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© 2003 American Society for Clinical Oncology Automated, Multiplex Assay for High-Frequency Microsatellite Instability in Colorectal Cancer
From the Departments of Surgery and Pathology, Memorial Sloan-Kettering Cancer Center, New York; and the Department of Microbiology, Weill Medical College of Cornell University, Ithaca, NY. Address reprint requests to Philip B. Paty, MD, Department of Surgery, Memorial Sloan-Kettering Cancer Center, 1275 York Ave, New York, NY 10021; email: patyp{at}mskcc.org.
Purpose: In a series of hereditary nonpolyposis colorectal cancer (HNPCC) patients, we evaluated the sensitivities of the individual microsatellites recommended by the National Cancer Institute (NCI) consensus workshop for detection of high-frequency microsatellite instability (MSI-H). On the basis of this evaluation, we developed a three-marker assay that assigns microsatellite instability (MSI) in a multiplex polymerase chain reaction. Methods: Individual marker sensitivity was assessed in 18 HNPCC tumors. Multiplex and NCI assays were then assessed in a series of 120 patients with early-onset colon cancer. Results: The sensitivity of microsatellite markers BAT25, BAT26, D2S123, D5S346, and D17S250 for ASI in HNPCC cancers was 100%, 94%, 72%, 50%, and 50%, respectively. The three most accurate markers were combined and optimized in a multiplex assay that assigned MSI-H whenever at least two of three markers revealed ASI. In early-onset colon cancers, the prevalence of MSI-H determined by the multiplex assay and by the NCI assay was 16% and 23%, respectively. The additional MSI-H tumors and patients with MSI-H identified by the NCI assay lacked the traits characteristic of MSI-H seen in tumors and patients identified by the multiplex assay: retention of heterozygosity (NCI additional 22% v multiplex 84%; P = .003), characteristic tumor morphology (0% v 64%; P = .006), and 5-year cancer survival rate (44% v 100%; P = .0003). Conclusion: The multiplex assay identifies colon cancers with MSI-H by assessing three highly accurate microsatellite markers. This assay identifies a smaller MSI-H cohort with more homogeneous clinical features and is superior as a marker of favorable prognosis. It merits prospective evaluation as a marker of prognosis and as a screening test for HNPCC.
TWO MAJOR pathways of genomic instability have been identified in colorectal cancer: a chromosomal instability (CIN) pathway and a high-frequency microsatellite instability (MSI-H) pathway.15 CIN is found in the majority of cancers and is characterized by aneuploidy, loss of heterozygosity (LOH), chromosomal amplifications, and translocations. MSI-H is found in 10% to 20% of primary colorectal cancers (CRCs) and is characterized by diploidy and mutation or methylation silencing of mismatch repair (MMR) genes.617 In cancers with MSI-H, the MMR pathway is defective and cancer cells are unable to repair slippage mutations that occur during DNA replication. The cancers accumulate unrepaired slippage events throughout the genome but particularly in microsatellites.2,12,13 Routine evaluation of tumors for the presence or absence of MSI-H at the time of clinical presentation with CRC has significant potential for improving patient management. MSI-H is present in more than 85% of CRCs that occur in families with hereditary nonpolyposis colon cancer (HNPCC).13,18 MSI-H is also found in approximately 10% to 15% of cancers not associated with HNPCC, many of which have lost MMR function because of methylation silencing of the MLH1 gene.10,11 At present, MSI-H testing remains primarily a research tool, but it can be helpful in the clinical assessment and management of CRC patients. MSI-H may serve as a screening test for patients with heritable mutations in MMR genes that cannot be identified accurately by clinical presentation or family history alone.13,1922 In addition, retrospective studies have shown that MSI-H is an important prognostic marker because CRCs with MSI-H have a favorable prognosis after surgical resection.14,15 Moreover, the response of CRCs with MSI-H to treatment with chemotherapeutic agents may be different from that of microsatellite stable (MSS) cancers.2328 Thus, the currently available data present a strong rationale for routine assessment of MSI-H in primary CRCs, particularly for patients who enter chemoprevention or adjuvant therapy trials. The accuracy of MSI-H as a marker to identify colon cancers that have lost MMR function is variable and is dependent on the technical details of the assay. Molecular diagnosis of MSI-H using polymerase chain reaction (PCR) assays, although not technically demanding, has not been fully standardized.29 MSI-H analyses have varied with regard to the microsatellite markers used, the method for detecting allele size instability (ASI), and the number and proportion of microsatellite markers with size instability required for a positive diagnosis of MSI-H. To standardize the molecular definition of MSI-H, in 1997 a National Cancer Institute (NCI) workshop recommended a panel of five microsatellite markers. These loci were selected for their efficacy in identifying colorectal adenocarcinomas with loss of hMSH2 or hMLH1 expression.29,30 The panel consisted of two mononucleotide microsatellites (BAT25, BAT26) and three dinucleotide microsatellites (D2S123, D5S346, and D17S250).31 MSI-H tumors are defined by the NCI workshop as having at least two of five microsatellite markers demonstrating instability. Low-frequency microsatellite instability (MSI-L) and MSS are defined by size instability in one or zero markers, respectively.31 The NCI panel of microsatellite markers, or variations of it, has been used for correlative studies of survival and molecular profiling in CRC and for screening patients for HNPCC tumors. However, no rigorous evaluation of the accuracy of these markers has been published, despite evidence that ASI, especially among dinucleotide markers, may occur in tumors that retain an intact DNA MMR pathway.32 It was our aim to examine the individual sensitivities of the markers for microsatellite slippage events in HNPCC tumors and their specificity in a larger series of all CRCs. To facilitate more informative clinical correlative studies, we wished to develop a rapid, automated MSI assay. We reasoned that MSI analysis would be made simpler, faster, less costly, and possibly more accurate if only the most sensitive microsatellite markers were used and they could be combined in a single, automated reaction. In this article, we compare results of an optimized, multiplex, three-marker MSI assay to the established five-marker assay recommended by the 1997 NCI workshop.
