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van Dongen J, Willemsen G, de Geus EJC, Boomsma DI, Neale MC. Effects of smoking on genome-wide DNA methylation profiles: A study of discordant and concordant monozygotic twin pairs. eLife 2023; 12:e83286. [PMID: 37643467 PMCID: PMC10501767 DOI: 10.7554/elife.83286] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 08/08/2023] [Indexed: 08/31/2023] Open
Abstract
Background Smoking-associated DNA methylation levels identified through epigenome-wide association studies (EWASs) are generally ascribed to smoking-reactive mechanisms, but the contribution of a shared genetic predisposition to smoking and DNA methylation levels is typically not accounted for. Methods We exploited a strong within-family design, that is, the discordant monozygotic twin design, to study reactiveness of DNA methylation in blood cells to smoking and reversibility of methylation patterns upon quitting smoking. Illumina HumanMethylation450 BeadChip data were available for 769 monozygotic twin pairs (mean age = 36 years, range = 18-78, 70% female), including pairs discordant or concordant for current or former smoking. Results In pairs discordant for current smoking, 13 differentially methylated CpGs were found between current smoking twins and their genetically identical co-twin who never smoked. Top sites include multiple CpGs in CACNA1D and GNG12, which encode subunits of a calcium voltage-gated channel and G protein, respectively. These proteins interact with the nicotinic acetylcholine receptor, suggesting that methylation levels at these CpGs might be reactive to nicotine exposure. All 13 CpGs have been previously associated with smoking in unrelated individuals and data from monozygotic pairs discordant for former smoking indicated that methylation patterns are to a large extent reversible upon smoking cessation. We further showed that differences in smoking level exposure for monozygotic twins who are both current smokers but differ in the number of cigarettes they smoke are reflected in their DNA methylation profiles. Conclusions In conclusion, by analysing data from monozygotic twins, we robustly demonstrate that DNA methylation level in human blood cells is reactive to cigarette smoking. Funding We acknowledge funding from the National Institute on Drug Abuse grant DA049867, the Netherlands Organization for Scientific Research (NWO): Biobanking and Biomolecular Research Infrastructure (BBMRI-NL, NWO 184.033.111) and the BBRMI-NL-financed BIOS Consortium (NWO 184.021.007), NWO Large Scale infrastructures X-Omics (184.034.019), Genotype/phenotype database for behaviour genetic and genetic epidemiological studies (ZonMw Middelgroot 911-09-032); Netherlands Twin Registry Repository: researching the interplay between genome and environment (NWO-Groot 480-15-001/674); the Avera Institute, Sioux Falls (USA), and the National Institutes of Health (NIH R01 HD042157-01A1, MH081802, Grand Opportunity grants 1RC2 MH089951 and 1RC2 MH089995); epigenetic data were generated at the Human Genomics Facility (HuGe-F) at ErasmusMC Rotterdam. Cotinine assaying was sponsored by the Neuroscience Campus Amsterdam. DIB acknowledges the Royal Netherlands Academy of Science Professor Award (PAH/6635).
