Autori prezentujú prípad parciálnej hydatidóznej moly, kde DNA analýza (STR – genotypizácia krátkych tandemových opakovaní) poukázala na triandrickú monogynickú tetraploidnú kompozíciu genómu s gonozómovým komplementom XXXY. Uvedený genetický nález, ktorý je zriedkavý v porovnaní s typickými, diandrickými monogynickými triploidnými parciálnymi molami, klinicko-patologicky koreluje s parciálnou molou. Genetická analýza definitívne potvrdila podozrenie na parciálnu molu. Pre vylúčenie možnosti pôvodu molárnej gravidity ako zadržané produkty koncepcie po predchádzajúcej tehotnosti ukončenej interrupciou, boli porovnané STR profily molárnej gravidity a produktu predcházajúcej koncepcie. Genotypizácia krátkych tandemových opakovaní je užitočná molekulárno-genetická metóda v diferenciálnej diagnostike parciálnej hydatidóznej moly, kde sú klinicko-patologické nálezy často nejednoznačné.
The authors present a case of a partial hydatidiform mole where DNA analysis (STR – short tandem repeat genotyping) showed a triandric monogynic tetraploid genome composition with a XXXY gonosomal complement. This genetic finding clinicopathologically correlates with a partial hydatidiform mole, although it is rare in comparison with the typical, diandric monogynic triploid partial moles. The genetic analysis definitively confirmed the suspected diagnosis of a partial mole. To exclude the possibility that molar pregnancy represented retained products of conception after elective pregnancy termination, STR profiles from molar pregnancy and previous products of conception were compared. Short tandem repeats genotyping is a useful molecular genetic method in the differential diagnosis of partial hydatidiform moles, where clinical-pathological findings are frequently ambiguous.
Cíl: Cílem práce bylo zhodnotit využívání farmakogenetického testování u nemocných s psychiatrickou diagnózou. Metoda: Od roku 1997 je ve FN Brno-Bohunice dostupná a hrazená pojišťovnou genotypizace a fenotypizace CYP2D6. Žádosti o farmakogenetickou analýzu poskytlo oddělení lékařské genetiky FN Brno-Bohunice. Výsledky: V letech 1997-2019 bylo vyžádáno 223 vyšetření u nemocných s psychiatrickou diagnózou. Nejvíce vyšetření bylo realizováno v první dekádě v rámci klinických studií zaměřených na vliv aktivity CYP2D6 na účinnost a toleranci léčby antidepresivy. Postupně pak počet žádostí soustavně klesal. Diskuse: Jsou rozebírány možné příčiny včetně neprovázanosti s dostupným stanovením plazmatických hladin. Závěr: Stanovení genotypu a/nebo fenotypů nejdůležitějších enzymů metabolizujících psychofarmaka usnadní a urychlí u nereagujícího jedince volbu další léčebné strategie. Farmakogenetické testování léky metabolizujících enzymů společně s terapeutickým monitorováním léků (TDM) by měly být dostupné alespoň v univerzitních nemocnicích, kde se kumulují obtížně léčitelní pacienti.
Aim: The aim of the paper is to evaluate the use of pharmacogenetic testing in patients with a psychiatric diagnosis. Methods: In the Faculty Hospital Brno-Bohunice the genotyping and phenotyping of CYP2D6 is available and covered by insurance since 1997. The requests for pharmacogenetic analysis were provided by the Department of Medical Genetics, University Hospital Brno. Results: Between 1997 and 2019 totally 223 requests were collected and pharmacogenetic analyses performed in patients with psychiatric diagnosis. Most of analyses were performed in the first decade. The patients were recruited in studies aiming at exploring the influence of CYP2D6 activity on efficacy and tolerability of treatment with antidepressants. In further years there was a progressive decrease of requests. Discussion: The possible reasons are discussed including absence of interconnection with drug plasma levels measurement. Conclusions: Genotyping and/or phenotyping of drug metabolising enzymes in unresponsive individuals facilitates and accelerates choice of further treatment strategy. Pharmacogenetic testing together with therapeutic drug monitoring should be available at least at university hospitals with cumulation of difficult to treat patients.
