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Díez-Villanueva A, Martín B, Moratalla-Navarro F, Morón-Duran FD, Galván-Femenía I, Obón-Santacana M, Carreras A, de Cid R, Peinado MA, Moreno V. Identification of intergenerational epigenetic inheritance by whole genome DNA methylation analysis in trios. Sci Rep 2023; 13:21266. [PMID: 38042866 PMCID: PMC10693549 DOI: 10.1038/s41598-023-48517-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 11/27/2023] [Indexed: 12/04/2023] Open
Abstract
Genome-wide association studies have identified thousands of loci associated with common diseases and traits. However, a large fraction of heritability remains unexplained. Epigenetic modifications, such as the observed in DNA methylation have been proposed as a mechanism of intergenerational inheritance. To investigate the potential contribution of DNA methylation to the missing heritability, we analysed the methylomes of four healthy trios (two parents and one offspring) using whole genome bisulphite sequencing. Of the 1.5 million CpGs (19%) with over 20% variability between parents in at least one family and compatible with a Mendelian inheritance pattern, only 3488 CpGs (0.2%) lacked correlation with any SNP in the genome, marking them as potential sites for intergenerational epigenetic inheritance. These markers were distributed genome-wide, with some preference to be located in promoters. They displayed a bimodal distribution, being either fully methylated or unmethylated, and were often found at the boundaries of genomic regions with high/low GC content. This analysis provides a starting point for future investigations into the missing heritability of simple and complex traits.
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Affiliation(s)
- Anna Díez-Villanueva
- Unit of Biomarkers and Susceptibility (UBS), Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L'Hospitalet del Llobregat, 08908, Barcelona, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), 28029, Madrid, Spain
| | - Berta Martín
- Germans Trias i Pujol Institute (IGTP), Translational Program in Cancer Research (CARE), Camí de les Escoles, s/n, Can Ruti Biomedical Campus, 08916, Badalona, Catalonia, Spain
| | - Ferran Moratalla-Navarro
- Unit of Biomarkers and Susceptibility (UBS), Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L'Hospitalet del Llobregat, 08908, Barcelona, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), 28029, Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine and Universitat de Barcelona Institute of Complex Systems (UBICS), University of Barcelona, 08907, Barcelona, Spain
| | - Francisco D Morón-Duran
- Unit of Biomarkers and Susceptibility (UBS), Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L'Hospitalet del Llobregat, 08908, Barcelona, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Spain
- Department of Clinical Sciences, Faculty of Medicine and Universitat de Barcelona Institute of Complex Systems (UBICS), University of Barcelona, 08907, Barcelona, Spain
| | - Iván Galván-Femenía
- Genomes for Life-GCAT lab., Germans Trias i Pujol Research Institute (IGTP), Camí de les Escoles, s/n, Can Ruti Biomedical Campus, 08916, Badalona, Catalonia, Spain
| | - Mireia Obón-Santacana
- Unit of Biomarkers and Susceptibility (UBS), Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L'Hospitalet del Llobregat, 08908, Barcelona, Spain
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), 28029, Madrid, Spain
| | - Anna Carreras
- Genomes for Life-GCAT lab., Germans Trias i Pujol Research Institute (IGTP), Camí de les Escoles, s/n, Can Ruti Biomedical Campus, 08916, Badalona, Catalonia, Spain
| | - Rafael de Cid
- Genomes for Life-GCAT lab., Germans Trias i Pujol Research Institute (IGTP), Camí de les Escoles, s/n, Can Ruti Biomedical Campus, 08916, Badalona, Catalonia, Spain
| | - Miguel A Peinado
- Germans Trias i Pujol Institute (IGTP), Translational Program in Cancer Research (CARE), Camí de les Escoles, s/n, Can Ruti Biomedical Campus, 08916, Badalona, Catalonia, Spain
| | - Victor Moreno
- Unit of Biomarkers and Susceptibility (UBS), Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology (ICO), L'Hospitalet del Llobregat, 08908, Barcelona, Spain.
- ONCOBELL Program, Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, 08908, Barcelona, Spain.
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP), 28029, Madrid, Spain.
- Department of Clinical Sciences, Faculty of Medicine and Universitat de Barcelona Institute of Complex Systems (UBICS), University of Barcelona, 08907, Barcelona, Spain.
