BACKGROUND: Noninvasive prenatal testing (NIPT) is the most recent modality widely used in prenatal diagnostics. Commercially available NIPT has high sensitivity and specificity for the common fetal chromosomal aneuploidies. As future advancements in NIPT sequencing technology are becoming promising and more reliable, the ability to detect beyond aneuploidies and to expand detection of submicroscopic genomic alterations, as well as single-gene disorders might become possible. CASE PRESENTATION: Here we present a case of a 34-year-old pregnant woman, G2P1, who had NIPT screening which detected a terminal microduplication of 10.34 Mb on the long arm of chromosome 15 (15q26.1q26.3). Subsequent prenatal diagnostic testing including karyotype, microarray and fluorescence in situ hybridization (FISH) analyses were performed. Microarray testing confirmed and particularized a copy number gain of 10.66 Mb of the distal end of the long arm of chromosome 15. The G-banding cytogenetic studies yielded results consistent with unbalanced translocation between chromosome 15 and 18. To further characterize the abnormality involving the long arm of chromosome 18 and to map the genomic location of the duplicated 15q more precisely, FISH analysis using specific sub-telomeric probes was performed. FISH analysis confirmed that the extra duplicated segment of chromosome 15 is translocated onto the distal end of the long arm of chromosome 18 at band 18q23. Parental karyotype and FISH studies were performed to see if this unbalanced rearrangement was inherited from a healthy balanced translocation carrier versus being a de novo finding. Parental chromosomal analysis provided no evidence of a rearrangement between chromosome 15 and chromosome 18. The final fetal karyotype was reported as 46,XX,der(18)t(15;18)(q26.2;q23)dn. CONCLUSIONS: In this case study, the microduplication of fetal chromosome 15q26.1q26.3 was accurately detected using NIPT. Our results suggest that further refinements in NIPT have the potential to evolve to a powerful and efficient screening method, which might be used to detect a broad range of chromosomal imbalances. Since microduplications and microdeletions are a potential reportable result with NIPT, this must be included in pre-test counseling. Prenatal diagnostic testing of such findings is strongly recommended.

• Publication type
• Journal Article MeSH

• MeSH
• Genetic Diseases, Inborn diagnosis   etiology   genetics   classification   MeSH
• Congenital, Hereditary, and Neonatal Diseases and Abnormalities diagnosis   etiology   genetics   classification   MeSH

• Conspectus
• Patologie. Klinická medicína
• NML Fields
• genetika, lékařská genetika
• embryologie a teratologie
• NML Publication type
• kolektivní monografie

BACKGROUND: Chromosomal microarray analysis has been shown to be a valuable and cost effective assay for elucidating copy number variants (CNVs) in children with intellectual disability and developmental delay (ID/DD). METHODS: In our study, we performed array-based comparative genomic hybridization (array-CGH) analysis using oligonucleotide-based platforms in 542 Czech patients with ID/DD, autism spectrum disorders and multiple congenital abnormalities. Prior to the array-CGH analysis, all the patients were first examined karyotypically using G-banding. The presence of CNVs and their putative derivation was confirmed using fluorescence in situ hybridization (FISH), multiplex ligation-dependent probe amplification (MLPA) and predominantly relative quantitative polymerase chain reaction (qPCR). RESULTS: In total, 5.9% (32/542) patients were positive for karyotypic abnormalities. Pathogenic/likely pathogenic CNVs were identified in 17.7% of them (96/542), variants of uncertain significance (VOUS) were detected in 4.8% (26/542) and likely benign CNVs in 9.2% of cases (50/542). We identified 6.6% (36/542) patients with known recurrent microdeletion (24 cases) and microduplication (12 cases) syndromes, as well as 4.8% (26/542) patients with non-recurrent rare microdeletions (21 cases) and microduplications (5 cases). In the group of patients with submicroscopic pathogenic/likely pathogenic CNVs (13.3%; 68/510) we identified 91.2% (62/68) patients with one CNV, 5.9% (4/68) patients with two likely independent CNVs and 2.9% (2/68) patients with two CNVs resulting from cryptic unbalanced translocations. Of all detected CNVs, 21% (31/147) had a de novo origin, 51% (75/147) were inherited and 28% (41/147) of unknown origin. In our cohort pathogenic/likely pathogenic microdeletions were more frequent than microduplications (69%; 51/74 vs. 31%; 23/74) ranging in size from 0.395 Mb to 10.676 Mb (microdeletions) and 0.544 Mb to 8.156 Mb (microduplications), but their sizes were not significantly different (P = 0.83). The pathogenic/likely pathogenic CNVs (median 2.663 Mb) were significantly larger than benign CNVs (median 0.394 Mb) (P < 0.00001) and likewise the pathogenic/likely pathogenic CNVs (median 2.663 Mb) were significantly larger in size than VOUS (median 0.469 Mb) (P < 0.00001). CONCLUSIONS: Our results confirm the benefit of array-CGH in the current clinical genetic diagnostics leading to identification of the genetic cause of ID/DD in affected children.

