheim, Southern California Kaiser Permanente Medical Group, CA 92806, USA
| | - Pasquale Striano
- Pediatric Neurology and Muscular Diseases Unit, IRCCS Istituto Giannina Gaslini, Genoa 16147, Italy
- Department of Neurosciences, Rehabilitation, Ophthalmology, Genetics, Maternal and Child Health, University of Genoa, Genoa 16132, Italy
| | - Amanda S Freed
- Department of Clinical Science, Kaiser Permanente Bernard J. Tyson School of Medicine, Pasadena, CA 91101, USA
| | - Line Futtrup
- Department of Paediatrics, Regional Hospital of Central Jutland, Viborg 8800, Denmark
| | - Thomas Balslev
- Department of Paediatrics, Regional Hospital of Central Jutland, Viborg 8800, Denmark
- Centre for Educational Development, Aarhus University, Aarhus 8200, Denmark
| | - Anna Abulí
- Department of Clinical and Molecular Genetics and Medicine Genetics Group, VHIR, University Hospital Vall d’Hebron, Barcelona 08035, Spain
| | - Leslie Danvoye
- Department of Neurology, Université catholique de Louvain, Cliniques universitaires Saint-Luc, Brussels 1200, Belgium
| | - Damien Lederer
- Centre for Human Genetics, Institute for Pathology and Genetics, Gosselies 6041, Belgium
| | - Tugce Balci
- Department of Pediatrics, Division of Medical Genetics, Western University, London, ON N6A3K7, Canada
- Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre and Children's Health Research Institute, London, ON N6A5A5, Canada
| | - Maryam Nabavi Nouri
- Department of Paediatrics, Division of Pediatric Neurology, London Health Sciences Centre, London, ON N6A5W9, Canada
| | | | - Sarah Drewes
- Department of Medical Genetics, UPMC Children’s Hospital of Pittsburgh, Pittsburgh, PA 15224, USA
| | - Kalene van Engelen
- Medical Genetics Program of Southwestern Ontario, London Health Sciences Centre, London, ON N6A5W9, Canada
| | - Katherine B Howell
- Department of Neurology, Royal Children’s Hospital, Melbourne, VIC 3052, Australia
- Department of Pediatrics, University of Melbourne, Melbourne, VIC 3052, Australia
- Murdoch Children’s Research Institute, Melbourne, VIC 3052, Australia
| | - Jean Khoury
- Genomic Medicine Institute and Epilepsy Center, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette 4362, Luxembourg
| | - Marena Trinidad
- Translational Genomics, BioMarin Pharmaceutical Inc., Novato, CA 94949, USA
| | - Steven Froelich
- Translational Genomics, BioMarin Pharmaceutical Inc., Novato, CA 94949, USA
| | - Johannes R Lemke
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig 04103, Germany
- Center for Rare Diseases, University of Leipzig Medical Center, Leipzig 04103, Germany
| | | | | | - Jing-Qiong Kang
- Department of Neurology, Vanderbilt University Medical Center, Nashville, TN 37240, USA
- Neuroscience Graduate Program, Vanderbilt University, Nashville, TN 37235, USA
- Department of Neurology, Vanderbilt Brain Institute, Nashville, TN 37235, USA
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232, USA
- Vanderbilt Kennedy Center of Human Development, Nashville, TN 37203, USA
| | - Arthur Wuster
- Translational Genomics, BioMarin Pharmaceutical Inc., Novato, CA 94949, USA
| | - Rikke S Møller
- Department of Epilepsy Genetics and Personalized Medicine, The Danish Epilepsy Centre, Dianalund 4293, Denmark
- Department of Regional Health Research, University of Southern Denmark, Odense 5000, Denmark
| | - Dennis Lal
- Genomic Medicine Institute and Epilepsy Center, Cleveland Clinic, Cleveland, OH 44195, USA
- Stanley Center of Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Department of Neurology, University of Texas Health Sciences Center at Houston, Houston, TX 77030, USA
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4
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Codina-Solà M, Trujillano L, Abulí A, Rovira-Moreno E, Muñoz-Cabello P, Campos B, Fernández-Álvarez P, Palau D, Carrasco E, Valenzuela I, Cueto-González AM, Lasa-Aranzasti A, Limeres J, Leno-Colorado J, Costa-Roger M, Moles-Fernández A, Balmaña J, Díez O, Cuscó I, Garcia-Arumí E, Tizzano EF. An spanish study of secondary findings in families affected with mendelian disorders: choices, prevalence and family history. Eur J Hum Genet 2023; 31:223-230. [PMID: 36446894 PMCID: PMC9905470 DOI: 10.1038/s41431-022-01240-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 09/30/2022] [Revised: 11/02/2022] [Accepted: 11/08/2022] [Indexed: 12/02/2022] Open
Abstract
Clinical exome sequencing has the potential to identify pathogenic variants unrelated to the purpose of the study (secondary findings, SFs). Data describing actual choices of SFs in participants in a clinical setting and factors influencing their decision are virtually non-existant in Europe. In this work, we report the acceptance rate of SFs, calculate their prevalence and study factors associated with the decision in a cohort of patients affected with a rare genetic disorder in a Spanish Hospital. Finally, we re-examine the presence of previously non reported family history in positive cases. We retrospectively reviewed informed consent choices and SF results from 824 unrelated probands affected with rare genetic disorders who underwent whole-genome or exome sequencing. Ninety percent of families (740/824) affected with rare disorders wished to be informed of SFs. Declining SFs was associated with a prenatal setting (30% vs. 8.7%, p = 0.025), consanguinity (19% vs. 8.7%, p = 0.013), male gender (10.6% vs. 1.5%, p = 0.00865) and the proband being a minor (10.6% vs. 1.5%, p = 0.014). Overall, 27 pathogenic or likely pathogenic variants were identified in 27 individuals, with an SF prevalence of 3.6%. Disclosure of SFs increased the percentage of positive family histories and resulted in early diagnosis or changes in the management of 10 individuals from five families. We show that the acceptance of SFs in Spain is high and the disclosure of SFs leads to a clinically meaningful change in the medical management of individuals.
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Affiliation(s)
- Marta Codina-Solà
- Medicine Genetics Group, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain.
- Department of Clinical and Molecular Genetics, Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain.
- European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability ERN-ITHACA, Barcelona, Spain.
| | - Laura Trujillano
- Medicine Genetics Group, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
- Department of Clinical and Molecular Genetics, Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
- Instituto de Salud Carlos III, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain
| | - Anna Abulí
- Medicine Genetics Group, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
- Department of Clinical and Molecular Genetics, Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
- European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability ERN-ITHACA, Barcelona, Spain
| | - Eulàlia Rovira-Moreno
- Medicine Genetics Group, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
- Department of Clinical and Molecular Genetics, Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
- European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability ERN-ITHACA, Barcelona, Spain
| | - Patricia Muñoz-Cabello
- Medicine Genetics Group, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
- Department of Clinical and Molecular Genetics, Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
| | - Berta Campos
- Medicine Genetics Group, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
- Department of Clinical and Molecular Genetics, Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
| | - Paula Fernández-Álvarez
- Medicine Genetics Group, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
- Department of Clinical and Molecular Genetics, Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
- European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability ERN-ITHACA, Barcelona, Spain
| | - Dolors Palau
- Medicine Genetics Group, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
| | - Estela Carrasco
- Hereditary Cancer Genetics Group, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Hospital Universitari Vall d'Hebron, Barcelona, Spain
- Medical Oncology Department, Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
| | - Irene Valenzuela
- Medicine Genetics Group, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
- Department of Clinical and Molecular Genetics, Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
- European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability ERN-ITHACA, Barcelona, Spain
| | - Anna Maria Cueto-González
- Medicine Genetics Group, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
- Department of Clinical and Molecular Genetics, Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
| | - Amaia Lasa-Aranzasti
- Medicine Genetics Group, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
- Department of Clinical and Molecular Genetics, Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
- European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability ERN-ITHACA, Barcelona, Spain
| | - Javier Limeres
- European Reference Networks for rare, low prevalence and complex diseases of the heart (ERN GUARD-Heart), Barcelona, Spain
- Unidad de Cardiopatías Familiares, Servicio de Cardiología, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
- Centre for Biomedical Network Research on Cardiovascular Diseases (CIBERCV), Madrid, Spain
| | - Jordi Leno-Colorado
- Medicine Genetics Group, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
- Department of Clinical and Molecular Genetics, Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
| | - Mar Costa-Roger
- Medicine Genetics Group, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
- Department of Clinical and Molecular Genetics, Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
| | - Alejandro Moles-Fernández
- Medicine Genetics Group, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
- Department of Clinical and Molecular Genetics, Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
| | - Judith Balmaña
- Hereditary Cancer Genetics Group, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Hospital Universitari Vall d'Hebron, Barcelona, Spain
- Medical Oncology Department, Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
| | - Orland Díez
- Department of Clinical and Molecular Genetics, Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
- Hereditary Cancer Genetics Group, Vall d'Hebron Institute of Oncology (VHIO), Vall d'Hebron Barcelona Hospital Campus, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Ivon Cuscó
- Medicine Genetics Group, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
- Department of Clinical and Molecular Genetics, Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
- European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability ERN-ITHACA, Barcelona, Spain
- Instituto de Salud Carlos III, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain
- Department of Genetics, Hospital Sant Pau, Barcelona, Spain
| | - Elena Garcia-Arumí
- Medicine Genetics Group, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
- Department of Clinical and Molecular Genetics, Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
- European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability ERN-ITHACA, Barcelona, Spain
- Instituto de Salud Carlos III, Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain
- Research Group on Neuromuscular and Mitochondrial Disorders, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
| | - Eduardo Fidel Tizzano
- Medicine Genetics Group, Vall d'Hebron Institut de Recerca (VHIR), Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
- Department of Clinical and Molecular Genetics, Vall d'Hebron Barcelona Hospital Campus, Vall d'Hebron Hospital Universitari, Barcelona, Spain
- European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability ERN-ITHACA, Barcelona, Spain
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5
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Abulí A, Costa-Roger M, Codina-Solà M, Valenzuela I, Leno-Colorado J, Rovira-Moreno E, Cueto-González A, Fernández-Álvarez P, García-Arumí E, Cuscó I, Tizzano EF. Experience using singleton exome sequencing of probands as an approach to preconception carrier screening in consanguineous couples. J Med Genet 2022; 60:540-546. [PMID: 36600615 DOI: 10.1136/jmg-2022-108607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 10/05/2022] [Indexed: 12/13/2022]
Abstract
BACKGROUND Consanguineous couples have an increased risk of severe diseases in offspring due to autosomal recessive disorders. Exome sequencing (ES) offers the possibility of extensive preconception carrier screening (PCS) in consanguineous couples who may be at risk of rare genetic disorders. METHODS We retrospectively analysed ES data from 65 probands affected with rare genetic disorders born from consanguineous couples. We explored diagnostic yield and carrier status for recessive disorders. RESULTS The overall diagnostic yield in a singleton approach was 53.8%, mostly recessive variants. In a hypothetical exome-based PCS, only 11.7% of these causative rare variants would have been missed in the filtering process. Carrier screening for recessive conditions allowed the identification of at least one additional pathogenic or likely pathogenic variant in 85.7% of the probands, being the majority with a gene carrier frequency <1 in 200. In addition, considering only clinically actionable conditions, we estimated that 12.3% of our close consanguineous couples may be at risk for an additional recessive disease. CONCLUSIONS Our results demonstrate that ES outperforms panel-based screening in a PCS context in consanguineous couples and could potentially increase their reproductive autonomy and facilitate informed decision-making.
