Numerous genomic tests are available for use in colorectal cancer, with a widely variable evidence base for their effectiveness and cost-effectiveness. In this review, we highlight many of these tests, with a focus on their proposed role, the evidence base to support that role, and the associated costs and risks. The tests with the strongest evidence base are KRAS genetic testing in the metastatic setting and microsatellite instability testing in selected patients and in stage II disease. There also may be a role for delineating recurrence-risk signatures for selected patients with stage II disease. The evidence to support broad utilization of uridine 5'-diphospho-glucuronosyltransferase 1A1 (UGT1A1) and dihydropyrimidine dehydrogenase (DPD) testing to guide irinotecan and fluorouracil dosing remains limited. There is much anticipation that next-generation sequencing will herald a new era of targeted therapy for patients with colorectal cancer; however, currently there are no data to support the introduction of widespread testing.
The introduction into clinical practice of the anti–epidermal growth factor receptor (EGFR) antibodies cetuximab and panitumumab has improved clinical outcomes for patients with metastatic colorectal cancer. It has been noted that KRAS mutations are negative predictive markers for response to these agents. Activating KRAS mutations in codon 12 are detected in approximately 35% to 45% of patients with colorectal cancer; these are a leading cause of resistance to EGFR inhibitors. Mutations in codon 13 of the KRAS gene have been identified and occur in about 6% of patients with colorectal cancer. However, the role of codon 13 mutations in the development of resistance to EGFR treatment remains a matter of controversy. At this point, in the absence of prospective trials and given the contradictory results of the two retrospective studies, the role of KRAS codon 13 mutation in resistance to EGFR inhibition requires further study.[35,36]
There is evidence that NRAS mutations and KRAS mutations in exons 3 and 4 are also negative predictive markers of response. The PRIME trial was a randomized phase III investigation of panitumumab with infusional FOLFOX vs FOLFOX alone as first-line treatment in patients with metastatic colorectal cancer. When patients with any RAS mutation were excluded in the PRIME study, improvement in OS was observed in the panitumumab arm compared with those receiving chemotherapy alone (26.0 vs 20.2 months; P = .043).[38,39] This finding was supported by similar findings in the PEAK trial, a randomized phase II study of panitumumab plus FOLFOX vs bevacizumab plus FOLFOX in patients with previously untreated, wild-type KRAS exon 2 metastatic colorectal cancer. A trend toward a worse outcome was noted with the addition of panitumumab in both the PRIME and PEAK studies in patients with NRAS and non–exon 2 KRAS mutations, suggesting that this group of patients does not benefit and may, in fact, be potentially harmed by anti-EGFR therapy.[38,41] The PICCOLO study analyzed the efficacy of adding panitumumab to irinotecan in patients with KRAS wild-type 5-FU–resistant advanced disease. Patients with any RAS mutation had worse outcomes than did patients with RAS wild-type cancer. In a study using next-generation sequencing on 299 samples from a KRAS wild-type subset of patients receiving panitumumab, similar conclusions were reached. Among KRAS wild-type patients, a treatment effect for progression-free survival (PFS) favoring panitumumab occurred in patients with NRAS wild-type (hazard ratio [HR] = 0.39) and BRAF wild-type (HR = 0.37) but not in those with NRAS mutant-type (HR = 1.94).
The CRYSTAL trial analyzed the survival benefit of adding cetuximab to irinotecan, 5-FU, and leucovorin (FOLFIRI) as first-line treatment for patients with metastatic colorectal cancer. This study confirmed that the addition of cetuximab significantly improved overall response rate (ORR), PFS, and OS compared with FOLFIRI alone in patients with KRAS wild-type disease. The FIRE-3 study compared bevacizumab with cetuximab when added to FOLFIRI in the first-line treatment setting for metastatic colorectal cancer that was exon-2 KRAS wild-type. A subgroup analysis was performed in patients who had KRAS mutations in exons 3 or 4 or NRAS mutations in exons 2, 3, or 4. This subgroup of 34 patients in the cetuximab arm had an ORR of 38%, compared with 65% for patients with wild-type cancers.
