SNP arrays in heterogeneous tissue: highly accurate collection of both germline and somatic genetic information from unpaired single tumor samples

Abstract

SNP arrays provide reliable genotypes and can detect chromosomal aberrations at a high resolution. However, tissue heterogeneity is currently a major limitation for somatic tissue analysis. We have developed SOMATICs, an original program for accurate analysis of heterogeneous tissue samples. Fifty-four samples (42 tumors and 12 normal tissues) were processed through Illumina Beadarrays and then analyzed with SOMATICs. We demonstrate that tissue heterogeneity-related limitations not only can be overcome but can also be turned into an advantage. First, admixture of normal cells with tumor can be used as an internal reference, thereby enabling highly sensitive detection of somatic deletions without having corresponding normal tissue. Second, the presence of normal cells allows for discrimination of somatic from germline aberrations, and the proportion of cells in the tissue sample that are harboring the somatic events can be assessed. Third, relatively early versus late somatic events can also be distinguished, assuming that late events occur only in subsets of cancer cells. Finally, admixture by normal cells allows inference of germline genotypes from a cancer sample. All this information can be obtained from any cancer sample containing a proportion of 40-75% of cancer cells. SOMATICs is a ready-to-use open-source program that integrates all of these features into a simple format, comprehensively describing each chromosomal event.

Figure 1

Automatic Detection of Chromosomal Aberrations in Heterogeneous Tissue Samples In each panel, the BAF and the logR ratio are plotted along chromosomal regions. The black boxes at the bottom represent detection with SOMATICs and other currently available methods, namely, Beadstudio LOH score (y axis range from 0 to 5), dChip (default detection threshold), and CNVPartition. (A) Small germline deletion is revealed as a decreased logR ratio (−0.5), and the band of heterozygous SNPs centered on 0.5 is absent on the BAF plot. (B–E) Various types of somatic deletions revealed on the BAF plot in which the single band of heterozygous SNPs is replaced by two bands and the logR ratio is decreased, but to a lesser extent as compared to germline deletions. The various types of somatic deletions are manifested by differences in the position and the size of the two-band patterns. Note that (E) shows a somatic deletion occurring in very few cells. In this situation, detection is easier with use of the BAF (two-band pattern) than with the logR (reduced shift downward). However, the copy number call as a “deletion” relies on a significant decrease of the logR (in this situation, p < 2.2e⁻¹⁶). (F) Wavy fluctuations of logR ratio, which is not reflected in the BAF, are artefacts. This artifact is responsible for false-positive detection by programs focusing only on logR ratio. (G) Two small germline duplications are revealed on the BAF plot as heterozygous SNPs showing a two-band pattern with a logR ratio that is increased. (H) In somatic duplication, the two bands are closer to one another and the increase in logR is less than that of germline amplification (G). As with (E), for (H), the BAF two-band pattern is easier to detect than is the logR shift upward. However, the copy number call as an “amplification” relies on a significant increase of the logR (in this case, p < 2.2e⁻¹⁶). SOMATICs can detect and differentiate the various types of alterations when other programs cannot.

Figure 2

Proportion of Cells, “c,” in a Heterogeneous Tumor Sample Harboring a Somatic Genetic Event (A) BAF and the logR ratio plots from one chromosome reveal three somatic hemizygous deletions occurring in three different proportions of cells. The BAF_del of heterozygote SNPs is measured after “folding” the BAF plot along an axis centered around 0.5. Then BAF_del is used to determine c with the formula designed for somatic deletions (see Appendices for details). (B) Frequency distribution showing the number of SNPs included in the somatic deletions by the proportion of cells, “c,” in which these events occur. Some somatic deletions occur in over 80% of cells (rightmost bar). Assuming that only cancer cells harbor somatic deletions, the proportion of cancer cells is then estimated as 80% in this sample. (C) Schematic illustrating the relationship between the chronology of somatic events during tumorigenesis and the proportion of cancer cells with these events. Early somatic events are present in all (or a great majority of) cancer cells, whereas late somatic events are only present in subsets of cells.

Figure 3

Germline Genotype Inference from a Heterogeneous Cancer Sample (A) Schematic representation of the calling methods used by SOMATICs and by BeadStudio. SOMATICs is specifically designed to generate appropriate calls in genomic regions with allelic imbalance. When bands of heterozygous AB SNPs can be discriminated from the bands of homozygous AA and BB SNPs, a reliable germline genotype call can be provided. (B) illustrates enotyping call rates in regions of allelic imbalance with SOMATICs and BeadStudio, and (C) illlustrates genotyping accuracy in regions of allelic imbalance with SOMATICs and BeadStudio. These results were obtained by comparison of genotypes inferred from tumors with genotypes read in normal corresponding tissue obtained with seven pairs of matched samples. The results in (B) and (C) are expressed as a function of the distance from the heterozygote bands to the homozygote bands, on a scale of 0 to 0.5, representing the mean BAF of the lower band of heterozygote SNPs. This mean BAF is converted into a proportion of cells, “c,” with allelic imbalance by use of the formula for somatic deletions (see Appendices for details).