Epilepsia je komplexné neurologické ochorenie, ktoré postihuje 40 - 60 miliónov ľudí na celom svete. V patogenéze epilepsie zohrávajú významnú úlohu viaceré genetické faktory, čo vedie k rastúcemu významu genetiky v oblasti epileptológie. S rozvojom metodík využívajúcich masívne paralelné sekvenovanie boli identifikované mnohé DNA varianty spôsobujúce epilepsiu, čím sa zlepšuje naše chápanie molekulárnych mechanizmov súvisiacich s klinickými prejavmi geneticky podmienených epilepsií. V tejto práci ponúkame prehľad súčasných, ale aj budúcich možností genetickej diagnostiky epilepsie, ktorá prostredníctvom určenia génových variantov u pacientov s monogénovou aj polygénovou epilepsiou môže otvoriť cestu k cielenej personalizovanej diagnostike a liečbe.
Epilepsy is a complex neurological disease that affects 40-60 million people worldwide. Multiple genetic factors play a significant role in the pathogenesis of epilepsy, leading to the growing importance of genetics in the field of epileptology. With the development of methodologies using massively parallel sequencing, many DNA variants causing epilepsy have been identified, improving our understanding of the molecular mechanisms involved in the clinical manifestations of genetically determined epilepsies. In this paper, we offer an overview of current but also future possibilities for genetic diagnostics of epilepsy, which, by identifying gene variants in patients with both monogenic and polygenic epilepsy, may open the way to targeted personalized diagnosis and treatment.
- MeSH
- diagnostické techniky molekulární metody MeSH
- epilepsie * diagnóza genetika klasifikace MeSH
- genetické testování * metody MeSH
- karyotypizace metody MeSH
- lidé MeSH
- sekvenování celého genomu metody MeSH
- sekvenování exomu metody MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- práce podpořená grantem MeSH
- přehledy MeSH
BACKGROUND: Whole exome sequencing (WES) and whole genome sequencing (WGS) have become standard methods in human clinical diagnostics as well as in population genomics (POPGEN). Blood-derived genomic DNA (gDNA) is routinely used in the clinical environment. Conversely, many POPGEN studies and commercial tests benefit from easy saliva sampling. Here, we evaluated the quality of variant call sets and the level of genotype concordance of single nucleotide variants (SNVs) and small insertions and deletions (indels) for WES and WGS using paired blood- and saliva-derived gDNA isolates employing genomic reference-based validated protocols. METHODS: The genomic reference standard Coriell NA12878 was repeatedly analyzed using optimized WES and WGS protocols, and data calls were compared with the truth dataset published by the Genome in a Bottle Consortium. gDNA was extracted from the paired blood and saliva samples of 10 participants and processed using the same protocols. A comparison of paired blood-saliva call sets was performed in the context of WGS and WES genomic reference-based technical validation results. RESULTS: The quality pattern of called variants obtained from genomic-reference-based technical replicates correlates with data calls of paired blood-saliva-derived samples in all levels of tested examinations despite a higher rate of non-human contamination found in the saliva samples. The F1 score of 10 blood-to-saliva-derived comparisons ranged between 0.8030-0.9998 for SNVs and between 0.8883-0.9991 for small-indels in the case of the WGS protocol, and between 0.8643-0.999 for SNVs and between 0.7781-1.000 for small-indels in the case of the WES protocol. CONCLUSION: Saliva may be considered an equivalent material to blood for genetic analysis for both WGS and WES under strict protocol conditions. The accuracy of sequencing metrics and variant-detection accuracy is not affected by choosing saliva as the gDNA source instead of blood but much more significantly by the genomic context, variant types, and the sequencing technology used.
- MeSH
- DNA genetika MeSH
- exom MeSH
- genom lidský MeSH
- genomika MeSH
- lidé MeSH
- metagenomika * MeSH
- sekvenování celého genomu MeSH
- sekvenování exomu MeSH
- sliny * MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
Circulating extracellular DNA (ecDNA) is known to worsen the outcome of many diseases. ecDNA released from neutrophils during infection or inflammation is present in the form of neutrophil extracellular traps (NETs). It has been shown that higher ecDNA concentration occurs in a number of inflammatory diseases including inflammatory bowel disease (IBD). Enzymes such as peptidyl arginine deiminases (PADs) are crucial for NET formation. We sought to describe the dynamics of ecDNA concentrations and fragmentation, along with NETosis during a mouse model of chemically induced colitis. Plasma ecDNA concentration was highest on day seven of dextran sulfate sodium (DSS) intake and the increase was time-dependent. This increase correlated with the percentage of cells undergoing NETosis and other markers of disease activity. Relative proportion of nuclear ecDNA increased towards more severe colitis; however, absolute amount decreased. In colon explant medium, the highest concentration of ecDNA was on day three of DSS consumption. Early administration of PAD4 inhibitors did not alleviate disease activity, but lowered the ecDNA concentration. These results uncover the biological characteristics of ecDNA in IBD and support the role of ecDNA in intestinal inflammation. The therapeutic intervention aimed at NETs and/or nuclear ecDNA has yet to be fully investigated.