Cieľ: Cieľom práce bola genetická charakterizácia súboru prípadov suspektných z parciálnej moly hydatidózy na základe nejednoznačného morfologického obrazu placentárneho tkaniva. Súbor a metodika: Práca predkladá výsledky genetickej analýzy súboru 10 pacientok s rôznymi klinickými prejavmi reprodukčných strát, u ktorých bola na základe histopatologického vyšetrenia suponovaná parciálna mola hydatidóza. Kompozícia genómu produktu koncepcie bola určená genotypizáciou krátkych tandemových opakovaní (STR – short tandem repeats) použitím komerčnej súpravy „Devyser Compact v3“ (Devyser). Výsledky a závery: Z 10 vyšetrených prípadov bol v piatich zistený diandrický monogynický triploidný genóm charakteristický pre parciálnu molu. V štyroch prípadoch boli vylúčené aneuploidie chromozómov 13, 18, 21, X a Y, v jednom prípade bol diagnostikovaný Patauov syndróm. Pri nejednoznačnom histopatologickom obraze môže patológom v diferenciálnej diagnostike parciálnej moly významne pomôcť konzultačná DNA analýza (ideálne STR genotypizácia). Histopatologický obraz parciálnej moly hydatidózy môže byť v skorých štádiách gravidity v niektorých prípadoch neúplný a nejednoznačný, čo môže viesť k falošne negatívnemu výsledku vyšetrenia. Na druhej strane, mnohé iné patológie, napr. aneuploidie alebo digynická triploidia, môžu mať histopatologický obraz podobný parciálnej mole, čo naopak vedie k falošnej pozitivite vyšetrenia. Presná diagnostika parciálnej moly hydatidózy použitím molekulárnych genetických metód prispeje k stanoveniu adekvátnej dispenzárnej starostlivosti.
Objective: The aim of the study was the genetic characterization of a set of cases with an unclear morphological profile of the placental tissue suspected of a partial hydatidiform mole. Patients and methods: This work presents the results of a genetic analysis of a group of 10 patients with various clinical manifestations of reproductive loss, where a partial hydatidiform mole was suspected on the basis of a histopathological examination. The composition of the genome of the products of conception was determined by short tandem repeats (STR) genotyping using a commercial kit “Devyser Compact v3 (Devyser) “. Results and conclusions: Out of 10 analyzed cases, five had diandric monogynic triploid genome, characteristic for a partial mole. Aneuploidies of chromosomes 13, 18, 21, X and Y were excluded in four cases and Patau‘s syndrome was diagnosed in one case. In the case of an unclear histopathological profile, consultative DNA analysis (ideally STR genotyping) can significantly help the pathologist in the differential diagnosis of a partial mole. The histopathological profile of a partial hydatidiform mole may be in some cases incomplete and unclear, especially in the early weeks of gestation, which can lead to false negativity of the examination. On the other hand, other pathologies, for example aneuploides or digynic triploidy, may produce a histopathological profile similar to a partial mole, which leads to false positivity. Accurate diagnosis of a partial hydatidiform mole using molecular genetic methods contributes to the determination of adequate dispensary care for patients.
Závěrečná zpráva o řešení grantu Agentury pro zdravotnický výzkum MZ ČR
Nestr.
Roma are an ethnic minority originating from a small group of ancestors from India. This endanger them by hereditary recessive disorders much more than our majority population. The ignorance of the ethnic origin in the diagnostics represents big health and financial costs for our healthcare system. The hereditary disorders in Roma are almost always due to a specific homozygous mutations in genes mutated also in the common population or in the specific genes. Homozygozity mapping is very effective for finding candidate regions with known recessive genes or new genes with disease causing mutations. This approach also improves data filtering from exome sequencing. From DNA diagnostics we recruited 50 Roma unrelated patients or families with hereditary neuropathy or hearing loss, in some of them the homozygosity mapping was done already and are the candidates for exome sequencing. We hope to clarify hereditary diseases in Roma by this approach. It will improve and rationalize the DNA diagnostics and genetic counselling for Roma patients and families and save the significant costs.
Romové jsou etnickou menšinou, pocházející z malého počtu prapředků z Indie, což je ohrožuje recesívně dědičnými chorobami více než většinovou populaci. Neznalost etnicky specifických chorob této menšiny představuje m.j. značné finanční zatížení pro systém zdravotní péče. U Romů jsou dědičná onemocnění téměř vždy v důsledku specifických homozygotních mutací, v genech způsobujících onemocnění i v běžné populaci nebo často ve specifických genech. Homozygotní mapování je účinné k určení oblastí, kde leží známé geny s recesivními mutacemi nebo nové geny zodpovědné za onemocnění. Tento přístup zefektivňuje filtrování dat z exomového sekvenování. Shromážděno je 50 pacientů - Romů, s dědičnou neuropatií nebo hluchotou, kde jsou vyloučeny běžné příčiny. U části je provedeno homozygotní mapování a jsou kandidáty pro exomové sekvenování. Tímto postupem je velká šance na objasnění příčin dědičných onemocnění u Romů. Náš projekt by měl zlepšit a zefektivnit DNA diagnostiku i genetické poradenství pro pacienty a rodiny romského etnika a ušetřit většinou zbytečné diagnostické peripetie i náklady.
