Východiska: Karcinom ovaria, závažné nádorové onemocnění s vysokou mortalitou, je v České republice diagnostikováno každým rokem přibližně u 1 000 žen. Riziko vzniku onemocnění je zvýšeno u nosiček mutací v některých nádorových predispozičních genech. S vysokým relativním rizikem (RR > 5) jsou spojeny mutace v genech BRCA1, BRCA2, BRIP1, geny Lynchova syndromu, RAD51C, RAD51D, STK11; s možným zvýšením rizika mutace v genech ATM, CHEK2, NBN, PALB2, BARD1. Cílem práce bylo určit frekvenci mutací v nádorových predispozičních genech v naší populaci. Metody a výsledky: Celkem 1 057 pacientek s karcinomem ovaria a 617 nenádorových kontrol bylo vyšetřeno pomocí panelového sekvenování nové generace na platformě Illumina. Patogenní mutace ve vysoko rizikových genech, vč. velkých genomových přestaveb, byly v našem souboru zachyceny u 30,6 % pacientek; u neselektovaných pacientek byla frekvence mutací téměř 25 %, u pacientek s negativní rodinnou anamnézou 18 %. Nejčastěji mutovanými predispozičními geny byly BRCA1 a BRCA2, součet frekvence mutací v ostatních ovariálních predispozičních genech odpovídal frekvenci mutací v genu BRCA2. Záchyt mutací u pacientek starších 70 let byl více než třikrát vyšší v porovnání s pacientkami ve věku pod 30 let. Závěr: Karcinom ovaria je heterogenní onemocnění s vysokým podílem dědičné formy onemocnění. Vzhledem k nedostatku adekvátních screeningových modalit pro včasnou diagnostiku onemocnění je identifikace nosiček mutací v ovariálních predispozičních genech klíčová, s vysokým potenciálem k celkovému snížení mortality z důvodu karcinomu ovaria.

Background: Ovarian cancer is a disease with high mortality. Approximately 1,000 women are diagnosed with ovarian cancer in the Czech Republic annually. Women harboring a mutation in cancer-predisposing genes face an increased risk of tumor development. Mutations in BRCA1, BRCA2, BRIP1, and Lynch syndrome genes (RAD51C, RAD51D, and STK11) are associated with a high risk of ovarian cancer, and mutations in ATM, CHEK2, NBN, PALB2, and BARD1 appear to increase the risk. Our aim was to examine the frequency of mutations in cancer-predisposing genes in the Czech Republic. Materials and methods: We analyzed 1,057 individuals including ovarian cancer patients and 617 non-cancer controls using CZECANCA panel next-generation sequencing on the Illumina platform. Pathogenic mutations in high-risk genes, including CNVs, were detected in 30.6% of patients. The mutation frequency reached 25.0% and 18.2% in subgroups of unselected ovarian cancer patients and patients with a negative family cancer history, respectively. The most frequently mutated genes were BRCA1 and BRCA2. The overall frequency of mutations in non-BRCA genes was comparable to that in BRCA2. The mutation frequency in ovarian cancer patients aged > 70 years was three times higher than that in patients diagnosed before the age of 30. Conclusion: Ovarian cancer is a heterogeneous disease with a high proportion of hereditary cases. The lack of efficient screening for early diagnosis emphasizes the importance of identifying carriers of mutations in ovarian cancer-predisposing genes; this is because proper follow-up and prevention strategies can reduce overall ovarian cancer-related mortality.

• Keywords
• panel genů,
• MeSH
• Genes, Neoplasm MeSH
• Clinical Studies as Topic MeSH
• Humans MeSH
• Mutation MeSH
• Ovarian Neoplasms * genetics   MeSH
• High-Throughput Nucleotide Sequencing methods   MeSH
• Check Tag
• Humans MeSH
• Female MeSH
• Publication type
• Research Support, Non-U.S. Gov't MeSH
• Geographicals
• Czech Republic MeSH

The aim of this study was to identify the molecular genetic cause of disease in posterior polymorphous corneal dystrophy (PPCD) probands of diverse origin and to assess the utility of massively parallel sequencing in the detection of ZEB1 mutations. We investigated a total of 12 families (five British, four Czech, one Slovak and two Swiss). Ten novel and two recurrent disease-causing mutations in ZEB1, were identified in probands by Sanger (n = 5), exome (n = 4) and genome (n = 3) sequencing. Sanger sequencing was used to confirm the mutations detected by massively parallel sequencing, and to perform segregation analysis. Genome sequencing revealed that one proband harboured a novel ∼0.34 Mb heterozygous de novo deletion spanning exons 1-7 and part of exon 8. Transcript analysis confirmed that the ZEB1 transcript is detectable in blood-derived RNA samples and that the disease-associated variant c.482-2A>G leads to aberrant pre-mRNA splicing. De novo mutations, which are a feature of PPCD3, were found in the current study with an incidence rate of at least 16.6%. In general, massively parallel sequencing is a time-efficient way to detect PPCD3-associated mutations and, importantly, genome sequencing enables the identification of full or partial heterozygous ZEB1 deletions that can evade detection by both Sanger and exome sequencing. These findings contribute to our understanding of PPCD3, for which currently, 49 pathogenic variants have been identified, all of which are predicted to be null alleles.