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Affiliation(s)
- Anna Abulí
- Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron, Barcelona, Spain .,Medicine Genetics Group Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Mar Costa-Roger
- Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Medicine Genetics Group Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Marta Codina-Solà
- Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Medicine Genetics Group Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Irene Valenzuela
- Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Medicine Genetics Group Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Jordi Leno-Colorado
- Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Medicine Genetics Group Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Eulàlia Rovira-Moreno
- Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Medicine Genetics Group Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Anna Cueto-González
- Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Medicine Genetics Group Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Paula Fernández-Álvarez
- Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Medicine Genetics Group Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
| | - Elena García-Arumí
- Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Medicine Genetics Group Vall d'Hebron Research Institute (VHIR), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
| | - Ivon Cuscó
- Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Medicine Genetics Group Vall d'Hebron Research Institute (VHIR), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
| | - Eduardo F Tizzano
- Department of Clinical and Molecular Genetics, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Medicine Genetics Group Vall d'Hebron Research Institute (VHIR), Barcelona, Spain
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6
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Carrasco E, López-Fernández A, Codina-Sola M, Valenzuela I, Cueto-González AM, Villacampa G, Navarro V, Torres-Esquius S, Palau D, Cruellas M, Torres M, Perez-Dueñas B, Abulí A, Diez O, Sábado-Álvarez C, García-Arumí E, Tizzano EF, Moreno L, Balmaña J. Clinical and psychological implications of secondary and incidental findings in cancer susceptibility genes after exome sequencing in patients with rare disorders. J Med Genet 2022:jmg-2022-108929. [DOI: 10.1136/jmg-2022-108929] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 11/11/2022] [Indexed: 12/03/2022]
Abstract
Background/ObjectivesExome sequencing may identify pathogenic variants unrelated with the purpose of the analysis. We investigated the frequency of secondary and incidental findings (SF/IF) in cancer susceptibility genes (CSG), their clinical actionability and the psychological impact in individuals with an SF/IF (cases) compared with individuals tested due to their cancer history (controls).MethodsThis study analysed 533 exomes ordered for non-cancer conditions. Medical records were reviewed for clinical actionability of SF/IF. Psychological impact was analysed using the Multidimensional Impact of Cancer Risk Assessment (MICRA) scale and compared between cases and controls with a propensity score weighting method.ResultsThe frequency of SF/IF in CSG was 2.1% (95% CI 1.1% to 3.8%): threeBRCA2, threePMS2, twoSDHB, and one each inBRCA1,MLH1andRAD51C. Among the relatives, 18 were carriers. Twenty enrolled for surveillance, and a neoplasm was diagnosed in 20%: three paragangliomas and one breast cancer. Cases presented higher MICRA mean scores than controls (21.3 vs 16.2 in MICRA total score, 6.3 vs 4.2 in the distress subscale, and 8.3 vs 6.6 in the uncertainty subscale; all p<0.001).ConclusionSF/IF in CSG were identified in 2.1% of patients. Despite a numerically higher psychological impact, the identification of SF/IF allowed early detection and cancer prevention in families without cancer history.
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7
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Keraite I, Becker P, Canevazzi D, Frias-López C, Dabad M, Tonda-Hernandez R, Paramonov I, Ingham MJ, Brun-Heath I, Leno J, Abulí A, Garcia-Arumí E, Heath SC, Gut M, Gut IG. A method for multiplexed full-length single-molecule sequencing of the human mitochondrial genome. Nat Commun 2022; 13:5902. [PMID: 36202811 PMCID: PMC9537161 DOI: 10.1038/s41467-022-33530-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 09/21/2022] [Indexed: 11/09/2022] Open
Abstract
Methods to reconstruct the mitochondrial DNA (mtDNA) sequence using short-read sequencing come with an inherent bias due to amplification and mapping. They can fail to determine the phase of variants, to capture multiple deletions and to cover the mitochondrial genome evenly. Here we describe a method to target, multiplex and sequence at high coverage full-length human mitochondrial genomes as native single-molecules, utilizing the RNA-guided DNA endonuclease Cas9. Combining Cas9 induced breaks, that define the mtDNA beginning and end of the sequencing reads, as barcodes, we achieve high demultiplexing specificity and delineation of the full-length of the mtDNA, regardless of the structural variant pattern. The long-read sequencing data is analysed with a pipeline where our custom-developed software, baldur, efficiently detects single nucleotide heteroplasmy to below 1%, physically determines phase and can accurately disentangle complex deletions. Our workflow is a tool for studying mtDNA variation and will accelerate mitochondrial research. Accurate analysis of mitochondrial DNA is important for mitochondrial disease clinical research and diagnostics. Here, authors present a method using Cas9 cleavage, nanopore sequencing and a custom pipeline to identify pathogenic variants, deletions and accurately quantify heteroplasmy to below 1%.
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Affiliation(s)
- Ieva Keraite
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Philipp Becker
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Qiagen, Hilden, Germany
| | - Davide Canevazzi
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Cristina Frias-López
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Marc Dabad
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Raúl Tonda-Hernandez
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Ida Paramonov
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Matthew John Ingham
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Isabelle Brun-Heath
- Institute for Research in Biomedicine (IRB Barcelona) - The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Joint IRB-BSC Program in Computational Biology, Barcelona, Spain
| | - Jordi Leno
- Department of Clinical and Molecular Genetics and Rare Disease, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Medicine Genetics Group, VHIR, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Anna Abulí
- Department of Clinical and Molecular Genetics and Rare Disease, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Medicine Genetics Group, VHIR, Hospital Universitari Vall d'Hebron, Barcelona, Spain
| | - Elena Garcia-Arumí
- Department of Clinical and Molecular Genetics and Rare Disease, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Research Group on Neuromuscular and Mitochondrial Disorders, VHIR, Hospital Universitari Vall d'Hebron, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
| | - Simon Charles Heath
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain. .,Universitat Pompeu Fabra, Barcelona, Spain.
| | - Ivo Glynne Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology (BIST), Barcelona, Spain. .,Universitat Pompeu Fabra, Barcelona, Spain.
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8
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Álvaro-Sánchez S, Abreu-Rodríguez I, Abulí A, Serra-Juhe C, Garrido-Navas MDC. Current Status of Genetic Counselling for Rare Diseases in Spain. Diagnostics (Basel) 2021; 11:2320. [PMID: 34943558 PMCID: PMC8700506 DOI: 10.3390/diagnostics11122320] [Citation(s) in RCA: 1] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/05/2021] [Accepted: 12/06/2021] [Indexed: 12/29/2022] Open
Abstract
Genetic Counselling is essential for providing personalised information and support to patients with Rare Diseases (RD). Unlike most other developed countries, Spain does not recognize geneticists or genetic counsellors as healthcare professionals Thus, patients with RD face not only challenges associated with their own disease but also deal with lack of knowledge, uncertainty, and other psychosocial issues arising as a consequence of diagnostic delay. In this review, we highlight the importance of genetic counsellors in the field of RD as well as evaluate the current situation in which rare disease patients receive genetic services in Spain. We describe the main units and strategies at the national level assisting patients with RD and we conclude with a series of future perspectives and unmet needs that Spain should overcome to improve the management of patients with RD.
