Cohort profile: genomic data for 26 622 individuals from the Canadian Longitudinal Study on Aging (CLSA)

Figures

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  Figure 1. Pairwise plot of allele frequency of SNPs that pass all four tests from genotype batches 1–5. The SNPs are considered as passed if they have non-significant p value (Fisher’s p>3.5×10−10) below the multiple testing corrected threshold for the respective test on discordant genotype frequency between batch, departure from Hardy-Weinberg equilibrium, discordance between the positive control replicates and on discordant genotype frequency between male and female. SNP, single-nucleotide polymorphism

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  Figure 2. Determining the CLSA European ancestry subset. (A) Top four principal components from all 1000 Genomes populations labelled and coloured (population code refers to https://wwwinternationalgenomeorg/category/population/). (B) Top four principal components from CLSA colour coded and labelled by cluster number. CLSA, Canadian Longitudinal Study on Aging.

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  Figure 3. BAF (top) and log2 ratio (bottom) of chromosomes X and Y are shown for sex chromosome abnormalities. (A) In 46, XY, the BAF is either 0 or 1, and the expected log2 ratio is less than 0 on chromosome X. However, in the PAR and the chrY11.2/chrXq21.3 homology block, there are heterozygous calls in male shown as BAF of 0.5. The red line shows the locally weighted scatterplot smoothing curve for log2 ratio. The BAF is either 0 or 1, and the expected log2 ratio is 0 on chromosome Y. (B) In 46, XX, the BAF is either 0 (AA), ½ (AB) or 1 (BB), and the expected log2 ratio is 0 on chromosome X as in a normal diploid cell. The BAF is between 0 and 1, and the log2 ratio is less than 0 on chromosome Y. (C) For Klinefelter syndrome (47, XXY), the log2 ratio is around 0 on chromosome X, which indicates ploidy as 2N. Compared with 46, XY, there are relatively lower peaks of log2 ratio at PAR and chrX21.3/chrY11.2 homology block region. Moreover, BAF of heterozygous calls at PAR and chrX21.3/chrY11.2 homology block region shifted from 0.5 to intermediate values. They both indicated an extra copy of chromosome X. Chromosome Y intensity profile showed a clear male pattern. (D) For Turner syndrome…