@article {32, title = {Exome Sequencing Identifies Biallelic MSH3 Germline Mutations as a Recessive Subtype of Colorectal Adenomatous Polyposis.}, journal = {Am J Hum Genet}, volume = {99}, year = {2016}, month = {2016 Aug 04}, pages = {337-51}, abstract = {

In \~{}30\% of families affected by colorectal adenomatous polyposis, no germline mutations have been identified in the previously implicated genes APC, MUTYH, POLE, POLD1, and NTHL1, although a hereditary etiology is likely. To uncover further genes with high-penetrance causative mutations, we performed exome sequencing of leukocyte DNA from 102 unrelated individuals with unexplained adenomatous polyposis. We identified two unrelated individuals with differing compound-heterozygous loss-of-function (LoF) germline mutations in the mismatch-repair gene MSH3. The impact of the MSH3 mutations (c.1148delA, c.2319-1G>A, c.2760delC, and c.3001-2A>C) was indicated at the RNA and protein levels. Analysis of the diseased individuals{\textquoteright} tumor tissue demonstrated high microsatellite instability of di- and tetranucleotides (EMAST), and immunohistochemical staining illustrated a complete loss of nuclear MSH3 in normal and tumor tissue, confirming the LoF effect and causal relevance of the mutations. The pedigrees, genotypes, and frequency of MSH3 mutations in the general population are consistent with an autosomal-recessive mode of inheritance. Both index persons have an affected sibling carrying the same mutations. The tumor spectrum in these four persons comprised colorectal and duodenal adenomas, colorectal cancer, gastric cancer, and an early-onset astrocytoma. Additionally, we detected one unrelated individual with biallelic PMS2 germline mutations, representing constitutional mismatch-repair deficiency. Potentially causative variants in 14 more candidate genes identified in 26 other individuals require further workup. In the present study, we identified biallelic germline MSH3 mutations in individuals with a suspected hereditary tumor syndrome. Our data suggest that MSH3 mutations represent an additional recessive subtype of colorectal adenomatous polyposis.

}, keywords = {Adenomatous Polyposis Coli, Adolescent, Adult, Alleles, Child, Preschool, Colorectal Neoplasms, DNA Mutational Analysis, DNA-Binding Proteins, Exome, Female, Genes, Recessive, Germ-Line Mutation, Humans, Male, Middle Aged, Mismatch Repair Endonuclease PMS2, MutS Homolog 3 Protein, Pedigree}, issn = {1537-6605}, doi = {10.1016/j.ajhg.2016.06.015}, author = {Adam, Ronja and Spier, Isabel and Zhao, Bixiao and Kloth, Michael and Marquez, Jonathan and Hinrichsen, Inga and Kirfel, Jutta and Tafazzoli, Aylar and Horpaopan, Sukanya and Uhlhaas, Siegfried and Stienen, Dietlinde and Friedrichs, Nicolaus and Altm{\"u}ller, Janine and Laner, Andreas and Holzapfel, Stefanie and Peters, Sophia and Kayser, Katrin and Thiele, Holger and Holinski-Feder, Elke and Marra, Giancarlo and Kristiansen, Glen and N{\"o}then, Markus M and B{\"u}ttner, Reinhard and M{\"o}slein, Gabriela and Betz, Regina C and Brieger, Angela and Lifton, Richard P and Aretz, Stefan} } @article {93, title = {Exome sequencing identifies potential novel candidate genes in patients with unexplained colorectal adenomatous polyposis.}, journal = {Fam Cancer}, volume = {15}, year = {2016}, month = {2016 Apr}, pages = {281-8}, abstract = {