- MeSH
- biologické markery metabolismus MeSH
- deoxyribonukleasy metabolismus MeSH
- DNA krev metabolismus MeSH
- endoskopie MeSH
- extracelulární pasti účinky léků metabolismus MeSH
- extracelulární prostor metabolismus MeSH
- kolitida krev chemicky indukované patologie MeSH
- mitochondriální DNA krev MeSH
- myši inbrední C57BL MeSH
- ornithin analogy a deriváty farmakologie MeSH
- peptidylarginindeiminasa typu 4 metabolismus MeSH
- síran dextranu MeSH
- streptonigrin farmakologie MeSH
- střeva účinky léků patologie MeSH
- střevní sliznice účinky léků patologie MeSH
- stupeň závažnosti nemoci MeSH
- zánět krev patologie MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Ten published DNA-based analytical methods aiming at detecting material of almond (Prunus dulcis) were in silico evaluated for potential cross-reactivity with other stone fruits (Prunus spp.), including peach, apricot, plum, cherry, sour cherry and Sargent cherry. For most assays, the analysis of nucleotide databases suggested none or insufficient discrimination of at least some stone fruits. On the other hand, the assay targeting non-specific lipid transfer protein (Röder et al., 2011, Anal Chim Acta 685:74-83) was sufficiently discriminative, judging from nucleotide alignments. Empirical evaluation was performed for three of the published methods, one modification of a commercial kit (SureFood allergen almond) and one attempted novel method targeting thaumatin-like protein gene. Samples of leaves and kernels were used in the experiments. The empirical results were favourable for the method from Röder et al. (2011) and a modification of SureFood allergen almond kit, both showing cross-reactivity <10(-3) compared to the model almond.
Vydanie prvé 654 stran, strana 609-624 se opakuje : ilustrace (některé barevné) ; 24 cm
V monográfii sú prezentované výsledky analýz 17 ochorení u slovenských pacientov. Výsledky genetickej analýzy jednotlivých ochorení sú prezentované historicky, od prvých molekulárno genetických výsledkov až po súčasný stav poznatkov, doplnené získanými výsledkami u slovenských pacientov. Nakladatelská anotace. Kráceno
- Klíčová slova
- Slovensko,
- MeSH
- genetické nemoci vrozené MeSH
- lékařská genetika MeSH
- Konspekt
- Patologie. Klinická medicína
- NLK Obory
- genetika, lékařská genetika
- NLK Publikační typ
- kolektivní monografie
Myotonická dystrofia (MD) je geneticky podmienené progresívne degeneratívne ochorenie priečne pruhovaných svalov. Okrem postihnutia svalstva sa fakultatívne vyskytujú viaceré orgánové komplikácie, ktoré postihujú oči, srdce, gonády, endokrinné žľazy a mozog. MD sa v súčasnosti rozdeľuje na dve geneticky odlišné formy. MD1 je zapríčinená expanziou CTG trinukleotidového repetitívneho motívu v géne DMPK, kým expanzia CCTG tetranukleotidového motívu v géne ZNF9 (CNBP) má za následok MD2. Podobné fenotypové prejavy oboch typov MD môžu byť zapríčinené rovnakými molekulárnymi procesmi, ktoré sú spojené pravdepodobne s RNA transkriptmi obsahujúcimi dané expandované trakty. Na druhej strane, odlišnosti medzi MD1 a MD2 môžu byť výsledkom špecifických interakcií CUG a CCUG transkriptov, ako aj lokus špecifických efektov týchto expanzií. Spolu so stále sa rozširujúcimi vedomosťami o patogenických procesoch vedúcich k MD, pribúdajú aj klinické štúdie zamerané na vývoj vhodných liečebných postupov. V starostlivosti o pacientov s MD preto zohrávajú čoraz významnejšiu úlohu metódy vhodné na molekulárnu identifikáciu daných expanzií a vytváranie národných a medzinárodných registrov pacientov s MD.
Myotonic dystrophy (DM) is genetically determined progressive and degenerative disorder of skeletal muscles. Besides involvement of skeletal muscles, DM may cause eye, heart, endocrine and brain disorders. DM comprises at least two genetically distinct forms. DM1 is caused by an expansion of a CTG repeat in the DMPK gene, while expansion of a CCTG repeat in the ZNF9 (CNBP) gene causes DM2. Strikingly similar phenotypic presentations of both types may be a consequence of common pathogenic mechanisms likely connected to the expansion containing RNA transcripts. On the other hand, the differences between DM1 and DM2 may be a consequence of specific interactions of the CUG and CCUG transcripts, and of locus specific effects of these expansions. Together with the extending knowledge about the pathogenic processes leading to DM, there are also a grooving number of clinical studies aimed to find possible therapeutic approaches. Therefore, molecular methods suitable for the direct identification of the expansions and the establishment of national and international patient registries will play crucial role in the healthcare of the patients with DM in the near future.
