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Permutation-based significance analysis reduces the type 1 error rate in bisulfite sequencing data analysis of human umbilical cord blood samples

Laajala, Essi (författare)
Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland; InFLAMES Research Flagship Center, University of Turku, Turku Finland; Turku Doctoral Programme of Molecular Medicine, University of Turku, Turku, Finland; Department of Computer Science, Aalto University, Espoo, Finland
Halla-Aho, Viivi (författare)
Department of Computer Science, Aalto University, Espoo, Finland
Grönroos, Toni (författare)
Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland; InFLAMES Research Flagship Center, University of Turku, Turku Finland
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Kalim, Ubaid Ullah (författare)
Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland; InFLAMES Research Flagship Center, University of Turku, Turku Finland
Vähä-Mäkilä, Mari (författare)
Research Centre for Integrative Physiology and Pharmacology, Institute of Biomedicine, University of Turku, Turku, Finland
Nurmio, Mirja (författare)
Research Centre for Integrative Physiology and Pharmacology, Institute of Biomedicine, University of Turku, Turku, Finland
Kallionpää, Henna (författare)
Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
Lietzén, Niina (författare)
Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
Mykkänen, Juha (författare)
Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland; Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland
Rasool, Omid (författare)
Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland; InFLAMES Research Flagship Center, University of Turku, Turku Finland
Toppari, Jorma (författare)
Research Centre for Integrative Physiology and Pharmacology, Institute of Biomedicine, University of Turku, Turku, Finland; Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland; Department of Pediatrics, Turku University Hospital, Turku, Finland
Oresic, Matej, 1967- (författare)
Örebro universitet,Institutionen för medicinska vetenskaper,Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland; InFLAMES Research Flagship Center, University of Turku, Turku Finland
Knip, Mikael (författare)
Pediatric Research Center, Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland; Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Center for Child Health Research, Tampere University Hospital, Tampere, Finland
Lund, Riikka (författare)
Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
Lahesmaa, Riitta (författare)
Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland; InFLAMES Research Flagship Center, University of Turku, Turku Finland; Institute of Biomedicine, University of Turku, Turku, Finland
Lähdesmäki, Harri (författare)
Department of Computer Science, Aalto University, Espoo, Finland
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 (creator_code:org_t)
2022-03-04
2022
Engelska.
Ingår i: Epigenetics. - : Taylor & Francis. - 1559-2294 .- 1559-2308. ; 17:12, s. 1608-1627
Relaterad länk:
https://doi.org/10.1...
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https://www.tandfonl...
https://urn.kb.se/re...
https://doi.org/10.1...
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  • Tidskriftsartikel (refereegranskat)
Abstract Ämnesord
Stäng  
  • DNA methylation patterns are largely established in-utero and might mediate the impacts of in-utero conditions on later health outcomes. Associations between perinatal DNA methylation marks and pregnancy-related variables, such as maternal age and gestational weight gain, have been earlier studied with methylation microarrays, which typically cover less than 2% of human CpG sites. To detect such associations outside these regions, we chose the bisulphite sequencing approach. We collected and curated clinical data on 200 newborn infants; whose umbilical cord blood samples were analysed with the reduced representation bisulphite sequencing (RRBS) method. A generalized linear mixed-effects model was fit for each high coverage CpG site, followed by spatial and multiple testing adjustment of P values to identify differentially methylated cytosines (DMCs) and regions (DMRs) associated with clinical variables, such as maternal age, mode of delivery, and birth weight. Type 1 error rate was then evaluated with a permutation analysis. We discovered a strong inflation of spatially adjusted P values through the permutation analysis, which we then applied for empirical type 1 error control. The inflation of P values was caused by a common method for spatial adjustment and DMR detection, implemented in tools comb-p and RADMeth. Based on empirically estimated significance thresholds, very little differential methylation was associated with any of the studied clinical variables, other than sex. With this analysis workflow, the sex-associated differentially methylated regions were highly reproducible across studies, technologies, and statistical models.

Ämnesord

MEDICIN OCH HÄLSOVETENSKAP  -- Medicinska och farmaceutiska grundvetenskaper -- Medicinsk genetik (hsv//swe)
MEDICAL AND HEALTH SCIENCES  -- Basic Medicine -- Medical Genetics (hsv//eng)

Nyckelord

DNA methylation
RRBS
analysis workflow
bisulphite sequencing
differential methylation
pregnancy
sex
spatial correlation
type 1 error
umbilical cord blood

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