In up to 30\% of patients with colorectal adenomatous polyposis, no germline mutation in the known genes APC, causing familial adenomatous polyposis, MUTYH, causing MUTYH-associated polyposis, and POLE or POLD1, causing Polymerase-Proofreading-associated polyposis can be identified, although a hereditary etiology is likely. To uncover new causative genes, exome sequencing was performed using DNA from leukocytes and a total of 12 colorectal adenomas from seven unrelated patients with unexplained sporadic adenomatous polyposis. For data analysis and variant filtering, an established bioinformatics pipeline including in-house tools was applied. Variants were filtered for rare truncating point mutations and copy-number variants assuming a dominant, recessive, or tumor suppressor model of inheritance. Subsequently, targeted sequence analysis of the most promising candidate genes was performed in a validation cohort of 191 unrelated patients. All relevant variants were validated by Sanger sequencing. The analysis of exome sequencing data resulted in the identification of rare loss-of-function germline mutations in three promising candidate genes (DSC2, PIEZO1, ZSWIM7). In the validation cohort, further variants predicted to be pathogenic were identified in DSC2 and PIEZO1. According to the somatic mutation spectra, the adenomas in this patient cohort follow the classical pathways of colorectal tumorigenesis. The present study identified three candidate genes which might represent rare causes for a predisposition to colorectal adenoma formation. Especially PIEZO1 (FAM38A) and ZSWIM7 (SWS1) warrant further exploration. To evaluate the clinical relevance of these genes, investigation of larger patient cohorts and functional studies are required.

}, keywords = {Adenomatous Polyposis Coli, Adenomatous Polyps, Aged, Desmocollins, Exome, Female, Genetic Predisposition to Disease, Germ-Line Mutation, High-Throughput Nucleotide Sequencing, Humans, Ion Channels, Male, Middle Aged, Reproducibility of Results}, issn = {1573-7292}, doi = {10.1007/s10689-016-9870-z}, author = {Spier, Isabel and Kerick, Martin and Drichel, Dmitriy and Horpaopan, Sukanya and Altm{\"u}ller, Janine and Laner, Andreas and Holzapfel, Stefanie and Peters, Sophia and Adam, Ronja and Zhao, Bixiao and Becker, Tim and Lifton, Richard P and Holinski-Feder, Elke and Perner, Sven and Thiele, Holger and N{\"o}then, Markus M and Hoffmann, Per and Timmermann, Bernd and Schweiger, Michal R and Aretz, Stefan} } @article {112, title = {Low-level APC mutational mosaicism is the underlying cause in a substantial fraction of unexplained colorectal adenomatous polyposis cases.}, journal = {J Med Genet}, volume = {53}, year = {2016}, month = {2016 Mar}, pages = {172-9}, abstract = {

BACKGROUND: In 30-50\% of patients with colorectal adenomatous polyposis, no germline mutation in the known genes APC, causing familial adenomatous polyposis, MUTYH, causing MUTYH-associated polyposis, or POLE or POLD1, causing polymerase-proofreading-associated polyposis can be identified, although a hereditary aetiology is likely. This study aimed to explore the impact of APC mutational mosaicism in unexplained polyposis.

METHODS: To comprehensively screen for somatic low-level APC mosaicism, high-coverage next-generation sequencing of the APC gene was performed using DNA from leucocytes and a total of 53 colorectal tumours from 20 unrelated patients with unexplained sporadic adenomatous polyposis. APC mosaicism was assumed if the same loss-of-function APC mutation was present in >= 2 anatomically separated colorectal adenomas/carcinomas per patient. All mutations were validated using diverse methods.

RESULTS: In 25\% (5/20) of patients, somatic mosaicism of a pathogenic APC mutation was identified as underlying cause of the disease. In 2/5 cases, the mosaic level in leucocyte DNA was slightly below the sensitivity threshold of Sanger sequencing; while in 3/5 cases, the allelic fraction was either very low (0.1-1\%) or no mutations were detectable. The majority of mosaic mutations were located outside the somatic mutation cluster region of the gene.

CONCLUSIONS: The present data indicate a high prevalence of pathogenic mosaic APC mutations below the detection thresholds of routine diagnostics in adenomatous polyposis, even if high-coverage sequencing of leucocyte DNA alone is taken into account. This has important implications for both routine work-up and strategies to identify new causative genes in this patient group.

