Evaluation of Five Candidate Genes from GWAS for Association with Oligozoospermia in a Han Chinese Population

<div><p>Background</p><p>Oligozoospermia is one of the severe forms of idiopathic male infertility. However, its pathology is largely unknown, and few genetic factors have been defined. Our previous genome-wide association study (GWAS) has identified four risk loci for non-obstructive azoospermia (NOA).</p><p>Objective</p><p>To investigate the potentially functional genetic variants (including not only common variants, but also less-common and rare variants) of these loci on spermatogenic impairment, especially oligozoospermia.</p><p>Design, Setting, and Participants</p><p>A total of 784 individuals with oligozoospermia and 592 healthy controls were recruited to this study from March 2004 and January 2011.</p><p>Measurements</p><p>We conducted a two-stage study to explore the association between oligozoospermia and new makers near NOA risk loci. In the first stage, we used next generation sequencing (NGS) in 96 oligozoospermia cases and 96 healthy controls to screen oligozoospermia-susceptible genetic variants. Next, we validated these variants in a large cohort containing 688 cases and 496 controls by SNPscan for high-throughput Single Nucleotide Polymorphism (SNP) genotyping.</p><p>Results and Limitations</p><p>Totally, we observed seven oligozoospermia associated variants (rs3791185 and rs2232015 in <i>PRMT6</i>, rs146039840 and rs11046992 in <i>Sox5</i>, rs1129332 in <i>PEX10</i>, rs3197744 in <i>SIRPA</i>, rs1048055 in <i>SIRPG</i>) in the first stage. In the validation stage, rs3197744 in <i>SIRPA</i> and rs11046992 in <i>Sox5</i> were associated with increased risk of oligozoospermia with an odds ratio (OR) of 4.62 (<i>P</i>  =  0.005, 95%CI 1.58-13.4) and 1.82 (<i>P</i>  =  0.005, 95%CI 1.01-1.64), respectively. Further investigation in larger populations and functional characterizations are needed to validate our findings.</p><p>Conclusions</p><p>Our study provides evidence of independent oligozoospermia risk alleles driven by variants in the potentially functional regions of genes discovered by GWAS. Our findings suggest that integrating sequence data with large-scale genotyping will serve as an effective strategy for discovering risk alleles in the future.</p></div

The distributions of selected variables among cases and control subjects.

a<p>Independent-samples T-test for comparing the mean of the age, BMI and Pack-years of smoking between the cases and controls.</p>b<p>Two-sided chi-squared test for either selected variable distributions between cases and controls.</p>*<p>p<0.05 for two-sided chi-squared test for either selected characteristics distributions or allele frequencies between control and case group.</p

The meiotic program initiation pathway genes and polymorphisms evaluated in this study.

<p>Abbreviations: nsSNP, non-synonymous; UTR, untranslated region; MAF, minor allele frequency; HWE, Hardy-Weinberg equilibrium.</p>a<p>Minimum allele frequency in the general Han Chinese population, as reported in dbSNP database.</p

Prediction of the binding of microRNA to the 3’ UTR of <i>SIRPA</i> with the substitution of rs3197744 G>T.

<p>(A) the original binding of -miR-4277 to the 3’ UTR of <i>SIRPA</i> (B) the substitution of rs3197744 G>T may increase the binding sites of miR-148b-5p, miR-148a-5p, miR-506-5p etc.</p

Association of seven identified genetic variations in solexa sequence with oligozoospermia in a Chinese population.

<p>MAF, minor allele frequency;</p>a<p>ORs and <i>P</i> were obtained from multivariate logistic regression analysis;</p>b<p><i>P</i>-value was survived after Bonferroni correction.</p

Associations of selected meiotic program initiation pathway gene polymorphisms and the risk of idiopathic male infertility.