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Affiliation(s)
- Jenny van Dongen
- Department of Biological Psychology, Vrije Universiteit AmsterdamAmsterdamNetherlands
- Amsterdam Public Health Research InstituteAmsterdamNetherlands
- Amsterdam Reproduction and Development (AR&D) Research InstituteAmsterdamNetherlands
| | - Gonneke Willemsen
- Department of Biological Psychology, Vrije Universiteit AmsterdamAmsterdamNetherlands
- Amsterdam Public Health Research InstituteAmsterdamNetherlands
| | - Eco JC de Geus
- Department of Biological Psychology, Vrije Universiteit AmsterdamAmsterdamNetherlands
- Amsterdam Public Health Research InstituteAmsterdamNetherlands
| | - Dorret I Boomsma
- Department of Biological Psychology, Vrije Universiteit AmsterdamAmsterdamNetherlands
- Amsterdam Public Health Research InstituteAmsterdamNetherlands
- Amsterdam Reproduction and Development (AR&D) Research InstituteAmsterdamNetherlands
| | - Michael C Neale
- Virginia Institute for Psychiatric and Behavioral Genetics, Virginia Commonwealth UniversityRichmondUnited States
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2
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Beck JJ, Ahmed T, Finnicum CT, Zwinderman K, Ehli EA, Boomsma DI, Hottenga JJ. Genetic Ancestry Estimates within Dutch Family Units and Across Genotyping Arrays: Insights from Empirical Analysis Using Two Estimation Methods. Genes (Basel) 2023; 14:1497. [PMID: 37510400 PMCID: PMC10379078 DOI: 10.3390/genes14071497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/12/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
Accurate inference of genetic ancestry is crucial for population-based association studies, accounting for population heterogeneity and structure. This study analyzes genome-wide SNP data from the Netherlands Twin Register to compare genetic ancestry estimates. The focus is on the comparison of ancestry estimates between family members and individuals genotyped on multiple arrays (Affymetrix 6.0, Affymetrix Axiom, and Illumina GSA). Two conventional methods, principal component analysis and ADMIXTURE, were implemented to estimate ancestry, each serving its specific purpose, rather than for direct comparison. The results reveal that as the degree of genetic relatedness decreases, the Euclidean distances of genetic ancestry estimates between family members significantly increase (empirical p < 0.001), regardless of the estimation method and genotyping array. Ancestry estimates among individuals genotyped on multiple arrays also show statistically significant differences (empirical p < 0.001). Additionally, this study investigates the relationship between the ancestry estimates of non-identical twin offspring with ancestrally diverse parents and those with ancestrally similar parents. The results indicate a statistically significant weak correlation between the variation in ancestry estimates among offspring and differences in ancestry estimates among parents (Spearman's rho: 0.07, p = 0.005). This study highlights the utility of current methods in inferring genetic ancestry, emphasizing the importance of reference population composition in determining ancestry estimates.
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Affiliation(s)
- Jeffrey J Beck
- Avera Institute for Human Genetics, Avera McKennan Hospital and University Health Center, Sioux Falls, SD 57105, USA
| | - Talitha Ahmed
- Department of Biological Psychology, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands
| | - Casey T Finnicum
- Avera Institute for Human Genetics, Avera McKennan Hospital and University Health Center, Sioux Falls, SD 57105, USA
| | - Koos Zwinderman
- Department of Clinical Epidemiology, Biostatistics, and Bioinformatics, Academic Medical Center Amsterdam, 1105 AZ Amsterdam, The Netherlands
- Amsterdam Public Health (APH) Research Institute, 1081 BT Amsterdam, The Netherlands
| | - Erik A Ehli
- Avera Institute for Human Genetics, Avera McKennan Hospital and University Health Center, Sioux Falls, SD 57105, USA
| | - Dorret I Boomsma
- Avera Institute for Human Genetics, Avera McKennan Hospital and University Health Center, Sioux Falls, SD 57105, USA
- Department of Biological Psychology, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands
- Amsterdam Public Health (APH) Research Institute, 1081 BT Amsterdam, The Netherlands
| | - Jouke Jan Hottenga
- Department of Biological Psychology, Vrije Universiteit, 1081 HV Amsterdam, The Netherlands
- Amsterdam Public Health (APH) Research Institute, 1081 BT Amsterdam, The Netherlands
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3
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Bignardi G, Chamberlain R, Kevenaar ST, Tamimy Z, Boomsma DI. On the etiology of aesthetic chills: a behavioral genetic study. Sci Rep 2022; 12:3247. [PMID: 35228562 PMCID: PMC8885664 DOI: 10.1038/s41598-022-07161-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 02/02/2022] [Indexed: 12/22/2022] Open
Abstract
Aesthetic chills, broadly defined as a somatic marker of peak emotional-hedonic responses, are experienced by individuals across a variety of human cultures. Yet individuals vary widely in the propensity of feeling them. These individual differences have been studied in relation to demographics, personality, and neurobiological and physiological factors, but no study to date has explored the genetic etiological sources of variation. To partition genetic and environmental sources of variation in the propensity of feeling aesthetic chills, we fitted a biometrical genetic model to data from 14,127 twins (from 8995 pairs), collected by the Netherlands Twin Register. Both genetic and unique environmental factors accounted for variance in aesthetic chills, with heritability estimated at 0.36 ([0.33, 0.39] 95% CI). We found females more prone than males to report feeling aesthetic chills. However, a test for genotype x sex interaction did not show evidence that heritability differs between sexes. We thus show that the propensity of feeling aesthetic chills is not shaped by nurture alone, but it also reflects underlying genetic propensities.
