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Journal of Clinical Oncology, Vol 21, Issue 16 (August), 2003: 3105-3112
© 2003 American Society for Clinical Oncology

Automated, Multiplex Assay for High-Frequency Microsatellite Instability in Colorectal Cancer

G.M. Nash, M. Gimbel, J. Shia, A.T. Culliford, D.R. Nathanson, M. Ndubuisi, Y. Yamaguchi, Z.S. Zeng, F. Barany, P.B. Paty

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.


    ABSTRACT
 TOP
 ABSTRACT
 INTRODUCTION
 METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 
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.


    INTRODUCTION
 TOP
 ABSTRACT
 INTRODUCTION
 METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 
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.1–5 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.6–17 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.13,19–22 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.23–28 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.


    METHODS
 TOP
 ABSTRACT
 INTRODUCTION
 METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 
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 marker’s 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
Oligonucleotide primers for BAT25, BAT26, BAT40, D2S123, D5S346, and D17S250 were fluorescently labeled.34 The amplification of each microsatellite marker was optimized for identical PCR conditions using AmpliTaqGold DNA Polymerase (Applied Biosystems, Foster City, CA). Every colon cancer specimen and its corresponding normal tissue (100 ng DNA per reaction) were analyzed for all six microsatellite markers by uniplex PCRs. The PCR products were resolved in an ABI PRISM 377 DNA Sequencer (Applied Biosystems).

ASI Analysis
ASI of microsatellite markers in cancer specimens was detected and distinguished from PCR stutter using Genotyper 2.5 software (Applied Biosystems). Following their detection during electrophoresis, peaks were ordered by size (smallest to largest) and individually labeled with their sizes in base pairs. Then, using parameters provided by Applied Biosystems, labels were removed from peaks that were followed within 3.0 base pairs, or preceded within 1.6 base pairs, by a higher amplitude peak. Thus, only the true allele peaks remained labeled. Allelic size instability was defined as the identification in a tumor of a novel-size allele; that is, an allele with a length not seen in normal colonic mucosa from the same individual.

LOH Analysis
The dinucleotide markers D2S123, D5S346, and D17S250 were also examined for LOH events. Allele peak heights were measured in relative fluorescent units using Genotyper 2.5 software. For each marker that was informative (ie, yielded two alleles) in normal tissue, the peak heights in normal and tumor tissue were noted. An LOH event was defined as a 50% to 100% change in height of allele number one relative to allele number two when comparing tumor to normal tissue.

Multiplexing
Each microsatellite marker’s sensitivity for ASI was assessed from the uniplex PCRs performed on tumor and normal tissues from the 18 HNPCC patients. The three most sensitive microsatellite markers were then combined in a multiplex assay in which the three PCR reactions were performed simultaneously in a single tube. PCR primer concentrations for BAT25 and D2S123 were reduced to 30% of that used in uniplex PCRs. To achieve similar peak amplitudes for all three markers, the concentration of BAT26 primers was reduced to 10% of the uniplex level. Multiplex PCRs for these three microsatellite markers were performed on tumor and normal tissues for all 120 patients. In addition, uniplex PCRs for the three microsatellite markers were performed in 120 patients. MSI was scored as present when at least two of three markers showed size instability for both methods.

Morphology
Using 3-µm sections taken from paraffin blocks and stained with hematoxylin and eosin, a pathologist evaluated the morphology of CRCs from 16 of the 18 HNPCC patients and 72 of the 120 patients. Tumors were assigned as possible MSI if they showed poor differentiation, medullary component, histologic heterogeneity, or apparently increased tumor-infiltrating lymphocytes.35–37 Slides for 48 sporadic and two HNPCC cancers were unavailable for pathology review.

Statistics
The Pearson’s {chi}2 or Fisher’s exact tests were applied to the results as appropriate. All reported P values are two-sided, and P values of <= .05 were considered significant. Survival curves were generated by the Kaplan-Maier method and subjected to the log-rank test.


