We evaluated copy number variation (CNV) for four genes in rat strains differing in nervous system excitability. rpl13a copy number is significantly reduced in hippocampus and bone marrow in rats with a high excitability threshold and stress. The observed phenomenon may be associated with a role for rpl13a in lipid metabolism.

• MeSH
• hipokampus metabolismus   fyziologie   MeSH
• kortikální excitabilita genetika   fyziologie   MeSH
• kostní dřeň metabolismus   fyziologie   MeSH
• krysa rodu rattus MeSH
• nervový systém - fyziologické jevy genetika   MeSH
• ribozomální proteiny genetika   MeSH
• variabilita počtu kopií segmentů DNA genetika   MeSH
• zvířata MeSH
• Check Tag
• krysa rodu rattus MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH

Východiska: Přestože je bevacizumab prvním biologickým léčivem schváleným pro léčbu metastatického kolorektálního karcinomu (mCRC), neexistuje žádný zavedený DNA biomarker, který by zlepšil jeho účinnost a personalizoval léčbu. Materiál a metody: Sledováno bylo 30 pacientů s mCRC na terapii bevacizumabem (15 s dobrou odpovědí a 15 se špatnou odpovědí) z Fakultní nemocnice Olomouc. Pro analýzu variací v počtu kopií genů (copy number variation – CNV) byly použity vzorky FFPE a OncoScan FFPE Assay Kit, který zachycuje přibližně 900 nádorových genů. Výsledky: Ve skupině dobře reagujících pacientů bylo jako potenciálně významné pozitivní prediktivní nádorové biomarkery léčby bevacizumabem identifikováno 102 genů (klasifikovaných jako ATPázy, typ AAA, neuronální přenos signálu, regulace transkripce a domény typu PH superior). Ve špatně reagující skupině bylo identifikováno 74 potenciálně negativních prediktivních genů (klasifikovaných jako galektiny, signální dráha Jak-STAT, kaskáda MAPK, diferenciace a doména asociovaná s F-boxem). Závěr: V pilotní studii jsme našli slibné biomarkery variace počtu kopií odpovědi na bevacizumab v FFPE vzorcích nádorů pacientů s mCRC. Validační fáze by měla být zaměřena zejména na geny spojené s angiogenezí (AGRN, MAPK8, ARHGAP22, LGALS13, LGALS4, ZFP36 a MYC), tumorigenezí (DVL1) a proliferací tumoru (IFNL1, IFNL2, IFNL3, MAP3K10 a MAP4K1).

Background: Despite bevacizumab being the first biological agent approved for the treatment of metastatic colorectal cancer (mCRC), there is not any established DNA biomarker to improve its efficacy and personalize the treatment. Materials and methods: Thirty patients with mCRC on bevacizumab therapy (15 with a good response and 15 with a poor response) from the University Hospital Olomouc were followed. Formalin-fixed paraffin-embedded (FFPE) samples were used for copy number variation (CNV) analysis using the OncoScan FFPE Assay Kit in order to capture approx. 900 tumor genes. Results: In the group of good responding patients, 102 genes (classified as ATPases, type AAA, neuronal signal transmission, regulation of transcription, and superior domain PH type), potentially significant positive predictive tumor biomarkers of bevacizumab treatment, were found. In the poorly responding group, 74 potentially negative predictive genes (classified as galectines, Jak-STAT signalling pathway, MAPK cascade, differentiation, and F-box associated domain) were identified. Conclusion: In the pilot study, we found promising copy number variation biomarkers of bevacizumab response in FFPE samples of mCRC patients. The validation phase should be focused especially on the genes associated with angiogenesis (AGRN, MAPK8, ARHGAP22, LGALS13, LGALS4, ZFP36, and MYC), tumorigenesis (DVL1), and tumor proliferation (IFNL1, IFNL2, IFNL3, MAP3K10, and MAP4K1).