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Affiliation(s)
| | - Irene Abreu-Rodríguez
- Genetics Service, Hospital del Mar Research Institute, IMIM, 08003 Barcelona, Spain;
| | - Anna Abulí
- Department of Clinical and Molecular Genetics, Hospital Vall d’Hebron, 08035 Barcelona, Spain;
- Medicine Genetics Group, Vall d’Hebron Research Institute (VHIR), 08035 Barcelona, Spain
| | - Clara Serra-Juhe
- U705 CIBERER, Genetics Department, Hospital de la Santa Creu i Sant Pau, Universitat Autònoma de Barcelona, 08193 Barcelona, Spain;
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), 28029 Madrid, Spain
| | - Maria del Carmen Garrido-Navas
- CONGEN, Genetic Counselling Services, C/Albahaca 4, 18006 Granada, Spain;
- Genetics Department, Faculty of Sciences, Universidad de Granada, 18071 Granada, Spain
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9
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Abulí A, Boada M, Rodríguez-Santiago B, Coroleu B, Veiga A, Armengol L, Barri PN, Pérez-Jurado LA, Estivill X. NGS-Based Assay for the Identification of Individuals Carrying Recessive Genetic Mutations in Reproductive Medicine. Hum Mutat 2016; 37:516-23. [PMID: 26990548 DOI: 10.1002/humu.22989] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [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: 01/27/2016] [Accepted: 03/09/2016] [Indexed: 12/25/2022]
Abstract
Next-generation sequencing (NGS) has the capacity of carrier screening in gamete donation (GD) programs. We have developed and validated an NGS carrier-screening test (qCarrier test) that includes 200 genes associated with 368 disorders (277 autosomal recessive and 37 X-linked). Carrier screening is performed on oocyte donation candidates and the male partner of oocyte recipient. Carriers of X-linked conditions are excluded from the GD program, whereas donors are chosen who do not carry mutations for the same gene/disease as the recipients. The validation phase showed a high sensitivity (>99% sensitivity) detecting all single-nucleotide variants, 13 indels, and 25 copy-number variants included in the validation set. A total of 1,301 individuals were analysed with the qCarrier test, including 483 candidate oocyte donors and 635 receptor couples, 105 females receiving sperm donation, and 39 couples seeking pregnancy. We identified 56% of individuals who are carriers for at least one genetic condition and 1.7% of female donors who were excluded from the program due to a carrier state of X-linked conditions. Globally, 3% of a priori assigned donations had a high reproductive risk that could be minimized after testing. Genetic counselling at different stages is essential for helping to facilitate a successful and healthy pregnancy.
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Affiliation(s)
- Anna Abulí
- Unit of Medical Genomics, Department of Obstetrics, Gynaecology and Reproduction, Dexeus Women's Health, Barcelona, Spain
| | - Montserrat Boada
- Service of Reproduction Medicine, Obstetrics, Department of Obstetrics, Gynaecology and Reproduction, Dexeus Women's Health, Barcelona, Spain
| | | | - Buenaventura Coroleu
- Service of Reproduction Medicine, Obstetrics, Department of Obstetrics, Gynaecology and Reproduction, Dexeus Women's Health, Barcelona, Spain
| | - Anna Veiga
- Service of Reproduction Medicine, Obstetrics, Department of Obstetrics, Gynaecology and Reproduction, Dexeus Women's Health, Barcelona, Spain
| | - Lluís Armengol
- Research and Development Department, qGenomics Laboratory, Barcelona, Spain
| | - Pedro N Barri
- Service of Reproduction Medicine, Obstetrics, Department of Obstetrics, Gynaecology and Reproduction, Dexeus Women's Health, Barcelona, Spain
| | - Luis A Pérez-Jurado
- Genetics Unit, Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), Barcelona, Spain.,Hospital del Mar Research Institute (IMIM), Barcelona, Spain.,CIBER in Rare Disorders (CIBERER), Barcelona, Spain
| | - Xavier Estivill
- Unit of Medical Genomics, Department of Obstetrics, Gynaecology and Reproduction, Dexeus Women's Health, Barcelona, Spain.,Genetics Unit, Department of Experimental and Health Sciences, Pompeu Fabra University (UPF), Barcelona, Spain.,Hospital del Mar Research Institute (IMIM), Barcelona, Spain.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,CIBER in Epidemiology and Public Health (CIBERESP), Barcelona, Spain.,Experimental Genetics Division, Sidra Medical and Research Centre, Doha, Qatar
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10
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Abulí A, Castells A, Bujanda L, Lozano JJ, Bessa X, Hernández C, Álvarez-Urturi C, Pellisé M, Esteban-Jurado C, Hijona E, Burón A, Macià F, Grau J, Guayta R, Castellví-Bel S, Andreu M. Genetic Variants Associated with Colorectal Adenoma Susceptibility. PLoS One 2016; 11:e0153084. [PMID: 27078840 PMCID: PMC4831735 DOI: 10.1371/journal.pone.0153084] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [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: 12/08/2015] [Accepted: 03/23/2016] [Indexed: 01/11/2023] Open
Abstract
Background Common low-penetrance genetic variants have been consistently associated with colorectal cancer risk. Aim To determine if these genetic variants are associated also with adenoma susceptibility and may improve selection of patients with increased risk for advanced adenomas and/or multiplicity (≥ 3 adenomas). Methods We selected 1,326 patients with increased risk for advanced adenomas and/or multiplicity and 1,252 controls with normal colonoscopy from population-based colorectal cancer screening programs. We conducted a case-control association study analyzing 30 colorectal cancer susceptibility variants in order to investigate the contribution of these variants to the development of subsequent advanced neoplasia and/or multiplicity. Results We found that 14 of the analyzed genetic variants showed a statistically significant association with advanced adenomas and/or multiplicity: the probability of developing these lesions increased with the number of risk alleles reaching a 2.3-fold risk increment in individuals with ≥ 17 risk alleles. Conclusions Nearly half of the genetic variants associated with colorectal cancer risk are also related to advanced adenoma and/or multiplicity predisposition. Assessing the number of risk alleles in individuals within colorectal cancer screening programs may help to identify better a subgroup with increased risk for advanced neoplasia and/or multiplicity in the general population.
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Affiliation(s)
- Anna Abulí
- Department of Gastroenterology, Hospital del Mar, IMIM (Hospital del Mar Medical Research Institute), Pompeu Fabra University, Passeig Marítim 25–29, 08003, Barcelona, Catalonia, Spain
| | - Antoni Castells
- Department of Gastroenterology, Hospital Clínic, CIBERehd, IDIBAPS, University of Barcelona, Villarroel 170, 08036, Barcelona, Catalonia, Spain
| | - Luis Bujanda
- Department of Gastroenterology, Hospital Donostia/Instituto Biodonostia, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Universidad del País Vasco (UPV/EHU), Doctor Begiristain Kalea, 20014, Donostia/Gipuzkoa, Spain
| | - Juan José Lozano
- Plataforma de Bioinformática, CIBERehd, Villarroel 170, 08036, Barcelona, Catalonia, Spain
| | - Xavier Bessa
- Department of Gastroenterology, Hospital del Mar, IMIM (Hospital del Mar Medical Research Institute), Pompeu Fabra University, Passeig Marítim 25–29, 08003, Barcelona, Catalonia, Spain
| | - Cristina Hernández
- Department of Epidemiology and Evaluation, Hospital del Mar, IMIM (Hospital del Mar Medical Research Institute), Passeig Marítim 25–29, 08003, Barcelona, Catalonia, Spain
| | - Cristina Álvarez-Urturi
- Department of Gastroenterology, Hospital del Mar, IMIM (Hospital del Mar Medical Research Institute), Pompeu Fabra University, Passeig Marítim 25–29, 08003, Barcelona, Catalonia, Spain
| | - Maria Pellisé
- Department of Gastroenterology, Hospital Clínic, CIBERehd, IDIBAPS, University of Barcelona, Villarroel 170, 08036, Barcelona, Catalonia, Spain
| | - Clara Esteban-Jurado
- Department of Gastroenterology, Hospital Clínic, CIBERehd, IDIBAPS, University of Barcelona, Villarroel 170, 08036, Barcelona, Catalonia, Spain
| | - Elizabeth Hijona
- Department of Gastroenterology, Hospital Donostia/Instituto Biodonostia, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Universidad del País Vasco (UPV/EHU), Doctor Begiristain Kalea, 20014, Donostia/Gipuzkoa, Spain
| | - Andrea Burón
- Department of Epidemiology and Evaluation, Hospital del Mar, IMIM (Hospital del Mar Medical Research Institute), Passeig Marítim 25–29, 08003, Barcelona, Catalonia, Spain
| | - Francesc Macià
- Department of Epidemiology and Evaluation, Hospital del Mar, IMIM (Hospital del Mar Medical Research Institute), Passeig Marítim 25–29, 08003, Barcelona, Catalonia, Spain
| | - Jaume Grau
- Unitat d’Avaluació, Suport i Preventiva, Hospital Clínic, Roselló 138, 08036, Barcelona, Catalonia, Spain
| | - Rafael Guayta
- Planning and Research Unit, Consell de Collegis Farmacèutics de Catalunya, Girona 64, 08009, Barcelona, Catalonia, Spain
| | - Sergi Castellví-Bel
- Department of Gastroenterology, Hospital Clínic, CIBERehd, IDIBAPS, University of Barcelona, Villarroel 170, 08036, Barcelona, Catalonia, Spain
| | - Montserrat Andreu
- Department of Gastroenterology, Hospital del Mar, IMIM (Hospital del Mar Medical Research Institute), Pompeu Fabra University, Passeig Marítim 25–29, 08003, Barcelona, Catalonia, Spain
- * E-mail:
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11
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Abulí A, Bujanda L, Muñoz J, Buch S, Schafmayer C, Valeria Maiorana M, Veneroni S, van Wezel T, Liu T, Westers H, Esteban-Jurado C, Ocaña T, Piqué JM, Andreu M, Jover R, Carracedo A, Xicola RM, Llor X, Castells A, Dunlop M, Hofstra R, Lindblom A, Wijnen J, Peterlongo P, Hampe J, Ruiz-Ponte C, Castellví-Bel S. The MLH1 c.1852_1853delinsGC (p.K618A) variant in colorectal cancer: genetic association study in 18,723 individuals. PLoS One 2014; 9:e95022. [PMID: 24743384 PMCID: PMC3990597 DOI: 10.1371/journal.pone.0095022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [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: 12/16/2013] [Accepted: 03/21/2014] [Indexed: 12/25/2022] Open
Abstract
Colorectal cancer is one of the most frequent neoplasms and an important cause of mortality in the developed world. Mendelian syndromes account for about 5% of the total burden of CRC, being Lynch syndrome and familial adenomatous polyposis the most common forms. Lynch syndrome tumors develop mainly as a consequence of defective DNA mismatch repair associated with germline mutations in MLH1, MSH2, MSH6 and PMS2. A significant proportion of variants identified by screening these genes correspond to missense or noncoding changes without a clear pathogenic consequence, and they are designated as “variants of uncertain significance”, being the c.1852_1853delinsGC (p.K618A) variant in the MLH1 gene a clear example. The implication of this variant as a low-penetrance risk variant for CRC was assessed in the present study by performing a case-control study within a large cohort from the COGENT consortium-COST Action BM1206 including 18,723 individuals (8,055 colorectal cancer cases and 10,668 controls) and a case-only genotype-phenotype correlation with several clinical and pathological characteristics restricted to the Epicolon cohort. Our results showed no involvement of this variant as a low-penetrance variant for colorectal cancer genetic susceptibility and no association with any clinical and pathological characteristics including family history for this neoplasm or Lynch syndrome.
