Mapping a new spontaneous preterm birth susceptibility gene, IGF1R, using linkage, haplotype sharing, and association analysis

Abstract

Preterm birth is the major cause of neonatal death and serious morbidity. Most preterm births are due to spontaneous onset of labor without a known cause or effective prevention. Both maternal and fetal genomes influence the predisposition to spontaneous preterm birth (SPTB), but the susceptibility loci remain to be defined. We utilized a combination of unique population structures, family-based linkage analysis, and subsequent case-control association to identify a susceptibility haplotype for SPTB. Clinically well-characterized SPTB families from northern Finland, a subisolate founded by a relatively small founder population that has subsequently experienced a number of bottlenecks, were selected for the initial discovery sample. Genome-wide linkage analysis using a high-density single-nucleotide polymorphism (SNP) array in seven large northern Finnish non-consanginous families identified a locus on 15q26.3 (HLOD 4.68). This region contains the IGF1R gene, which encodes the type 1 insulin-like growth factor receptor IGF-1R. Haplotype segregation analysis revealed that a 55 kb 12-SNP core segment within the IGF1R gene was shared identical-by-state (IBS) in five families. A follow-up case-control study in an independent sample representing the more general Finnish population showed an association of a 6-SNP IGF1R haplotype with SPTB in the fetuses, providing further evidence for IGF1R as a SPTB predisposition gene (frequency in cases versus controls 0.11 versus 0.05, P = 0.001, odds ratio 2.3). This study demonstrates the identification of a predisposing, low-frequency haplotype in a multifactorial trait using a well-characterized population and a combination of family and case-control designs. Our findings support the identification of the novel susceptibility gene IGF1R for predisposition by the fetal genome to being born preterm.

Figure 1. Study design.

Figure 2. Heterogeneity LOD (HLOD) scores in parametric linkage analysis of spontaneous preterm birth.

For the affected fetus phenotype (left panel), initial linkage signals (HLOD>2) were detected on chromosomes 2p24.3 (SNP rs6531074, HLOD = 2.05), 4q12 (SNP rs2037046, HLOD = 2.16), 10p12.1 (SNP SNP_A-419261, HLOD = 2.54), 12q21.3 (SNP rs7138288, HLOD = 2.08), 13q13.3 (SNP rs4245377, HLOD = 2.39), and 15q26.3 (SNP rs2715416, HLOD = 2.59) as indicated by arrows. For the mothers (right panel), the three maximum HLOD scores were detected on chromosomes 8q24.3 (SNP rs11167102, HLOD = 1.53) and 15q26.3 (SNPs rs11247268 and rs329292, HLODs of 1.48 and 1.51, respectively).

Figure 3. IGF1R haplotype segregation in family 70.

Each successive column represents a single chromosome, with the paternal (p) and maternal (m) origin indicated above the haplotype. The individuals genotyped are indicated by the same numbers as in Figure S1. The bracketed () haplotypes were imputed for untyped individuals. Green-shaded areas indicate within-family haplotype sharing. Haplotype core segment I (55 kb), shared IBS between families 24, 70, 126, 253, and 150, is indicated by a solid box. The location of maximal haplotype sharing (rs11630259–rs1357112 haplotype AT) in all disease-cosegregating chromosomes in all families is shown by white letters on a black background. See text for details and Figure S2 for IGF1R haplotypes in all of the linked families.

Figure 4. Pairwise D prime and r² LD plots of IGF1R SNPs in the association analysis.

The largest 55 kb region of LD spans the two associating SNPs rs7165181 (marker 8) and rs4966038 (marker 9), extending to the SNPs rs2684811 (between markers 11 and 12; the highest linkage signal) and rs2715416 (marker 12; the original linkage signal).

Figure 5. Illustration of SNPs yielding the most significant linkage and association signals on chromosome 15q26.3.

The most significant linkage (black symbols) and association (gray symbols) signals in the infants (triangles) and mothers (rounded dots) are shown. IGF1R contains 21 exons at 97.0–97.3 Mb with the IGF-1R alpha and beta subunits encoded by exons 1–11 and 11–21, respectively. Black asterisk represents the initial linkage peak obtained from the infants using the 6,377 LD-pruned SNPs (rs2715416 at position 97,271,554). The region of linkage and association localizes at a 55-kb LD interval extending from intron 2 to intron 6 (gray line). A statistically significant association was detected for haplotype TGCAAG (unadjusted P = 0.001, log10(P) = 2.89, and permutation-corrected P = 0.021).