Tumor Samples Tumor and normal tissue was collected under Institutional Review Board protocol from patients having surgery for CRC at Memorial Sloan-Kettering Cancer Center, New York, NY. The operations were performed between November 1992 and November 2000. Tissue was obtained at time of surgical resection and snap frozen in liquid nitrogen. DNA was extracted and purified using a proteinase K, phenol-chloroform, LiCl, and EtOH protocol. Tissue from 18 patients with HNPCC, defined by Amsterdam Criteria, served as positive controls for MSI.33 These positive controls were used to evaluate each microsatellite markers sensitivity for detecting ASI. To compare the performance of the NCI and multiplex assays, a series of 120 early-onset (age 60 years) colon cancer patients were identified from our frozen tumor bank (stage I, n = 14; stage II, n = 27; stage III, n = 35; and stage IV, n = 44).
PCR
ASI Analysis
LOH Analysis
Multiplexing
Morphology
Statistics
There was successful PCR amplification of all microsatellite loci in 100% of samples for both uniplex and multiplex reactions.
HNPCC Specimens
Early-Onset Cancer Specimens When the NCI panel of five loci was used, ASI was seen in at least two loci in 23% of specimens (28 of 120), at one locus in 11% (13 of 120), and at no loci in 66% (79 of 120; Table 2
At least one LOH event was observed in 55% (66 of 120) of early-onset cancers. LOH was observed in 36% (10 of 28) of the tumors with MSI-H by NCI criteria (MSI-H/NCI) and in 61% (56 of 92) of the tumors with MSS by NCI criteria (MSS/NCI). LOH was observed in 46% (six of 13) of the tumors with MSI-L by NCI criteria (MSI-L/NCI).
Mononucleotide Repeat Versus Dinucleotide Repeat Size Instability
Multiplexing
Multiplex Assay Versus NCI Assay There were fewer cancers identified as having MSI by the multiplex assay compared with the NCI assay (Table 2
Morphology
Survival
BAT40 The mononucleotide BAT40 was assessed in all tumors to determine if use of a third mononucleotide marker in place of D2S123 might improve the accuracy of MSI-H assessment. In the HNPCC patients, BAT40 had intermediate sensitivity for ASI (evident in 13 of 18 patients), which was comparable to that of D2S123 (evident in 13 of 18 patients). In the 120 early-onset colon cancers, BAT40 showed ASI in 57% (16 of 28) of MSI-H/NCI patients, in 31% (four of 13) of MSI-L/NCI patients, and in 6% (five of 79) of MSS/NCI patients. If BAT40 was substituted for D2S123 in the multiplex assay, only one tumor among the 120 early-onset cancers would have changed its MSI designation (from MSI-H to MSS; Table 3
MSI-H has particular clinical importance in the assessment of CRC patients. Each year, there are an estimated 20,000 patients diagnosed with CRCs with MSI-H in the United States.38 Patients with HNPCC represent approximately 5% of all patients with CRC,39 and patients with sporadic MSI account for an additional 10% to 15%.14 In both instances, MSI indicates disruption of the MMR pathway within the cancer cells. The availability of an MSI test that is rapid and highly accurate in identifying the presence or absence of MMR deficiency in colorectal tumors is crucial for successful use of MSI testing in clinical and research applications. Clinical uses include screening patients with early-onset, familial, or metachronous colon cancer for germline mutation testing for HNPCC, as well as individualizing prognosis for all patients with colon cancer. The research applications are numerous and include studies of cancer surveillance, chemoprevention, cancer progression, molecular profiling, and adjuvant therapy.