• MeSH
• Child MeSH
• Cohort Studies MeSH
• Infant MeSH
• Humans MeSH
• Intellectual Disability genetics   MeSH
• Adolescent MeSH
• Infant, Newborn MeSH
• Child, Preschool MeSH
• Oligonucleotide Array Sequence Analysis * MeSH
• Comparative Genomic Hybridization * MeSH
• DNA Copy Number Variations * MeSH
• Developmental Disabilities genetics   MeSH
• Check Tag
• Child MeSH
• Infant MeSH
• Humans MeSH
• Adolescent MeSH
• Male MeSH
• Infant, Newborn MeSH
• Child, Preschool MeSH
• Female MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH
• Geographicals
• Czech Republic MeSH

Chromosomal band 17q12 is a gene-rich region flanked by segmental duplications, making the region prone to deletions and duplications via the non-allelic homologous recombination mechanism. While deletions cause a well-described disorder with a specific phenotype called renal cysts and diabetes mellitus, the phenotype caused by reciprocal duplications is less specific, primarily because of variable expressivity, and incomplete penetrance. We present an unusual family with four children carrying the 17q12 microduplication inherited from their clinically healthy mother, who was a carrier of both the duplication and, interestingly, also of an atypical deletion of the 17q12 region. The duplication was inherited from her diabetic father and the deletion from her diabetic mother who also suffered from a renal disorder. Clinical manifestations in the family were variable, but all children showed some degree of a neurodevelopmental disorder, such as epilepsy, intellectual disability, delayed speech development, or attention deficit disorder. The simultaneous occurrence of a deletion and duplication in the same chromosomal region in one family is very rare, and to our knowledge, individuals carrying both a deletion and a duplication of this region have never been described.

• MeSH
• Chromosome Deletion MeSH
• Chromosome Duplication genetics   MeSH
• Phenotype MeSH
• Humans MeSH
• Intellectual Disability * genetics   MeSH
• Abnormalities, Multiple * genetics   MeSH
• Check Tag
• Humans MeSH
• Female MeSH
• Publication type
• Case Reports MeSH
• Research Support, Non-U.S. Gov't MeSH
• Geographicals
• Czech Republic 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
• Adult MeSH
• Dystonic Disorders diagnosis   genetics   MeSH
• Dystonia diagnosis   genetics   MeSH
• Cohort Studies MeSH
• Humans MeSH
• Exome Sequencing * MeSH
• DNA Copy Number Variations * genetics   MeSH
• Check Tag
• Adult MeSH
• Humans MeSH
• Male MeSH
• Female MeSH
• Publication type
• Journal Article MeSH
• Research Support, Non-U.S. Gov't MeSH

Background: Copy number variants (CNVs) are the genetic bases for microdeletion/ microduplication syndromes (MMSs). Couples with an affected child and desire to have further children are routinely tested for a potential parental origin of a specific CNV either by molecular karyotyping or by two color fluorescence in situ hybridization (FISH), yet. In the latter case a critical region probe (CRP) is combined with a control probe for identification of the chromosome in question. However, CNVs can arise also due to other reasons, like a recombination-event based on a submicroscopic, cryptic inversion in one of the parents. Results: Seventy-four patients with different MMSs and overall 81 CNVs were studied here by a novel three color FISH approach. The way how three locus-specific probes are selected (one is the CRP and two are flanking it in a distance of 5-10 Mb) enables to detect or exclude two possible parental conditions as origins of the CNV seen in the index: (i) direct parental origin of the CNV (deletion or duplication) or (ii) a parental cryptic inversion. Thus, for overall 51/81 CNVs (63%) a parental origin could be determined. 36/51 (70.5%) inherited the CNV directly from one of the parents, but 15/51 (29.5%) were due to an exclusively by three color FISH detectable parental inversion. A 2:1 ratio of maternal versus paternal inheritance was found. Also almost two times more male than female were among the index patients. Conclusion: The new, here suggested three color FISH approach is suited for more comprehensive parental studies of patients with MMS. The detection rate for parental origin was increased by 140% in this study. Still, for 30/81 cases (37%) no reason for the 'de novo' MMS in the affected index patient could be found by the here suggested FISH-probe set.