• MeSH
• Corneal Dystrophies, Hereditary diagnosis   genetics   metabolism   MeSH
• Child MeSH
• DNA genetics   MeSH
• Adult MeSH
• Exons MeSH
• Heterozygote MeSH
• Middle Aged MeSH
• Humans MeSH
• Adolescent MeSH
• Young Adult MeSH
• Mutation * MeSH
• DNA Mutational Analysis MeSH
• Child, Preschool MeSH
• Pedigree MeSH
• Base Sequence MeSH
• Sequence Deletion MeSH
• Aged MeSH
• Zinc Finger E-box-Binding Homeobox 1 genetics   metabolism   MeSH
• High-Throughput Nucleotide Sequencing MeSH
• Zinc Fingers MeSH
• Check Tag
• Child MeSH
• Adult MeSH
• Middle Aged MeSH
• Humans MeSH
• Adolescent MeSH
• Young Adult MeSH
• Child, Preschool MeSH
• Aged MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH

Metagenomic high-throughput sequencing (mHTS) is a hypothesis-free, universal pathogen detection technique for determination of the DNA/RNA sequences in a variety of sample types and infectious syndromes. mHTS is still in its early stages of translating into clinical application. To support the development, implementation and standardization of mHTS procedures for virus diagnostics, the European Society for Clinical Virology (ESCV) Network on Next-Generation Sequencing (ENNGS) has been established. The aim of ENNGS is to bring together professionals involved in mHTS for viral diagnostics to share methodologies and experiences, and to develop application recommendations. This manuscript aims to provide practical recommendations for the wet lab procedures necessary for implementation of mHTS for virus diagnostics and to give recommendations for development and validation of laboratory methods, including mHTS quality assurance, control and quality assessment protocols.

• MeSH
• Metagenomics * MeSH
• Viruses * genetics   MeSH
• High-Throughput Nucleotide Sequencing MeSH
• Publication type
• Journal Article MeSH

Sekvenování nové generace, nazývané také masivně paralelní sekvenování (MPS), je v současnosti nejrychleji se rozvíjející metodou molekulární genetiky, která přinese zlom v oblasti personalizované medicíny. V tomto přehledu stručně popisujeme hlavní typy MPS, kterými jsou celogenomová a exomová sekvenace, sekvenace transkriptomu a amplikonové sekvenování. Dále je uveden souhrn výhod, nevýhod a možných aplikací technologií nabízených v současnosti v České republice.

Next generation or massive parallel sequencing (MPS) is a rapidly advancing method in molecular genetics that will bring significant changes in the personalized medicine field. In this review we briefly describe major types of MPS, including whole-genome, -exome, -transcriptome and amplicon sequencing. We also present an overview of the advantages, drawbacks and possible applications of sequencing technologies available in the Czech Republic.

• Keywords
• masivně paralelní sekvenování, amplikonové sekvenování, sekvenování nové generace,
• MeSH
• Exome MeSH
• Humans MeSH
• Sequence Analysis, DNA * economics   instrumentation   trends   MeSH
• Sequence Analysis, RNA methods   MeSH
• Transcriptome MeSH
• High-Throughput Nucleotide Sequencing * economics   methods   instrumentation   MeSH
• Check Tag
• Humans MeSH
• Publication type
• Research Support, Non-U.S. Gov't MeSH
• Review MeSH

Dědičná onemocnění ledvin jsou příčinou renálního selhání u 10–15 % pacientů. K vývojovým anomáliím ledvin přispívají i genetické faktory, které se mohou vyskytovat v rodinách opakovaně. V článku jsou prezentovány dvě kazuistiky molekulárněgenetického vyšetření genů asociovaných s onemocněním ledvin. Na těchto případech je popisován proces klinické a genetické indikace lékařem, následné zpracování vzorku metodou masivního paralelního sekvenování (MPS, NGS – next generation sequencing), Sangerova sekvenování a bioinformatické zpracování hrubých dat. Ta jsou dále hodnocena a interpretována pomocí predikčních programů a odborných databází. V první případové studii byla v rodině nalezena genetická etiologie onemocnění a potvrzena diagnóza. V druhé případové studii nemohla být genetická etiologie onemocnění potvrzena z důvodu nejasné patogenity nalezených variant. Nicméně přesto bude docházet k dispenzarizaci jedinců, u kterých budou tyto varianty nalezeny.