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Affiliation(s)
- Anna Abulí
- Department of Gastroenterology, Hospital Clínic, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Barcelona, Catalonia, Spain
- Department of Gastroenterology, Hospital del Mar-IMIM (Hospital del Mar Medical Research Centre), Pompeu Fabra University, Barcelona, Catalonia, Spain
| | - Luis Bujanda
- Gastroenterology Department, Hospital Donostia, Networked Biomedical Research Centre for Hepatic and Digestive Diseases (CIBEREHD), Basque Country University, San Sebastián, Spain
| | - Jenifer Muñoz
- Department of Gastroenterology, Hospital Clínic, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Barcelona, Catalonia, Spain
| | - Stephan Buch
- Department of Medine I, University Hospital Dresden, Dresden, Germany
| | - Clemens Schafmayer
- Department of General and Thoracic Surgery, University Hospital Schleswig-Holstein, Kiel, Germany
| | | | - Silvia Veneroni
- Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori, Milan, Italy
| | - Tom van Wezel
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Tao Liu
- Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
| | - Helga Westers
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Clara Esteban-Jurado
- Department of Gastroenterology, Hospital Clínic, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Barcelona, Catalonia, Spain
| | - Teresa Ocaña
- Department of Gastroenterology, Hospital Clínic, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Barcelona, Catalonia, Spain
| | - Josep M. Piqué
- Department of Gastroenterology, Hospital Clínic, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Barcelona, Catalonia, Spain
| | - Montserrat Andreu
- Department of Gastroenterology, Hospital del Mar-IMIM (Hospital del Mar Medical Research Centre), Pompeu Fabra University, Barcelona, Catalonia, Spain
| | - Rodrigo Jover
- Department of Gastroenterology, Hospital General d'Alacant, Alicante, Spain
| | - Angel Carracedo
- Galician Public Foundation of Genomic Medicine (FPGMX), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Genomics Medicine Group, Hospital Clínico, Santiago de Compostela, University of Santiago de Compostela, Galicia, Spain
- Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
| | - Rosa M. Xicola
- Section of Digestive Diseases and Nutrition, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Xavier Llor
- Section of Digestive Diseases and Nutrition, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Antoni Castells
- Department of Gastroenterology, Hospital Clínic, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Barcelona, Catalonia, Spain
| | | | - Malcolm Dunlop
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Edinburgh, United Kingdom
| | - Robert Hofstra
- Department of Genetics, University Medical Center Groningen, Groningen, The Netherlands
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institute, Stockholm, Sweden
| | - Juul Wijnen
- Departments of Human Genetics and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Paolo Peterlongo
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milan, Italy
| | - Jochen Hampe
- Department of Medine I, University Hospital Dresden, Dresden, Germany
| | - Clara Ruiz-Ponte
- Galician Public Foundation of Genomic Medicine (FPGMX), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Genomics Medicine Group, Hospital Clínico, Santiago de Compostela, University of Santiago de Compostela, Galicia, Spain
| | - Sergi Castellví-Bel
- Department of Gastroenterology, Hospital Clínic, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Barcelona, Catalonia, Spain
- * E-mail:
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12
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Abulí A, Lozano JJ, Rodríguez-Soler M, Jover R, Bessa X, Muñoz J, Esteban-Jurado C, Fernández-Rozadilla C, Carracedo A, Ruiz-Ponte C, Cubiella J, Balaguer F, Bujanda L, Reñé JM, Clofent J, Morillas JD, Nicolás-Pérez D, Xicola RM, Llor X, Piqué JM, Andreu M, Castells A, Castellví-Bel S. Genetic susceptibility variants associated with colorectal cancer prognosis. Carcinogenesis 2013; 34:2286-2291. [PMID: 23712746 DOI: 10.1093/carcin/bgt179] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023] Open
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13
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Dunlop MG, Tenesa A, Farrington SM, Ballereau S, Brewster DH, Koessler T, Pharoah P, Schafmayer C, Hampe J, Völzke H, Chang-Claude J, Hoffmeister M, Brenner H, von Holst S, Picelli S, Lindblom A, Jenkins MA, Hopper JL, Casey G, Duggan D, Newcomb PA, Abulí A, Bessa X, Ruiz-Ponte C, Castellví-Bel S, Niittymäki I, Tuupanen S, Karhu A, Aaltonen L, Zanke B, Hudson T, Gallinger S, Barclay E, Martin L, Gorman M, Carvajal-Carmona L, Walther A, Kerr D, Lubbe S, Broderick P, Chandler I, Pittman A, Penegar S, Campbell H, Tomlinson I, Houlston RS. Cumulative impact of common genetic variants and other risk factors on colorectal cancer risk in 42,103 individuals. Gut 2013; 62:871-81. [PMID: 22490517 PMCID: PMC5105590 DOI: 10.1136/gutjnl-2011-300537] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
OBJECTIVE Colorectal cancer (CRC) has a substantial heritable component. Common genetic variation has been shown to contribute to CRC risk. A study was conducted in a large multi-population study to assess the feasibility of CRC risk prediction using common genetic variant data combined with other risk factors. A risk prediction model was built and applied to the Scottish population using available data. DESIGN Nine populations of European descent were studied to develop and validate CRC risk prediction models. Binary logistic regression was used to assess the combined effect of age, gender, family history (FH) and genotypes at 10 susceptibility loci that individually only modestly influence CRC risk. Risk models were generated from case-control data incorporating genotypes alone (n=39,266) and in combination with gender, age and FH (n=11,324). Model discriminatory performance was assessed using 10-fold internal cross-validation and externally using 4187 independent samples. The 10-year absolute risk was estimated by modelling genotype and FH with age- and gender-specific population risks. RESULTS The median number of risk alleles was greater in cases than controls (10 vs 9, p<2.2 × 10(-16)), confirmed in external validation sets (Sweden p=1.2 × 10(-6), Finland p=2 × 10(-5)). The mean per-allele increase in risk was 9% (OR 1.09; 95% CI 1.05 to 1.13). Discriminative performance was poor across the risk spectrum (area under curve for genotypes alone 0.57; area under curve for genotype/age/gender/FH 0.59). However, modelling genotype data, FH, age and gender with Scottish population data shows the practicalities of identifying a subgroup with >5% predicted 10-year absolute risk. CONCLUSION Genotype data provide additional information that complements age, gender and FH as risk factors, but individualised genetic risk prediction is not currently feasible. Nonetheless, the modelling exercise suggests public health potential since it is possible to stratify the population into CRC risk categories, thereby informing targeted prevention and surveillance.
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Affiliation(s)
- Malcolm G Dunlop
- Colon Cancer Genetics Group, Institute of Genetics and Molecular Medicine, University of Edinburgh and MRC Human Genetics Unit, Edinburgh EH4 2XU, UK.