• Publication type
• Journal Article MeSH

Cíl studie: Syndrom Noonanové (NS), jedna z nejčastějších RASopatií, má odhadovanou incidenci 1 z 1000 až 2500 živě narozených jedinců. V prenatálním období lze u postižených plodů s tímto syndromem pozorovat zvýšené šíjové projasnění, hygroma colli, hydrops plodu, vrozené srdeční vady, vady ledvin, lymfatické vaky nebo větší množství plodové vody. U plodů s těmito nálezy byla při nálezu normálního karyotypu a po vyloučení mikrodelečních/mikroduplikačních syndromů doplněna prenatální diagnostika i o vyšetření vybraných genů pro RASopatie. Cílem studie bylo zhodnotit klinický přínos masivně paralelního sekvenování (MPS, massively parallel sequencing) DNA plodů suspektních pro NS, tj. diagnostickou výtěžnost na jedné straně a podíl detekovaných variant nejasného významu na straně druhé. Typ studie: Klinicky diagnostická. Název a sídlo pracoviště: Centrum prenatální diagnostiky, Brno, s.r.o.; Cytogenetická laboratoř Brno, s.r.o. Metodika: Analyzovány byly vzorky plodových vod, resp. choriových klků. Z nich izolovaná DNA byla po zjištění normálního karyotypu a array-CGH (aCGH) postoupena k analýze genů asociovaných s RASopatiemi metodou MPS. Výsledky: Ve sledovaném dvouletém období byl NS potvrzen celkem u 10 z 95 vyšetřovaných plodů. To představuje 10,5% diagnostickou výtěžnost metody. Celkem u 10 plodů byla detekována varianta DNA nejasného významu (VOUS, variants of unknown significance), následná segregační analýza pomohla objasnit její význam u šesti plodů. Závěr: MPS umožňuje rychlou molekulárně-genetickou diagnostiku RASopatií již v prenatálním období. Tato metoda tak přispívá k objasnění nejen fenotypových projevů u již narozených jedinců, ale také ultrazvukových nálezů u plodů s normálním karyotypem i aCGH.

Objective: Noonan syndrome (NS), one of the most common RASopathies, has an estimated incidence of 1 in 1,0002,500 live births. In the prenatal period increased nuchal translucency, hygroma colli, hydrops fetus, congenital heart disease, kidney defects, larger amount of amniotic fluid can be observed in affected fetuses with this syndrome. In the fetuses with normal karyotype and no microdeletion/microduplication syndromes the examination of selected genes for RASopathies was added. The aim of the study was to evaluate the clinical benefit of massively parallel sequencing (MPS) of susceptible fetal DNA for NS, i.e., the diagnostic yield on the one hand and the proportion of detected variants of unknown significance (VOUS) on the other. Design: Clinically diagnostic. Setting: Centrum prenatální diagnostiky, Brno, s.r.o; Cytogenetická laboratoř Brno, s.r.o. Methods: Samples of amniotic fluid or chorionic villus were analyzed. Selected genes associated with RASopathies were analyzed in case of the negative result of karyotype and array-CGH. A panel of twenty genes was investigated by MPS. Results: In the two-years period, Noonan syndrome was detected in 10 from 95 investigated fetuses. This represents a 10.5% diagnostic efficiency of the method. DNA variants of unknown significance were detected in 10 fetuses. A segregation analysis helped to clarify their meaning in six fetuses. Conclusion: MPS allows fast molecular-genetic diagnosis of RASopathies already in the prenatal period. This method contributes to the clarification not only of phenotypic manifestations in already born individuals but also of ultrasound findings in fetuses with both normal karyotype and aCGH.

• Keywords
• cystický hygrom,
• MeSH
• Hydrops Fetalis MeSH
• Pregnancy Complications MeSH
• Humans MeSH
• Nuchal Translucency Measurement methods   MeSH
• Noonan Syndrome * diagnosis   MeSH
• Prenatal Diagnosis * methods   MeSH
• Retrospective Studies MeSH
• Pregnancy MeSH
• Heart Defects, Congenital diagnosis   MeSH
• High-Throughput Nucleotide Sequencing methods   MeSH
• Check Tag
• Humans MeSH
• Pregnancy MeSH
• Female MeSH

