392 APC MLH1 TP53 SMAD4 KRAS BRAF Table 1. Genes commonly involved in sporadic CRC Gene Protein function Negative regulator of WNT signaling involved in controlling cell proliferation in the colon and small intestine DNA single nucleotide mismatch repair Transcription factor regulating downstream target genes involved in cell cycle regulation Component of the TGF- signaling pathway GDP/GTP binding protein facilitating ligand dependent TK growth factor signaling Serine–threonine protein kinase that acts as a downstream effector of KRAS-mediated signaling Biomarkers in Colon Cancer Adjuvant Treatment Defect in CRC Inactivation by mutations leading to loss of function of APC protein (protein truncation) and constitutive activation of WNT signaling Epigenetic silencing leading to loss of protein expression and the accumulation of cellular mutations Inactivating (nonsense and misense) mutations leading to loss of function of wild-type protein Target of AI on chromosome 18q, gene inactivation by homozygous deletion/ mutation Activation (most commonly through codon 12/13 misense mutations) leading to activation of the RAF–MEK–ERK pathway Activation most commonly through a valine-to-glutamic acid amino acid (V600E) substitution Frequency (%) 85 15–25 35–55 10–35 35–45 8–12 Abbreviations: AI, allelic imbalance; CRC, colorectal cancer; ERK, extracellular signal–related kinase; MEK, mitogen- activated protein kinase/extracellular signal–related kinase kinase; TGF- , transforming growth factor ; TK, tyrosine kinase. tumor suppressor gene [11–15]. A summary of the genes involved in sporadic colon cancer development is shown in Table 1. A more detailed molecular analysis of colon can- cers revealed colon tumors to be heterogeneous with regard to molecular alterations and potentially categorizable into specific tumor phenotypes based on their molecular pro- files. Two of these represent genetic instability classes. The majority of sporadic cases (up to 85%) display chromo- somal instability (CIN), which manifests as aneuploid and polyploid karyotypes and multiple structural chromosomal changes [12, 13, 16, 17]. This phenotype is thought to arise through defects in a number of processes, including aber- rant expression or mutation of mitotic checkpoint genes, microtubule spindle defects, and telomere dysfunction [18]. In contrast, the remaining 15% of sporadic colon can- cers demonstrate a microsatellite instability (MSI) pheno- type, in which tumors display insertion– deletion mutations, most commonly in short tandemly repeated nucleotides (microsatellites) [19, 20]. Chromosome losses are rarer in these tumors, which tend to have a diploid karyotype [17, 21]. The underlying genetic mechanism responsible for this phenotype is loss of function, predominantly through gene silencing of DNA mismatch repair (MMR) genes, in partic- ular, MLH1 in sporadic CRC [22, 23]. Consequently, this phenotype is also often referred to as the MMR deficient (dMMR) phenotype, and in 2%–3% of CRC is caused by germline mutations to one of a number of MMR genes (MLH1, MSH2, MSH6, and PMS2) that form part of the pre- sentation of Lynch syndrome, or hereditary nonpolyposis CRC [24]. Whereas patients with an MSI/dMMR tumor phenotype have a relatively stable karyotype, a deficient re- pair process in tumors leads to loss of function mutations in tumor suppressor genes, including TGFBR2, IGF2R, and PTEN, and is associated with gain-of-function mutations in oncogenes such as BRAF [25–27]; this phenomenon, in turn, is often referred to as a “mutator” phenotype. Finally, the analysis of CpG island methylation in the silencing of genes in colon tumors has led to the identifica- tion of the CpG island methylator phenotype, which ap- pears to partially overlap the MSI phenotype [28, 29]. A summary of the clinical utility of a number of prom- ising candidate markers in the adjuvant setting is presented in Table 2 and reviewed below. Genomic Instability Phenotypes as Biomarkers MSI MSI can be detected in tumors by a number of complemen- tary approaches. Using the polymerase chain reaction (PCR) to amplify specific microsatellite repeats, the pres- ence of instability can be monitored through a comparison of the length of repeats obtained from normal DNA (typi- cally extracted from adjacent normal mucosa cells) with those from the DNA extracted from the tumor cells. A ref-