• MeSH
• bevacizumab aplikace a dávkování   terapeutické užití   MeSH
• kolorektální nádory * diagnóza   farmakoterapie   genetika   patologie   MeSH
• lidé MeSH
• metastázy nádorů farmakoterapie   MeSH
• mutační analýza DNA metody   MeSH
• nádorové biomarkery analýza   genetika   MeSH
• pilotní projekty MeSH
• protinádorové látky imunologicky aktivní aplikace a dávkování   terapeutické užití   MeSH
• variabilita počtu kopií segmentů DNA MeSH
• Check Tag
• lidé MeSH

BACKGROUND: The incidence of squamous cell carcinoma of the oral tongue (SCCOT) is increasing in people under age 40. There is an urgent need to identify prognostic markers that help identify young SCCOT patients with poor prognosis in order to select these for individualized treatment. MATERIALS AND METHODS: To identify genetic markers that can serve as prognostic markers for young SCCOT patients, we first investigated four young (≤40 years) and five elderly patients (≥50 years) using global RNA sequencing and whole-exome sequencing. Next, we combined our data with data on SCCOT from the cancer genome atlas (TCGA), giving a total of 16 young and 104 elderly, to explore the correlations between genomic variations and clinical outcomes. RESULTS: In agreement with previous studies, we found that SCCOT from young and elderly patients was transcriptomically and also genomically similar with no significant differences regarding cancer driver genes, germline predisposition genes, or the burden of somatic single nucleotide variations (SNVs). However, a disparate copy number variation (CNV) was found in young patients with distinct clinical outcome. Combined with data from TCGA, we found that the overall survival was significantly better in young patients with low-CNV (n = 5) compared to high-CNV (n = 11) burden (P = 0.044). CONCLUSIONS: Copy number variation burden is a useful single prognostic marker for SCCOT from young, but not elderly, patients. CNV burden thus holds promise to form an important contribution when selecting suitable treatment protocols for young patients with SCCOT.

• MeSH
• dospělí MeSH
• lidé středního věku MeSH
• lidé MeSH
• míra přežití MeSH
• mladý dospělý MeSH
• nádorové biomarkery * MeSH
• nádory jazyka diagnóza   genetika   mortalita   MeSH
• prognóza MeSH
• sekvenování exomu MeSH
• senioři MeSH
• spinocelulární karcinom diagnóza   genetika   mortalita   MeSH
• variabilita počtu kopií segmentů DNA * MeSH
• věkové faktory MeSH
• Check Tag
• dospělí MeSH
• lidé středního věku MeSH
• lidé MeSH
• mladý dospělý MeSH
• mužské pohlaví MeSH
• senioři MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH

Long transgenes are often used in mammalian genetics, e.g., to rescue mutations in large genes. In the course of experiments addressing the genetic basis of hybrid sterility caused by meiotic defects in mice bearing different alleles of Prdm9, we discovered that introduction of copy-number variation (CNV) via two independent insertions of long transgenes containing incomplete Prdm9 decreased testicular weight and epididymal sperm count. Transgenic animals displayed increased occurrence of seminiferous tubules with apoptotic cells at 18 days postpartum (dpp) corresponding to late meiotic prophase I, but not at 21 dpp. We hypothesized that long transgene insertions could cause asynapsis, but the immunocytochemical data revealed that the adult transgenic testes carried a similar percentage of asynaptic pachytene spermatocytes as the controls. These transgenic spermatocytes displayed less crossovers but similar numbers of unrepaired meiotic breaks. Despite slightly increased frequency of metaphase I spermatocytes with univalent chromosome(s) and reduced numbers of metaphase II spermatocytes, cytological studies did not reveal increased apoptosis in tubules containing the metaphase spermatocytes, but found an increased percentage of tubules carrying apoptotic spermatids. Sperm counts of subfertile animals inversely correlated with the transcription levels of the Psmb1 gene encoded within these two transgenes. The effect of the transgenes was dependent on sex and genetic background. Our results imply that the fertility of transgenic hybrid animals is not compromised by the impaired meiotic synapsis of homologous chromosomes, but can be negatively influenced by the increased expression of the introduced genes.

