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Determination of obesity associated gene variants related to TMEM18 through ultra-deep targeted re-sequencing in a case-control cohort for pediatric obesity.
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience. (Functional Pharmacology)
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience. (Functional Pharmacology)
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience. (Functional Pharmacology)
Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Immunology, Genetics and Pathology.ORCID iD: 0000-0001-6085-6749
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2015 (English)In: Genetical Research, ISSN 0016-6723, E-ISSN 1469-5073, Vol. 97, e16Article in journal (Refereed) Published
Abstract [en]

Genome-wide association studies (GWAS) have revealed association of a locus approximately 25b downstream of the TMEM18 gene with body mass and obesity. We utilized targeted re-sequencing of the body mass associated locus in proximity of TMEM18 in a case-control population of severely obese children and adolescents from the Stockholm area. We expanded our study to include the TMEM18 gene itself, with the aim of identifying body mass associated genetic variants. Sequencing was performed on the SOLiD platform, on long-range PCR fragments generated through targeted amplification of the regions of interest. Candidate single nucleotide polymorphisms (SNPs) were validated by TaqMan genotyping. We were able to observe 131 SNPs across the re-sequenced regions. Chi squared tests comparing the allele frequencies between cases and controls revealed 57 SNPs as candidates for association with obesity. Validation and replication genotyping revealed robust associations for SNPs within the haplotype block region located downstream from the TMEM18 gene. This study provides a high resolution map of the genetic variation pattern in the TMEM18 gene, as well as the associated haplotype block, and further strengthens the association of variants within the proximal haplotype block with obesity and body mass.

Place, publisher, year, edition, pages
2015. Vol. 97, e16
National Category
Medical Genetics
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URN: urn:nbn:se:uu:diva-275285DOI: 10.1017/S0016672315000117ISI: 000367181100015PubMedID: 26365393OAI: oai:DiVA.org:uu-275285DiVA: diva2:899682
Funder
Swedish Research CouncilThe Swedish Brain FoundationNovo NordiskSwedish Research Council, 80576801Swedish Research Council, 70374401
Available from: 2016-02-02 Created: 2016-02-02 Last updated: 2017-11-30Bibliographically approved

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Rask-Andersen, MathiasSällman Almén, MarkusAmeur, AdamGyllensten, UlfFredriksson, RobertSchiöth, Helgi B

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Rask-Andersen, MathiasSällman Almén, MarkusAmeur, AdamGyllensten, UlfFredriksson, RobertSchiöth, Helgi B
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Department of NeuroscienceDepartment of Immunology, Genetics and PathologyMedicinsk genetik och genomik
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