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14
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Fernandez-Rozadilla C, Cazier JB, Tomlinson IP, Carvajal-Carmona LG, Palles C, Lamas MJ, Baiget M, López-Fernández LA, Brea-Fernández A, Abulí A, Bujanda L, Clofent J, Gonzalez D, Xicola R, Andreu M, Bessa X, Jover R, Llor X. A colorectal cancer genome-wide association study in a Spanish cohort identifies two variants associated with colorectal cancer risk at 1p33 and 8p12. BMC Genomics 2013; 14:55. [PMID: 23350875 PMCID: PMC3616862 DOI: 10.1186/1471-2164-14-55] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 01/23/2013] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is a disease of complex aetiology, with much of the expected inherited risk being due to several common low risk variants. Genome-Wide Association Studies (GWAS) have identified 20 CRC risk variants. Nevertheless, these have only been able to explain part of the missing heritability. Moreover, these signals have only been inspected in populations of Northern European origin. RESULTS Thus, we followed the same approach in a Spanish cohort of 881 cases and 667 controls. Sixty-four variants at 24 loci were found to be associated with CRC at p-values <10-5. We therefore evaluated the 24 loci in another Spanish replication cohort (1481 cases and 1850 controls). Two of these SNPs, rs12080929 at 1p33 (Preplication=0.042; Ppooled=5.523x10-03; OR (CI95%)=0.866(0.782-0.959)) and rs11987193 at 8p12 (Preplication=0.039; Ppooled=6.985x10-5; OR (CI95%)=0.786(0.705-0.878)) were replicated in the second Phase, although they did not reach genome-wide statistical significance. CONCLUSIONS We have performed the first CRC GWAS in a Southern European population and by these means we were able to identify two new susceptibility variants at 1p33 and 8p12 loci. These two SNPs are located near the SLC5A9 and DUSP4 loci, respectively, which could be good functional candidates for the association signals. We therefore believe that these two markers constitute good candidates for CRC susceptibility loci and should be further evaluated in other larger datasets. Moreover, we highlight that were these two SNPs true susceptibility variants, they would constitute a decrease in the CRC missing heritability fraction.
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Affiliation(s)
- Ceres Fernandez-Rozadilla
- Galician Public Fundation of Genomic Medicine (FPGMX)-Grupo de Medicina Xenómica-Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERer)-IDIS, Santiago de Compostela, 15706, Spain
| | - Jean-Baptiste Cazier
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Ian P Tomlinson
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
- NIHR Comprehensive Biomedical Research Centre, University of Oxford, Oxford, OX3 7BN, UK
| | - Luis G Carvajal-Carmona
- Department of Biochemistry and Molecular Medicine School of Medicine University of California, Davis, California, USA
| | - Claire Palles
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - María J Lamas
- Oncology Pharmacy Unit, Complejo Hospitalario Universitario of Santiago (CHUS), Santiago de Compostela, 15706, Spain
| | - Montserrat Baiget
- Genetics Department, Hospital de Santa Creu I Sant Pau, Barcelona, 08025, Spain
| | - Luis A López-Fernández
- Pharmacogenetics & Pharmacogenomics Laboratory, Servicio de Farmacia, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón,, Madrid, 28007, Spain
| | - Alejandro Brea-Fernández
- Galician Public Fundation of Genomic Medicine (FPGMX)-Grupo de Medicina Xenómica-Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERer)-IDIS, Santiago de Compostela, 15706, Spain
| | - Anna Abulí
- Gastroenterology Department, Hospital del Mar, Barcelona, 08003, Spain
- Department of Gastroenterology, Hospital Clínic, CIBERehd, IDIBAPS, University of Barcelona, Barcelona, 08036, Spain
| | - Luis Bujanda
- Gastroenterology Department, Donostia Hospital, CIBERehd, University of the Basque Country, San Sebastián, 20014, Spain
| | - Juan Clofent
- Gastroenterology Department, Hospital do Meixoeiro, Vigo, 36214, Spain
- Section of Digestive Diseases, Internal Medicine Department, Hospital Sagunto, Valencia, 46520, Spain
| | - Dolors Gonzalez
- Servicio de Patologia Digestiva, Hospital Sant PAu, Barcelona, 08003, Spain
| | - Rosa Xicola
- Section of Digestive Diseases and Nutrition, University of Illinois at Chicago, Chicago, IL, 60607, USA
| | - Montserrat Andreu
- Gastroenterology Department, Hospital del Mar, Barcelona, 08003, Spain
| | - Xavier Bessa
- Gastroenterology Department, Hospital del Mar, Barcelona, 08003, Spain
| | - Rodrigo Jover
- Gastroenterology Department, Hospital General Universitario de Alicante, Alicante, 03010, Spain
| | - Xavier Llor
- Section of Digestive Diseases and Nutrition, University of Illinois at Chicago, Chicago, IL, 60607, USA
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Castellví-Bel S, Abulí A, Castells A. Meta-analysis of several GWAS sets yields additional genetic susceptibility variants for colorectal cancer: first X-linked component identified. Gastroenterology 2012; 143:1684-5. [PMID: 23073136 DOI: 10.1053/j.gastro.2012.10.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Affiliation(s)
- Sergi Castellví-Bel
- IDIBAPS/Hospital Clínic/CIBERehd, Centre Esther Koplovitz, Barcelona, Catalonia, Spain
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16
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Fernandez-Rozadilla C, Brea-Fernández A, Bessa X, Álvarez-Urturi C, Abulí A, Clofent J, Payá A, Jover R, Xicola R, Llor X, Andreu M, Castells A, Carracedo Á, Castellví-Bel S, Ruiz-Ponte C. BMPR1Amutations in early-onset colorectal cancer with mismatch repair proficiency. Clin Genet 2012; 84:94-6. [DOI: 10.1111/cge.12023] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- C Fernandez-Rozadilla
- Fundación Pública Galega de Medicina Xenómica (FPGMX)-Grupo de Medicina Xenómica; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERer), IDIS; Santiago de Compostela; 15706; Spain
| | - A Brea-Fernández
- Fundación Pública Galega de Medicina Xenómica (FPGMX)-Grupo de Medicina Xenómica; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERer), IDIS; Santiago de Compostela; 15706; Spain
| | - X Bessa
- Gastroenterology Department, Hospital del Mar; IMIM-Research Institut; Barcelona; 08003; Spain
| | - C Álvarez-Urturi
- Gastroenterology Department, Hospital del Mar; IMIM-Research Institut; Barcelona; 08003; Spain
| | | | - J Clofent
- Section of Digestive Diseases, Internal Medicine Department; Hospital Sagunto; Valencia; 46520; Spain
| | - A Payá
- Pathologic Department; Hospital General Universitario de Alicante; Alicante; 03010; Spain
| | - R Jover
- Gastroenterology Department; Hospital General Universitario de Alicante; Alicante; 03010; Spain
| | - R Xicola
- Section of Digestive Diseases and Nutrition, Department of Medicine and Cancer Center; University of Illinois at Chicago; Chicago; IL; 60607; USA
| | - X Llor
- Section of Digestive Diseases and Nutrition, Department of Medicine and Cancer Center; University of Illinois at Chicago; Chicago; IL; 60607; USA
| | - M Andreu
- Gastroenterology Department, Hospital del Mar; IMIM-Research Institut; Barcelona; 08003; Spain
| | - A Castells
- Department of Gastroenterology, Hospital Clínic, CIBERehd, IDIBAPS; University of Barcelona; Barcelona; 08036; Spain
| | - Á Carracedo
- Fundación Pública Galega de Medicina Xenómica (FPGMX)-Grupo de Medicina Xenómica; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERer), IDIS; Santiago de Compostela; 15706; Spain
| | - S Castellví-Bel
- Department of Gastroenterology, Hospital Clínic, CIBERehd, IDIBAPS; University of Barcelona; Barcelona; 08036; Spain
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17
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Castellví-Bel S, Ruiz-Ponte C, Fernández-Rozadilla C, Abulí A, Muñoz J, Bessa X, Brea-Fernández A, Ferro M, Giráldez MD, Xicola RM, Llor X, Jover R, Piqué JM, Andreu M, Castells A, Carracedo A. Seeking genetic susceptibility variants for colorectal cancer: the EPICOLON consortium experience. Mutagenesis 2012; 27:153-9. [PMID: 22294762 DOI: 10.1093/mutage/ger047] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
The EPICOLON consortium was initiated in 1999 by the Gastrointestinal Oncology Group of the Spanish Gastroenterology Association. It recruited consecutive, unselected, population-based colorectal cancer (CRC) cases and control subjects matched by age and gender without personal or familial history of cancer all over Spain with the main goal of gaining knowledge in Lynch syndrome and familial CRC. This epidemiological, prospective and multicentre study collected extensive clinical data and biological samples from ∼2000 CRC cases and 2000 controls in Phases 1 and 2 involving 25 and 14 participating hospitals, respectively. Genetic susceptibility projects in EPICOLON have included candidate-gene approaches evaluating single-nucleotide polymorphisms/genes from the historical category (linked to CRC risk by previous studies), from human syntenic CRC susceptibility regions identified in mouse, from the CRC carcinogenesis-related pathways Wnt and BMP, from regions 9q22 and 3q22 with positive linkage in CRC families, and from the mucin gene family. This consortium has also participated actively in the identification 5 of the 16 common, low-penetrance CRC genetic variants identified so far by genome-wide association studies. Finishing their own pangenomic study and performing whole-exome sequencing in selected CRC samples are among EPICOLON future research prospects.
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Affiliation(s)
- Sergi Castellví-Bel
- Department of Gastroenterology, Hospital Clínic, CIBERehd, IDIBAPS, University of Barcelona, Villarroel 170, 08036 Barcelona, Catalonia, Spain.
