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Noncoding Variations in the Gene Encoding Ceramide Synthase 6 are Associated with Type 2 Diabetes in a Large Indigenous Australian Pedigree

Published online by Cambridge University Press:  23 April 2019

David A. Good
Affiliation:
Diabetes Research Laboratories, School of Clinical Medicine Prince Charles Hospital Northside Clinical Unit, Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
David L. Duffy
Affiliation:
QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
Manuela Good
Affiliation:
Diabetes Research Laboratories, School of Clinical Medicine Prince Charles Hospital Northside Clinical Unit, Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
Cheng Xia Guo
Affiliation:
Diabetes Research Laboratories, School of Clinical Medicine Prince Charles Hospital Northside Clinical Unit, Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
Frances Busfield
Affiliation:
Diabetes Research Laboratories, School of Clinical Medicine Prince Charles Hospital Northside Clinical Unit, Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
Anthony Shaw
Affiliation:
Diabetes Research Laboratories, School of Clinical Medicine Prince Charles Hospital Northside Clinical Unit, Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
Joanne T. E. Shaw*
Affiliation:
Diabetes Research Laboratories, School of Clinical Medicine Prince Charles Hospital Northside Clinical Unit, Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
*
*Author for correspondence: Joanne T. E. Shaw, Email: jteshaw@gmail.com

Abstract

Type 2 diabetes (T2D) is a chronic disease that disproportionately affects Indigenous Australians. We have previously reported the localization of a novel T2D locus by linkage analysis to chromosome 2q24 in a large admixed Indigenous Australian pedigree (Busfield et al. (2002). American Journal of Human Genetics, 70, 349–357). Here we describe fine mapping of this region in this pedigree, with the identification of SNPs showing strong association with T2D: rs3845724 (diabetes p = 7 × 10−4), rs4668106 (diabetes p = 9 × 10−4) and rs529002 (plasma glucose p = 3 × 10−4). These associations were successfully replicated in an independent collection of Indigenous Australian T2D cases and controls. These SNPs all lie within the gene encoding ceramide synthase 6 (CERS6) and thus may regulate ceramide synthesis.

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Articles
Copyright
© The Author(s) 2019 
Figure 0

Fig. 1. Plot of the –log10p value for association of SNPs with T2D in pedigree members. Upper panel shows results for genotyped SNPs and the original multipoint linkage results converted into p values (recall linkage analysis uses a less severe multiple testing threshold). The result for rs4668106 combining the pedigree and replicate samples is labeled. The lower panel shows results for imputed SNPs, along with Fisher-combined p values from two large published GWAS meta-analyses. The position of the published T2D and FPG SNPs rs7607980 in COLBB1 and rs560887 in G6PC2 are indicated at the bottom (meta-analysis p = 10−18 and 10−128, respectively).

Figure 1

Table 1. SNPs and their association with type 2 diabetes in members of a large indigenous Australian pedigree

Figure 2

Table 2. Genotype frequencies for rs4668106 in original pedigree and indigenous replication sample and combined association analysis

Figure 3

Table 3. Frequency of top diabetes-associated SNPs

Figure 4

Table 4. Proportions of rs4668089-rs4668102-rs4668106-rs3845724 haplotypes in diabetic patients and unaffected individuals from this study compared with U.S. population controls

Figure 5

Fig. 2. Relationship between rs4668089 genotype and blood glucose, body mass index and waist-to-hip ratio adjusting for age. The red curve is locally weighted regression curve for the T/T genotype, and the blue curve is for the G/T genotype.

Figure 6

Fig. 3. SNP genotype association with waist circumference for members of the Indigenous Australian pedigree.

Figure 7

Fig. 4. The plot from Islet Regulome Browser (http://www.isletregulome.org) showing Virtual 4C estimates for interaction between ‘bait’ region on G6PC2 and distal CERS6/CERS6-AS1. The chromatin interaction map is constructed from promoter capture HiC data (four human islet samples) centered on the queried bait region, hence, virtual 4C. A CHiCAGO score >5 is a high-confidence interaction (Miguel-Escalada et al., 2018).