PMC

Schematic classification of colorectal cancers (CRCs). MSI, microsatellite instability.

Microsatellite instability (MSI) determination of two microsatellites in the same, multiplexed run. The upper tracing is from blood DNA showing (A)n mononucleotide marker BAT26 at 120 bp and (CA)n dinucleotide marker D2S123 at 170 bp. The patient is homozygous for both markers. The lower tracing is from the same patient's tumor DNA. Arrows point to the new alleles in BAT26 at 114 bp and in D2S123 at 172 and 160 bp. The fact that D2S123 displays two novel alleles suggests that the tumor consists of at least two different clonal expansions. Note the “stutter” bands that occur both in the dinucleotide marker and, more strongly, in the mononucleotide marker. These are believed to be produced during the polymerase chain reaction and do not occur in vivo.

Tracings of polymerase chain reaction (PCR) amplicons containing microsatellite D2S123, a highly polymorphic (CA)n dinucleotide. One PCR primer was end labeled with fluorescent dye, the amplicon was run on a sequencer, and it was analyzed by the Genotyper software. Lengths of the amplicons containing the microsatellite and the strength of the signal are indicated. The upper tracing is from blood DNA displaying heterozygosity, with one allele measuring 164 bp and the other allele measuring 184 bp in length (arrows). The lower tracing is from the same patient's colorectal tumor showing two new alleles, which measure 162 bp and 178 bp in length (arrows). This means that both of the germline alleles were mutated in the tumor. The persistence of the germline alleles most likely emanates from noncancerous tissue present in the tumor specimen (eg, tumor-infiltrating lymphocytes, stroma, blood vessels).