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
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
OBJECTIVES: Direct genotyping of adenovirus or enterovirus from clinical material using polymerase chain reaction (PCR) followed by Sanger sequencing is often difficult due to the presence of multiple virus types in a sample, or due to varying efficacy of PCR amplifying the capsid gene on the background of foreign nucleic acids. Here we present a simple protocol for virus genotyping using massive parallel amplicon sequencing. METHODS: The protocol utilized a set of 16 tailed degenerate primers flanking the seventh hypervariable region of the adenovirus hexon gene and 9 tailed degenerate primers targeted to the proximal portion of the enterovirus VP1 gene. Subsequent addition of dual indices enabled simultaneous sequencing of 384 different samples on an Illumina MiSeq instrument. Downstream bioinformatic analysis was based on remapping to a set of references representative of the presently known repertoire of virus types. RESULTS: After validation with known virus types, the sequencing method was applied on 301 adenovirus-positive samples and 350 enterovirus-positive samples from a longitudinally collected series of stools from 83 children aged 3 to 36 months. We detected 7 different adenovirus types and 27 different enterovirus types. There were 37 (6.2%) samples containing more than one genotype of the same viral genus. At least one dual infection was experienced by 23 of 83 (28%) of the children observed over the 3 years' observation period. CONCLUSIONS: Amplicon sequencing with a multiplex set of degenerate primers seems to be a rapid and reliable technical solution for genotyping of large collections of samples where simultaneous infections with multiple strains can be expected.
- MeSH
- Adenoviridae classification genetics isolation & purification MeSH
- Adenoviridae Infections virology MeSH
- DNA Primers genetics MeSH
- Enterovirus Infections virology MeSH
- Enterovirus classification genetics isolation & purification MeSH
- Genotype * MeSH
- Genotyping Techniques methods MeSH
- Infant MeSH
- Humans MeSH
- Longitudinal Studies MeSH
- Child, Preschool MeSH
- Sequence Analysis, DNA methods MeSH
- Computational Biology MeSH
- Animals MeSH
- Check Tag
- Infant MeSH
- Humans MeSH
- Male MeSH
- Child, Preschool MeSH
- Female MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Evaluation Study MeSH
- Research Support, Non-U.S. Gov't MeSH
- Geographicals
- Norway MeSH
AIMS: Amyloidosis is caused by deposition of abnormal protein fibrils, leading to damage of organ function. Hereditary amyloidosis represents a monogenic disease caused by germline mutations in 11 amyloidogenic precursor protein genes. One of the important but non-specific symptoms of amyloidosis is hypertrophic cardiomyopathy. Diagnostics of hereditary amyloidosis is complicated and the real cause can remain overlooked. We aimed to design hereditary amyloidosis gene panel and to introduce new next-generation sequencing (NGS) approach to investigate hereditary amyloidosis in a cohort of patients with hypertrophic cardiomyopathy of unknown significance. METHODS: Design of target enrichment DNA library preparation using Haloplex Custom Kit containing 11 amyloidogenic genes was followed by MiSeq Illumina sequencing and bioinformatics identification of germline variants using tool VarScan in a cohort of 40 patients. RESULTS: We present design of NGS panel for 11 genes (TTR, FGA, APOA1, APOA2, LYZ, GSN, CST3, PRNP, APP, B2M, ITM2B) connected to various forms of amyloidosis. We detected one mutation, which is responsible for hereditary amyloidosis. Some other single nucleotide variants are so far undescribed or rare variants or represent common polymorphisms in European population. CONCLUSIONS: We report one positive case of hereditary amyloidosis in a cohort of patients with hypertrophic cardiomyopathy of unknown significance and set up first panel for NGS in hereditary amyloidosis. This work may facilitate successful implementation of the NGS method by other researchers or clinicians and may improve the diagnostic process after validation.
