Optimal detection of clinically relevant mutations in colorectal carcinoma: sample pooling overcomes intra-tumoral heterogeneity

Abstract

Intra-tumoral genomic heterogeneity is a well-established biologic property of human malignancies with emerging roles in cancer progression and therapy resistance. However, its impact on the clinical utility of genomic testing in patient management remains unclear. Furthermore, best practices to account for heterogeneity in the provision of highly accurate, clinically valid molecular testing have yet to be firmly established. Genomic biomarkers for the management of colorectal carcinoma are both well-established (ie, KRAS, NRAS) and emerging (BRAF, PIK3CA, and others) in respect to therapy selection and clinical trial eligibility. Critically, standard colorectal carcinoma management requires the exclusion of KRAS and NRAS mutations; thus optimal procedures to control for potential intra-tumoral heterogeneity are clinically important. Here, we assessed heterogeneity among three intra-tumoral sites within 99 colorectal carcinomas cases on a CLIA-validated oncology next generation sequencing assay and examined whether a pooling strategy overcame any discordant results. Overall, 11% of cases demonstrated discordant mutation results between sites; 2% of cases were discrepant for mutations within RAS genes while the remainder was discrepant in PIK3CA. Half of the discrepant cases were associated with borderline tumor cellularity assessment. Further, a sample pooling strategy across all three sites successfully detected the relevant mutation in all but one case. Our results indicate that intra-tumoral genomic heterogeneity of clinically relevant genes within colorectal carcinoma is a relatively infrequent occurrence and that a simple strategy to pool DNA from several tumor sites with adequate cellularity minimizes the risk of false negative results even further to ensure optimal patient management.

Characterizing MRI features of rectal cancers with different KRAS status

“…In daily practice, the biopsy is still the routine way to get tumour mutant status before treatment. Considering the spatial and temporal intra-tumour molecular heterogeneity, the results for biopsy samples are yet to be consistent [11][12][13]50]. Recently, a large prospective study [50] showed that the concordance ratio between paired biopsy and resection specimens was 82% for KRAS status.…”

“…Nevertheless, since condons 12 and 13 KRAS mutations represent the majority of RAS mutations in CRC, our results provide a reasonable representation for tumors with RAS mutation in some degree. Fourth, considering the potential discrepancy between pre-treatment biopsy and final pathology [11][12][13], only the outcome from final surgical specimen were enrolled in the study. Fifth, this was a single-center study with a limited sample size, which may be the reason why only moderate predictive value of MRI features for identifying KRAS status has been observed.…”

“…On the other hand, different molecular subtypes correlate with various discriminating morphological features [1]. Various MR imaging modules [11][12][13][14][15][16] (i.e. diffusionweighted MR imaging [DWI], magnetic resonance spectroscopy [MRS], arterial spin labelling [ASL]) and advanced analysis for routine MR imaging [17][18][19][20][21] have been introduced in the oncologic field to evaluate tumoral biological characteristics and predict KRAS status.…”

Intratumor heterogeneity: A new perspective on colorectal cancer research

“…37 Some studies have indicated that sampling at three tumor-rich sites rich may reduce the negative results of DNA testing, increase the accuracy of gene detection and improve overall ITH assessment. 38 Sequencing tumor tissue DNA by multiregion sampling, however, may also be challenging. The contrast sampling method of tumor center, tumor periphery, and normal tissue obtained by diagnostic puncture method cannot achieve the function of multipoint sampling to obtain the information of intratumor heterogeneity.…”

Radiomics Features of 18F-fluorodeoxyglucose Positron-Emission Tomography as a Novel Prognostic Signature in Colorectal Cancer

“…Radiomics has frequently been adopted for subtype classification, evaluation of lymph node metastasis or distant metastasis, and prediction of treatment response or prognosis in many types of cancers [12][13][14][15]. It is regarded as somewhat difficult to assess intra-tumoral heterogeneity using a single spatially-biased biopsy [16]. Detection of unseen information reflecting intra-tumoral heterogeneity might be the main motivation for applying a radiomics approach in the oncology field.…”