Genome-wide Allelic State Analysis on Flow-Sorted Tumor Fractions Provides an Accurate Measure of Chromosomal Aberrations

Abstract

Chromosomal aberrations are a common characteristic of cancer and are associated with copy number abnormalities and loss of heterozygosity (LOH). Tumor heterogeneity, low tumor cell percentage, and lack of knowledge of the DNA content impair the identification of these alterations especially in aneuploid tumors. To accurately detect allelic changes in carcinomas, we combined flow-sorting and single nucleotide polymorphism arrays. Cells derived from archival cervical and colon cancers were flow-sorted based on differential vimentin and keratin expression and DNA content and analyzed on single nucleotide polymorphism arrays. A new algorithm, the lesser allele intensity ratio, was used to generate a molecular measure of chromosomal aberrations for each case. Flow-sorting significantly improved the detection of copy number abnormalities; 31.8% showed an increase in amplitude and 23.2% were missed in the unsorted fraction, whereas 15.9% were detected but interpreted differently. Fluorescence in situ hybridization copy numbers, as well as the high similarity between the DNA index and the allelic state index, which is the average of the allelic states across the genome, validated the method. This new approach provides an individual molecular measure of chromosomal aberrations and will likely have repercussions for preoperative molecular staging, classification, and prognostic profiling of tumors, particularly for heterogeneous aneuploid tumors, and allows the study of the underlying molecular genetic mechanisms and clonal evolution of tumor subpopulations. [Cancer Res 2008;68(24):10333-40]

The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line

“…LOH encompassed 15.7% of the genome, including several entire chromosome arms (5p, 6q, Xp, Xq) or large distal portions (2q, 3q, 6p, 11q, 13q, 19p, 22q) (Supplementary Fig. 7, Supplementary Table 9), consistent with previous descriptions of LOH in cervical carcinomas 17 . The overall profile is consistent with published karyotypes of various HeLa strains 4 , suggesting that the hypertriploid state arose either during tumorigenesis or early in the establishment of the HeLa cell line.…”

Glioblastomas are composed of genetically divergent clones with distinct tumourigenic potential and variable stem cell-associated phenotypes

“…Genomic analysis of cellular subpopulations that differ in ploidy has been performed in other cancers, including breast [37], cervical, colorectal [14], prostate and pancreas [3, 45]. Compared with other genomic techniques, such as gene expression arrays and next-generation sequencing, which measure signals from a complex mixture of cell types, our approach has the advantage to dissect this complex mixture into distinct tumour clones and stromal cells.…”

Inferring tumor progression from genomic heterogeneity

“…Previous studies have shown that FACS can be used to separate tumor cells by ploidy for genomic analysis (Corver et al 2008). FACS separates subpopulations of tumor cells, and tumor cells from normal cells, by differences in their total genomic DNA content, or ploidy.…”