Cíl studie: Zhodnocení kaskádového vyšetření metodami kvantitativní fluorescenční PCR (QF-PCR – quantitative fluorescence PCR) a SNP array (single nucleotide polymorphism array) při identifikaci chromozomálních abnormalit u potracených plodů. Soubor a metodika: V průběhu let 2018–2020 bylo v laboratořích Gennetu zpracováno 1 094 vzorků potracených plodů. Standardní schéma kaskádového vyšetření zahrnovalo screening základních aneuploidií metodou QF-PCR setem Omnibor (STR markery 13, 18, 21, X a Y), setem SAB-nadstavba I (STR markery 2, 7, 15, 16, 22), setem SAB-nadstavba II (od listopadu 2019, STR markery 4, 6, 14) a následně vyšetření metodou SNP array (Illumina). U všech vzorků bylo provedeno ověření/vyloučení maternální kontaminace. Výsledky: Po vyloučení maternální kontaminace (32 % vzorků) bylo metodou QF-PCR vyšetřeno 742 vzorků, 469 (63,2 %) z nich mělo negativní nález a 273 (36,8 %) patologický nález. Vzorky 469 plodů s negativním QF-PCR nálezem byly následně vyšetřeny metodou SNP array. Normální ženský/mužský profil byl potvrzen u 402 plodů (85,7 %), chromozomální aneuploidie a velké chromozomální aberace (delece/duplikace > 10 Mb) u 51 vzorků (10,9 %). U 16 (3,4 %) vyšetřených plodů byla nalezena mikrodelece nebo mikroduplikace, ve dvou případech se jednalo o patogenní mikrodelece a ve 14 o variantu nejasného významu bez přímé souvislosti s abortem. Byl potvrzen statisticky významný vyšší záchyt chromozomálních aberací u plodů žen s věkem > 35 let. Mezi skupinami vyšetřených abortů u gravidit po spontánní koncepci a po in vitro fertilizaci nebyl prokázán statisticky významný rozdíl. Závěr: Kaskádovým vyšetřením metodami QF-PCR a SNP array byla objasněna genetická příčina u 43 % všech vyšetřených abortů. Záchyt chromozomálních abnormalit u časných abortů v I. trimestru byl 50,4 %.

Objective: The evaluation of quantitative fluorescence PCR (QF-PCR) and single nucleotide polymorphism array (SNP array) analysis for the identification of chromosomal abnormalities in products of conception (POC). Materials and methods: A total of 1,094 POC samples were processed at Gennet in the years 2018–2020. Chromosomal aneuploidies were tested by QF-PCR using a Omnibor set (STR markers 13, 18, 21, X a Y), SAB-I set (STR markers 2, 7, 15, 16, 22), SAB-II set (from November 2019, STR markers 4, 6, 14) followed by SNP array analysis (Illumina) on samples with a negative QF-PCR result. All POC samples were tested for maternal contamination. Results: After exclusion of maternal contamination (32% samples) the total number of 742 POC samples were tested by QF-PCR. Chromosomal aneuploidies were found in 273 POC samples (36.8%). Then, 469 QF-PCR negative POC samples were tested by SNP array analysis. Normal female/male profile was confirmed in 402 samples (85.7%) and chromosomal aneuploidies and chromosomal aberrations (deletion/duplication > 10 Mb) in 51 samples (10.9%). Microdeletion/microduplication was found in 16 POC samples (3.4%), two were classified as pathogenic variants and 14 as variants of unknown significance. In a group of women > 35 years of age, statistically significant increase of the chromosomal abnormalities was confirmed. No statistically significant difference between the in vitro fertilization group and the group of spontaneous conception was found. Conclusion: The application of the molecular work-up based on the stepwise use of QF-PCR and SNP array clarifies the cause of the abortion in 43% POC samples. The overall detection rate in the I. trimester was 50.4%.

• MeSH
• Aneuploidy MeSH
• Chromosome Aberrations embryology   MeSH
• Chromosome Deletion MeSH
• Polymorphism, Single Nucleotide MeSH
• Real-Time Polymerase Chain Reaction * MeSH
• Humans MeSH
• Aborted Fetus * abnormalities   embryology   MeSH
• Check Tag
• Humans MeSH

V oblasti genetiky duševních poruch je současná pozornost vědců zaměřena na celogenomové asociační studie a vyšetřování mikrodelecí/ mikroduplikací DNA. Ty se ukazují být podstatné jako jedna z příčin schizofrenie. Zobrazovací metody mozku se pokoušejí hledat biomarkery, využitelné při diagnostice a léčbě duševních poruch. Na základě nových poznatků se hledají nové léčebné postupy u demence u Alzheimerovy choroby, například antiamyloidní terapie nebo ovlivňování metabolizmu mitochondrií. Katatonie stále hledá své místo v nové koncepci klasifikace duševních nemocí. Jednotlivé typy katatonie se od sebe mohou etiopatogeneticky i terapeuticky lišit. V oblasti farmakoterapie duševních poruch byla nyní publikována zejména řada vodítek Světové federace společností pro biologickou psychiatrii. Nové stimulační metody mozku se prosazují zejména v léčbě deprese a schizofrenie.