Hereditary kidney diseases are the cause of renal failure in 10-15 % of patients. What also contributes to the development of renal abnormalities are genetic factors that can appear in families repeatedly. The article presents two case studies of molecular genetic testing of genes associated with kidney diseases. The clinical and genetic indication process carried out by the physician is described in these cases, together with the following processing of samples by massive parallel sequencing (MPS, NGS – next-generation sequencing), Sanger sequencing, and bioinformatic processing of raw data. These are further evaluated and interpreted using prediction programs and professional databases. In the first case study, a genetic etiology for the disease was discovered in the family and a diagnosis was confirmed. In the second case study, the genetic etiology of the disease could not have been confirmed due to the unclear pathogenicity of the variants found. Nevertheless, there will be dispensarization of individuals in whom these variants will be found.

• MeSH
• Molecular Diagnostic Techniques MeSH
• Child MeSH
• Genetic Diseases, Inborn * MeSH
• Labor, Induced MeSH
• Humans MeSH
• Kidney Diseases * congenital   MeSH
• Fetus abnormalities   MeSH
• Polycystic Kidney Diseases diagnosis   genetics   MeSH
• Polycystic Kidney, Autosomal Recessive diagnosis   genetics   MeSH
• Sequence Analysis, DNA MeSH
• Check Tag
• Child MeSH
• Humans MeSH
• Male MeSH
• Publication type
• Case Reports MeSH

The information on candidate cancer driver alterations available from public databases is often descriptive and of limited mechanistic insight, which poses difficulties for reliable distinction between true driver and passenger events. To address this challenge, we performed in-depth analysis of whole-exome sequencing data from cell lines generated by a barrier bypass-clonal expansion (BBCE) protocol. The employed strategy is based on carcinogen-driven immortalization of primary mouse embryonic fibroblasts and recapitulates early steps of cell transformation. Among the mutated genes were almost 200 COSMIC Cancer Gene Census genes, many of which were recurrently affected in the set of 25 immortalized cell lines. The alterations affected pathways regulating DNA damage response and repair, transcription and chromatin structure, cell cycle and cell death, as well as developmental pathways. The functional impact of the mutations was strongly supported by the manifestation of several known cancer hotspot mutations among the identified alterations. We identified a new set of genes encoding subunits of the BAF chromatin remodeling complex that exhibited Ras-mediated dependence on PRC2 histone methyltransferase activity, a finding that is similar to what has been observed for other BAF subunits in cancer cells. Among the affected BAF complex subunits, we determined Smarcd2 and Smarcc1 as putative driver candidates not yet fully identified by large-scale cancer genome sequencing projects. In addition, Ep400 displayed characteristics of a driver gene in that it showed a mutually exclusive mutation pattern when compared with mutations in the Trrap subunit of the TIP60 complex, both in the cell line panel and in a human tumor data set. We propose that the information generated by deep sequencing of the BBCE cell lines coupled with phenotypic analysis of the mutant cells can yield mechanistic insights into driver events relevant to human cancer development.

• MeSH
• Exome genetics   MeSH
• Fibroblasts MeSH
• Humans MeSH
• Mutation MeSH
• Mice MeSH
• Cell Transformation, Neoplastic genetics   MeSH
• Neoplasm Proteins genetics   MeSH
• Neoplasms genetics   MeSH
• Primary Cell Culture MeSH
• High-Throughput Nucleotide Sequencing * MeSH
• Animals MeSH
• Check Tag
• Humans MeSH
• Mice MeSH
• Animals MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Research Support, N.I.H., Extramural MeSH

Although genetic lesions responsible for some mendelian disorders can be rapidly discovered through massively parallel sequencing of whole genomes or exomes, not all diseases readily yield to such efforts. We describe the illustrative case of the simple mendelian disorder medullary cystic kidney disease type 1 (MCKD1), mapped more than a decade ago to a 2-Mb region on chromosome 1. Ultimately, only by cloning, capillary sequencing and de novo assembly did we find that each of six families with MCKD1 harbors an equivalent but apparently independently arising mutation in sequence markedly under-represented in massively parallel sequencing data: the insertion of a single cytosine in one copy (but a different copy in each family) of the repeat unit comprising the extremely long (~1.5-5 kb), GC-rich (>80%) coding variable-number tandem repeat (VNTR) sequence in the MUC1 gene encoding mucin 1. These results provide a cautionary tale about the challenges in identifying the genes responsible for mendelian, let alone more complex, disorders through massively parallel sequencing.