• MeSH
• apoptóza genetika   MeSH
• dvouřetězcové zlomy DNA MeSH
• fertilita genetika   MeSH
• genetické pozadí MeSH
• kontrolní body buněčného cyklu genetika   MeSH
• myši MeSH
• pachytenní stadium genetika   MeSH
• počet spermií MeSH
• spermatocyty metabolismus   MeSH
• testis anatomie a histologie   metabolismus   MeSH
• transgeny * MeSH
• variabilita počtu kopií segmentů DNA * MeSH
• velikost orgánu MeSH
• zvířata MeSH
• Check Tag
• mužské pohlaví MeSH
• myši MeSH
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Ciele: Analýza prenatálnych vzoriek za obdobie 2015–2020. Porovnanie miery detekcie klinicky relevantných variant cytogenetickou analýzou karyotypu a cytogenomickými metódami MLPA (Multiplex Ligation-Depent Probe Amplification) a mikročipmi (CMA – chromosomal microarray). Súbor a metodika: Analyzovaných bolo 1 029 prenatálnych vzoriek cytogenetickým hodnotením karyotypu (n = 1 029), cytogenomickými metódami MLPA (n = 144) a CMA (n = 111). Všetky nebalansované zmeny boli potvrdené metódou MLPA alebo CMA. Výsledky: Z analyzovaného súboru plodov, po odčítaní aneuploidií – 107 (10,40 %, n = 1 029), bolo analýzou karyotypu zachytených 22 štruktúrnych aberácií (2,39 %, n = 922) – deväť nebalansovaných zmien (0,98 %), 10 balansovaných zmien (1,08 %), jeden prípad nejasnej mozaiky (0,09 %), jeden prípad prítomnosti marker chromozómu (0,09 %) a jeden prípad diskordancie pohlavia (0,09 %). U 255 vzoriek s fyziologickým karyotypom indikovaných k cytogenomickému vyšetreniu bolo zachytených celkom osem (7,21 %, n = 111) patologických variant metódou CMA. Metódou MLPA bolo z týchto ôsmich patogénnych variant zachytených päť (3,47 %, n = 144). Celkový záchyt patogénnych variant metódami MLPA a CMA vrátane konfirmačných vyšetrení patologického karyotypu je 14 (5,14 %) a 17 (6,25 %) (n = 272). Záchyt patologických variant v skupine s izolovanými poruchami bol nižší než v skupine s mnohopočetnými poruchami (5,08 vs. 21,42 %). Záver: Potvrdila sa vyššia úspešnosť záchytu patologických variant so zmenou v počte kópií, metódou CMA než MLPA.

Objective: Analysis of prenatal samples from 2015 to 2020. Comparison detection rates of clinically relevant variants by cytogenetic karyotype analysis and cytogenomic MLPA (Multiplex Ligation-Depent Probe Amplification) and microarray methods (CMA – chromosomal microarray). Material and method: 1,029 prenatal samples were analyzed by cytogenetic karyotyping (N = 1,029), cytogenomic methods – MLPA (N = 144) and CMA (N = 111). All unbalanced changes were confirmed by MLPA or CMA. Results: From the analyzed set of fetuses, after subtraction of aneuploidies – 107 (10.40%, N = 1,029), 22 structural aberrations (2.39%, N = 922) – nine unbalanced changes (0.98%), 10 balanced changes (1.08%), one case of unclear mosaicism (0.09%), one case of presence of a marker chromosome (0.09%) and one case of sex discordance (0.09%) – were detected by karyotype analysis. A total of eight (7.21%, N = 111) pathological variants were detected by CMA in 255 samples with physiological karyotype indicated for cytogenomic examination. Five (3.47%, N = 144) of eight pathogenic variants were detected by MLPA method. The total capture of pathogenic variants by MLPA and CMA methods was 14 (5.14%) and 17 (6.25%) (N = 272), including confirmatory pathological karyotype testing. Detection of pathological variants in the isolated disorders group was lower than in the multiple disorders group (5.08 vs. 21.42%). Conclusion: A higher success rate for the detection of pathological copy number variation variants by the microarray method than by the MLPA method was confirmed.

• MeSH
• klinická studie jako téma MeSH
• lidé MeSH
• mikročipová analýza metody   MeSH
• mozaicismus MeSH
• multiplexová polymerázová řetězová reakce metody   MeSH
• plod MeSH
• prenatální diagnóza * MeSH
• těhotenství MeSH
• variabilita počtu kopií segmentů DNA MeSH
• vrozené vady * diagnóza   genetika   MeSH
• Check Tag
• lidé MeSH
• těhotenství MeSH
• ženské pohlaví MeSH

