Novel genetic and epigenetic alterations in ... - Ous-research.no

RØYRVIK ET AL.the PubMed database; search terms were compositions of mononucleotide, microsatellites,repeats, genes, frameshift, and the MeSH term neoplasms. From therelevant articles, with the cut-off date for inclusion being December 2006, mutationfrequency data for genes with coding microsatellites (or microsatellites in intronsand UTRs, as mentioned below) was pooled. Included were studies on MSItumors and cell lines of all tissue types in which the MSI phenotype occurs, theoverwhelming majority being gastrointestinal and endometrial tumors. Inclusionof mutation data on cell lines was kept to a minimum, as cell lines cannot be usedto represent the situation in primary tumors with regard to the frequencies offrameshift mutations of this type. 44,49 Table I encompasses those genes and studiessuitable for pooling, across tissue types but with particular attention to sporadic,primary colorectal tumors.TABLE IMutation frequencies of microsatellite-containing genesGene symbol—the most common name for any given gene in the scientific corpussurveyed; HGNC symbol—the name approved by the Human Genome NomenclatureCommittee, updated to October, 2007; Repeat—the repeat unit andnumber of units of microsatellites that were tested; Gene location—the location ofthe repeat within the gene, taken when possible from the scientific corpus, otherwisefrom Ensembl Exon View of a representative transcript; Chr. Location—the location of the gene on a chromosome, taken when possible from the scientificcorpus, otherwise from Ensembl or GeneCards.org; Mut%(tot)—the mutationfrequency across all studies of any microsatellite unstable tumor type; Mut S/C—the number of mutated samples across studies of colorectal carcinomas (mostlysporadic, but with HNPCC cases and cell lines where these could not be separated)over the total number of samples; Mut% S/C—the mutation frequencyacross studies of colorectal carcinomas (mostly sporadic, but with HNPCC casesand cell lines where these could not be separated); Ref—Articles from which mutationfrequency information was pooled.Gene HGNC RepeatChr. Location(tot)%(S/C)Mut %MutMut. S/CRefs.ABCF1 ABCF1 (A)10 6p21.33 29 % 17/58 29 %44,52AC1 C4orf6 (T)10 4p16.2 68 % 14/20 70 %53,54ACTRII ACVR2A (A)8 2q22.3 70 % 95/140 68 %55-59AD7c-NTP (T)8 1p36 6 % 2/35 6 %55AIM2 AIM2 (A)10 1q22 52 % 46/81 57 %44,55,56AMYB MYBL1 (A)8 8q22 11 %56ANG2 ANGPT2 (A)9 8p23.1 4 % 2/57 4 %49APAF-1 APAF1 (A)8 12q23 8 % 5/79 6 %60-62ATM ATM (T)7 11q22-23 13 % 4/44 9 %63-65ATR ATR (A)10 3q23 23 % 55/252 22 %17,44,49,53,66,67AXIN2 AXIN2(G)7,59,68,6917q24.1 20 % 18/81 22 %(C)6,(A)6,(C)5234