Genotyping Techniques to Address Diversity in Tumors

Abstract

Array based genotyping platforms have during recent years been established as a valuable tool for the characterization of genomic alterations in cancer. The analysis of tumor samples, however, presents challenges for data analysis and interpretation. For example, tumor samples are often admixed with nonaberrant cells that define the tumor microenvironment, such as infiltrating lymphocytes and fibroblasts, or vasculature. Furthermore, tumors often comprise subclones harboring divergent aberrations that are acquired subsequent to the tumorinitiating event. The combined analysis of both genotype and copy number status obtained by array based genotyping platforms provide opportunities to address these challenges. In this review, we present the basic principles for current array based genotyping platforms and how they can be used to infer genotype and copy number for acquired genomic alterations. We describe how these techniques can be used to resolve tumor ploidy, normal cell admixture, and subclonality. We also exemplify how genotyping techniques can be applied in tumor studies to elucidate the hierarchy among tumor clones, and thus, provide means to study clonal expansion and tumor evolution.

Intra-tumor Genetic Heterogeneity and Mortality in Head and Neck Cancer: Analysis of Data from The Cancer Genome Atlas

“…More generally, MATH will be straightforward to apply clinically in other types of cancer, for there is nothing specific to HNSCC in the underlying analysis of exome sequence data. Unlike approaches to measuring intra-tumor heterogeneity that require pre-identification of subclone markers [ 17 , 18 ], detailed analysis of SNP arrays [ 26 , 50 ], or analysis of multiple portions down to single cells of a tumor [ 13 , 20 , 22 , 25 ], MATH calculations require no information beyond a list of tumor-specific mutations and their MAFs, derived directly from a patient’s tumor and normal DNA. Thus, as WES enters the practice of clinical oncology [ 8 , 32 ], MATH will provide a novel and straightforward way to incorporate information about intra-tumor heterogeneity into clinical research and practice.…”

Intratumoral genome diversity parallels progression and predicts outcome in pediatric cancer

“…It provides a stark contrast to current strategies for biomarker evaluation, with mutation status, genome profile or protein expression typically being evaluated in merely a single tumour sample-resting on the assumption that tumours are biologically homogeneous 5 . Microdiversity would be a particularly attractive clinical marker as it is a parameter possible to quantify using standard genome arrays and relatively simple bioinformatic operations 17 . The fact that we found a potential prognostic value of microdiversity in preoperatively treated nephroblastoma may be of particular interest because there is currently no standard molecular prognosticator for the many children worldwide treated for nephroblastoma under protocols with mandatory preoperative chemotherapy.…”

“…The cancer cell fraction ranged from 60 to 99%, well in agreement with clearly deviant SNP array profiles, which fulfilled local criteria for clinical analysis ( Supplementary Figs 8-11). The method for estimating the proportion of cells containing a certain allelic imbalance from Illumina arrays has previously been validated by us and others 9,17,35,36 . In brief, the fraction of cells within single tumour samples that harboured each detected allelic imbalance was calculated using mirrored B-allele frequency (mBAF) values from the BAF-segmentation algorithm for Illumina arrays 35 .…”

“…The many data points given by such array-based analyses allow for precise quantification in single tumour samples of the proportion of cells harbouring each detected abnormality (Fig. 1a,b) 9,17 . Intratumoral diversity can thereby be monitored not only by comparing genomes from different locations in the same tumour (intratumoral macrodiversity) but also by dissecting genetic heterogeneity within tumour samples only a few millimetres in size (intratumoral microdiversity; Fig.…”

Heterogeneous Challenges for Urologic Cancers

“…The existence of clonal karyotypic heterogeneity has been documented for several tumor types, and cytogenetic investigations have revealed coexisting related but divergent subclones in several tumor types. In addition, comparative genome hybridization analyses have indicated an underlying heterogeneity with respect to copy number alterations and to the presence of subclones with different sets of genomic alterations [1]. Furthermore, investigations based on the sequencing of more than one gene in the same biopsy revealed that some mutations are present in all tumor cells, whereas others are not.…”