OBJECTIVES: The term "copy number variation/variant" (CNV) denotes a DNA sequence with a magnitude of 1 kb at least which is differently represented among individuals based on its deletion or duplication. Since 2008, multiple studies have reported copy number variations in schizophrenia, and they seem to fill in a gap in our knowledge on the genetic background of schizophrenia. The aim of this review is to sum up the current findings related to CNVs in schizophrenia in order to facilitate further research. METHODS: We searched the PubMed computer database using the key words "schizophrenia AND CNVs" on 26th October 2011. Out of 91 obtained results, we selected the references based on their relevance. RESULTS: The CNVs at genome loci 1q21.1, 2p16.3, 3q29, 15q11.2, 15q13.3, 16p13.1 and 22q11.2 were associated with schizophrenia most frequently. The data provide evidence for low prevalent, but highly penetrant CNVs associated with schizophrenia. CNV deletions show higher penetrance than duplications. Larger CNVs often have higher penetrance than smaller CNVs. Although the vast majority of CNVs are inherited, CNVs that have newly occurred as de novo mutations have more readily been implicated in schizophrenia. De novo CNVs may be responsible for the presence of schizophrenia in only one of the two monozygotic twins, who otherwise have identical genomes. CONCLUSION: Identifying CNVs in schizophrenia can lead to changes in the treatment and genetic counselling. Our knowledge on the genetic background of neurodevelopmental disorders may also reduce stigma in schizophrenia.

• MeSH
• celogenomová asociační studie statistika a číselné údaje   MeSH
• genetická predispozice k nemoci genetika   MeSH
• genom lidský genetika   MeSH
• lidé MeSH
• schizofrenie genetika   MeSH
• variabilita počtu kopií segmentů DNA genetika   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH

OBJECTIVE: Recent studies have integrated copy number variant (CNV) and gene analysis using target enrichment. Here, we transferred this concept to our routine genetics laboratory, which is not linked to centralized non-invasive prenatal testing (NIPT) facilities. METHOD: From a cohort of 100 pregnant women, 22 were selected for the analysis of maternal genomic DNA (gDNA) along with fetal cell-free DNA. Using targeted enrichment, 135 genes were analyzed, combined with aberrations of chromosomes 21, 18, 13, X, and Y. The data were subjected to specificity and sensitivity analyses, and correlated with the results from invasive testing methods. RESULTS: The sensitivity/specificity was determined for the CNV analysis of chromosomes: 21 (80%/75%), 18 (-/82%), 13 (100%/67%), and Y (100%/100%). The gene detection was valid for maternal gDNA. However, for cell-free fetal DNA, it was not possible to determine the boundary between an artifact and a real sequence variant. CONCLUSION: The target enrichment method combining CNV and gene detection seems feasible in a regular laboratory. However, this method can only be responsibly optimized with a sufficient number of controls and further validation on a strong bioinformatic background. The present results showed that NIPT should be performed in specialized centers, and that its introduction to isolated laboratories may not provide valid data.

• MeSH
• laboratoře * MeSH
• lidé MeSH
• lidské chromozomy, pár 21 MeSH
• těhotenství MeSH
• variabilita počtu kopií segmentů DNA MeSH
• volné cirkulující nukleové kyseliny * MeSH
• vysoce účinné nukleotidové sekvenování MeSH
• Check Tag
• lidé MeSH
• těhotenství MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH

The genetic correlates of extreme impulsive violence are poorly understood, and there have been no studies that have systematically characterized a large group of affected individuals both clinically and genetically. We performed a genome-wide rare copy number variant (CNV) analysis in 281 males from four Czech prisons who met strict clinical criteria for extreme impulsive violence. Inclusion criteria included age ≥ 18 years, an ICD-10 diagnosis of Dissocial Personality Disorder, and the absence of an organic brain disorder. Participants underwent a structured psychiatric assessment to diagnose extreme impulsive violence and then provided a blood sample for genetic analysis. DNA was genotyped and CNVs were identified using Illumina HumanOmni2.5 single-nucleotide polymorphism array platform. Comparing with 10851 external population controls, we identified 828 rare CNVs (frequency ≤ 0.1% among control samples) in 264 participants. The CNVs impacted 754 genes, with 124 genes impacted more than once (2-25 times). Many of these genes are associated with autosomal dominant or X-linked disorders affecting adult behavior, cognition, learning, intelligence, specifically expressed in the brain and relevant to synapses, neurodevelopment, neurodegeneration, obesity and neuropsychiatric phenotypes. Specifically, we identified 31 CNVs of clinical relevance in 31 individuals, 59 likely clinically relevant CNVs in 49 individuals, and 17 recurrent CNVs in 65 individuals. Thus, 123 of 281 (44%) individuals had one to several rare CNVs that were indirectly or directly relevant to impulsive violence. Extreme impulsive violence is genetically heterogeneous and genomic analysis is likely required to identify, further research and specifically treat the causes in affected individuals.