The high cost of these targeted therapies remains a concern. A cost-effectiveness analysis showed that without genetic testing, the addition of cetuximab had an ICER of $2.9 million per life year (LY) gained. This is well beyond the threshold of $50,000 to $100,000 per QALY that is considered to be the benchmark of cost-effectiveness. When using KRAS testing as a biomarker, the ICER improved, but only to $2.8 million per LY. While EGFR-targeted therapies do not appear to reach the criteria that warrant their being described as cost-effective, they are commonly used in clinical practice. Due to the observation that RAS testing improves the cost-effectiveness of EGFR-targeted therapies, we therefore support the use of this approach for patients who have metastatic colorectal cancer. However, since there is no evidence to support the use of EGFR-targeted therapy in the adjuvant setting, there is no indication to test for RAS mutations in patients with early-stage disease.
BRAF is the main downstream effector of KRAS. Mutations in B-Raf proto-oncogene, serine/threonine kinase (BRAF), are found in less than 10% of patients with colorectal cancer. BRAF mutations are a negative prognostic marker regardless of treatment received, with significant differences in median OS: BRAF-mutant, 8.8 months; KRAS-mutant, 14.4 months; and KRAS wild-type, 20.1 months. CRYSTAL analyzed the efficacy of adding cetuximab to irinotecan in the first line of treatment. In a subset analysis of this trial, the impact of utilizing BRAF mutations as a predictive tool in relation to the efficacy of anti-EGFR therapy was examined.[48,49] Patients with mutated BRAF had low response rates and markedly shorter median PFS (5.1 vs 8.3 months) and OS (9.5 vs 22.0 months) compared with patients with wild-type tumors. BRAF inhibition by vemurafenib has been attempted, but with limited responses.[51,52]
The value of BRAF mutation analysis is limited, since it provides prognostic information but does not provide predictive information. However, it does have additional utility in patients with microsatellite instability (MSI). The presence of a BRAF mutation indicates sporadic disease and excludes a diagnosis of Lynch syndrome. Given that prognostic information does not ultimately change management, we propose that it is only necessary to check for BRAF mutation status in patients who have been found to have MSI in order to determine whether it is sporadic or inherited. Furthermore, BRAF and KRAS mutations are mutually exclusive. Therefore, if a KRAS mutation is detected, BRAF status will be wild-type, and there is no need to check for BRAF. For this reason, many institutions use a reflex BRAF test if KRAS is wild-type.
Microsatellite instability testing
The first genetic mutation to cause MSI was discovered in 1993; it was linked to the development of hereditary colon cancer. Further mutations were subsequently discovered, and extensive work has been done to understand the best method of testing and the clinical implications of mutation. Mismatch repair (MMR) genes are responsible for the correction of nucleotide base mispairings and small insertions or deletions that occur during DNA replication. These genes include MSH2, MLH1, PMS1, PMS2, MSH6, and MLH3. Germline mutations in one of the MMR genes is the underlying defect in hereditary nonpolyposis colon cancer, also known as Lynch syndrome.
Approximately 15% of colorectal cancers demonstrate MSI. MSI is the result of germline mutations causing Lynch syndrome in 3%, and the result of sporadic mutations, with no clinical relevance for other family members, in 12%; the remaining 85% of colorectal cancers do not demonstrsate MSI. The presence of a BRAF mutation indicates sporadic rather than hereditary disease and excludes a diagnosis of Lynch syndrome. Sporadic tumors do not contain MMR gene mutations; instead, they have acquired hypermethylation of the MLH1 gene, which silences gene expression. Cells with MMR deficiency accumulate DNA errors throughout the genome. When comparing colorectal cancer that is microsatellite stable (MSS) with colorectal cancer that demonstrates MSI, MSI tumors are seen to have characteristic clinicopathologic features: they tend to occur in the proximal colon, to have a greater mucinous component, to contain lymphocytic infiltration, and to be poorly differentiated.
