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Background  Changes in the number of alleles of a chromosome may have an impact upon gene expression. Loss of heterozygosity (LOH) indicates that one allele of a gene has been lost, and knowing the exact copy number of the gene would indicate whether duplication of the remaining allele has occurred. We were interested to determine the copy number of the  Adenomatous Polyposis Coli  ( APC ) gene in sporadic colorectal cancers with LOH.    Methods  We selected 38 carcinomas with LOH for the  APC  gene region of chromosome 5, as determined by amplification of the CA repeat region within the D5S346 loci. The copy number status of  APC  was ascertained using the SALSA® MLPA® P043-B1 APC Kit. LOH for the  DCC  gene,  KRAS  gene mutation, and microsatellite instability were also evaluated for each tumor, utilizing standard polymerase chain reaction methods.    Results  No tumor demonstrated microsatellite instability. LOH of the  DCC  gene was also present in 33 of 36 (91.7 %) informative tumors. A  KRAS  gene mutation was present in 16 of the 38 (42.1 %) tumors. Twenty-four (63.2 %) of the tumors were copy number neutral, 10 (26.3 %) tumors demonstrated major loss, while two (5.3 %) showed partial loss. Two tumors (5.3 %) had copy number gain.    Conclusions  Results of  APC  and  DCC  LOH,  KRAS  and microsatellite instability indicate our colorectal cancer cases were typical of sporadic cancers following the ‘chromosomal instability’ pathway. The majority of our colorectal carcinomas with LOH for  APC  gene are copy number neutral. However, one-third of our cases showed copy number loss, suggesting that duplication of the remaining allele is not required for the development of a colorectal carcinoma.

Copy number of the Adenomatous Polyposis Coli gene is not always neutral in sporadic colorectal cancers with loss of heterozygosity for the gene