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Valls-Margarit J, Galván-Femenía I, Matías-Sánchez D, Blay N, Puiggròs M, Carreras A, Salvoro C, Cortés B, Amela R, Farre X, Lerga-Jaso J, Puig M, Sánchez-Herrero J, Moreno V, Perucho M, Sumoy L, Armengol L, Delaneau O, Cáceres M, de Cid R, Torrents D. GCAT|Panel, a comprehensive structural variant haplotype map of the Iberian population from high-coverage whole-genome sequencing. Nucleic Acids Res 2022; 50:2464-2479. [PMID: 35176773 PMCID: PMC8934637 DOI: 10.1093/nar/gkac076] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 07/20/2021] [Revised: 12/24/2021] [Accepted: 02/09/2022] [Indexed: 11/17/2022] Open
Abstract
The combined analysis of haplotype panels with phenotype clinical cohorts is a common approach to explore the genetic architecture of human diseases. However, genetic studies are mainly based on single nucleotide variants (SNVs) and small insertions and deletions (indels). Here, we contribute to fill this gap by generating a dense haplotype map focused on the identification, characterization, and phasing of structural variants (SVs). By integrating multiple variant identification methods and Logistic Regression Models (LRMs), we present a catalogue of 35 431 441 variants, including 89 178 SVs (≥50 bp), 30 325 064 SNVs and 5 017 199 indels, across 785 Illumina high coverage (30x) whole-genomes from the Iberian GCAT Cohort, containing a median of 3.52M SNVs, 606 336 indels and 6393 SVs per individual. The haplotype panel is able to impute up to 14 360 728 SNVs/indels and 23 179 SVs, showing a 2.7-fold increase for SVs compared with available genetic variation panels. The value of this panel for SVs analysis is shown through an imputed rare Alu element located in a new locus associated with Mononeuritis of lower limb, a rare neuromuscular disease. This study represents the first deep characterization of genetic variation within the Iberian population and the first operational haplotype panel to systematically include the SVs into genome-wide genetic studies.
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Affiliation(s)
| | | | | | - Natalia Blay
- Genomes for Life-GCAT lab Group, Institute for Health Science Research Germans Trias i Pujol (IGTP), Badalona 08916, Spain
| | - Montserrat Puiggròs
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain
| | - Anna Carreras
- Genomes for Life-GCAT lab Group, Institute for Health Science Research Germans Trias i Pujol (IGTP), Badalona 08916, Spain
| | - Cecilia Salvoro
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain
| | - Beatriz Cortés
- Genomes for Life-GCAT lab Group, Institute for Health Science Research Germans Trias i Pujol (IGTP), Badalona 08916, Spain
| | - Ramon Amela
- Life Sciences Department, Barcelona Supercomputing Center (BSC), Barcelona 08034, Spain
| | - Xavier Farre
- Genomes for Life-GCAT lab Group, Institute for Health Science Research Germans Trias i Pujol (IGTP), Badalona 08916, Spain
| | - Jon Lerga-Jaso
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
| | - Marta Puig
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
| | - Jose Francisco Sánchez-Herrero
- High Content Genomics and Bioinformatics Unit, Institute for Health Science Research Germans Trias i Pujol (IGTP), 08916 Badalona, Spain
| | - Victor Moreno
- Catalan Institute of Oncology, Hospitalet del Llobregat, 08908, Spain
- Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet del Llobregat, 08908, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid 28029, Spain
- Universitat de Barcelona (UB), Barcelona 08007, Spain
| | - Manuel Perucho
- Sanford Burnham Prebys Medical Discovery Institute (SBP), La Jolla, CA 92037, USA
- Cancer Genetics and Epigenetics, Program of Predictive and Personalized Medicine of Cancer (PMPPC), Health Science Research Institute Germans Trias i Pujol (IGTP), Badalona 08916, Spain
| | - Lauro Sumoy
- High Content Genomics and Bioinformatics Unit, Institute for Health Science Research Germans Trias i Pujol (IGTP), 08916 Badalona, Spain
| | - Lluís Armengol
- Quantitative Genomic Medicine Laboratories (qGenomics), Esplugues del Llobregat, 08950, Spain
| | - Olivier Delaneau
- Department of Computational Biology, University of Lausanne, Génopode, 1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics (SIB), University of Lausanne, Quartier Sorge – Batiment Amphipole, 1015 Lausanne, Switzerland
| | - Mario Cáceres
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona 08193, Spain
- ICREA, Barcelona 08010, Spain
| | - Rafael de Cid
- Correspondence may also be addressed to Rafael de Cid. Tel: +34 930330542;
| | - David Torrents
- To whom correspondence should be addressed. Tel: +34 934134074;
