DOI: 10.5061/dryad.nvx0k6dx5
title: Genetic insights into the age-specific biological mechanisms governing human ovarian ageing

description: There is currently little evidence that the genetic basis of human
 phenotype varies significantly across the lifespan. However, time-to-event
 phenotypes are understudied and can be thought of as reflecting an
 underlying hazard, which is unlikely to be constant through life when
 values take a broad range. Here, we find that 74% of 245 genome-wide
 significant genetic associations with age at natural menopause (ANM) in
 the UK Biobank show a form of age-specific effect. Nineteen of these
 replicated discoveries are identified only by our modelling framework,
 which determines the time-dependency of DNA variant-age-at-onset
 associations, without a significant multiple-testing burden. Across the
 range of early to late menopause, we find evidence for significantly
 different underlying biological pathways, changes in the sign of genetic
 correlations of ANM to health indicators and outcomes, and differences in
 inferred causal relationships. We find that DNA damage response processes
 only act to shape ovarian reserve and depletion for women of early ANM.
 Genetically mediated delays in ANM were associated with increased relative
 risk of breast cancer and leiomyoma at all ages, and with high cholesterol
 and heart failure for late-ANM women. These findings suggest that a better
 understanding of the age-dependency of genetic risk factor relationships
 among health indicators and outcomes is achievable through appropriate
 statistical modelling of large-scale biobank data.
description: We first restricted our analysis to a sample of European-ancestry
 UK Biobank individuals. To infer ancestry, we used both self-reported
 ethnic background (UK Biobank field 21000-0), selecting coding 1, and
 genetic ethnicity (UK Biobank field 22006-0), selecting coding 1. We
 projected the 488,377 genotyped participants onto the first two genotypic
 principal components (PC) calculated from 2,504 individuals of the 1,000
 Genomes project. Using the obtained PC loadings, we then assigned each
 participant to the closest 1,000 Genomes project population, selecting
 individuals with PC1 projection &lt; absolute value 4 and PC 2
 projection &lt; absolute value 3. Samples were also excluded based on
 UK Biobank quality control procedures with individuals removed of (i)
 extreme heterozygosity and missing genotype outliers; (ii) a genetically
 inferred gender that did not match the self-reported gender; (iii)
 putative sex chromosome aneuploidy; (iv) exclusion from kinship inference;
 (v) withdrawn consent. We used genotype probabilities from version 3 of
 the imputed autosomal genotype data provided by the UK Biobank to
 hard-call the genotypes for variants with an imputation quality score
 above 0.3. The hard-call-threshold was 0.1, setting the genotypes with
 probability leq0.9 as missing. From the good quality markers (with
 missingness less than 5% and p-value for Hardy-Weinberg test larger than
 10<sup>-6</sup>, as determined in the set of unrelated
 Europeans), we selected those with minor allele frequency (MAF) &gt;
 0.0002 and rs identifier, in the set of European-ancestry participants. We
 then took the overlap with the Estonian Biobank data described below to
 give a final set of 8.7 million SNPs using both autosomal chromosomes and
 the X chromosome. This provides a set of high-quality SNP markers present
 across both discovery and prediction data sets. We
 created the phenotypic data of age-at-menopause similarly to Ojavee et al
 2021, Nature Communications, doi.org/10.1038/s41467-021-22538-w. We used
 UKB field 3581 to obtain the time if available, and we excluded from the
 analysis 1) women who had reported of having and later not having had
 menopause or vice versa, 2) women who said they had menopause but there is
 no record of the time of menopause (UKB field 2724), 3) women who have had
 hysterectomy or the information about this is missing (UKB field 3591), 4)
 women whose menopause is before age 33 or after 65.
 Within the UK Biobank data, there were a total of 173,424
 unrelated (only one person kept from second-degree or closer relative
 pairs) European ancestry women, out of which 125,697 had experienced
 menopause and 47,727 had not had menopause based on data field 2724. For
 computational convenience when conducting the joint BayesW analysis we
 created an additional subset of markers by removing markers in very high
 LD, through the selection of the highest MAF marker from any set of
 markers with LD R<sup>2</sup> geq 0.8 within a 1Mb window.
 These filters resulted in a data set with 173,424 individuals and
 2,174,071 markers for the first-step estimation of the LOCO genetic
 predictors and then in the second-step age-specific Cox Proportional
 hazards we analysed 8.7 million SNPs using both autosomal chromosomes and
 the X chromosome.