In the genetics of mental disorders, the main effort of the scientists is recently aimed at genome-wide association studies and the detection of DNA microdeletions/microduplications. They seem to be important as one of the substantial parts of the genetic background of schizophrenia. Brain neuroimaging seeks to define biomarkers, useful in the diagnostics and treatment of mental disorders. Based on the new knowledge, modern treatments in dementia in Alzheimer´s disease are developed, e.g. anti-amyloid therapy or modulators of mitochondrial metabolism. Catatonia is still looking for its proper place in the new concepts of classification of mental disorders. Individual subtypes of catatonia are probably different from each other in etiopathogenesis and treatment. In the area of pharmacotherapy, several guidelines were recently published by the World Federation of Societies of Biological Psychiatry. New brain stimulation techniques may be efficient in the treatment of depression and schizophrenia.

• Keywords
• zobrazovací metody mozku, stimulační metody mozku,
• MeSH
• Alzheimer Disease diagnosis   therapy   MeSH
• Biological Psychiatry trends   MeSH
• Biomarkers MeSH
• Dementia diagnosis   therapy   MeSH
• Depression therapy   MeSH
• Mental Disorders diagnosis   genetics   therapy   MeSH
• Drug Therapy trends   MeSH
• Genetics MeSH
• Deep Brain Stimulation trends   MeSH
• Catatonia classification   MeSH
• Humans MeSH
• Brain Diseases therapy   MeSH
• Neuroimaging trends   utilization   MeSH
• Schizophrenia diagnosis   etiology   therapy   MeSH
• Check Tag
• Humans MeSH
• Publication type
• Review MeSH

Moderními metodami genetického výzkumu schizofrenie jsou celogenomové asociační studie a hledání mikrodelecí/mikroduplikací DNA. Takto mohou být významné geny či polymorfizmy nalezeny, neznáme však jejich roli v patogenezi onemocnění. Proto se pozornost obrací ke genetickému vyšetřování endofenotypů schizofrenie. Endofenotyp je nejčastěji neurobiologická či neuropsychologická charakteristika asociovaná s danou nemocí, je dědičná a celoživotní a vyskytuje se také u duševně zdravých příbuzných pacienta. U schizofrenie jsou studovány zejména endofenotypy neurofyziologické, neuromotorické, neurokognitivní, neuroanatomické a neurologické. V tomto přehledovém článku jsou nejvýznamnější endofenotypy schizofrenie popsány, zmíněn je jejich biologický podklad a možné významné genetické nálezy. Problémem popisovaného výzkumu je zejména skutečnost, že schizofrenie je klinicky velmi heterogenní a výskyt endofenotypů se u jejích jednotlivých podskupin může významně lišit. Budoucnost má multicentrický mezinárodní genetický výzkum endofenotypů schizofrenie, kdy však veškeré procedury musejí být prováděny jednotně. Nalezení a vysvětlení genetického podkladu schizofrenie může sloužit její léčbě, prevenci i destigmatizaci onemocnění.

Genome-wide association studies and studies of DNA microdeletions/microduplications represent modern genetic research methods applied in schizophrenia. It is possible to find important genes and their polymorphisms by these procedures, but the findings do not clarify schizophrenia pathogenesis. That is why the genetic research into schizophrenia endophenotypes has recently been emphas ized. Endophenotype is usually a neurobiological or neuropsychological marker associated with a certain disease, heritable and life-l ong, and also occurs in healthy relatives of the patients. Neurophysiological, neuromotoric, neurocognitive, neuroanatomical and neurolo gical endophenotypes are studied in schizophrenia most frequently. In this review article, we mention the most important schizophreni a endophenotypes including their biological background, and relevant genetic findings. The problem is that schizophrenia is a cli nically heterogenous mental disorder, so the appearance of individual endophenotypes in particular subgroups may be significantly diffe rent. A multisite international genetic research into schizophrenia endophenotypes seems to be promising, but the procedures must be performed uniformly in all centers. The finding and elucidation of the genetic background of schizophrenia may help in its trea tment, prevention, and destigmatization.

• Keywords
• etiopatogeneze,
• MeSH
• Endophenotypes MeSH
• Genetic Predisposition to Disease genetics   MeSH
• Genetic Association Studies MeSH
• Genetics MeSH
• Clinical Trials as Topic MeSH
• Humans MeSH
• Schizophrenia etiology   genetics   MeSH
• Check Tag
• Humans MeSH
• Publication type
• Review MeSH