394 erence panel of 5–10 microsatellite loci is used to diagnose MSI cases [30], for which three categories have been estab- lished: MSI-High (MSI-H), unstable for 30% of markers used; MSI-Low (MSI-L), unstable for 10%–30% of mark- ers used; and microsatellite stable (MSS), for cases that dis- play no MSI. Lack of expression of MMR proteins as assessed by immunohistochemistry (IHC) (primarily using antibodies to the MLH1 protein) is diagnostic for dMMR and is often used in MSI tumor analysis as an alternative to PCR, and additionally in the clinical setting to complement genetic testing for Lynch syndrome patients [24]. In clinical studies, MSI rates have been shown to vary with tumor stage—22% reported in stage II, 12% reported in stage III, and 2% reported in stage IV disease [31]. In the adjuvant setting, MSI tumor status has been shown to be a significant prognostic marker. The majority of retrospec- tive studies (Table 2) demonstrate that patients with MSI-H (or dMMR) colon cancers have higher survival rates than those with MSS tumors [32–34]. These findings were con- firmed in a meta-analysis of 32 trials, which confirmed the prognostic advantage in patients with MSI-H tumors and those treated with 5-FU– based adjuvant therapy [35]. In the PETACC-3 study, the prognostic value of MSI status was found to be more significant in patients with stage II disease than in stage III cases [36]. In addition, in a multivariate analysis of stage II colon cancer patients from the QUick and Simple And Reliable (QUASAR) study, Kerr and col- leagues demonstrated that MMR deficiency (hazard ratio [HR], 0.31; 95% confidence interval [CI], 0.15– 0.63; p .001) and T4 stage (HR, 1.94; 95% CI, 1.35–2.79; p .005) (together accounting for 25% of patients) were independent prognostic factors for tumor recurrence [37]. Similar find- ings were reported in a multivariate analysis of the PETACC-3 data [36]. The value of MSI tumor status as a predictive marker of adjuvant therapy is less clear. An early study suggested that MSI-H was predictive of response to 5-FU– based adjuvant therapy in patients with stage III colon cancer [38]. How- ever, an accumulating body of evidence suggests that pa- tients with MSI-H tumors do not benefit from 5-FU– based adjuvant therapy, compared with patients with MSS tumors [33, 35, 39, 40]. This is particularly relevant for patients with stage II disease, for whom adjuvant chemotherapy (5-FU alone) is reported to increase survival by approxi- mately 3%, and has led some investigators to recommend that stage II colon tumors should be analyzed for dMMR status to guide decisions on the use of adjuvant therapy [39]. Recently the CALGB 89803 study reported a higher 5-year DFS rate in stage III colon cancer patients with MMR-deficient/MSI-H tumors treated with irinotecan plus Biomarkers in Colon Cancer Adjuvant Treatment 5-FU than in patients treated with the same regimen with intact MMR proteins: this was not observed in patients treated with 5-FU and leucovorin (LV) alone, suggesting that tumor MSI status might be predictive of response to iri- notecan in stage III colon cancer [41]. In contrast, the PETACC-3 study, in 1,327 patients, failed to demonstrate a predictive effect of tumor MSI status for patients treated with irinotecan, 5-FU, and LV, compared with those receiv- ing 5-FU alone [36, 42]. To date, MSI is considered to be a strong and well- validated prognostic marker in adjuvant CRC, and it is cur- rently the only such biomarker in this setting. In the appropriate clinical setting, we would advocate that MSI data may be used in clinical decision making, particularly in stage II colon cancers, for which a favorable outcome of pa- tients with MSI-H tumors suggests that these patients should not receive adjuvant chemotherapy [43]. The assess- ment of MSI tumor status as a predictive marker for adju- vant therapy requires more data. It should also be considered, however, that the value of MSI tumor status as a prognostic or predictive marker in the adjuvant setting may be effected by mutations to other genes involved in co- lon cancer etiology, such the BRAF gene (discussed below) [44]. Chromosome 18q AI/CIN Chromosome 18q AI has been associated with poor prog- nosis in stage II and stage III CRC patients in some studies [45– 48], but not others [34, 49] (Table 2). Watanabe and colleagues reported that patients with stage III MSS colon tumors with no 18q AI had a higher survival rate following 5-FU– based treatment (70% versus 50%) than those whose tumors displayed 18q AI [50]. In the CALGB 89803 study, stage III colon cancer patients with 18q AI had lower 5-year DFS (0.78 versus 0.93) and OS (0.85 versus 0.98) rates than patients whose tumors displayed no 18q AI [51]. However, drawing conclusions from comparing chromosome 18q AI studies in colon cancer is difficult, and differences in the methodologies used, including the scoring of AI, possibly explains the contradictory findings reported. Thus, the in- consistency of the genetic markers used among studies leads to analysis of AI in different regions on chromosome 18q. An additional complication comes from the stage-spe- cific effects of biomarkers. The PETACC group presented, at the 2009 American Society of Clinical Oncology Annual Meeting [36], that tumor 18q AI status was not found to be prognostic in stage II tumors, whereas an effect was found in stage III tumors on univariate analysis. This is important because the patient population most in need of prognostic markers is stage II patients, for whom treatment versus no treatment is based on the inherent prognostic features. Cur-