TY - JOUR
TI - Determination of the obesity-associated gene variants within the entire
FTO gene by ultra-deep targeted sequencing in obese and lean children
AU - Almen, M. Sallman
AU - Rask-Andersen, M.
AU - Jacobsson, J. A.
AU - Ameur,
AU - A.
AU - Kalnina, I.
AU - Moschonis, G.
AU - Juhlin, S.
AU - Bringeland, N.
AU - and Hedberg, L. A.
AU - Ignatovica, V.
AU - Chrousos, G. P.
AU - Manios, Y.
AU - and Klovins, J.
AU - Marcus, C.
AU - Gyllensten, U.
AU - Fredriksson, R.
AU - and Schioth, H. B.
JO - International Journal of Obesity Supplements
PY - 2013
VL - 37
TODO - 3
SP - 424-431
PB - Nature Publishing Group
SN - 2046-2166, 2046-2174
TODO - 10.1038/ijo.2012.57
TODO - genetics; NGS; next generation sequencing
TODO - 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.
International Journal of Obesity (2013) 37, 424-431;
doi:10.1038/ijo.2012.57; published online 24 April 2012
ER -