Genome-wide SNP and CNV analysis identifies common and low-frequency variants associated with severe early-onset obesity.
- Authors
- Wheeler, Eleanor; Huang, Ni; Bochukova, Elena G; Keogh, Julia M; Lindsay, Sarah; Garg, Sumedha; Henning, Elana; Blackburn, Hannah; Loos, Ruth J F; Wareham, Nick J; O'Rahilly, Stephen; Hurles, Matthew E; Barroso, InΓͺs; Farooqi, I Sadaf
- Year
- 2013
- Journal
- Nature genetics
- PMID
- 23563609
- DOI
- 10.1038/ng.2607
- PMCID
- PMC4106235
Common and rare variants associated with body mass index (BMI) and obesity account for <5% of the variance in BMI. We performed SNP and copy number variation (CNV) association analyses in 1,509 children with obesity at the extreme tail (>3 s.d. from the mean) of the BMI distribution and 5,380 controls. Evaluation of 29 SNPs (P < 1 Γ 10(-5)) in an additional 971 severely obese children and 1,990 controls identified 4 new loci associated with severe obesity (LEPR, PRKCH, PACS1 and RMST). A previously reported 43-kb deletion at the NEGR1 locus was significantly associated with severe obesity (P = 6.6 Γ 10(-7)). However, this signal was entirely driven by a flanking 8-kb deletion; absence of this deletion increased risk for obesity (P = 6.1 Γ 10(-11)). We found a significant burden of rare, single CNVs in severely obese cases (P < 0.0001). Integrative gene network pathway analysis of rare deletions indicated enrichment of genes affecting G protein-coupled receptors (GPCRs) involved in the neuronal regulation of energy homeostasis.
Genome wide SNP association study in severe early onset obesity. Manhattan plot showing the significance (βlog10(p)) of all SNPs in the discovery analysis. SNPs taken for replication (circled), established loci (dark grey) and novel loci (green) are shown. Horizontal dashed line indicates p=1Γ10β6.
A quantile-quantile plot of βlog10(p) of 481 common CNVs. Concentration band represents 95% confidence intervals. The data generally conform to the βlog10 transformed uniform distribution expected under the null hypothesis of no association, with the exception of strong associations with the two deletions upstream of NEGR1.
NEGR1 locus on chromosome 1p31.1. a. Schematic of the locus with the positions of the two deletions (8-kb and 43-kb) and neighbouring genes. b. Sequence conservation of the small 8-kb deletion sequence. Nucleotide Percent Identity Plot (PIP) for the region is shown. Orthologous sequences from multiple species were aligned to the human sequence using MultiPIP maker, and sequence identity >50% (light grey) and >75% (dark grey) is highlighted, with the details shown below. The predicted NKX6.1 binding site is located in the most conserved region (arrow). c. Transcription factor NKX6.1 binding was confirmed using EMSA assay, electromobility shift (arrow) was specific to the sequence contained in the 8-kb deletion. n/s (non-specific band).
| Name | Type |
|---|---|
| 1958BC local | cohort |
| 1958 British Birth Cohort | cohort |
| 8βkb deletion local | variant |
| affected status | phenotype |
| Affy6 SNPs local | variant |
| Affymetrix Human SNP Array 6.0 local | drug |
| Applied Biosystems | drug |
| BMI | phenotype |
| case cohort | cohort |
| cases | cohort |
| CEU | cohort |
| CHB+JPT | drug |
| CNV | variant |
| common CNVEs local | variant |
| control | cohort |
| controls | cohort |
| developmental delay | phenotype |
| early-onset obesity | phenotype |
| EPIC-Norfolk | cohort |
| EPIC-Obesity Study local | cohort |
| ethnic outliers local | phenotype |
| European population | cohort |
| Europeans | cohort |
| genetic distance local | phenotype |
| Genetics of Obesity Study local | cohort |
| GIH local | cohort |
| GOOS local | cohort |
| HBD burden local | phenotype |
| iPLEX Gold Assay local | drug |
| Light Shift Chemiluminescent EMSA Kit local | drug |
| MUT oligonucleotide local | drug |
| NEGR1 | gene |
| NEGR1 deletions local | variant |
| NKX6.1 local | gene |
| rare variant | cohort |
| rs17025867 local | variant |
| rs7255638 local | variant |
| SCOOP local | cohort |
| SCOOP cohort local | cohort |
| Sequenom | drug |
| SNP | cohort |
| TaqMan assay | drug |
| UK Blood Service Collection local | cohort |
| UKBS local | cohort |
| Wellcome Trust Case-Control Consortium local | cohort |
| Wellcome Trust Case Control Consortium 2 | cohort |
| WTCCC2 | cohort |
| WT oligonucleotide local | drug |
| WTSIby local | drug |
| YRI | cohort |
| Ξ±βNKX6.1 antibody local | drug |
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