<p>SNPs, single-nucleotide polymorphisms; OR, odds ratios; CI, confidence interval.</p>a<p>Subjects consisted of proven fertility men with semen volume ≥2 ml, sperm counts ≥20×10⁶/ml and sperm motility ≥50% motile sperm.</p>b<p>Subjects consisted of idiopathic infertile men with sperm counts <20×10⁶/ml.</p>c<p>Subjects consisted of idiopathic infertile men with sperm counts = 0/ml.</p>d<p>Subjects consisted of idiopathic infertile men with sperm counts from 0.1 to 20×10⁶/ml.</p>e<p>Subjects consisted of idiopathic infertile men with sperm counts ≥20×10⁶/ml.</p>f<p>ORs were obtained from multivariate logistic regression analysis.</p>g<p>Two-sided χ2 test for genotype distributions between cases and controls.</p

Supplemental Material, DS1_TPX_10.1177_0192623318789398 - Exome Sequencing of Fresh-frozen or Formalin-fixed Paraffin-embedded B6C3F1/N Mouse Hepatocellular Carcinomas Arising Either Spontaneously or due to Chronic Chemical Exposure

<p>Supplemental Material, DS1_TPX_10.1177_0192623318789398 for Exome Sequencing of Fresh-frozen or Formalin-fixed Paraffin-embedded B6C3F1/N Mouse Hepatocellular Carcinomas Arising Either Spontaneously or due to Chronic Chemical Exposure by Scott S. Auerbach, Miaofei Xu, B. Alex Merrick, Mark J. Hoenerhoff, Dhiral Phadke, Debra J. Taxman, Ruchir Shah, Hue-Hua L. Hong, Thai-Vu Ton, Ramesh C. Kovi, Robert C. Sills, and Arun R. Pandiri in Toxicologic Pathology</p

Supplemental Material, TS4_TPX_10.1177_0192623318789398 - Exome Sequencing of Fresh-frozen or Formalin-fixed Paraffin-embedded B6C3F1/N Mouse Hepatocellular Carcinomas Arising Either Spontaneously or due to Chronic Chemical Exposure

<p>Supplemental Material, TS4_TPX_10.1177_0192623318789398 for Exome Sequencing of Fresh-frozen or Formalin-fixed Paraffin-embedded B6C3F1/N Mouse Hepatocellular Carcinomas Arising Either Spontaneously or due to Chronic Chemical Exposure by Scott S. Auerbach, Miaofei Xu, B. Alex Merrick, Mark J. Hoenerhoff, Dhiral Phadke, Debra J. Taxman, Ruchir Shah, Hue-Hua L. Hong, Thai-Vu Ton, Ramesh C. Kovi, Robert C. Sills, and Arun R. Pandiri in Toxicologic Pathology</p

Supplemental Material, TS5_TPX_10.1177_0192623318789398 - Exome Sequencing of Fresh-frozen or Formalin-fixed Paraffin-embedded B6C3F1/N Mouse Hepatocellular Carcinomas Arising Either Spontaneously or due to Chronic Chemical Exposure

<p>Supplemental Material, TS5_TPX_10.1177_0192623318789398 for Exome Sequencing of Fresh-frozen or Formalin-fixed Paraffin-embedded B6C3F1/N Mouse Hepatocellular Carcinomas Arising Either Spontaneously or due to Chronic Chemical Exposure by Scott S. Auerbach, Miaofei Xu, B. Alex Merrick, Mark J. Hoenerhoff, Dhiral Phadke, Debra J. Taxman, Ruchir Shah, Hue-Hua L. Hong, Thai-Vu Ton, Ramesh C. Kovi, Robert C. Sills, and Arun R. Pandiri in Toxicologic Pathology</p

Supplemental Material, DS2a_TPX_10.1177_0192623318789398 - Exome Sequencing of Fresh-frozen or Formalin-fixed Paraffin-embedded B6C3F1/N Mouse Hepatocellular Carcinomas Arising Either Spontaneously or due to Chronic Chemical Exposure

<p>Supplemental Material, DS2a_TPX_10.1177_0192623318789398 for Exome Sequencing of Fresh-frozen or Formalin-fixed Paraffin-embedded B6C3F1/N Mouse Hepatocellular Carcinomas Arising Either Spontaneously or due to Chronic Chemical Exposure by Scott S. Auerbach, Miaofei Xu, B. Alex Merrick, Mark J. Hoenerhoff, Dhiral Phadke, Debra J. Taxman, Ruchir Shah, Hue-Hua L. Hong, Thai-Vu Ton, Ramesh C. Kovi, Robert C. Sills, and Arun R. Pandiri in Toxicologic Pathology</p