• MeSH
• asociální osobnost genetika   MeSH
• dospělí MeSH
• impulzivní chování * MeSH
• lidé středního věku MeSH
• lidé MeSH
• mladiství MeSH
• násilí * MeSH
• senioři MeSH
• variabilita počtu kopií segmentů DNA * MeSH
• Check Tag
• dospělí MeSH
• lidé středního věku MeSH
• lidé MeSH
• mladiství MeSH
• mužské pohlaví MeSH
• senioři MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, N.I.H., Extramural MeSH

INTRODUCTION: Next-generation sequencing is now used on a routine basis for molecular testing but studies on copy-number variant (CNV) detection from next-generation sequencing data are underrepresented. Utilizing an existing whole-exome sequencing (WES) dataset, we sought to investigate the contribution of rare CNVs to the genetic causality of dystonia. METHODS: The CNV read-depth analysis tool ExomeDepth was applied to the exome sequences of 953 unrelated patients with dystonia (600 with isolated dystonia and 353 with combined dystonia; 33% with additional neurological involvement). We prioritized rare CNVs that affected known disease genes and/or were known to be associated with defined microdeletion/microduplication syndromes. Pathogenicity assessment of CNVs was based on recently published standards of the American College of Medical Genetics and Genomics and the Clinical Genome Resource. RESULTS: We identified pathogenic or likely pathogenic CNVs in 14 of 953 patients (1.5%). Of the 14 different CNVs, 12 were deletions and 2 were duplications, ranging in predicted size from 124bp to 17 Mb. Within the deletion intervals, BRPF1, CHD8, DJ1, EFTUD2, FGF14, GCH1, PANK2, SGCE, UBE3A, VPS16, WARS2, and WDR45 were determined as the most clinically relevant genes. The duplications involved chromosomal regions 6q21-q22 and 15q11-q13. CNV analysis increased the diagnostic yield in the total cohort from 18.4% to 19.8%, as compared to the assessment of single-nucleotide variants and small insertions and deletions alone. CONCLUSIONS: WES-based CNV analysis in dystonia is feasible, increases the diagnostic yield, and should be combined with the assessment of single-nucleotide variants and small insertions and deletions.

• MeSH
• dospělí MeSH
• dystonické poruchy diagnóza   genetika   MeSH
• dystonie diagnóza   genetika   MeSH
• kohortové studie MeSH
• lidé MeSH
• sekvenování exomu * MeSH
• variabilita počtu kopií segmentů DNA * genetika   MeSH
• Check Tag
• dospělí MeSH
• lidé MeSH
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Transcriptome sequencing (RNA-seq) is widely used to detect gene rearrangements and quantitate gene expression in acute lymphoblastic leukemia (ALL), but its utility and accuracy in identifying copy number variations (CNVs) has not been well described. CNV information inferred from RNA-seq can be highly informative to guide disease classification and risk stratification in ALL due to the high incidence of aneuploid subtypes within this disease. Here we describe RNAseqCNV, a method to detect large scale CNVs from RNA-seq data. We used models based on normalized gene expression and minor allele frequency to classify arm level CNVs with high accuracy in ALL (99.1% overall and 98.3% for non-diploid chromosome arms, respectively), and the models were further validated with excellent performance in acute myeloid leukemia (accuracy 99.8% overall and 99.4% for non-diploid chromosome arms). RNAseqCNV outperforms alternative RNA-seq based algorithms in calling CNVs in the ALL dataset, especially in samples with a high proportion of CNVs. The CNV calls were highly concordant with DNA-based CNV results and more reliable than conventional cytogenetic-based karyotypes. RNAseqCNV provides a method to robustly identify copy number alterations in the absence of DNA-based analyses, further enhancing the utility of RNA-seq to classify ALL subtype.

• MeSH
• algoritmy MeSH
• karyotypizace MeSH
• lidé MeSH
• sekvenování transkriptomu MeSH
• variabilita počtu kopií segmentů DNA * genetika   MeSH
• vysoce účinné nukleotidové sekvenování * metody   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, N.I.H., Extramural MeSH