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Obón-Santacana M, Vilardell M, Carreras A, Duran X, Velasco J, Galván-Femenía I, Alonso T, Puig L, Sumoy L, Duell EJ, Perucho M, Moreno V, de Cid R. GCAT|Genomes for life: a prospective cohort study of the genomes of Catalonia. BMJ Open 2018; 8:e018324. [PMID: 29593016 PMCID: PMC5875652 DOI: 10.1136/bmjopen-2017-018324] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
PURPOSE The prevalence of chronic non-communicable diseases (NCDs) is increasing worldwide. NCDs are the leading cause of both morbidity and mortality, and it is estimated that by 2030, they will be responsible for 80% of deaths across the world. The Genomes for Life (GCAT) project is a long-term prospective cohort study that was designed to integrate and assess the role of epidemiological, genomic and epigenomic factors in the development of major chronic diseases in Catalonia, a north-east region of Spain. PARTICIPANTS At the end of 2017, the GCAT Study will have recruited 20 000 participants aged 40-65 years. Participants who agreed to take part in the study completed a self-administered computer-driven questionnaire, and underwent blood pressure, cardiac frequency and anthropometry measurements. For each participant, blood plasma, blood serum and white blood cells are collected at baseline. The GCAT Study has access to the electronic health records of the Catalan Public Healthcare System. Participants will be followed biannually at least 20 years after recruitment. FINDINGS TO DATE Among all GCAT participants, 59.2% are women and 83.3% of the cohort identified themselves as Caucasian/white. More than half of the participants have higher education levels, 72.2% are current workers and 42.1% are classified as overweight (body mass index ≥25 and <30 kg/m2). We have genotyped 5459 participants, of which 5000 have metabolome data. Further, the whole genome of 808 participants will be sequenced by the end of 2017. FUTURE PLANS The first follow-up study started in December 2017 and will end by March 2018. Residences of all subjects will be geocoded during the following year. Several genomic analyses are ongoing, and metabolomic and genomic integrations will be performed to identify underlying genetic variants, as well as environmental factors that influence metabolites.
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Affiliation(s)
- Mireia Obón-Santacana
- Genomes for Life -GCAT lab Group, Program of Predictive and Personalized Medicine of Cancer (PMPPC), Institute for Health Science Research Germans Trias i Pujol (IGTP), Badalona, Spain
- Cancer Prevention and Control Program, Catalan Institute of Oncology (ICO-IDIBELL), Hospitalet del Llobregat, Spain
| | - Mireia Vilardell
- Genomes for Life -GCAT lab Group, Program of Predictive and Personalized Medicine of Cancer (PMPPC), Institute for Health Science Research Germans Trias i Pujol (IGTP), Badalona, Spain
| | - Anna Carreras
- Genomes for Life -GCAT lab Group, Program of Predictive and Personalized Medicine of Cancer (PMPPC), Institute for Health Science Research Germans Trias i Pujol (IGTP), Badalona, Spain
| | - Xavier Duran
- Genomes for Life -GCAT lab Group, Program of Predictive and Personalized Medicine of Cancer (PMPPC), Institute for Health Science Research Germans Trias i Pujol (IGTP), Badalona, Spain
| | - Juan Velasco
- Genomes for Life -GCAT lab Group, Program of Predictive and Personalized Medicine of Cancer (PMPPC), Institute for Health Science Research Germans Trias i Pujol (IGTP), Badalona, Spain
| | - Iván Galván-Femenía
- Genomes for Life -GCAT lab Group, Program of Predictive and Personalized Medicine of Cancer (PMPPC), Institute for Health Science Research Germans Trias i Pujol (IGTP), Badalona, Spain
| | - Teresa Alonso
- Genomes for Life -GCAT lab Group, Program of Predictive and Personalized Medicine of Cancer (PMPPC), Institute for Health Science Research Germans Trias i Pujol (IGTP), Badalona, Spain
| | - Lluís Puig
- Banc de Sang i Teixits (BST), Barcelona, Spain
| | - Lauro Sumoy
- Program of Predictive and Personalized Medicine of Cancer (PMPPC), Institute for Health Science Research Germans Trias i Pujol (IGTP), Badalona, Spain
| | - Eric J Duell
- Unit of Nutrition and Cancer, Cancer Epidemiology Research Program, Catalan Institute of Oncology (ICO-IDIBELL), Hospitalet del Llobregat, Spain
| | - Manuel Perucho
- Program of Predictive and Personalized Medicine of Cancer (PMPPC), Institute for Health Science Research Germans Trias i Pujol (IGTP), Badalona, Spain
| | - Victor Moreno
- Cancer Prevention and Control Program, Catalan Institute of Oncology (ICO-IDIBELL), Hospitalet del Llobregat, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Hospitalet del Llobregat, Madrid, Spain
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Rafael de Cid
- Genomes for Life -GCAT lab Group, Program of Predictive and Personalized Medicine of Cancer (PMPPC), Institute for Health Science Research Germans Trias i Pujol (IGTP), Badalona, Spain
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