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Affiliation(s)
- Giacomo Bignardi
- Department of Language & Genetics, Max Planck Institute for Psycholinguistics, Nijmegen, The Netherlands.
- Department of Psychology, Goldsmiths University of London, London, UK.
- Max Planck School of Cognition, Stephanstrasse 1a, Leipzig, Germany.
| | | | - Sofieke T Kevenaar
- Department of Biological Psychology, Netherlands Twin Register, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Zenab Tamimy
- Department of Biological Psychology, Netherlands Twin Register, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Dorret I Boomsma
- Department of Biological Psychology, Netherlands Twin Register, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
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4
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Kreeke JA, Nguyen H, Haan J, Konijnenberg E, Tomassen J, Braber A, Kate M, Collij L, Yaqub M, Berckel B, Lammertsma AA, Boomsma DI, Tan HS, Verbraak FD, Visser PJ. Retinal layer thickness in preclinical Alzheimer's disease. Acta Ophthalmol 2019; 97:798-804. [PMID: 31058465 PMCID: PMC6900176 DOI: 10.1111/aos.14121] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 03/28/2019] [Indexed: 12/26/2022]
Abstract
Purpose There is urgent need for non‐invasive diagnostic biomarkers in the preclinical phase of Alzheimer's Disease (AD). Several studies suggest that retinal thickness is reduced in AD. Here, we aim to test the diagnostic value of retinal thickness in preclinical AD, as defined by cognitively normal individuals with amyloid pathology on PET. Methods One hundred and sixty five cognitively healthy monozygotic twins aged ≥ 60 were included from the Netherlands Twin Register taking part in the European Medical Information Framework for Alzheimer's Disease PreclinAD study. Participants underwent [18F] flutemetamol PET that was visually rated for presence or absence of cortical amyloid beta (Aβ). Binding potential (BPND) was calculated as continuous measure for Aβ. Spectral Domain OCT was used to asses total and individual inner retinal layer thickness in the macular region (ETDRS circles) as well as peripapillary retinal nerve fibre layer (pRNFL) thickness. Differences between Aβ+ and Aβ− individuals and associations between BPND and retinal thickness were analyzed. Results No differences were found in retinal layer thickness in the macula or pRNFL between Aβ+ and Aβ− individuals. A positive associations between BPND and macular total retinal thickness was observed in the inner ring (p = 0.018), but this was not statistically significant after correction for multiple testing (p = 0.144). Brain/eye parameters had moderate to high intra‐twin correlations (p < 0.001) except visual rating score of Aβ, which did not correlate (r = 0.21, p = 0.068). Conclusion Variation in retinal thickness likely reflects genetic differences between individuals, but cannot discriminate between healthy and preclinical AD cases, making its use as biomarker in these early stages limited.
