No abstract

Insertion-deletion polymorphisms (INDELs) are diallelic markers derived from a single mutation event. Their low mutation frequency makes them suitable for forensic and parentage testing. The examination of INDELs thus combines advantages of both short tandem repeats (STR) and single nucleotide polymorphisms (SNP). This type of polymorphisms may be examined using as small amplicon size as SNP (about 100 bp) but could be analyzed by techniques used for routine STR analysis. For our population study, we genotyped 55 unrelated Czech individuals. We also genotyped 11 trios to analyze DIPplex Kit (QIAGEN, Germany) suitability for parentage testing. DIPplex Kit contains 30 diallelic autosomal markers. INDELs in DIPplex Kit were tested with linkage disequilibrium test, which showed that they could be treated as independent markers. All 30 loci fulfill Hardy–Weinberg equilibrium. There were several significant differences between Czech and African populations, but no significant ones within European population. Probability of a match in the Czech population was 1 in 6.8 × 1012; combined power of discrimination was 99.9999999999%. Average paternity index was 1.13–1.77 for each locus; combined paternity index reached about 27,000 for a set of 30 loci. We can conclude that DIPplex kit is useful as an additional panel of markers in paternity cases when mutations in STR polymorphisms are present. For application on degraded or inhibited samples, further optimization of buffer and primer concentrations is needed.Electronic supplementary materialThe online version of this article (doi:10.1007/s00414-011-0649-3) contains supplementary material, which is available to authorized users.

An expanded polyglutamine stretch in the huntingtin protein has been identified as the pathogenetic cause of Huntington's disease (HD). Although the length of the expanded polyglutamine repeat is inversely correlated with the age-at-onset, additional genetic factors are thought to modify the variance in the disease onset. As linkage analysis suggested a modifier locus on chromosome 4p, we investigated the functional relevance of S18Y polymorphism of the ubiquitin carboxy-terminal hydrolase L1 in 946 Caucasian HD patients. In this group, the allelic variation on locus S18Y is responsible for 1.1% of the variance in the HD age-at-onset, and the rare Y allele is associated with younger-aged cases.

Familial adenomatous polyposis (FAP) is an autosomal dominant predisposition to colorectal cancer and is caused by germline mutations in the adenomatous polyposis coli gene. The most prominent clinical manifestation is the presence of hundreds to thousands of colorectal polyps.A milder phenotype is found in patients affected with AFAP/ multiple adenomas. We screened the entire APC coding region using the combination of DGGE, PTT and direct sequencing and identified causative mutations in 52 of 77 patients. Thirteen of the mutations found were novel. In addition, we also tested 21 APC mutation/negative probands for the two most common mutations in the MYH gene. Four patients showed neither dominant transmission of the disease nor evidence of APC mutations. In one of them the most common biallelic germline mutation in the MYH gene was detected. Correlations between the localization of germline mutations and clinical manifestations of the diseases are discussed. © 2004 Wiley-Liss, Inc.KEY WORDS: adenomatous polyposis coli; APC; familial adenomatous polyposis; FAP; MYH; multiple adenomas INTRODUCTIONFamilial adenomatous polyposis (FAP, MIM# 175100) is a dominantly inherited colorectal cancer predisposition caused by germline mutations in the adenomatous polyposis coli gene ( APC, Gene Bank NM_000038.2). Its prevalence in the Czech Republic has been estimated to be 1 per 5000-7500. Clinically FAP is characterized by the development of hundreds to thousands of polyps, which are present mainly in the colon. The polyps appear during the teenage years and if left untreated they progress to colorectal cancer at the average age of 39 years. Because FAP shows nearly 100% penetration (Bisgaard et al., 1994) genetic testing of the at-risk relatives and the early prevention of cancer development are very important.The APC gene encodes a tumor suppressor protein expressed in a wide variety of tissues. In colonic epithelial 2 Vandrovcová et al.cells APC protein plays an essential role in the control of the cell cycle progression by preventing β-catenin accumulation. β-catenin activates transcription of specific target genes such as protooncogenes cyclin D1 and c-myc (Sieber et al., 2000). Germline mutations in the APC gene are found in about 80% of patients affected with FAP while inactivating somatic mutations occur in FAP tumors and i n most cases of sporadic colorectal carcinomas (Powell et al., 1992(Powell et al., , 1993Hutter et al., 2001). Germline mutations are scattered thorough the whole APC gene, however, they are predominantly distributed in the 5' half of the gene. About 95% of the mutations are nonsense or truncating frameshift mutations. Mutational analysis has revealed that there is an apparent correlation between the mutation site and the phenotype of patients. This concordance has been proved especially for the severity of the disease and some extracolonic manifestations, such as desmoid tumors and congenital hypertrophy of the retinal pigment epithelium (CHRPE) (Fearnhead et al., 2001). In addition to the class...

The expansion of a polymorphic CAG repeat in the HD gene encoding huntingtin has been identified as the major cause of Huntington's disease (HD) and determines 42-73% of the variance in the age-at-onset of the disease. Polymorphisms in huntingtin interacting or associated genes are thought to modify the course of the disease. To identify genetic modifiers influencing the age at disease onset, we searched for polymorphic markers in the GRIK2, TBP, BDNF, HIP1 and ZDHHC17 genes and analysed seven of them by association studies in 980 independent European HD patients. Screening for unknown sequence variations we found besides several silent variations three polymorphisms in the ZDHHC17 gene. These and polymorphisms in the GRIK2, TBP and BDNF genes were analysed with respect to their association with the HD age-at-onset. Although some of the factors have been defined as genetic modifier factors in previous studies, none of the genes encoding GRIK2, TBP, BDNF and ZDHHC17 could be identified as a genetic modifier for HD.