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Giráldez MD, López-Dóriga A, Bujanda L, Abulí A, Bessa X, Fernández-Rozadilla C, Muñoz J, Cuatrecasas M, Jover R, Xicola RM, Llor X, Piqué JM, Carracedo A, Ruiz-Ponte C, Cosme A, Enríquez-Navascués JM, Moreno V, Andreu M, Castells A, Balaguer F, Castellví-Bel S. Susceptibility genetic variants associated with early-onset colorectal cancer. Carcinogenesis 2012; 33:613-9. [PMID: 22235025 DOI: 10.1093/carcin/bgs009] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [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] Open
Abstract
Colorectal cancer (CRC) is the second most common cancer in Western countries. Hereditary forms only correspond to 5% of CRC burden. Recently, genome-wide association studies have identified common low-penetrant CRC genetic susceptibility loci. Early-onset CRC (CRC<50 years old) is especially suggestive of hereditary predisposition although 85-90% of heritability still remains unidentified. CRC<50 patients (n = 191) were compared with a late-onset CRC group (CRC>65 years old) (n = 1264). CRC susceptibility variants at 8q23.3 (rs16892766), 8q24.21 (rs6983267), 10p14 (rs10795668), 11q23.1 (rs3802842), 15q13.3 (rs4779584), 18q21 (rs4939827), 14q22.2 (rs4444235), 16q22.1 (rs9929218), 19q13.1 (rs10411210) and 20p12.3 (rs961253) were genotyped in all DNA samples. A genotype-phenotype correlation with clinical and pathological characteristics in both groups was performed. Risk allele carriers for rs3802842 [Odds ratio (OR) = 1.5, 95% confidence interval (CI) 1.1-2.05, P = 0.0096, dominant model) and rs4779584 (OR = 1.39, 95% CI 1.02-1.9, P = 0.0396, dominant model) were more frequent in the CRC<50 group, whereas homozygotes for rs10795668 risk allele were also more frequent in the early-onset CRC (P = 0.02, codominant model). Regarding early-onset cases, 14q22 (rs4444235), 11q23 (rs3802842) and 20p12 (rs961253) variants were more associated with family history of CRC or tumors of the Lynch syndrome spectrum excluding CRC. In our entire cohort, sum of risk alleles was significantly higher in patients with a CRC family history (OR = 1.40, 95% CI 1.06-1.85, P = 0.01). In conclusion, variants at 10p14 (rs10795668), 11q23.1 (rs3802842) and 15q13.3 (rs4779584) may have a predominant role in predisposition to early-onset CRC. Association of CRC susceptibility variants with some patient's familiar and personal features could be relevant for screening and surveillance strategies in this high-risk group and it should be explored in further studies.
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Affiliation(s)
- María Dolores Giráldez
- Department of Gastroenterology, Hospital Clínic, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), IDIBAPS, University of Barcelona, Villarroel 170, 08036 Barcelona, Catalonia, Spain
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19
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Bessa X, Alenda C, Paya A, Álvarez C, Iglesias M, Seoane A, Dedeu JM, Abulí A, Ilzarbe L, Navarro G, Pellise M, Balaguer F, Castellvi-Bel S, LLor X, Castells A, Jover R, Andreu M. Validation Microsatellite Path Score in a Population-Based Cohort of Patients With Colorectal Cancer. J Clin Oncol 2011; 29:3374-80. [DOI: 10.1200/jco.2010.34.3947] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Purpose Bethesda guidelines are used to recognize patients at risk for Lynch syndrome. However, obtaining personal and familial tumor data can sometimes be difficult. The Microsatellite Path Score (MsPath), a pathological score, based on age, tumor location, and pathologic features, has been developed to effectively predict colorectal cancer with DNA mismatch repair (MMR) deficiencies. However, the MsPath model's performance in an unselected, population-based colorectal cancer (CRC) population is unknown. Patients and Methods We analyzed all patients with CRC regardless of age, personal or family history, and tumor characteristics from the EPICOLON study, an independent, prospective, multicenter, population-based cohort (N = 1,222). All patients underwent tumor microsatellite instability (MSI) analysis and immunostaining for MLH1/MSH2, and those with MMR underwent tumor BRAF mutation analysis and MLH1/MSH2 germline testing. All the pathologic features were centralized and evaluated blinded to the MMR status. Results MsPath score for prediction of having MSI high, with the recommended MsPath cutoff score ≥1.0, had a sensitivity, specificity, and positive predictive value (PPV) of 92.8% (95% CI, 86.9 to 98.3), 64.1% (95% CI, 61.1 to 66.8), and 15.8% (95% CI, 12.2 to 18.6), respectively. MsPath score had a sensitivity, specificity, and PPV of 81.8% (95% CI, 59.0 to 99.8), 60.6% (95% CI, 57.8 to 63.4), and 1.9% (95% CI, 0.7 to 3.1), respectively, for the identification of MLH1/MSH2 gene carriers. Application of the MsPath score, resulted in two (18%) of 11 mutation carriers being missed, both pathogenic germline MSH2 mutations. Conclusion In the general nonselected population, the MsPath score accurately predicted the probability of bearing a MSI high CRC, but it was insufficiently accurate to use for the selection of patients warranting MLH1/MSH2 mutation testing in the setting of Lynch syndrome.
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Affiliation(s)
- Xavier Bessa
- Xavier Bessa, Cristina Álvarez, Mar Iglesias, Agustín Seoane, Josep Maria Dedeu, Anna Abulí, Lucas Ilzarbe, Gemma Navarro, Montserrat Andreu, Hospital del Mar, Parc de Salut Mar, Institut Municipal d'Investigació Mèdica, Pompeu Fabra and Autonoma University; Maria Pellise, Francesc Balaguer, Sergi Castellvi-Bel, Antoni Castells, Institut de Malalties Digestives i Metabòliques, Hospital Clínic, CIBERehd, IDIBAPS, University of Barcelona, Barcelona, Catalonia; Cristina Alenda, Artemio Paya, Rodrigo Jover,
| | - Cristina Alenda
- Xavier Bessa, Cristina Álvarez, Mar Iglesias, Agustín Seoane, Josep Maria Dedeu, Anna Abulí, Lucas Ilzarbe, Gemma Navarro, Montserrat Andreu, Hospital del Mar, Parc de Salut Mar, Institut Municipal d'Investigació Mèdica, Pompeu Fabra and Autonoma University; Maria Pellise, Francesc Balaguer, Sergi Castellvi-Bel, Antoni Castells, Institut de Malalties Digestives i Metabòliques, Hospital Clínic, CIBERehd, IDIBAPS, University of Barcelona, Barcelona, Catalonia; Cristina Alenda, Artemio Paya, Rodrigo Jover,
| | - Artemio Paya
- Xavier Bessa, Cristina Álvarez, Mar Iglesias, Agustín Seoane, Josep Maria Dedeu, Anna Abulí, Lucas Ilzarbe, Gemma Navarro, Montserrat Andreu, Hospital del Mar, Parc de Salut Mar, Institut Municipal d'Investigació Mèdica, Pompeu Fabra and Autonoma University; Maria Pellise, Francesc Balaguer, Sergi Castellvi-Bel, Antoni Castells, Institut de Malalties Digestives i Metabòliques, Hospital Clínic, CIBERehd, IDIBAPS, University of Barcelona, Barcelona, Catalonia; Cristina Alenda, Artemio Paya, Rodrigo Jover,
| | - Cristina Álvarez
- Xavier Bessa, Cristina Álvarez, Mar Iglesias, Agustín Seoane, Josep Maria Dedeu, Anna Abulí, Lucas Ilzarbe, Gemma Navarro, Montserrat Andreu, Hospital del Mar, Parc de Salut Mar, Institut Municipal d'Investigació Mèdica, Pompeu Fabra and Autonoma University; Maria Pellise, Francesc Balaguer, Sergi Castellvi-Bel, Antoni Castells, Institut de Malalties Digestives i Metabòliques, Hospital Clínic, CIBERehd, IDIBAPS, University of Barcelona, Barcelona, Catalonia; Cristina Alenda, Artemio Paya, Rodrigo Jover,
| | - Mar Iglesias
- Xavier Bessa, Cristina Álvarez, Mar Iglesias, Agustín Seoane, Josep Maria Dedeu, Anna Abulí, Lucas Ilzarbe, Gemma Navarro, Montserrat Andreu, Hospital del Mar, Parc de Salut Mar, Institut Municipal d'Investigació Mèdica, Pompeu Fabra and Autonoma University; Maria Pellise, Francesc Balaguer, Sergi Castellvi-Bel, Antoni Castells, Institut de Malalties Digestives i Metabòliques, Hospital Clínic, CIBERehd, IDIBAPS, University of Barcelona, Barcelona, Catalonia; Cristina Alenda, Artemio Paya, Rodrigo Jover,
| | - Agustín Seoane
- Xavier Bessa, Cristina Álvarez, Mar Iglesias, Agustín Seoane, Josep Maria Dedeu, Anna Abulí, Lucas Ilzarbe, Gemma Navarro, Montserrat Andreu, Hospital del Mar, Parc de Salut Mar, Institut Municipal d'Investigació Mèdica, Pompeu Fabra and Autonoma University; Maria Pellise, Francesc Balaguer, Sergi Castellvi-Bel, Antoni Castells, Institut de Malalties Digestives i Metabòliques, Hospital Clínic, CIBERehd, IDIBAPS, University of Barcelona, Barcelona, Catalonia; Cristina Alenda, Artemio Paya, Rodrigo Jover,
| | - Josep Maria Dedeu
- Xavier Bessa, Cristina Álvarez, Mar Iglesias, Agustín Seoane, Josep Maria Dedeu, Anna Abulí, Lucas Ilzarbe, Gemma Navarro, Montserrat Andreu, Hospital del Mar, Parc de Salut Mar, Institut Municipal d'Investigació Mèdica, Pompeu Fabra and Autonoma University; Maria Pellise, Francesc Balaguer, Sergi Castellvi-Bel, Antoni Castells, Institut de Malalties Digestives i Metabòliques, Hospital Clínic, CIBERehd, IDIBAPS, University of Barcelona, Barcelona, Catalonia; Cristina Alenda, Artemio Paya, Rodrigo Jover,
