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. 2019 Sep;43(6):704-716.
doi: 10.1002/gepi.22214. Epub 2019 Jun 6.

A systematic genetic analysis and visualization of phenotypic heterogeneity among orofacial cleft GWAS signals

Jenna C Carlson  1   2 , Deepti Anand  3 , Azeez Butali  4 , Carmen J Buxo  5 , Kaare Christensen  6 , Frederic Deleyiannis  7 , Jacqueline T Hecht  8 , Lina M Moreno  9 , Ieda M Orioli  10   11 , Carmencita Padilla  12   13 , John R Shaffer  2   14 , Alexandre R Vieira  14 , George L Wehby  15 , Seth M Weinberg  2   14   16 , Jeffrey C Murray  17 , Terri H Beaty  18 , Irfan Saadi  19 , Salil A Lachke  3   20 , Mary L Marazita  2   14   16 , Eleanor Feingold  1   2   16 , Elizabeth J Leslie  21
Affiliations

A systematic genetic analysis and visualization of phenotypic heterogeneity among orofacial cleft GWAS signals

Jenna C Carlson et al. Genet Epidemiol. 2019 Sep.

Abstract

Phenotypic heterogeneity is a hallmark of complex traits, and genetic studies of such traits may focus on them as a single diagnostic entity or by analyzing specific components. For example, in orofacial clefting (OFC), three subtypes-cleft lip (CL), cleft lip and palate (CLP), and cleft palate (CP) have been studied separately and in combination. To further dissect the genetic architecture of OFCs and how a given associated locus may be contributing to distinct subtypes of a trait we developed a framework for quantifying and interpreting evidence of subtype-specific or shared genetic effects in complex traits. We applied this technique to create a "cleft map" of the association of 30 genetic loci with three OFC subtypes. In addition to new associations, we found loci with subtype-specific effects (e.g., GRHL3 [CP], WNT5A [CLP]), as well as loci associated with two or all three subtypes. We cross-referenced these results with mouse craniofacial gene expression datasets, which identified additional promising candidate genes. However, we found no strong correlation between OFC subtypes and expression patterns. In aggregate, the cleft map revealed that neither subtype-specific nor shared genetic effects operate in isolation in OFC architecture. Our approach can be easily applied to any complex trait with distinct phenotypic subgroups.

Keywords: birth defects; genome-wide association studies; orofacial clefts; subtypes.

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Figures

Figure 1
Figure 1. Design and analytical strategy to study phenotypic heterogeneity of orofacial clefts.
Analyses consisted of four major steps: (1) GWAS for OFC subtypes, (2) selection of SNPs for analysis (p<10−5), (3) calculation of heterogeneity Q-statistic p-values and differences in log odds ratios, and (4) plotting each point as a sum of two vectors, each given by the –log10 p-value of the heterogeneity test times the sign of the direction of effect.
Figure 2
Figure 2. Subtype effects for SNPs at representative loci.
For each SNP per locus, the effects for CL and CLP, and CLP and CP were compared with heterogeneity Q-statistics. The direction of association was determined by the difference in absolute values of the log odds ratios (i.e. |log(ORCLP)| - |log(ORCL)|, |log(ORCLP)| - |log(ORCP)|). The coordinates of each SNP were determined by the sum of two vectors, each given by the –log10 p-value of the Q statistic times the sign of the direction. The x-axis of the cleft map represents the CL vs. CLP comparison and the y-axis represents that CLP vs. CP comparison. Concentric circles around the origin based on p-values of the Q-statistics are given for reference (0.01, 0.0001, increasing by 10−2). The centroid of each cluster of SNPs is represented by an “X”.
Figure 3
Figure 3. The Cleft Map.
Each of the 29 loci are represented by a single point as the centroid of all SNPs at the locus. The size of the point is scaled to the –log10 p-value for the most significant SNP in the meta-analyses of CL, CLP, and CP. Concentric circles about the origin based on p-values of the Q-statistics are given for reference (0.01, 0.0001, increasing by 10−2). Point size is scaled to represent the best p-value observed in the meta-analyses. Points are colored for clarity of gene name labels.
See this image and copyright information in PMC

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