Exome sequencing of women with surgically confirmed endometriosis identifies new candidate genes

Abstract

ObjectiveEndometriosis is a common gynecological condition with complex etiology defined by the presence of endometrial glands and stroma outside the womb Endometriosis is a highly familial disorder; yet genome-wide association studies (GWAS) to date have explained only ∼2-3% of the heritability. CNV studies have added to our understanding, but they have not uncovered the missing heritability. Next Generation Sequencing (NGS) gives the opportunity to look for rare variants with larger. In this study, we looked for coding variants predicted to have a functional effect using exome sequencing on 567 women with surgically confirmed endometriosis.DesignWhole exome sequencing was performed on patients with surgically confirmed endometriosis. Cases were compared to population controls from ExAc database(n=31,000). Most subjects were of European ancestry (>95%).Materials and MethodsExome sequencing was performed on Ion Proton platform (LifeScience Technologies). Variants were determined using Ion Proton protocol and confirmed using the GATK (Genome Analysis Toolkit) pipeline. We applied a series of filters to reduce sequencing artifacts. Single marker association was tested (in two stages) using Fisher's Exact Test. In silico prediction of protein function was evaluated using Polyphen 2. In silico prediction of evolutionary conserved bases was calculated using Siphy.ResultsWe identified several novel endometriosis associated loci; five of the leading candidate loci are shown in Table1. These gene variants have larger odds ratios than those discovered by GWAS. Replication studies will be required to determine whether these variants are recent mutations limited to Caucasian subjects in North America or whether they are prevalent in other populations.ConclusionsTabled 1Loci Associated with EndometriosisChromPositionVarAlleleEndoFreqPopulFreqp valueORGenePolyphen 2 / Siphy Score2/128324362T0.00350.00010.00000947MYO7B0.7/11.612/88523494G0.03700.01660.0000132.3CEP2901.0/17.94/2065507A0.00260.00000.000019173NAT8L1.0/19.11/33960171G0.00620.00070.0000289ZSCAN200.8/10.82/27355201A0.00350.00010.00003629PRED0.7/18.2 Open table in a new tab ObjectiveEndometriosis is a common gynecological condition with complex etiology defined by the presence of endometrial glands and stroma outside the womb Endometriosis is a highly familial disorder; yet genome-wide association studies (GWAS) to date have explained only ∼2-3% of the heritability. CNV studies have added to our understanding, but they have not uncovered the missing heritability. Next Generation Sequencing (NGS) gives the opportunity to look for rare variants with larger. In this study, we looked for coding variants predicted to have a functional effect using exome sequencing on 567 women with surgically confirmed endometriosis. Endometriosis is a common gynecological condition with complex etiology defined by the presence of endometrial glands and stroma outside the womb Endometriosis is a highly familial disorder; yet genome-wide association studies (GWAS) to date have explained only ∼2-3% of the heritability. CNV studies have added to our understanding, but they have not uncovered the missing heritability. Next Generation Sequencing (NGS) gives the opportunity to look for rare variants with larger. In this study, we looked for coding variants predicted to have a functional effect using exome sequencing on 567 women with surgically confirmed endometriosis. DesignWhole exome sequencing was performed on patients with surgically confirmed endometriosis. Cases were compared to population controls from ExAc database(n=31,000). Most subjects were of European ancestry (>95%). Whole exome sequencing was performed on patients with surgically confirmed endometriosis. Cases were compared to population controls from ExAc database(n=31,000). Most subjects were of European ancestry (>95%). Materials and MethodsExome sequencing was performed on Ion Proton platform (LifeScience Technologies). Variants were determined using Ion Proton protocol and confirmed using the GATK (Genome Analysis Toolkit) pipeline. We applied a series of filters to reduce sequencing artifacts. Single marker association was tested (in two stages) using Fisher's Exact Test. In silico prediction of protein function was evaluated using Polyphen 2. In silico prediction of evolutionary conserved bases was calculated using Siphy. Exome sequencing was performed on Ion Proton platform (LifeScience Technologies). Variants were determined using Ion Proton protocol and confirmed using the GATK (Genome Analysis Toolkit) pipeline. We applied a series of filters to reduce sequencing artifacts. Single marker association was tested (in two stages) using Fisher's Exact Test. In silico prediction of protein function was evaluated using Polyphen 2. In silico prediction of evolutionary conserved bases was calculated using Siphy. ResultsWe identified several novel endometriosis associated loci; five of the leading candidate loci are shown in Table1. These gene variants have larger odds ratios than those discovered by GWAS. Replication studies will be required to determine whether these variants are recent mutations limited to Caucasian subjects in North America or whether they are prevalent in other populations. We identified several novel endometriosis associated loci; five of the leading candidate loci are shown in Table1. These gene variants have larger odds ratios than those discovered by GWAS. Replication studies will be required to determine whether these variants are recent mutations limited to Caucasian subjects in North America or whether they are prevalent in other populations. ConclusionsTabled 1Loci Associated with EndometriosisChromPositionVarAlleleEndoFreqPopulFreqp valueORGenePolyphen 2 / Siphy Score2/128324362T0.00350.00010.00000947MYO7B0.7/11.612/88523494G0.03700.01660.0000132.3CEP2901.0/17.94/2065507A0.00260.00000.000019173NAT8L1.0/19.11/33960171G0.00620.00070.0000289ZSCAN200.8/10.82/27355201A0.00350.00010.00003629PRED0.7/18.2 Open table in a new tab