| | - Anna Abulí
- Xavier Bessa, Cristina Álvarez, Mar Iglesias, Agustín Seoane, Josep Maria Dedeu, Anna Abulí, Lucas Ilzarbe, Gemma Navarro, Montserrat Andreu, Hospital del Mar, Parc de Salut Mar, Institut Municipal d'Investigació Mèdica, Pompeu Fabra and Autonoma University; Maria Pellise, Francesc Balaguer, Sergi Castellvi-Bel, Antoni Castells, Institut de Malalties Digestives i Metabòliques, Hospital Clínic, CIBERehd, IDIBAPS, University of Barcelona, Barcelona, Catalonia; Cristina Alenda, Artemio Paya, Rodrigo Jover,
| | - Lucas Ilzarbe
- Xavier Bessa, Cristina Álvarez, Mar Iglesias, Agustín Seoane, Josep Maria Dedeu, Anna Abulí, Lucas Ilzarbe, Gemma Navarro, Montserrat Andreu, Hospital del Mar, Parc de Salut Mar, Institut Municipal d'Investigació Mèdica, Pompeu Fabra and Autonoma University; Maria Pellise, Francesc Balaguer, Sergi Castellvi-Bel, Antoni Castells, Institut de Malalties Digestives i Metabòliques, Hospital Clínic, CIBERehd, IDIBAPS, University of Barcelona, Barcelona, Catalonia; Cristina Alenda, Artemio Paya, Rodrigo Jover,
| | - Gemma Navarro
- Xavier Bessa, Cristina Álvarez, Mar Iglesias, Agustín Seoane, Josep Maria Dedeu, Anna Abulí, Lucas Ilzarbe, Gemma Navarro, Montserrat Andreu, Hospital del Mar, Parc de Salut Mar, Institut Municipal d'Investigació Mèdica, Pompeu Fabra and Autonoma University; Maria Pellise, Francesc Balaguer, Sergi Castellvi-Bel, Antoni Castells, Institut de Malalties Digestives i Metabòliques, Hospital Clínic, CIBERehd, IDIBAPS, University of Barcelona, Barcelona, Catalonia; Cristina Alenda, Artemio Paya, Rodrigo Jover,
| | - Maria Pellise
- Xavier Bessa, Cristina Álvarez, Mar Iglesias, Agustín Seoane, Josep Maria Dedeu, Anna Abulí, Lucas Ilzarbe, Gemma Navarro, Montserrat Andreu, Hospital del Mar, Parc de Salut Mar, Institut Municipal d'Investigació Mèdica, Pompeu Fabra and Autonoma University; Maria Pellise, Francesc Balaguer, Sergi Castellvi-Bel, Antoni Castells, Institut de Malalties Digestives i Metabòliques, Hospital Clínic, CIBERehd, IDIBAPS, University of Barcelona, Barcelona, Catalonia; Cristina Alenda, Artemio Paya, Rodrigo Jover,
| | - Francesc Balaguer
- Xavier Bessa, Cristina Álvarez, Mar Iglesias, Agustín Seoane, Josep Maria Dedeu, Anna Abulí, Lucas Ilzarbe, Gemma Navarro, Montserrat Andreu, Hospital del Mar, Parc de Salut Mar, Institut Municipal d'Investigació Mèdica, Pompeu Fabra and Autonoma University; Maria Pellise, Francesc Balaguer, Sergi Castellvi-Bel, Antoni Castells, Institut de Malalties Digestives i Metabòliques, Hospital Clínic, CIBERehd, IDIBAPS, University of Barcelona, Barcelona, Catalonia; Cristina Alenda, Artemio Paya, Rodrigo Jover,
| | - Sergi Castellvi-Bel
- Xavier Bessa, Cristina Álvarez, Mar Iglesias, Agustín Seoane, Josep Maria Dedeu, Anna Abulí, Lucas Ilzarbe, Gemma Navarro, Montserrat Andreu, Hospital del Mar, Parc de Salut Mar, Institut Municipal d'Investigació Mèdica, Pompeu Fabra and Autonoma University; Maria Pellise, Francesc Balaguer, Sergi Castellvi-Bel, Antoni Castells, Institut de Malalties Digestives i Metabòliques, Hospital Clínic, CIBERehd, IDIBAPS, University of Barcelona, Barcelona, Catalonia; Cristina Alenda, Artemio Paya, Rodrigo Jover,
| | - Xavier LLor
- Xavier Bessa, Cristina Álvarez, Mar Iglesias, Agustín Seoane, Josep Maria Dedeu, Anna Abulí, Lucas Ilzarbe, Gemma Navarro, Montserrat Andreu, Hospital del Mar, Parc de Salut Mar, Institut Municipal d'Investigació Mèdica, Pompeu Fabra and Autonoma University; Maria Pellise, Francesc Balaguer, Sergi Castellvi-Bel, Antoni Castells, Institut de Malalties Digestives i Metabòliques, Hospital Clínic, CIBERehd, IDIBAPS, University of Barcelona, Barcelona, Catalonia; Cristina Alenda, Artemio Paya, Rodrigo Jover,
| | - Antoni Castells
- Xavier Bessa, Cristina Álvarez, Mar Iglesias, Agustín Seoane, Josep Maria Dedeu, Anna Abulí, Lucas Ilzarbe, Gemma Navarro, Montserrat Andreu, Hospital del Mar, Parc de Salut Mar, Institut Municipal d'Investigació Mèdica, Pompeu Fabra and Autonoma University; Maria Pellise, Francesc Balaguer, Sergi Castellvi-Bel, Antoni Castells, Institut de Malalties Digestives i Metabòliques, Hospital Clínic, CIBERehd, IDIBAPS, University of Barcelona, Barcelona, Catalonia; Cristina Alenda, Artemio Paya, Rodrigo Jover,
| | - Rodrigo Jover
- Xavier Bessa, Cristina Álvarez, Mar Iglesias, Agustín Seoane, Josep Maria Dedeu, Anna Abulí, Lucas Ilzarbe, Gemma Navarro, Montserrat Andreu, Hospital del Mar, Parc de Salut Mar, Institut Municipal d'Investigació Mèdica, Pompeu Fabra and Autonoma University; Maria Pellise, Francesc Balaguer, Sergi Castellvi-Bel, Antoni Castells, Institut de Malalties Digestives i Metabòliques, Hospital Clínic, CIBERehd, IDIBAPS, University of Barcelona, Barcelona, Catalonia; Cristina Alenda, Artemio Paya, Rodrigo Jover,
| | - Montserrat Andreu
- Xavier Bessa, Cristina Álvarez, Mar Iglesias, Agustín Seoane, Josep Maria Dedeu, Anna Abulí, Lucas Ilzarbe, Gemma Navarro, Montserrat Andreu, Hospital del Mar, Parc de Salut Mar, Institut Municipal d'Investigació Mèdica, Pompeu Fabra and Autonoma University; Maria Pellise, Francesc Balaguer, Sergi Castellvi-Bel, Antoni Castells, Institut de Malalties Digestives i Metabòliques, Hospital Clínic, CIBERehd, IDIBAPS, University of Barcelona, Barcelona, Catalonia; Cristina Alenda, Artemio Paya, Rodrigo Jover,
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20
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Abulí A, Fernández-Rozadilla C, Alonso-Espinaco V, Muñoz J, Gonzalo V, Bessa X, González D, Clofent J, Cubiella J, Morillas JD, Rigau J, Latorre M, Fernández-Bañares F, Peña E, Riestra S, Payá A, Jover R, Xicola RM, Llor X, Carvajal-Carmona L, Villanueva CM, Moreno V, Piqué JM, Carracedo A, Castells A, Andreu M, Ruiz-Ponte C, Castellví-Bel S. Case-control study for colorectal cancer genetic susceptibility in EPICOLON: previously identified variants and mucins. BMC Cancer 2011; 11:339. [PMID: 21819567 PMCID: PMC3176240 DOI: 10.1186/1471-2407-11-339] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Accepted: 08/05/2011] [Indexed: 11/10/2022] Open
Abstract
Background Colorectal cancer (CRC) is the second leading cause of cancer death in developed countries. Familial aggregation in CRC is also important outside syndromic forms and, in this case, a polygenic model with several common low-penetrance alleles contributing to CRC genetic predisposition could be hypothesized. Mucins and GALNTs (N-acetylgalactosaminyltransferase) are interesting candidates for CRC genetic susceptibility and have not been previously evaluated. We present results for ten genetic variants linked to CRC risk in previous studies (previously identified category) and 18 selected variants from the mucin gene family in a case-control association study from the Spanish EPICOLON consortium. Methods CRC cases and matched controls were from EPICOLON, a prospective, multicenter, nationwide Spanish initiative, comprised of two independent stages. Stage 1 corresponded to 515 CRC cases and 515 controls, whereas stage 2 consisted of 901 CRC cases and 909 controls. Also, an independent cohort of 549 CRC cases and 599 controls outside EPICOLON was available for additional replication. Genotyping was performed for ten previously identified SNPs in ADH1C, APC, CCDN1, IL6, IL8, IRS1, MTHFR, PPARG, VDR and ARL11, and 18 selected variants in the mucin gene family. Results None of the 28 SNPs analyzed in our study was found to be associated with CRC risk. Although four SNPs were significant with a P-value < 0.05 in EPICOLON stage 1 [rs698 in ADH1C (OR = 1.63, 95% CI = 1.06-2.50, P-value = 0.02, recessive), rs1800795 in IL6 (OR = 1.62, 95% CI = 1.10-2.37, P-value = 0.01, recessive), rs3803185 in ARL11 (OR = 1.58, 95% CI = 1.17-2.15, P-value = 0.007, codominant), and rs2102302 in GALNTL2 (OR = 1.20, 95% CI = 1.00-1.44, P-value = 0.04, log-additive 0, 1, 2 alleles], only rs3803185 achieved statistical significance in EPICOLON stage 2 (OR = 1.34, 95% CI = 1.06-1.69, P-value = 0.01, recessive). In the joint analysis for both stages, results were only significant for rs3803185 (OR = 1.12, 95% CI = 1.00-1.25, P-value = 0.04, log-additive 0, 1, 2 alleles) and borderline significant for rs698 and rs2102302. The rs3803185 variant was not significantly associated with CRC risk in an external cohort (MCC-Spain), but it still showed some borderline significance in the pooled analysis of both cohorts (OR = 1.08, 95% CI = 0.98-1.18, P-value = 0.09, log-additive 0, 1, 2 alleles). Conclusions ARL11, ADH1C, GALNTL2 and IL6 genetic variants may have an effect on CRC risk. Further validation and meta-analyses should be undertaken in larger CRC studies.
