New molecular biology methods have specified the evidence of chromosomal changes in the tumor tissue. These alterations can be proven to exist in the majority of malignant tumors. The fast progress of whole genome molecular biological methods has helped to improve the knowledge of tumor genetics. The evidence of genetic changes is a component of currently used diagnostic and prognostic schemes in particular cancer diseases. Karyotyping was the first method used in the clinical practice but its importance has decreased with the arrival of new molecular biological methods. The most common methods used for the detection of chromosomal deletions or amplifications are CGH, array-CGH and SNP array. The first two methods are based on the principle of comparison between tumor DNA and control DNA. The principle of SNP array uses the presence of single nucleotide polymorphisms that are located in the whole genome in each individual. SNP array can prove not only deletions or amplifications of the chromosomes but unlike CGH techniques it can also detect a loss of heterozygosity or uniparental disomy. The screening of chromosomal changes has nowadays become routine. These techniques are used for diagnosis, prognosis and treatment of cancer disease in certain cases.

• MeSH
• chromozomální aberace MeSH
• DNA nádorová analýza   genetika   MeSH
• jednonukleotidový polymorfismus genetika   MeSH
• lidé MeSH
• nádory diagnóza   genetika   MeSH
• sekvenční analýza hybridizací s uspořádaným souborem oligonukleotidů metody   MeSH
• srovnávací genomová hybridizace metody   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH
• Názvy látek
• DNA nádorová MeSH

Alterations in the genome that lead to changes in DNA sequence copy number are characteristic features of solid tumors. We used CGH+SNP microarray and HPV-FISH techniques for detailed screening of copy number alterations (CNAs) in a cohort of 26 patients with cervical carcinoma (CC). This approach identified CNAs in 96.2% (25/26) of tumors. Array-CGH discovered CNAs in 73.1% (19/26) of samples, HPV-FISH experiments revealed CNAs in additional 23.1% (6/26) of samples. Common gains of genetic sequences were observed in 3q (50.0%), 1q (42.4%), 19q (23.1%), while losses were frequently found in 11q (30.8%), 4q (23.1%) and 13q (19.2%). Chromosomal regions involved in loss of heterozygosity were observed in 15.4% of samples in 8q21, 11q23, 14q21 and 18q12.2. Incidence of gain 3q was associated with HPV 16 and HPV 18 positive samples and simultaneous presence of gain 1q (P = 0.033). We did not found a correlation between incidence of CNAs identified by array-CGH and HPV strain infection and incidence of lymph node metastases. Subsequently, HPV-FISH was used for validation of array-CGH results in 23 patients for incidence of hTERC (3q26) and MYC (8q24) amplification. Using HPV-FISH, we found chromosomal lesions of hTERC in 87.0% and MYC in 65.2% of specimens. Our findings confirmed the important role of HPV infection and specific genomic alterations in the development of invasive cervical cancer. This study also indicates that CGH+SNP microarrays allow detecting genome-wide CNAs and copy-neutral loss of heterozygosity more precisely, however, it may be less sensitive than FISH in samples with low level clonal CNAs.

• Klíčová slova
• CGH+SNP microarrays, Cervical carcinoma, HPV-FISH, copy number alterations, whole-genome profiling,
• MeSH
• dospělí MeSH
• hybridizace in situ fluorescenční MeSH
• infekce papilomavirem komplikace   genetika   MeSH
• karcinom genetika   virologie   MeSH
• lidé středního věku MeSH
• lidé MeSH
• nádory děložního čípku genetika   virologie   MeSH
• sekvenční analýza hybridizací s uspořádaným souborem oligonukleotidů metody   MeSH
• senioři MeSH
• senzitivita a specificita MeSH
• srovnávací genomová hybridizace metody   MeSH
• stanovení celkové genové exprese metody   MeSH
• variabilita počtu kopií segmentů DNA MeSH
• ztráta heterozygozity genetika   MeSH
• Check Tag
• dospělí MeSH
• lidé středního věku MeSH
• lidé MeSH
• senioři MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

BACKGROUND: We investigated the features of the genomic rearrangements in a cohort of 50 male individuals with proteolipid protein 1 (PLP1) copy number gain events who were ascertained with Pelizaeus-Merzbacher disease (PMD; MIM: 312080). We then compared our new data to previous structural variant mutagenesis studies involving the Xq22 region of the human genome. The aggregate data from 159 sequenced join-points (discontinuous sequences in the reference genome that are joined during the rearrangement process) were studied. Analysis of these data from 150 individuals enabled the spectrum and relative distribution of the underlying genomic mutational signatures to be delineated. METHODS: Genomic rearrangements in PMD individuals with PLP1 copy number gain events were investigated by high-density customized array or clinical chromosomal microarray analysis and breakpoint junction sequence analysis. RESULTS: High-density customized array showed that the majority of cases (33/50; ~ 66%) present with single duplications, although complex genomic rearrangements (CGRs) are also frequent (17/50; ~ 34%). Breakpoint mapping to nucleotide resolution revealed further previously unknown structural and sequence complexities, even in single duplications. Meta-analysis of all studied rearrangements that occur at the PLP1 locus showed that single duplications were found in ~ 54% of individuals and that, among all CGR cases, triplication flanked by duplications is the most frequent CGR array CGH pattern observed. Importantly, in ~ 32% of join-points, there is evidence for a mutational signature of microhomeology (highly similar yet imperfect sequence matches). CONCLUSIONS: These data reveal a high frequency of CGRs at the PLP1 locus and support the assertion that replication-based mechanisms are prominent contributors to the formation of CGRs at Xq22. We propose that microhomeology can facilitate template switching, by stabilizing strand annealing of the primer using W-C base complementarity, and is a mutational signature for replicative repair.

• Klíčová slova
• BIR, Duplication, Genome instability, Genomic rearrangements, HR, LCR, MMBIR, Microhomeology, PMD, RBM,
• MeSH
• body zlomu chromozomu MeSH
• duplikace genu MeSH
• genetická predispozice k nemoci MeSH
• genetické asociační studie MeSH
• genom lidský MeSH
• genomika metody   MeSH
• genová přestavba * MeSH
• jednonukleotidový polymorfismus MeSH
• lidé MeSH
• mutace * MeSH
• myelinový proteolipidový protein genetika   MeSH
• nestabilita genomu MeSH
• srovnávací genomová hybridizace MeSH
• variabilita počtu kopií segmentů DNA * MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, N.I.H., Extramural MeSH
• Názvy látek
• myelinový proteolipidový protein MeSH
• PLP1 protein, human MeSH Prohlížeč