Common and rare genetic variants predisposing females to unexplained recurrent pregnancy loss

Abstract

Recurrent pregnancy loss (RPL) is a major reproductive health issue with multifactorial causes, affecting 2.6% of all pregnancies worldwide. Nearly half of the RPL cases lack clinically identifiable causes (e.g., antiphospholipid syndrome, uterine anomalies, and parental chromosomal abnormalities), referred to as unexplained RPL (uRPL). Here, we perform a genome-wide association study focusing on uRPL in 1,728 cases and 24,315 female controls of Japanese ancestry. We detect significant associations in the major histocompatibility complex (MHC) region at 6p21 (lead variant=rs9263738; P = 1.4 × 10^-10; odds ratio [OR] = 1.51 [95% CI: 1.33-1.72]; risk allele frequency = 0.871). The MHC associations are fine-mapped to the classical HLA alleles, HLA-C*12:02, HLA-B*52:01, and HLA-DRB1*15:02 (P = 1.1 × 10^-10, 1.5 × 10^-10, and 1.2 × 10^-9, respectively), which constitute a population-specific common long-range haplotype with a protective effect (P = 2.8 × 10^-10; OR = 0.65 [95% CI: 0.57-0.75]; haplotype frequency=0.108). Genome-wide copy-number variation (CNV) calling demonstrates rare predicted loss-of-function (pLoF) variants of the cadherin-11 gene (CDH11) conferring the risk of uRPL (P = 1.3 × 10^-4; OR = 3.29 [95% CI: 1.78-5.76]). Our study highlights the importance of reproductive immunology and rare variants in the uRPL etiology.

Fig. 1. Genome-wide association study of unexplained recurrent pregnancy loss.

Genome-wide associations of imputed genetic variants are shown. The pink horizontal line indicates the genome-wide significance threshold of P = 5.0 × 10^–8. P-values were computed using SAIGE. All statistical tests are two-sided and unadjusted for multiple comparisons. MHC, major histocompatibility complex.

Fig. 2. MHC fine-mapping analysis on the association with uRPL.

Regional associations of the imputed HLA variants in the MHC region with uRPL are shown. a Nominal regional associations. b Regional associations conditioned on HLA-C*12:02. c Regional associations conditioned on HLA-B*52:01. d Regional associations conditioned on HLA-DRB1*15:02. e Regional associations conditioned on HLA-C*12:02–HLA-B*52:01–HLA-DRB1*15:02 haplotype. Each diamond represents the −log₁₀(P) of the variants, including the single-nucleotide variants, two-, four-, and six-digit HLA alleles, and amino acid variants of HLA genes. The horizontal dashed line represents the genome-wide significance threshold of P = 5.0 × 10^–8. Detailed association results are available in Supplementary Data 1. P-values were computed by logistic regression. All statistical tests are two-sided and unadjusted for multiple comparisons.

Fig. 3. Associations of HLA-C*12:02–HLA-B*52:01–HLA-DRB1*15:02 haplotype in the stratified analysis.

Odds ratios of HLA-C*12:02–HLA-B*52:01–HLA-DRB1*15:02 haplotype in the stratified analysis are shown. The marker size is proportional to the case sample size. Error bars indicate 95% CI, and the measure of center is the maximum likelihood estimate by logistic regression. case group (A), uRPL cases with confirmed embryonic euploid or undetermined karyotype; case group (B), ANA(+) uRPL cases with confirmed embryonic euploid or undetermined karyotype; case group (C), autoantibody and hypothyroidism(-) uRPL cases with confirmed embryonic euploid or undetermined karyotype; case group (D), uRPL cases with confirmed embryonic euploid; case group (E), uRPL cases with confirmed embryonic aneuploid.

Fig. 4. Predicted loss-of-function copy-number variation associated with uRPL.

a A quantile–quantile plot of the P-values of tested genes from the pLoF CNV burden test. The gray diagonal dashed line is the identity line. The pink horizontal dashed line indicates the Bonferroni-corrected significance threshold of α = 0.05. Detailed association results are available in Supplementary Data 2. All statistical tests are two-sided and unadjusted for multiple comparisons. b Locations of the CDH11 pLoF CNVs in the uRPL cases are shown.