    RESULTS
 TOP
 ABSTRACT
 INTRODUCTION
 METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 
There was successful PCR amplification of all microsatellite loci in 100% of samples for both uniplex and multiplex reactions.

HNPCC Specimens
BAT25, BAT26, D2S123, D5S346, and D17S250 showed different sensitivities for detection of ASI. The size instability detection rate in HNPCC tumors was 100%, 94%, 72%, 50%, and 50%, respectively (Table 1Go). LOH was not observed in the HNPCC tumors.


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Table 1. Allele Size Instability in Hereditary Nonpolyposis Cancer Tumors, by Microsatellite Marker
 
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 2Go). By NCI guidelines, cancers with ASI in at least two loci would be classified as MSI-H, cancers with ASI in one locus would be classified as MSI-L, and cancers with ASI at no loci would be classified as MSS.


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Table 2. Allele Size Instability in Early Onset Colorectal Adenocarcinoma, by Microsatellite Marker
 
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
Mononucleotide ASI was present in all 18 HNPCC tumors and dinucleotide ASI was present in 14 HNPCC tumors (Table 1Go). Among early-onset cancers, size instability in BAT25 or BAT26 was less frequent than size instability in at least one dinucleotide marker (17% v 33% of cancers, respectively). ASI of mononucleotide repeat sequences BAT25 and BAT26 was present almost exclusively in the 19 patients identified as having MSI tumors by the multiplex assay. There was BAT25 ASI observed in one MSS/MSI-L patient and BAT26 ASI observed in no MSS/MSI-L patients. Differences in the prevalence of LOH were also observed. LOH was lower in tumors with BAT25/26 ASI compared with those with only dinucleotide ASI (15% v 62%). Twenty-three percent (nine of 40) of tumors with dinucleotide ASI had both LOH and ASI at the same locus.

Multiplexing
Of the five NCI panel markers, BAT25, BAT26, and D2S123 had the greatest sensitivity (100%, 94%, and 72%, respectively) for ASI in HNPCC cancers. These three markers were combined into a multiplex assay (Fig 1Go). The multiplex assay assigns MSI status when two or more of the three markers show allelic size instability. There was identical scoring of ASI and LOH for the individual primers (BAT25, BAT26, and D2S123) in every tumor sample, whether the PCR was uniplex or multiplex.



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Fig 1. Polyacrylamide gel image and electropherograms for a hereditary nonpolyposis colorectal cancer tumor paired with normal tissue.

 
Multiplex Assay Versus NCI Assay
There were fewer cancers identified as having MSI by the multiplex assay compared with the NCI assay (Table 2Go). When the NCI assay was used, the prevalence of MSI (MSI/NCI) was 23% (n = 28) in 120 early-onset colon cancers. Using the multiplex assay, the prevalence of MSI (MSI/multiplex) was 16% (n = 19). All clinical stages of cancer were present in each MSI cohort (MSI/multiplex: I, n = 4; II, n = 10; III, n = 3; IV, n = 2; and MSI/NCI: I, n = 5; II, n = 11; III, n = 6; IV, n = 6). LOH was observed in three of 19 (16%) MSI/multiplex patients and in 63 of 101 (63%) MSS/multiplex patients (P = .0001). LOH was observed in 10 of 28 (36%) MSI/NCI patients and in 56 of 92 (61%) MSS/NCI patients (P = .03). The additional patients identified as MSI-H by the NCI assay had a significantly higher prevalence of LOH compared with the MSI/multiplex patients (78% v 16%; P = .003).

Morphology
HNPCC tumors showed MSI morphology in 63% (10 of 16) of patients. Morphology consistent with MSI was demonstrated in 64% (nine of 14) of MSI/multiplex patients. None of the additional eight MSI/NCI patients examined demonstrated morphology consistent with MSI (P = .006). Morphology consistent with MSI was demonstrated in only 9% (five of 58) of the MSS/multiplex patients examined.