Developments in PCR technology, fluorescent labeling of DNA fragments, and computer-aided detection and analysis of gel banding patterns have improved the use of microsatellites in DNA diagnostics.40,41 These advances prompted us to examine the molecular diagnosis of MSI in CRC as outlined by the NCI workshop in 1997. Our goal was a simpler, more rapid, and more accurate method of MSI-H assessment. Because the value of an individual microsatellite marker is based on its ability to report accurately the status of the MMR pathway within tumors, we evaluated the performance of the five microsatellite markers used in the NCI assay in reporting ASI in HNPCC cancers and in reporting ASS in sporadic MSS cancers. We found marker sensitivities for ASI ranged from 100% to 50% (Table 1
In the test group of patients with early-onset CRC (age The NCI consensus group defined MSI-L as one of five markers with ASI. In contrast to MSI-H tumors, MSI-L tumors do not have loss of MSH2 or MLH1 expression.42 Phenotypically MSI-L tumors appear to be indistinguishable from MSS tumors.43 Recently, evidence has emerged indicating that MSI-L tumors represent a third pathway of colorectal carcinogenesis. Much controversy remains regarding the genetic origin and background of MSS and MSI-L tumors.4447 The analysis of MSI-L is difficult because the greater the number of microsatellites that are interrogated, the larger the MSI-L group becomes.48 Our assay does not attempt to distinguish MSS from MSI-L. Given that these groups are clinically indistinguishable with our current knowledge, the distinction of these groups remains a research endeavor. Our purpose was to improve the accuracy and usefulness of MSI-H assessment. Published reports indicate that mononucleotide markers have greater sensitivity and specificity for MMR deficiency than dinucleotide markers;29,32 this conclusion is supported by our own analysis. In HNPCC tumors, BAT25 and BAT26 were highly sensitive for microsatellite instability (ASI in 33 of 36 inquiries), whereas in sporadic tumors presumed to be competent in MMR (MSS and MSI-L), ASI was rare (with ASI in one of 184 inquiries). In contrast, dinucleotide instability was only moderately sensitive for microsatellite instability in HNPCC tumors (ASI in 31 of 54 inquiries), and was also present at low frequency in MSS and MSI-L tumors (ASI in 12 of 276 inquiries). However, the high sensitivity and specificity of mononucleotide markers for MSI-H did not extend to BAT40. Using BAT40, we found ASI in 13 of 18 inquiries in HNPCC tumors and in nine of 92 inquiries in MSS and MSI-L tumors. This 10% rate of ASI in MSS/MSI-L tumors indicates poor specificity for MSI-H, second only to D17S250 among the six markers tested. A multiplex assay designed with only the mononucleotide markers (BAT25, BAT26, and BAT40) would not have reclassified any tumors as MSI-H; one tumor with four of five markers positive by the NCI assay would have been dubiously reclassified as MSS. In contrast, we have shown that D2S123 is 72% sensitive for HNPCC and 99% specific for MSS, and others have shown that it is 100% reproducible.29 To exclude D2S123 in favor of a less reliable mononucleotide would ignore these experimental data. These findings do not support the use of BAT40 in our MSI-H assay. Investigators have argued that BAT26 alone may be sufficient to identify MSI-H.49,50 However, no single microsatellite marker is likely to have perfect accuracy for identifying colon cancers with DNA MMR deficiency.4953 We recorded one HNPCC tumor and two sporadic MSI-H tumors with ASS at BAT26. On the other hand, evaluating many microsatellite markers to increase sensitivity can leave the assay vulnerable to loss of specificity. The multiplex assay addresses this problem by retaining the three most sensitive markers and requiring two markers with ASI for a positive result and two markers with ASS for a negative result. By relying on concordance of at least two markers, a high degree of accuracy is obtained. If microsatellite analysis is to be useful for detection of MMR deficiency, the MSI assay must achieve high specificity. If the true prevalence of MMR deficiency in a series of CRCs is 12% and if an MSI-H assay has a sensitivity of 100% but a specificity of only 85%, more than half of the patients identified with MSI-H will not have true MMR deficiency. This large number of misclassified patients would result in high costs of germline mutation screening and would severely handicap investigators in correlative studies. A simple, rapid, and highly accurate MSI-H assay has the potential to improve the management of CRC patients both in routine practice and in clinical research. The multiplex assay presented here is well suited for this task.
Supported by a grant from the National Cancer Institute (2 P01 CA65930-05A2) and by the philanthropy of Marie and William Bianco. This work was presented, in part, as a poster at the May 2002 meeting of the American Society of Clinical Oncology under the title, "An Objective, Multiplex Microsatellite Instability (MSI) Assay for Colorectal Adenocarcinoma."
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Copyright © 2003 by the American Society of Clinical Oncology, Online ISSN: 1527-7755. Print ISSN: 0732-183X
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