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Affiliation(s)
- Anna Abulí
- Department of Gastroenterology, IDIBAPS, Hospital Clínic, CIBERehd, University of Barcelona, Barcelona, Catalonia, Spain
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Fernández-Rozadilla C, de Castro L, Clofent J, Brea-Fernández A, Bessa X, Abulí A, Andreu M, Jover R, Xicola R, Llor X, Castells A, Castellví-Bel S, Carracedo A, Ruiz-Ponte C. Single nucleotide polymorphisms in the Wnt and BMP pathways and colorectal cancer risk in a Spanish cohort. PLoS One 2010; 5. [PMID: 20844743 PMCID: PMC2936577 DOI: 10.1371/journal.pone.0012673] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2010] [Accepted: 08/06/2010] [Indexed: 12/27/2022] Open
Abstract
Background Colorectal cancer (CRC) is considered a complex disease, and thus the majority of the genetic susceptibility is thought to lie in the form of low-penetrance variants following a polygenic model of inheritance. Candidate-gene studies have so far been one of the basic approaches taken to identify these susceptibility variants. The consistent involvement of some signaling routes in carcinogenesis provided support for pathway-based studies as a natural strategy to select genes that could potentially harbour new susceptibility loci. Methodology/Principal Findings We selected two main carcinogenesis-related pathways: Wnt and BMP, in order to screen the implicated genes for new risk variants. We then conducted a case-control association study in 933 CRC cases and 969 controls based on coding and regulatory SNPs. We also included rs4444235 and rs9929218, which did not fulfill our selection criteria but belonged to two genes in the BMP pathway and had consistently been linked to CRC in previous studies. Neither allelic, nor genotypic or haplotypic analyses showed any signs of association between the 37 screened variants and CRC risk. Adjustments for sex and age, and stratified analysis between sporadic and control groups did not yield any positive results either. Conclusions/Significance Despite the relevance of both pathways in the pathogenesis of the disease, and the fact that this is indeed the first study that considers these pathways as a candidate-gene selection approach, our study does not present any evidence of the presence of low-penetrance variants for the selected markers in any of the considered genes in our cohort.
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Affiliation(s)
- Ceres Fernández-Rozadilla
- Galician Public Foundation of Genomic Medicine (FPGMX), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Genomics Medicine Group, Hospital Clínico, Santiago de Compostela, University of Santiago de Compostela, Galicia, Spain
| | - Luisa de Castro
- Gastroenterology Department, Hospital Meixoeiro, Vigo, Galicia, Spain
| | - Juan Clofent
- Gastroenterology Department, Hospital La Fe, Valencia, Spain
| | - Alejandro Brea-Fernández
- Galician Public Foundation of Genomic Medicine (FPGMX), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Genomics Medicine Group, Hospital Clínico, Santiago de Compostela, University of Santiago de Compostela, Galicia, Spain
| | - Xavier Bessa
- Gastroenterology Department, Hospital del Mar, Institut Municipal d'Investigació Médica (IMIM), Pompeu Fabra University, Barcelona, Catalonia, Spain
| | - Anna Abulí
- Gastroenterology Department, Hospital del Mar, Institut Municipal d'Investigació Médica (IMIM), Pompeu Fabra University, Barcelona, Catalonia, Spain
| | - Montserrat Andreu
- Gastroenterology Department, Hospital del Mar, Institut Municipal d'Investigació Médica (IMIM), Pompeu Fabra University, Barcelona, Catalonia, Spain
| | - Rodrigo Jover
- Unidad de Gastroenterología, Hospital General Universitario de Alicante, Alicante, Spain
| | - Rosa Xicola
- Section of Digestive Diseases and Nutrition, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Xavier Llor
- Section of Digestive Diseases and Nutrition, University of Illinois at Chicago, Chicago, Illinois, United States of America
| | - Antoni Castells
- Department of Gastroenterology, Hospital Clínic, CIBERehd, IDIBAPS, University of Barcelona, Barcelona, Catalonia, Spain
| | - Sergi Castellví-Bel
- Department of Gastroenterology, Hospital Clínic, CIBERehd, IDIBAPS, University of Barcelona, Barcelona, Catalonia, Spain
| | - Angel Carracedo
- Galician Public Foundation of Genomic Medicine (FPGMX), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Genomics Medicine Group, Hospital Clínico, Santiago de Compostela, University of Santiago de Compostela, Galicia, Spain
| | - Clara Ruiz-Ponte
- Galician Public Foundation of Genomic Medicine (FPGMX), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Genomics Medicine Group, Hospital Clínico, Santiago de Compostela, University of Santiago de Compostela, Galicia, Spain
- * E-mail:
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Abulí A, Bessa X, González JR, Ruiz-Ponte C, Cáceres A, Muñoz J, Gonzalo V, Balaguer F, Fernández-Rozadilla C, González D, de Castro L, Clofent J, Bujanda L, Cubiella J, Reñé JMA, Morillas JD, Lanas A, Rigau J, García AMA, Latorre M, Saló J, Fernández Bañares F, Argüello L, Peña E, Vilella A, Riestra S, Carreño R, Paya A, Alenda C, Xicola RM, Doyle BJ, Jover R, Llor X, Carracedo A, Castells A, Castellví-Bel S, Andreu M. Susceptibility genetic variants associated with colorectal cancer risk correlate with cancer phenotype. Gastroenterology 2010; 139:788-96, 796.e1-6. [PMID: 20638935 DOI: 10.1053/j.gastro.2010.05.072] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2010] [Revised: 05/10/2010] [Accepted: 05/17/2010] [Indexed: 12/30/2022]
Abstract
BACKGROUND & AIMS Ten common low-penetrant genetic variants have been consistently associated with colorectal cancer (CRC) risk; little is known about the correlation between these variants and CRC phenotype. Characterization of such a correlation would improve CRC management and prevention programs. We assessed the association between these genetic variants and CRC phenotype in patients and modeled pairwise combinations to detect epistasis. METHODS The validation population corresponded to a prospective, multicenter, population-based cohort (EPICOLON I) of 1096 patients with newly diagnosed CRC. The replication set was an independent, prospective, multicenter Spanish cohort (EPICOLON II) of 895 patients with newly diagnosed CRC. For individual single nucleotide polymorphism (SNP) association analyses, a multivariate method using logistic regression was applied in EPICOLON I and subsequently prospectively validated in EPICOLON II. Interactions between SNPs were assessed using the likelihood ratio test. RESULTS Validated results confirmed that the C allele on 8q23.3 (rs16892766) was significantly associated with advanced-stage tumors (odds ratio [OR], 1.48; 95% confidence interval [CI], 1.15-1.90; P value = 4.9 x 10(-3)). The G allele on 8q24.21 (rs6983267) was more common in patients with a familial history of CRC (OR, 2.02; 95% CI, 1.35-3.03; P value = 3.9 x 10(-4)). The combination of rs6983267 on 8q24.21 and rs9929218 on 16q22.2 was associated with a history of colorectal adenoma (carriers of GG and AA, respectively; OR, 2.28; 95% CI, 1.32-3.93; P = 5.0 x 10(-4)). CONCLUSIONS CRC susceptibility variants at 8q23.3, 8q24.21, and 16q22.2 appear to be associated with cancer phenotype. These findings might be used to develop screening and surveillance strategies.
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Affiliation(s)
- Anna Abulí
- Department of Gastroenterology, Hospital del Mar, Institut Municipal d'Investigació Mèdica, Pompeu Fabra University, Barcelona, Catalonia, Spain
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