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Affiliation(s)
- Jacoba A. Kreeke
- Ophthalmology Department Amsterdam UMC, location VUmc Amsterdam The Netherlands
| | - Hoang‐Ton Nguyen
- Ophthalmology Department Amsterdam UMC, location VUmc Amsterdam The Netherlands
| | - Jurre Haan
- Alzheimer Center Neuroscience Amsterdam Amsterdam UMC, location VUmc Amsterdam The Netherlands
| | - Elles Konijnenberg
- Alzheimer Center Neuroscience Amsterdam Amsterdam UMC, location VUmc Amsterdam The Netherlands
| | - Jori Tomassen
- Alzheimer Center Neuroscience Amsterdam Amsterdam UMC, location VUmc Amsterdam The Netherlands
| | - Anouk Braber
- Alzheimer Center Neuroscience Amsterdam Amsterdam UMC, location VUmc Amsterdam The Netherlands
- Department of Biological Psychology VU University Amsterdam Amsterdam The Netherlands
| | - Mara Kate
- Alzheimer Center Neuroscience Amsterdam Amsterdam UMC, location VUmc Amsterdam The Netherlands
| | - Lyduine Collij
- Department of Radiology and Nuclear Medicine Amsterdam UMC, location VUmc Amsterdam The Netherlands
| | - Maqsood Yaqub
- Department of Radiology and Nuclear Medicine Amsterdam UMC, location VUmc Amsterdam The Netherlands
| | - Bart Berckel
- Department of Radiology and Nuclear Medicine Amsterdam UMC, location VUmc Amsterdam The Netherlands
| | - Adriaan A. Lammertsma
- Department of Radiology and Nuclear Medicine Amsterdam UMC, location VUmc Amsterdam The Netherlands
| | - Dorret I. Boomsma
- Department of Biological Psychology VU University Amsterdam Amsterdam The Netherlands
| | - Hendra Stevie Tan
- Ophthalmology Department Amsterdam UMC, location VUmc Amsterdam The Netherlands
| | - Frank D. Verbraak
- Ophthalmology Department Amsterdam UMC, location VUmc Amsterdam The Netherlands
| | - Pieter Jelle Visser
- Alzheimer Center Neuroscience Amsterdam Amsterdam UMC, location VUmc Amsterdam The Netherlands
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Darby CA, Fitch JR, Brennan PJ, Kelly BJ, Bir N, Magrini V, Leonard J, Cottrell CE, Gastier-Foster JM, Wilson RK, Mardis ER, White P, Langmead B, Schatz MC. Samovar: Single-Sample Mosaic Single-Nucleotide Variant Calling with Linked Reads. iScience 2019; 18:1-10. [PMID: 31271967 PMCID: PMC6609817 DOI: 10.1016/j.isci.2019.05.037] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 05/06/2019] [Accepted: 05/24/2019] [Indexed: 12/25/2022] Open
Abstract
Linked-read sequencing enables greatly improves haplotype assembly over standard paired-end analysis. The detection of mosaic single-nucleotide variants benefits from haplotype assembly when the model is informed by the mapping between constituent reads and linked reads. Samovar evaluates haplotype-discordant reads identified through linked-read sequencing, thus enabling phasing and mosaic variant detection across the entire genome. Samovar trains a random forest model to score candidate sites using a dataset that considers read quality, phasing, and linked-read characteristics. Samovar calls mosaic single-nucleotide variants (SNVs) within a single sample with accuracy comparable with what previously required trios or matched tumor/normal pairs and outperforms single-sample mosaic variant callers at minor allele frequency 5%-50% with at least 30X coverage. Samovar finds somatic variants in both tumor and normal whole-genome sequencing from 13 pediatric cancer cases that can be corroborated with high recall with whole exome sequencing. Samovar is available open-source at https://github.com/cdarby/samovar under the MIT license.
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Affiliation(s)
- Charlotte A Darby
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - James R Fitch
- The Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Patrick J Brennan
- The Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Benjamin J Kelly
- The Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Natalie Bir
- The Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Vincent Magrini
- The Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Jeffrey Leonard
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA; Department of Neurosurgery, Nationwide Children's Hospital, Columbus, OH, USA
| | - Catherine E Cottrell
- The Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Julie M Gastier-Foster
- The Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Richard K Wilson
- The Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Elaine R Mardis
- The Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Peter White
- The Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA; Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA
| | - Ben Langmead
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA.