• MeSH
• Cytosine metabolism   MeSH
• Genetic Linkage MeSH
• Haplotypes MeSH
• Humans MeSH
• Minisatellite Repeats * genetics   MeSH
• Mucin-1 * genetics   metabolism   MeSH
• Mutation * MeSH
• Polycystic Kidney, Autosomal Dominant * MeSH
• High-Throughput Nucleotide Sequencing MeSH
• Check Tag
• Humans MeSH
• Male MeSH
• Female MeSH

Circulating tumor DNA (ctDNA) sequencing is being rapidly adopted in precision oncology, but the accuracy, sensitivity and reproducibility of ctDNA assays is poorly understood. Here we report the findings of a multi-site, cross-platform evaluation of the analytical performance of five industry-leading ctDNA assays. We evaluated each stage of the ctDNA sequencing workflow with simulations, synthetic DNA spike-in experiments and proficiency testing on standardized, cell-line-derived reference samples. Above 0.5% variant allele frequency, ctDNA mutations were detected with high sensitivity, precision and reproducibility by all five assays, whereas, below this limit, detection became unreliable and varied widely between assays, especially when input material was limited. Missed mutations (false negatives) were more common than erroneous candidates (false positives), indicating that the reliable sampling of rare ctDNA fragments is the key challenge for ctDNA assays. This comprehensive evaluation of the analytical performance of ctDNA assays serves to inform best practice guidelines and provides a resource for precision oncology.

• MeSH
• Circulating Tumor DNA genetics   MeSH
• Precision Medicine * MeSH
• Medical Oncology * MeSH
• Humans MeSH
• Limit of Detection MeSH
• Neoplasms genetics   MeSH
• Reproducibility of Results MeSH
• Sequence Analysis, DNA standards   MeSH
• Practice Guidelines as Topic MeSH
• High-Throughput Nucleotide Sequencing methods   MeSH
• Check Tag
• Humans MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Research Support, N.I.H., Extramural MeSH
• Research Support, N.I.H., Intramural MeSH
• Validation Study MeSH

• MeSH
• Nephritis, Interstitial * diagnosis   genetics   MeSH
• Humans MeSH
• Mucin-1 * genetics   MeSH
• Mutation MeSH
• Kidney Diseases genetics   MeSH
• Pedigree MeSH
• High-Throughput Nucleotide Sequencing MeSH
• Check Tag
• Humans MeSH
• Publication type
• Letter MeSH
• Research Support, Non-U.S. Gov't MeSH

Technologie sekvenování DNA nové generace mají v současné době nezastupitelné místo ve výzkumu a postupně nacházejí cestu i do oblasti klinické praxe. Sekvenační přístroje produkují velké množství dat, jejichž analýza metodami bioinformatiky je nezbytná k získání relevantních výsledků. Sekvenování se tak bez pokročilého výpočetního zpracování specializovanými algoritmy naprosto neobejde. V tomto přehledu jsou představeny základní koncepty výpočetního zpracování sekvenačních dat s přihlédnutím ke specifickým aspektům oblasti onkologie. Rovněž jsou uvedeny nejčastější problémy a překážky komplikující zpracování a biologickou interpretaci výsledků.

Next-generation sequencing technologies are currently well‑established in the research field and progressively find their way towards clinical applications. Sequencers produce vast amounts of data and therefore bioinformatics methods are needed for processing. Without computational methods, sequencing would not be able to produce relevant biological information. In this review, we introduce the basics of common NGS‑related bioinformatics methods used in oncological research. We also state some of the common problems complicating data processing and interpretation of the results. Key words: bioinformatics – high‑throughput nucleotide sequencing – mutations – cancer research – clinical application This study was supported by the European Regional Development Fund and the State Budget of the Czech Republic (RECAMO, CZ.1.05/2.1.00/03.0101), by the project MEYS – NPS I – LO1413, MH CZ – DRO (MMCI, 00209805) and BBMRI_CZ (LM2010004). The authors declare they have no potential conflicts of interest concerning drugs, products, or services used in the study. The Editorial Board declares that the manuscript met the ICMJE “uniform requirements” for biomedical papers. Submitted: 21. 4. 2015 Accepted: 26. 6. 2015

• Keywords
• technologie masivně paralelního sekvenování, referenční genom,
• MeSH
• Genome MeSH
• Data Interpretation, Statistical MeSH
• Humans MeSH
• Neoplasms genetics   MeSH
• Computational Biology * MeSH
• High-Throughput Nucleotide Sequencing * methods   MeSH
• Check Tag
• Humans MeSH
• Publication type
• Research Support, Non-U.S. Gov't MeSH
• Review MeSH