title: Determination of the obesity-associated gene variants within the entire FTO gene by ultra-deep targeted sequencing in obese and lean children.
abstract: BACKGROUND
  The Fat mass and obesity-associated gene (FTO) was the first gene reliably associated with body mass index in genome-wide association studies on a population level. At present, the genetic variations within the FTO gene are still the common variants that have the largest influence on body mass index.
  
  
  METHODS
  In the current study, we amplified the entire FTO gene, in total 412 Kbp, in over 200 long-range PCR fragments from each individual, from 524 severely obese and 527 lean Swedish children, and sequenced the products as two DNA pools using massive parallel sequencing (SOLiD).
  
  
  RESULTS
  The sequencing achieved very high coverage (median 18 000 reads) and we detected and estimated allele frequencies for 705 single nucleotide polymorphisms (SNPs) (19 novel) and 40 indels (24 novel) using a sophisticated statistical approach to remove false-positive SNPs. We identified 19 obesity-associated SNPs within intron one of the FTO gene, and validated our findings with genotyping. Ten of the validated obesity-associated SNPs have a stronger obesity association (P<0.007) than the commonly studied rs9939609 SNP (P<0.012).
  
  
  CONCLUSIONS
  This study provides a comprehensive obesity-associated variation map of FTO, identifies novel lead SNPs and evaluates putative causative variants. We conclude that intron one is the only region within the FTO gene associated with obesity, and finally, we establish next generation sequencing of pooled DNA as a powerful method to investigate genetic association with complex diseases and traits.
authors.affiliation: Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Uppsala, Sweden.
authors.forename: M
authors.initials: M
authors.lastname: Sällman Almén
authors.forename: M
authors.initials: M
authors.lastname: Rask-Andersen
authors.forename: J A
authors.initials: JA
authors.lastname: Jacobsson
authors.forename: A
authors.initials: A
authors.lastname: Ameur
authors.forename: I
authors.initials: I
authors.lastname: Kalnina
authors.forename: G
authors.initials: G
authors.lastname: Moschonis
authors.forename: S
authors.initials: S
authors.lastname: Juhlin
authors.forename: N
authors.initials: N
authors.lastname: Bringeland
authors.forename: L A
authors.initials: LA
authors.lastname: Hedberg
authors.forename: V
authors.initials: V
authors.lastname: Ignatovica
authors.forename: G P
authors.initials: GP
authors.lastname: Chrousos
authors.forename: Y
authors.initials: Y
authors.lastname: Manios
authors.forename: J
authors.initials: J
authors.lastname: Klovins
authors.forename: C
authors.initials: C
authors.lastname: Marcus
authors.forename: U
authors.initials: U
authors.lastname: Gyllensten
authors.forename: R
authors.initials: R
authors.lastname: Fredriksson
authors.forename: H B
authors.initials: HB
authors.lastname: Schiöth
mesh_terms: D000293:Adolescent; D000071516:Alpha-Ketoglutarate-Dependent Dioxygenase FTO; D001823:Body Composition / Q000235:genetics; D015992:Body Mass Index; D002648:Child; D005260:Female; D005787:Gene Frequency; D020022:Genetic Predisposition to Disease; D014644:Genetic Variation; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D008297:Male; D009765:Obesity / Q000453:epidemiology / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D011506:Proteins / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*; D013851:Thinness / Q000453:epidemiology / Q000235:genetics*; D044465:White People / Q000235:genetics*
chemical_list: D011506:Proteins; D000071516:Alpha-Ketoglutarate-Dependent Dioxygenase FTO; C526492:FTO protein, human