| | - Michael C Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA; Department of Biology, Johns Hopkins University, Baltimore, MD, USA; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
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6
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Pendergrass C, Peraza J. A comparison of neuropsychological function between monozygotic twins with neurofibromatosis, type 1: A case report. Clin Neuropsychol 2019; 34:1049-1064. [PMID: 31154935 DOI: 10.1080/13854046.2019.1621381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Objective: Neurofibromatosis type 1 (NF-1) is an autosomal dominant genetic disorder that commonly presents with cognitive impairment and greater rates of learning disorders and academic difficulty compared to the general population. Investigations of neurological and physiological expression of NF-1 in monozygotic twins identified intrapair similarities and differences. Monozygotic twins with NF-1 have been found to have similar IQ scores as well as concordant diagnoses of attention-deficit/hyperactivity disorder and learning disabilities. There have been no previous reports on similarities and differences in neuropsychological profiles between monozygotic twins with NF-1. The purpose of this article is to examine the results of comprehensive neuropsychological evaluations for a pair of monozygotic twins with NF-1.Method: A pair of 19-year-old female, African-American monozygotic twins with NF-1 underwent neuropsychological evaluations in an outpatient clinic. Findings are reported following the CAse REport (CARE) guidelines.Results: The twins demonstrated similar impairment in processing speed, working memory, and attention span; however, differences also were found.Conclusions: Intrapair similarities and differences on neuropsychological assessment were found between monozygotic twins with NF-1. Primary deficits were suggestive of a frontal-subcortical pattern and could be consistent with remote neuroimaging. When differences did occur, performance was typically better for Twin A, who had also showed greater improvement on neuroimaging. Implications and directions for future research are discussed. Specifically, this case demonstrates the need for inclusion of neuropsychological assessment in studies of larger cohorts of monozygotic twins with NF-1 and correlation of neuropsychological findings with neuroimaging and postzygotic mutations.
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Affiliation(s)
- Cody Pendergrass
- Graduate School of Professional Psychology, University of Denver, Denver, CO, USA.,Outpatient Behavioral Health Services, Denver Health Medical Center, Denver, CO, USA
| | - Jennifer Peraza
- Outpatient Behavioral Health Services, Denver Health Medical Center, Denver, CO, USA.,Department of Psychiatry, University of Colorado, Aurora, CO, USA
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Ouwens KG, Jansen R, Tolhuis B, Slagboom PE, Penninx BW, Boomsma DI. A characterization of postzygotic mutations identified in monozygotic twins. Hum Mutat 2018; 39:1393-1401. [PMID: 29980163 PMCID: PMC6175188 DOI: 10.1002/humu.23586] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 06/15/2018] [Accepted: 07/03/2018] [Indexed: 01/09/2023]
Abstract
Postzygotic mutations are DNA changes acquired from the zygote stage onwards throughout the lifespan. These changes lead to differences in DNA sequence among cells of an individual, potentially contributing to the etiology of complex disorders. Here we compared whole genome DNA sequence data of two monozygotic twin pairs, 40 and 100 years old, to detect somatic mosaicism. DNA samples were sequenced twice on two Illumina platforms (13X and 40X read depth) for increased specificity. Using differences in allelic ratios resulted in sets of 1,720 and 1,739 putative postzygotic mutations in the 40-year-old twin pair and 100-year-old twin pair, respectively, for subsequent enrichment analysis. This set of putative mutations was strongly (p < 4.37e-91) enriched in both twin pairs for regulatory elements. The corresponding genes were significantly enriched for genes that are alternatively spliced, and for genes involved in GTPase activity. This research shows that somatic mosaicism can be detected in monozygotic twin pairs by using allelic ratios calculated from DNA sequence data and that the mutations which are found by this approach are not randomly distributed throughout the genome.