Multiple studies have demonstrated that the presence of MSI is a good prognostic marker, being associated with decreased rates of recurrence compared with MSS tumors. Furthermore, there is evidence to suggest that MSI patients have a lack of benefit from 5-FU in the adjuvant setting, although the Quick and Simple and Reliable (QUASAR) study had conflicting results with regard to this endpoint.
The revised Bethesda criteria indicate which patients should be tested for MSI. Tumor tissue can be tested using immunohistochemistry to evaluate for the presence of MMR proteins. This method is advantageous, as very few tumor cells are needed, and most pathology labs are able to perform the test simply and quickly. Alternatively, MSI testing can be performed by a polymerase chain reaction assay. This is a more complex and expensive process requiring more tumor cells; however, because of tissue fixation, it has the benefit that results do not vary between laboratories.
We propose that MSI testing be performed in patients who fulfill the revised Bethesda criteria and in any patient with stage II disease, as results may influence decision making regarding the value of adjuvant chemotherapy.
Gene expression profiling to guide decision making in stage II colorectal cancer
In resected stage II colorectal cancer, 5-FU–based chemotherapy confers a 5% improvement in OS at 8 years of follow-up, compared with observation alone. The current standard of care is to give adjuvant chemotherapy only to patients with clinicopathologic factors indicating high risk, such as T4 disease, perforation, obstruction, or lymphovascular/perineural involvement. However, a number of genomic signatures are now available to provide prognostic information based on molecular features of the tumor.
Oncotype DX. This 12-gene expression assay uses a recurrence score, which was validated retrospectively on 1,436 cancer specimens from the QUASAR study, to predict the risk of recurrence. Patients who were found to be at high risk had a 6% absolute improvement in 3-year recurrence rates with adjuvant therapy, while “low-risk” patients had a 3% absolute improvement. This study also confirmed that T4 disease (high-risk) and MSI (low-risk) were the strongest predictors of recurrence. Therefore, in patients with these features, there is no value to the test. In the remainder of stage II tumors, the 3-year risk of recurrence is between 12% and 22%. Although the test provides only prognostic and not predictive information, it appears to be useful in guiding high-risk patients toward and low-risk patients away from adjuvant therapy. A cost-effectiveness analysis projected that Oncotype DX testing would reduce adjuvant chemotherapy use by 17%, compared with current treatment patterns. With the test priced at $3,200, direct medical costs were expected to decrease by an average of $2,971 per patient. This cost reduction is accompanied by the benefit of adjuvant therapy being individually targeted to the patients most likely to benefit.
ColoPrint. This assay classifies a sample as being either high risk or low risk, based on the expression of 18 genes; it was validated prospectively on 114 samples. Low-risk patients had a 5-year relapse-free survival rate of 90%, while high-risk patients had a rate of 74%. The investigators concluded that two-thirds of patients are at low risk and can safely be spared the toxicity and cost of adjuvant therapy. However, it has been noted that these results may have been confounded by unusually high numbers of tumors that had either BRAF mutations or MSI, both of which confer an improved prognosis. A major limitation of this assay is the need for fresh frozen tissue.
With the recent decrease in the cost of next-generation sequencing (NGS), multiple academic and private institutions have developed panels to check tumors for mutations that may have clinical significance and lead to a more personalized approach to therapy. Currently, there is a wide range of panels evaluating from 5 to 500 mutations. Some of these mutations will lead to clinically actionable information, but many will not. There is no consensus regarding if, when, and how tumors should be sequenced using this method. Furthermore, opinions range widely, and there is no evidence base to employ when deciding how to use the results.