- MeSH
- Adult MeSH
- Amyloidosis, Familial diagnosis genetics MeSH
- Phenotype MeSH
- Gene Frequency MeSH
- Genetic Predisposition to Disease MeSH
- Genetic Markers MeSH
- Cardiomyopathy, Hypertrophic diagnosis genetics MeSH
- Polymorphism, Single Nucleotide * MeSH
- Middle Aged MeSH
- Humans MeSH
- Mutation * MeSH
- DNA Mutational Analysis methods MeSH
- Pilot Projects MeSH
- Predictive Value of Tests MeSH
- Reproducibility of Results MeSH
- Risk Factors MeSH
- Aged, 80 and over MeSH
- Aged MeSH
- Gene Expression Profiling methods MeSH
- Transcriptome * MeSH
- Computational Biology MeSH
- High-Throughput Nucleotide Sequencing * MeSH
- Check Tag
- Adult MeSH
- Middle Aged MeSH
- Humans MeSH
- Male MeSH
- Aged, 80 and over MeSH
- Aged MeSH
- Female MeSH
- Publication type
- Journal Article 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
We describe a patient with early onset severe axonal Charcot-Marie-Tooth disease (CMT2) with dominant inheritance, in whom Sanger sequencing failed to detect a mutation in the mitofusin 2 (MFN2) gene because of a single nucleotide polymorphism (rs2236057) under the PCR primer sequence. The severe early onset phenotype and the family history with severely affected mother (died after delivery) was very suggestive of CMT2A and this suspicion was finally confirmed by a MFN2 mutation. The mutation p.His361Tyr was later detected in the patient by massively parallel sequencing with a gene panel for hereditary neuropathies. According to this information, new primers for amplification and sequencing were designed which bind away from the polymorphic sites of the patient's DNA. Sanger sequencing with these new primers then confirmed the heterozygous mutation in the MFN2 gene in this patient. This case report shows that massively parallel sequencing may in some rare cases be more sensitive than Sanger sequencing and highlights the importance of accurate primer design which requires special attention.
- MeSH
- Charcot-Marie-Tooth Disease diagnosis genetics MeSH
- DNA Primers MeSH
- GTP Phosphohydrolases genetics MeSH
- Polymorphism, Single Nucleotide * MeSH
- Humans MeSH
- Mitochondrial Proteins genetics MeSH
- Mutation * MeSH
- DNA Mutational Analysis MeSH
- Child, Preschool MeSH
- Pedigree MeSH
- High-Throughput Nucleotide Sequencing MeSH
- Check Tag
- Humans MeSH
- Male MeSH
- Child, Preschool MeSH
- Female MeSH
- Publication type
- Journal Article MeSH
- Case Reports MeSH
- Research Support, Non-U.S. Gov't MeSH
- Publication type
- Meeting Abstract 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
Patients below 55 years were genetically studied because the prevalence of isocitrate dehydrogenase 1 (IDH1) decreases in older patients and on grounds of cost-effectiveness, as suggested by the World Health Organization (WHO) in 2016. The aim of our study was to use novel massively parallel sequencing (MPS) approaches to examine rare variants of IDH1/2 in Czech diffuse astrocytic and oligodendroglial tumors (gliomas) patients below 55 years of age who had been immunohistochemically (IHC) diagnosed as IDH1 R132H negative. The IHC IDH1 status (wild type or mutant) of 275 tissue samples was analyzed using antibodies against the IDH1 R132H protein. Sixty-three samples of 55 years old patients with IHC IDH1 WT status were genotyped using two different MPS technologies to detect rare IDH1 and IDH2 variants. The tiered IHC (60 positive) and molecular (10 positive) approach thus revealed that 70 of the 275 samples (25%) bore IDH1/IDH2 mutations. The combined molecular and IHC approach thus revealed that 70 of the 275 samples (25%) considered in the study bore IDH1/IDH2 mutations. IHC detection of the IDH1 R132H variant should be routinely complemented with MPS to detect rare IDH1/2 variants in glioma patients below 55 years of age with negative IHC result of IDH R132H variant.
- MeSH
- Glioma * pathology MeSH
- Isocitrate Dehydrogenase genetics metabolism MeSH
- Middle Aged MeSH
- Humans MeSH
- Mutation MeSH
- Brain Neoplasms * diagnosis MeSH
- Retrospective Studies MeSH
- Aged MeSH
- High-Throughput Nucleotide Sequencing MeSH
- Check Tag
- Middle Aged MeSH
- Humans MeSH
- Aged MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't 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.