Survival
In total, 46 of the 120 early-onset patients died during a median follow-up of 4.9 years after surgery. The 5-year actuarial disease-free survival of patients with MSI/multiplex cancers was significantly better than that of patients with MSS/multiplex cancers (100% v 55%; P = .0004; Fig 2Go) and better than that of the additional patients identified as MSI by the NCI assay (100% v 44%; P = .0003; Fig 3Go).



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Fig 2. Disease-specific survival for patients 60 years of age (n = 41), stratified by multiplex assay. MSS, microsatellite stability.

 


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Fig 3. Disease-specific survival for patients 60 years of age (n = 41), stratified by National Cancer Institute (NCI) assay. MSI, microsatellite instability.

 
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 3Go). There was a discrepancy between BAT25 (ASI) and BAT26 (allele size stability [ASS]) in this patient, with D2S123, D5S346, and D17S250 all showing ASI, whereas BAT40 showed ASS. In the two other patient cases of disagreement between BAT25 and BAT26, BAT40 agreed with the remaining markers in both patients (Table 3Go). There were four MSI-L patients, defined by ASI in one dinucleotide marker, that also had ASI of BAT40. None of these four patients had MSI morphology, two had LOH, and two had died of disease at last follow-up.


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Table 3. BAT25 and BAT26 Disagreement
 

    DISCUSSION
 TOP
 ABSTRACT
 INTRODUCTION
 METHODS
 RESULTS
 DISCUSSION
 REFERENCES
 
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 1Go) and marker specificities ranged from 100% to 89% (Table 2Go). We selected the three microsatellites with the highest sensitivity for detecting ASI in HNPCC (BAT25, BAT26, and D2S123) to form a multiplex assay. We also designed the multiplex assay to exclude the marker (D17S250) with the greatest frequency (11%; 10 of 89 patients) of supplying what was suspected to be false-positive data; that is, ASI in tumors that were otherwise reported as ASS by the other four microsatellite markers. Moreover, the three microsatellite markers selected for the multiplex assay have been shown to be the most technically reliable and reproducible markers for MSI analysis.29 The multiplex assay also excludes D5S346, which has been shown to be the least reproducible marker among different laboratories using different techniques of microsatellite assessment.29

In the test group of patients with early-onset CRC (age <= 60 years; n = 120), the 19 tumors identified as MSI-H by the multiplex assay had infrequent detection of an LOH event (three of 19 patients). In contrast, of the nine additional tumors identified as MSI-H by the NCI assay, seven (77%) had an LOH event. This finding indicates that these seven tumors have allelic imbalance characteristic of CIN tumors and casts doubt on the validity of the assignment of the tumor as MSI-H by the NCI assay. Furthermore, the patients identified as having MSI-H tumors by the multiplex assay have a characteristic clinical phenotype not shared by the nine additional MSI-H patients. MSI tumor morphology was present in the majority of HNPCC tumors (63%) and MSI/multiplex tumors (64%), whereas it was infrequently seen in the additional MSI-H/NCI tumors (0%) and MSS tumors (9%). None of the MSI/multiplex patients died as a result of cancer (median follow-up, 7.4 years). However, in the MSI-H/NCI cohort, survival was much less consistent (5-year survival, 82%) because of five cancer deaths among the nine patients with MSI-H added by the NCI assay. It should be noted that the 5-year survival rate (82%) observed in our MSI-H/NCI cohort is similar to the survival rate (76%) previously reported for MSI-H using the NCI assay in a large, population-based study of early-onset CRC.14 Therefore, we believe that our data reflect an accurate molecular analysis of a representative population with early-onset CRC.

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.44–47 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.49–53 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.


    NOTES
 
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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 INTRODUCTION
 METHODS
 RESULTS
 DISCUSSION
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Submitted November 26, 2002; accepted May 29, 2003.


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