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Affiliation(s)
- Klaasjan G. Ouwens
- Department of Biological PsychologyVU University AmsterdamAmsterdamThe Netherlands
- Genalice Core BVNijkerkThe Netherlands
| | - Rick Jansen
- Department of PsychiatryVU University Medical CenterAmsterdamThe Netherlands
| | | | - P. Eline Slagboom
- Department of Molecular EpidemiologyLeids Universitair Medisch CentrumLeidenThe Netherlands
| | | | - Dorret I. Boomsma
- Department of Biological PsychologyVU University AmsterdamAmsterdamThe Netherlands
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8
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van Dongen J, Ehli EA, Jansen R, van Beijsterveldt CEM, Willemsen G, Hottenga JJ, Kallsen NA, Peyton SA, Breeze CE, Kluft C, Heijmans BT, Bartels M, Davies GE, Boomsma DI. Genome-wide analysis of DNA methylation in buccal cells: a study of monozygotic twins and mQTLs. Epigenetics Chromatin 2018; 11:54. [PMID: 30253792 PMCID: PMC6156977 DOI: 10.1186/s13072-018-0225-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 09/17/2018] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND DNA methylation arrays are widely used in epigenome-wide association studies and methylation quantitative trait locus (mQTL) studies. Here, we performed the first genome-wide analysis of monozygotic (MZ) twin correlations and mQTLs on data obtained with the Illumina MethylationEPIC BeadChip (EPIC array) and compared the performance of the EPIC array to the Illumina HumanMethylation450 BeadChip (HM450 array) for buccal-derived DNA. RESULTS Good-quality EPIC data were obtained for 102 buccal-derived DNA samples from 49 MZ twin pairs (mean age = 7.5 years, range = 1-10). Differences between MZ twins in the cellular content of buccal swabs were a major driver for differences in their DNA methylation profiles, highlighting the importance to adjust for cellular composition in DNA methylation studies of buccal-derived DNA. After adjusting for cellular composition, the genome-wide mean correlation (r) between MZ twins was 0.21 for the EPIC array, and cis mQTL analysis in 84 twins identified 1,296,323 significant associations (FDR 5%), encompassing 33,749 methylation sites and 616,029 genetic variants. MZ twin correlations were slightly larger (p < 2.2 × 10-16) for novel EPIC probes (N = 383,066, mean r = 0.22) compared to probes that are also present on HM450 (N = 406,822, mean r = 0.20). In line with this observation, a larger percentage of novel EPIC probes was associated with genetic variants (novel EPIC probes with significant mQTL 4.7%, HM450 probes with mQTL 3.9%, p < 2.2 × 10-16). Methylation sites with a large MZ correlation and sites associated with mQTLs were most strongly enriched in epithelial cell DNase I hypersensitive sites (DHSs), enhancers, and histone mark H3K4me3. CONCLUSIONS We conclude that the contribution of familial factors to individual differences in DNA methylation and the effect of mQTLs are larger for novel EPIC probes, especially those within regulatory elements connected to active regions specific to the investigated tissue.
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Affiliation(s)
- Jenny van Dongen
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Van Der Boechorststraat 1, 1081BT Amsterdam, The Netherlands
| | - Erik A. Ehli
- Avera Institute for Human Genetics, 3720 W. 69th Street, Sioux Falls, SD 57108 USA
| | - Rick Jansen
- Department of Psychiatry, VU University Medical Center, Oldenaller 1, 1081 HJ Amsterdam, The Netherlands
| | - Catharina E. M. van Beijsterveldt
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Van Der Boechorststraat 1, 1081BT Amsterdam, The Netherlands
| | - Gonneke Willemsen
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Van Der Boechorststraat 1, 1081BT Amsterdam, The Netherlands
| | - Jouke J. Hottenga
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Van Der Boechorststraat 1, 1081BT Amsterdam, The Netherlands
| | - Noah A. Kallsen
- Avera Institute for Human Genetics, 3720 W. 69th Street, Sioux Falls, SD 57108 USA
| | - Shanna A. Peyton
- Avera Institute for Human Genetics, 3720 W. 69th Street, Sioux Falls, SD 57108 USA
| | - Charles E. Breeze
- Altius Institute for Biomedical Sciences, 2211 Elliott Ave, Seattle, WA 98121 USA
| | - Cornelis Kluft
- Good Biomarker Sciences, Zernikedreef 8, 2333 CL Leiden, The Netherlands
| | - Bastiaan T. Heijmans
- Molecular Epidemiology Section, Leiden University Medical Center, Postal Zone S-05-P, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Meike Bartels
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Van Der Boechorststraat 1, 1081BT Amsterdam, The Netherlands
| | - Gareth E. Davies
- Avera Institute for Human Genetics, 3720 W. 69th Street, Sioux Falls, SD 57108 USA
| | - Dorret I. Boomsma
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrije Universiteit Amsterdam, Van Der Boechorststraat 1, 1081BT Amsterdam, The Netherlands
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