}, keywords = {Adenomatous Polyposis Coli, Adolescent, Adult, Colorectal Neoplasms, Genes, APC, High-Throughput Nucleotide Sequencing, Humans, Middle Aged, Mutation, Mutation Rate}, issn = {1468-6244}, doi = {10.1136/jmedgenet-2015-103468}, author = {Spier, Isabel and Drichel, Dmitriy and Kerick, Martin and Kirfel, Jutta and Horpaopan, Sukanya and Laner, Andreas and Holzapfel, Stefanie and Peters, Sophia and Adam, Ronja and Zhao, Bixiao and Becker, Tim and Lifton, Richard P and Perner, Sven and Hoffmann, Per and Kristiansen, Glen and Timmermann, Bernd and N{\"o}then, Markus M and Holinski-Feder, Elke and Schweiger, Michal R and Aretz, Stefan} } @article {202, title = {Frequency and phenotypic spectrum of germline mutations in POLE and seven other polymerase genes in 266 patients with colorectal adenomas and carcinomas.}, journal = {Int J Cancer}, volume = {137}, year = {2015}, month = {2015 Jul 15}, pages = {320-31}, abstract = {

In a number of families with colorectal adenomatous polyposis or suspected Lynch syndrome/HNPCC, no germline alteration in the APC, MUTYH, or mismatch repair (MMR) genes are found. Missense mutations in the polymerase genes POLE and POLD1 have recently been identified as rare cause of multiple colorectal adenomas and carcinomas, a condition termed polymerase proofreading-associated polyposis (PPAP). The aim of the present study was to evaluate the clinical relevance and phenotypic spectrum of polymerase germline mutations. Therefore, targeted sequencing of the polymerase genes POLD1, POLD2, POLD3, POLD4, POLE, POLE2, POLE3 and POLE4 was performed in 266 unrelated patients with polyposis or fulfilled Amsterdam criteria. The POLE mutation c.1270C>G;p.Leu424Val was detected in four unrelated patients. The mutation was present in 1.5\% (4/266) of all patients, 4\% (3/77) of all familial cases and 7\% (2/30) of familial polyposis cases. The colorectal phenotype in 14 affected individuals ranged from typical adenomatous polyposis to a HNPCC phenotype, with high intrafamilial variability. Multiple colorectal carcinomas and duodenal adenomas were common, and one case of duodenal carcinoma was reported. Additionally, various extraintestinal lesions were evident. Nine further putative pathogenic variants were identified. The most promising was c.1306C>T;p.Pro436Ser in POLE. In conclusion, a PPAP was identified in a substantial number of polyposis and familial colorectal cancer patients. Screening for polymerase proofreading mutations should therefore be considered, particularly in unexplained familial cases. The present study broadens the phenotypic spectrum of PPAP to duodenal adenomas and carcinomas, and identified novel, potentially pathogenic variants in four polymerase genes.

}, keywords = {Adenoma, Adolescent, Adult, Aged, Aged, 80 and over, Child, Colorectal Neoplasms, DNA Polymerase II, DNA-Directed DNA Polymerase, Family Health, Female, Gene Frequency, Genetic Predisposition to Disease, Germ-Line Mutation, Humans, Isoenzymes, Male, Middle Aged, Mutation, Missense, Pedigree, Phenotype, Phospholipase D, Poly-ADP-Ribose Binding Proteins, Polymorphism, Single Nucleotide, Sequence Analysis, DNA, Young Adult}, issn = {1097-0215}, doi = {10.1002/ijc.29396}, author = {Spier, Isabel and Holzapfel, Stefanie and Altm{\"u}ller, Janine and Zhao, Bixiao and Horpaopan, Sukanya and Vogt, Stefanie and Chen, Sophia and Morak, Monika and Raeder, Susanne and Kayser, Katrin and Stienen, Dietlinde and Adam, Ronja and N{\"u}rnberg, Peter and Plotz, Guido and Holinski-Feder, Elke and Lifton, Richard P and Thiele, Holger and Hoffmann, Per and Steinke, Verena and Aretz, Stefan} }