- MeSH
- dědičné senzorické a autonomní neuropatie genetika MeSH
- genotypizační techniky metody MeSH
- geny recesivní genetika MeSH
- hluchota genetika MeSH
- homozygot MeSH
- lidé MeSH
- Romové genetika MeSH
- sekvenování exomu metody MeSH
- spastická paraparéza genetika MeSH
- Check Tag
- lidé MeSH
- Konspekt
- Patologie. Klinická medicína
- NLK Obory
- genetika, lékařská genetika
- NLK Publikační typ
- závěrečné zprávy o řešení grantu AZV MZ ČR
BACKGROUND: Apple (Malus x domestica Borkh.) is one of the most important fruit tree crops of temperate areas, with great economic and cultural value. Apple cultivars can be maintained for centuries in plant collections through grafting, and some are thought to date as far back as Roman times. Molecular markers provide a means to reconstruct pedigrees and thus shed light on the recent history of migration and trade of biological materials. The objective of the present study was to identify relationships within a set of over 1400 mostly old apple cultivars using whole-genome SNP data (~ 253 K SNPs) in order to reconstruct pedigrees. RESULTS: Using simple exclusion tests, based on counting the number of Mendelian errors, more than one thousand parent-offspring relations and 295 complete parent-offspring families were identified. Additionally, a grandparent couple was identified for the missing parental side of 26 parent-offspring pairings. Among the 407 parent-offspring relations without a second identified parent, 327 could be oriented because one of the individuals was an offspring in a complete family or by using historical data on parentage or date of recording. Parents of emblematic cultivars such as 'Ribston Pippin', 'White Transparent' and 'Braeburn' were identified. The overall pedigree combining all the identified relationships encompassed seven generations and revealed a major impact of two Renaissance cultivars of French and English origin, namely 'Reinette Franche' and 'Margil', and one North-Eastern Europe cultivar from the 1700s, 'Alexander'. On the contrary, several older cultivars, from the Middle Ages or the Roman times, had no, or only single, identifiable offspring in the set of studied accessions. Frequent crosses between cultivars originating from different European regions were identified, especially from the nineteenth century onwards. CONCLUSIONS: The availability of over 1400 apple genotypes, previously filtered for genetic uniqueness and providing a broad representation of European germplasm, has been instrumental for the success of this large pedigree reconstruction. It enlightens the history of empirical selection and recent breeding of apple cultivars in Europe and provides insights to speed-up future breeding and selection.
- MeSH
- chov MeSH
- genom rostlinný * MeSH
- genotyp MeSH
- genotypizační techniky metody MeSH
- jednonukleotidový polymorfismus genetika MeSH
- Malus genetika MeSH
- rodokmen MeSH
- sekvenování celého genomu MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Evropa 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 klasifikace genetika izolace a purifikace MeSH
- adenovirové infekce virologie MeSH
- DNA primery genetika MeSH
- enterovirové infekce virologie MeSH
- Enterovirus klasifikace genetika izolace a purifikace MeSH
- genotyp * MeSH
- genotypizační techniky metody MeSH
- kojenec MeSH
- lidé MeSH
- longitudinální studie MeSH
- předškolní dítě MeSH
- sekvenční analýza DNA metody MeSH
- výpočetní biologie MeSH
- zvířata MeSH
- Check Tag
- kojenec MeSH
- lidé MeSH
- mužské pohlaví MeSH
- předškolní dítě MeSH
- ženské pohlaví MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- hodnotící studie MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Norsko MeSH
Bifidobacteria are widely known for their probiotic potential; however, little is known regarding the ecological significance and potential probiotic effects of the phylogenetically related 'scardovial' genera (Aeriscardovia, Alloscardovia, Bombiscardovia, Galliscardovia, Neoscardovia, Parascardovia, Pseudoscardovia and Scardovia) and Gardnerella classified with bifidobacteria within the Bifidobacteriaceae family. Accurate classification and genotyping of bacteria using certain housekeeping genes is possible, whilst current phylogenomic analyses allow for extremely precise classification. Studies of applicable genetic markers may provide results comparable to those obtained from phylogenomic analyses of the family Bifidobacteriaceae. Segments of the glyS (624 nucleotides), pheS (555 nucleotides), rpsA (630 nucleotides), and rpsB (432 nucleotides) genes and their concatenated sequence were explored. The mean glyS, pheS, rpsB and rpsA gene sequence similarities calculated for Bifidobacterium taxa were 84.8, 85.2, 90.2 and 86.8%, respectively. Interestingly, the average value of the Average Nucleotide Identity among 67 type strains of the family Bifidobacteriaceae (84.70%) calculated based on values published recently was in agreement with the average pairwise similarity (84.6%) among 75 type strains of Bifidobacteriaceae family computed in this study using the concatenated sequences of four gene fragments. Similar to phylogenomic analyses, several gene sequence and phylogenetic analyses revealed that concatenated gene regions allow for classification of Bifidobacteriaceae strains into particular phylogenetic clusters and groups. Phylogeny reconstructed from the concatenated sequences assisted in defining two novel phylogenetic groups, the Bifidobacterium psychraerophilum group consisting of B. psychraerophilum, Bifidobacterium crudilactis and Bifidobacterium aquikefiri species and the Bifidobacterium bombi group consisting of B. bombi, Bifidobacterium bohemicum and Bifidobacterium commune.
