Clinical background: Patient RM, YoB 1966 Her family were originally referred because of a history of breast and ovarian cancer. BRCA testing found a missense mutation which has been classified as a polymorphism. The cancer registry reported RM as having an endometrial cancer (another endometrial cancer confirmed in the family), therefore diagnosis of HNPCC considered. Tumour actually of ovarian origin. Testing: Jul 2009 IHC shows loss of MSH6 in adenocarcinoma MSI high 5/7 markers BRAF V600E negative MSH6 screening recommended Nov 2009 No pathogenic variants detected in MSH6 by sequence analysis or MLPA MLPA did detect a heterozygous duplication of MSH2 exons 1-6 (confirmed by 2 different MLPA kits)

Other information: IHC and MSI of cousin’s ovarian cancer have not shown any abnormalities. Discuss: How should this be reported? Is it clearly pathogenic? What follow-up, if any, should be recommended?

REPORT SUMMARY: Heterozygous duplication of exons 1 to 6 in the MSH2 gene. Report interpretation: RM has been referred for MSH6 gene analysis because she has clinical features of HNPCC. Previous studies of an ovarian tumour sample from her have shown evidence of microsatellite instability in 5 of the 7 markers tested. Immunohistochemistry showed loss of MSH6 protein expression from adenocarcinoma (see report dated xx/xx/xxxx for lab number). Molecular analysis has not detected any sequence variants in the MSH6 gene other than common polymorphisms of no known clinical significance. Furthermore MLPA analysis did not show any evidence of whole exon deletions or duplications of the MSH6 gene. The MLPA kit used for analysis of the MSH6 gene also contains a probe for exon 1 of the MSH2 gene, which showed evidence of a duplication. Further MLPA analysis of the MSH2 gene has identified a duplication of MSH2 exons 1 to 6. This duplication has not been previously reported in the literature or reported on the InSiGHT database. The clinical significance of this duplication of exons 1 to 6 is as yet unclear as the the location of the duplicated segment and its break points are unknown. It is therefore not appropriate to offer presymptomatic testing to at-risk relatives at this point. Further analysis of this duplication will be performed to attempt to elucidate any pathological significance and we would recommend screening of other affected family members to determine if the duplication segregates with the disease. If you wish to discuss this result further please contact the laboratory. These results are dependent upon the information supplied being correct and complete. Basis of test: Sequence analysis has been used to screen all coding exons of the MSH6 gene. Expected false negative rate is <1%. No known SNPs with a population frequency of >1% identified under the primers used. MLPA analysis of all exons of the MSH2 and MSH6 genes to detect exon deletions and duplications (MRC-Holland kit P003-B1/P008). Sequence nomenclature using HGVS guidelines. Genbank accession numbers: NM_ (MSH2)/NM_ (MSH6). DNA has been stored.