Perhaps the two best-known panels currently available in the United States are produced by Foundation Medicine and Caris Life Sciences. The FoundationOne panel interrogates the entire coding sequence of 315 cancer-related genes plus select introns from 28 genes that are often rearranged or altered in patients with cancer. Results are reported with suggestions for targeted therapies that may be active against the specific mutations identified. This panel was validated with reference samples of pooled cell lines that modeled key determinants of accuracy, including mutant allele frequency, indel length, and amplitude of copy change; it demonstrated a sensitivity and specificity of over 95%. FoundationOne investigators confirmed the accuracy of the panel using 249 formalin-fixed, paraffin-embedded cancer specimens that had been characterized by established assays. When the panel was applied to 2,221 cases, clinically actionable alterations were found in 76% of tumors.
Caris Life Sciences uses immunohistochemistry, fluorescence in situ hybridization, and polymerase chain reaction, in addition to NGS, in order to detect and interrogate each biomarker. A pilot study was performed in 86 patients with refractory cancer to compare PFS when using molecular profiling to guide therapy with PFS of the previous regimen on which the patient had experienced progression (ie, the patient serving as his or her own control). The results, however, have to be viewed with caution, since a comparison cohort was not used as a control population.
Overall, there is great potential for NGS to radically change the way clinical trials are developed and how we treat patients. However, until studies demonstrate the prognostic and/or predictive effectiveness of NGS approaches in specific colorectal cancer populations considering specific treatments, with appropriate comparison populations managed without NGS for validation, the use of these technologies should be limited.
Conclusions and Future Directions
A vast array of genomic tests are available for use in the management of colorectal cancer, with widely varying evidence in terms of their effectiveness and cost-effectiveness. The strongest evidence supports the role of KRAS testing in the metastatic setting and MSI testing in selected patients. There is currently no indication to test patients for DPD. UGT1A1 testing may ultimately be useful, but currently, insufficient data exist to support routine UGT1A1 testing in standard practice. For both 5-FU and irinotecan dosing, the most appropriate strategy is simply to reduce the dose if patients experience unacceptable toxicity. In the case of 5-FU, there may be a role for PK testing to guide dosing.[10,11] There may be a role for genomic signature testing, but only in selected patients with stage II disease. This strategy is now well established in the treatment of patients with breast cancer, and given that its use can prevent a significant proportion of women from receiving unnecessary chemotherapy, it appears to produce meaningful cost savings.[69-71]
Although this has not yet been fully established, prognostic signature testing may provide similar benefits in treating patients with colorectal cancer. The role of NGS is evolving. This is perhaps one of the most exciting areas of modern oncology, and recently the costs of sequencing have been falling. More research is desperately needed to establish a precise role for this strategy, in order for it to meet the criteria of being both an effective and a cost-effective test.
Although the arrival of NGS has generated much excitement in oncology, in many instances, research hopes have not translated into clinical advances. Much care must be taken when sequencing to ensure that there is an appropriate amount of viable tumor within the tested sample, since a single nucleotide polymorphism in DNA may have no implication for the subsequently transcribed RNA. This is one of many issues that have led researchers to take more interest in analyzing the downstream effects of mutations. Also, advances are being made in the emerging fields of transcriptomics (which analyzes RNA transcripts), proteomics (which analyzes the structure, function, and interactions of the proteins produced by particular genes or tissues), and epigenomics (which analyzes the methylation and histone modification of DNA, and the subsequent changes in gene expression that these processes give rise to). Advances in these disciplines will likely play an increasing role in future clinical research.
Financial Disclosure: Dr. Flowers is an unpaid consultant for Genentech and Millennium/Takeda. He also consults for Celgene, Seattle Genetics, OptumRx, Prescription Solutions, and Clinical Care Options. He reports research support from AbbVie, Acerta, Celgene, Gilead Sciences, Infinity Pharmaceuticals, Janssen, Millennium/Takeda, Onyx Pharmaceuticals, Pharmacyclics, and Spectrum. Dr. Goldstein and Dr. Shaib have no significant financial interest or other relationship with the manufacturers of any products or providers of any service mentioned in this article.
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