Rare mutations and potentially damaging missense variants in genes encoding fibrillar collagens and proteins involved in their production are candidates for risk for preterm premature rupture of membranes

Abstract

Preterm premature rupture of membranes (PPROM) is the leading identifiable cause of preterm birth with ~ 40% of preterm births being associated with PPROM and occurs in 1% - 2% of all pregnancies. We hypothesized that multiple rare variants in fetal genes involved in extracellular matrix synthesis would associate with PPROM, based on the assumption that impaired elaboration of matrix proteins would reduce fetal membrane tensile strength, predisposing to unscheduled rupture. We performed whole exome sequencing (WES) on neonatal DNA derived from pregnancies complicated by PPROM (49 cases) and healthy term deliveries (20 controls) to identify candidate mutations/variants. Genotyping for selected variants from the WES study was carried out on an additional 188 PPROM cases and 175 controls. All mothers were self-reported African Americans, and a panel of ancestry informative markers was used to control for genetic ancestry in all genetic association tests. In support of the primary hypothesis, a statistically significant genetic burden (all samples combined, SKAT-O p-value = 0.0225) of damaging/potentially damaging rare variants was identified in the genes of interest—fibrillar collagen genes, which contribute to fetal membrane strength and integrity. These findings suggest that the fetal contribution to PPROM is polygenic, and driven by an increased burden of rare variants that may also contribute to the disparities in rates of preterm birth among African Americans.

Mutations in fetal genes involved in innate immunity and host defense against microbes increase risk of preterm premature rupture of membranes (PPROM)

“…A DNA biobank at Virginia Commonwealth University and Hutzel Hospital of PPROM cases and term controls collected using the same criteria as those used for the WES cohort was employed for subsequent genotyping of selected mutations identified by WES (Modi et al. ).…”

“…The bioinformatics analysis for variant discovery and annotation was performed as described earlier (Modi et al. ). In brief, sequences were mapped to the human reference genome (build hg19) using BWA, followed by marking PCR duplicates using Picard tools and base quality recalibration using GATK (Modi et al.…”

“…Genotyping was performed on the Agena (previously Sequenom) MassArray iPLEX platform following manufacturer's instructions at the University of Minnesota Genomics Center (Modi et al. ). The primer sets used for iPlex genotyping are presented in Table .…”

“…Recently, we took a different approach based on the hypothesis that rare mutations or damaging variants in multiple genes (which might escape detection by GWAS or standard association studies, especially with small sample sizes) make significant contributions to PPROM (Modi et al. ). The approach was based on mutation/damaging variant detection using whole exome sequencing (WES), which we applied in this study to explore fetal gene mutations in the innate immune system and PPROM.…”

“…Moreover, attempts to identify loci contributing to prematurity through genome-wide association studies (GWAS) have not delivered strong candidates (Parets et al 2015), prompting investigators to pursue alternative approaches to identify genes contributing to preterm birth (Bacelis et al 2016;Brubaker et al 2016). Recently, we took a different approach based on the hypothesis that rare mutations or damaging variants in multiple genes (which might escape detection by GWAS or standard association studies, especially with small sample sizes) make significant contributions to PPROM (Modi et al 2017). The approach was based on mutation/damaging variant detection using whole exome sequencing (WES), which we applied in this study to explore fetal gene mutations in the innate immune system and PPROM.…”