Detectable clonal mosaicism from birth to old age and its relationship to cancer

Abstract

We detected clonal mosaicism for large chromosomal anomalies (duplications, deletions and uniparental disomy) using SNP microarray data from over 50,000 subjects recruited for genome-wide association studies. This detection method requires a relatively high frequency of cells with the same abnormal karyotype (>5-10%; presumably of clonal origin) in the presence of normal cells. The frequency of detectable clonal mosaicism in peripheral blood is low (<0.5%) from birth until 50 years of age, after which it rapidly rises to 2-3% in the elderly. Many of the mosaic anomalies are characteristic of those found in hematological cancers and identify common deleted regions with genes previously associated with these cancers. Although only 3% of subjects with detectable clonal mosaicism had any record of hematological cancer before DNA sampling, those without a previous diagnosis have an estimated tenfold higher risk of a subsequent hematological cancer (95% confidence interval = 6-18).

Figure 1

Expected values of B Allele Frequency (BAF) and Log R Ratio (LRR) for discrete copy number states. Mosaics have intermediate positions between these discrete states. Copy number is given above the horizontal lines in the LRR plot, while SNP genotypes are given in the BAF plot. M=maternal and P=paternal chromosome. States with M and P reversed are also possible. The scatter of points for copy number = 0 (homozygous deletion) represents background signal noise.

Figure 2

Expected and observed values of B Allele Frequency (BAF) and Log R Ratio (LRR) metrics for clonal mosaic anomalies detected in GENEVA subjects. (a) Expected. (b) Observed (N=514). In (b), “med”=median, “anom”=within the anomaly, “nonanom”=non-anomalous autosomal regions of the same sample. The solid purple and red circles represent the mean values of non-mosaic anomalies and the solid black and cyan circles are theoretical.

Figure 3

B Allele Frequency (BAF) and Log R Ratio (LRR) plots of four representative mosaic anomalies. Each pair of plots is for a different sample-chromosome combination and each point is a single SNP. Points in BAF plots are color-coded by genotype (red=AA, cyan=AB, purple-blue=BB, black=missing call). The vertical black lines indicate the breakpoint(s) of the anomaly. The vertical gray rectangle is the centromeric gap. Horizontal pink lines are drawn at 0, 1/3, 1/2, 2/3 and 1 in the BAF plots. The solid horizontal red line in each plot is the median value for non-anomalous regions of the autosomes. The horizontal dashed red line is the median value within the anomaly. (a) Mosaic acquired uniparental disomy for distal 12q is indicated by the split in the intermediate BAF band along with the lack of change in LRR. A non-mosaic uniparental isodisomy would have only two BAF bands (at 0 and 1). (b) Mosaic trisomy for chromosome 19 is indicated by a narrow split in the intermediate BAF band along with a small elevation of LRR. A non-mosaic trisomy would have a wider BAF split (at 1/3 and 2/3) and a larger elevation of LRR. (c) A mosaic deletion on 20q is indicated by a narrow split in the intermediate BAF band along with a small decrease in LRR. A non-mosaic heterozygous deletion would have no intermediate BAF bands and a larger decrease in LRR. (d) A mosaic deletion on 6q is indicated by a wide split in the intermediate BAF band along with a large decrease in LRR. The mosaic deletion in (d) has a greater proportion of cells containing the deletion than the one in (c). See Supplementary Figure 2 for additional examples.

Figure 4

The lengths and chromosomal positions of the 514 clonal mosaic anomalies detected in GENEVA subjects. An ideogram of each autosome is shown with scaled and color-coded representations of each mosaic anomaly to the right.

Figure 5

The percentage of subjects having one or more mosaic anomalies within 5-year age bins. Vertical bars are 95% confidence intervals. For two cells with zero counts, the upper bar connects zero to the frequency with a lower 95% confidence interval of zero given the sample size. Expected leukemia values are given for reference and calculated using age- and sex-specific prevalence estimates (http://seer.cancer.gov).

Figure 6

Fixed-effects meta-analysis for effect of age at DNA sampling on mosaic status. Effect estimates are from logistic regression of mosaic status on age at DNA sampling, with adjustment for case status specific to each study. The summary estimate of the log odds ratio is 0.05 (95% CI=0.04 – 0.07) and the corresponding odds ratio is 1.06 (95% CI=1.04 – 1.07). Cochran’s Q test of heterogeneity has p-value=0.89. The sizes of the black boxes are proportional to the inverse of the squared standard error and the gray lines are 95% confidence intervals. The horizontal points of the diamond span the 95% confidence interval of the summary estimate. See Table 1 for study descriptions. AA = African American and JL = Japanese/Latino.

Figure 7

A Kaplan-Meier plot of the proportion of living subjects who remain free of hematological cancer as a function of time since the time of DNA sampling and determination of mosaic status. Estimates for mosaic (red) and non-mosaic (black) subjects are given separately (solid lines), each with their 95% confidence intervals (dashed lines). The vertical ticks represent censoring times. For the 15 mosaic subjects with incident cancer, the times between DNA sampling and diagnosis are 3.5, 6.1, 12.7, 18.8, 25.0, 36.9, 37.5, 42.9, 44.0, 46.2, 48.0, 60.4, 61.8, 91.1, and 130.5 months.