The FIND results from genomewide linkage and sparse association scans in four American ethnic groups with DN confirm previous linkage findings and suggest new genetic loci contributing to DN and related phenotypes. Suggestive evidence for linkage was observed on chromosomes 6p and 7p for DN, and on 3p, 7q, 16q and 22q for urine ACR in one or more ethnic groups. No region displayed consistent evidence for linkage across all 4 ethnic groups, although the modest urine ACR linkage and association peak on chromosome 21 in AA received weak support from AI. Significant evidence for linkage was detected in overlapping regions of chromosome 7q for both DN and urine ACR in AA and EA families, respectively.
Expanding the FIND family study samples from the partial cohort previously examined [13
], altered the pattern of linkage across the autosomal genome. Newly detected linkage peaks with equivalent LOD scores ≥2.0 were observed on chromosomes 1q, 7p, 10p, 11p and 15q for DN, and on 2q, 3p, 16q and 22q for urine ACR. The full FIND sample provided greater power to detect genetic influences, as did modification of SIBPAL to include half-sib pairs in the Haseman-Elston regression. Moreover, use of a relatively dense set of 6,000 SNPs as a linkage panel, as opposed to a set of 400 microsatellite markers, ensures that a high level of information about linkage is available uniformly across each chromosome. The linkage peaks previously detected in a subset of these cases on chromosome 14q23 for DN and on 15q26 for urine ACR, now less prominent, were likely false positives, although genetic heterogeneity could also influence results. Similarly, there was no substantial overlap between the linkage findings reported here and in a linkage analysis of estimated glomerular filtration rate on the partial cohort [21
In general, these results did not closely overlap genomic regions implicated in previous non-FIND linkage studies for DN [5
] (online suppl. table S1
). Our linkage signals on chromosome 7p for DN in AI and 22q12.3 for urine ACR in MA, coincided with those for glomerular filtration rate and ACR, respectively, in type 2 diabetes from 63 mostly Caucasian extended pedigrees [22
]. The strongest evidence for linkage in this study occurred on chromosome 6p, with an empirical p value for linkage of 8.0 × 10−5
(LOD = 3.09) in EA for the binary DN trait.
The current report is the first of a linkage signal of such magnitude near the p terminus of chromosome 6 in a genomewide linkage study of DN or nondiabetic kidney disease. However, a genomewide scan for insulin resistance reported modest evidence for linkage in this location for acute insulin response to glucose in Hispanic families (LOD = 1.72 at 15 cM) [24
]. Suggestive evidence for linkage to urine ACR was found on chromosome 22 in MA (p = 5.9 × 10−4
, LOD = 2.29), with peak linkage near the nonmuscle myosin heavy chain 9/apolipoprotein L1 (MYH9/APOL1)
gene region implicated in diabetic and nondiabetic ESRD and focal segmental glomerulosclerosis in AA [9
]. Additional supporting evidence was observed in EA using the binary DN trait. However, no association signal was detected, which is reasonable since none of the reported MYH9/APOL1
kidney disease risk variants were included in our genotyping panels.
Several results from the FIND analyses occur in regions previously associated with DN phenotypes. Two SNPs near the candidate gene carnosinase 1 (CNDP1) showed evidence for association in at least one FIND cohort. The first SNP, rs999647, is 49 kb distal to CNDP1, with association specific to DN in AI families (p = 0.0057) and weak association with urine ACR in EA (p = 0.031; Fisher combined p = 0.028 over all cohorts). A neighboring SNP, rs872994, 919 kb distal to CNDP1 (at position 73,171,838, human genome build 18), displayed weak evidence for association in three ethnic groups, AI (p = 0.053), EA (p = 0.017) and MA (p = 0.033), with a combined Fisher p of 0.0043.
The chromosome 3p DN association in the AI population occurred at rs892605, approximately 400 kb proximal to the ghrelin (GHRL)
gene, for which association with kidney function in DM, but not DM itself, has been reported [27
Genomewide linkage scans for DN and related traits differ in many ways, including pedigree structures recruited, ascertainment criteria, definitions of DN and measurement of kidney function, diabetes type and duration. In contrast to other publications, FIND is a multiethnic sample of DN-affected and -unaffected subjects with extremes of phenotypic severity [12
]. This genomewide linkage and sparse association scan in the full FIND study sample provides evidence for both novel (e.g. on chromosomes 3p and 6p) and previously detected (chromosomes 7p and 22) genetic loci predisposing to renal impairment and DN. Genomewide association studies have the most power to detect genetic variants with relatively modest effect, but require that causal alleles be well captured (tagged) by the marker panel, which is true in practice mostly for common variants. The linkage study presented here only has power to detect variants with relatively large effect, but can do so regardless of the population allele frequency and number of tightly linked variants involved. These results should provide guidance for further exploration of the genetic basis for diabetic kidney disease using novel technologies.