Here we provide an overview of procedures for long-term cultivation, phenotyping, genotyping, and genetic transformation of cell cultures of tobacco cell lines BY-2 and VBI-0, and of A. thaliana, ecotype Landsberg erecta (LE) cell line. Notably, we present an improved protocol for BY-2 transformation and cloning and extend the available plant cell lines methodology toward high-throughput technologies like fluorescent-based cell sorting and transcriptomics.
- MeSH
- Arabidopsis cytologie genetika MeSH
- buněčné kultury metody MeSH
- buněčné linie MeSH
- geneticky modifikované rostliny cytologie genetika MeSH
- genotypizační techniky metody MeSH
- klonování DNA metody MeSH
- průtoková cytometrie metody MeSH
- stanovení celkové genové exprese metody MeSH
- tabák cytologie genetika MeSH
- transformace genetická MeSH
- transkriptom MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- MeSH
- epidemiologické faktory MeSH
- feces virologie MeSH
- fylogeneze MeSH
- genom virový MeSH
- genotypizační techniky metody MeSH
- klinické chemické testy metody MeSH
- lidé MeSH
- prasata virologie MeSH
- rizikové faktory MeSH
- Rotavirus * genetika izolace a purifikace MeSH
- virové zoonózy * epidemiologie přenos virologie MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
- Publikační typ
- práce podpořená grantem MeSH
BACKGROUND: The Meningococcal Antigen Typing System (MATS) was developed to identify meningococcus group B strains with a high likelihood of being covered by the 4CMenB vaccine, but is limited by the requirement for viable isolates from culture-confirmed cases. We examined if antigen genotyping could complement MATS in predicting strain coverage by the 4CMenB vaccine. METHODS: From a panel of 3912 MATS-typed invasive meningococcal disease isolates collected in England and Wales in 2007-2008, 2014-2015 and 2015-2016, and in 16 other countries in 2000-2015, 3481 isolates were also characterized by antigen genotyping. Individual associations between antigen genotypes and MATS coverage for each 4CMenB component were used to define a genetic MATS (gMATS). gMATS estimates were compared with England and Wales human complement serum bactericidal assay (hSBA) data and vaccine effectiveness (VE) data from England. RESULTS: Overall, 81% of the strain panel had genetically predictable MATS coverage, with 92% accuracy and highly concordant results across national panels (Lin's accuracy coefficient, 0.98; root-mean-square deviation, 6%). England and Wales strain coverage estimates were 72-73% by genotyping (66-73% by MATS), underestimating hSBA values after four vaccine doses (88%) and VE after two doses (83%). The gMATS predicted strain coverage in other countries was 58-88%. CONCLUSIONS: gMATS can replace MATS in predicting 4CMenB strain coverage in four out of five cases, without requiring a cultivable isolate, and is open to further improvement. Both methods underestimated VE in England. Strain coverage predictions in other countries matched or exceeded England and Wales estimates.
- MeSH
- antigeny bakteriální genetika MeSH
- celosvětové zdraví MeSH
- genotyp * MeSH
- genotypizační techniky metody MeSH
- lidé MeSH
- meningokoková meningitida epidemiologie mikrobiologie MeSH
- meningokokové vakcíny imunologie MeSH
- molekulární epidemiologie metody MeSH
- Neisseria meningitidis séroskupiny B klasifikace genetika izolace a purifikace MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- hodnotící studie MeSH
- práce podpořená grantem MeSH
