Genetics in prenatal diagnosis

The options for prenatal genetic testing have evolved rapidly in the past decade, and advances in sequencing technology now allow genetic diagnoses to be made down to the single-base-pair level, even before the birth of the child. This offers women the opportunity to obtain information regarding the foetus, thereby empowering them to make informed decisions about their pregnancy. As genetic testing becomes increasingly available to women, clinician knowledge and awareness of the options available to women is of great importance. Additionally, comprehensive pretest and posttest genetic counselling about the advantages, pitfalls and limitations of genetic testing should be provided to all women. This review article aims to cover the range of genetic tests currently available in prenatal screening and diagnosis, their current applications and limitations in clinical practice as well as what the future holds for prenatal genetics.

Clinical and genetic study of developmental and epileptic encephalopathy in argentinean pediatric patients / Estudio clínico y genético de encefalopatía epiléptica y del desarrollo en pacientes pediátricos argentinos

Abstract Introduction: The aim of this study was to extend our knowledge of the genetic background of Argentinean pediatric patients with developmental and epileptic encephalopathy (DEE) applying a next generation sequencing (NGS) panel. Methods: Thirty one patients with DEE were studied, including these phenotypes: Dravet syndrome (n:7), Dravet like syndrome (n:3), West syndrome (WS) (n:6), WS that evolved to Lennox-Gastaut syndrome (LGS) (n:4), epilepsy of infancy with migrating focal seizures (n:2), continuous spikes and waves during slow sleep evolving to LGS (n:1), LGS (n:1), myoclonic status in non-progressive encephalopathy (n:1), myoclonic atonic epilepsy (n:1), epileptic encephalopathy with multifocal spikes (n:1) and unclassified epileptic encephalopathy (n:4). Fifty-two genes frequently associated with DEE were studied by NGS in genomic DNA from peripheral blood. Results: Relevant variants were detected in 12 cases; 6 novel pathogenic or likely pathogenic variants, 6 previously reported as pathogenic and 1 variant of unknown sig nificance. Single-nucleotide heterozygous variants were identified in the SCN1A (5), GABRG2 (1), STXBP1 (2) genes, a mosaic variant in SCN2A (1) and a homozygous variant in SCN1B (1). Additionally, a heterozygous deletion involving the SCN1A, SCN2A and SCN3A genes (1), and the most frequent triplet repeat expansion in the ARX gene (1) were detected. Discussion: Genetic diagnosis was made in 39% of patients. We emphasize the importance of considering mosaic variants, copy number variants and hereditary forms when designing and interpreting molecular studies, to optimize diagnosis and management of patients. Approximately 42% of the de tected variants were novel, expanding the knowledge of the molecular basis of DEEs in Latin-American patients.

Resumen Introducción: El objetivo del estudio fue ampliar el conocimiento de las bases moleculares de las encefalopatías epilépticas y del desarrollo (EED) en pacientes pediátricos argentinos aplicando un panel de secuenciación de nueva generación (NGS). Métodos: Se analizaron 31 pacientes con los fenotipos clínicos de síndrome de Dra vet (n:7), síndrome símil Dravet (n:3), síndrome de West (SW) (n:6), SW que evoluciona a síndrome de Lennox Gastaut (SLG)(N:4), epilepsia de la infancia con crisis focales migratorias (n:2), actividad de punta onda continua durante el sueño que evolucionan a SLG (n:1), SLG (n:1), encefalopatía no progresiva con estatus mioclónico (n:1), epilepsia mioclónica atónica (n:1), encefalopatía epiléptica con espigas multifocales (n:1) y encefalopatía epiléptica indeterminada (n:4). Se estudiaron los 52 genes más frecuentemente asociados a EED a través de NGS, en ADN extraído de sangre periférica. Resultados: Se identificaron variantes relevantes en 12 casos, de las cuales 5 fueron nuevas y 6 previamente reportadas como patogénicas o posiblemente patogénicas, mien tras que una variante fue clasificada como de significado incierto. Variantes heterocigotas, de nucleótido único, se identificaron en los genes SCN1A (5), GABRG2 (1), STXBP1 (2), una variante en mosaico en SCN2A (1) y otra homocigota en SCN1B (1). Además, se detectó una deleción que involucra a los genes SCN1A, SCN2A y SCN3A (1) y la expansión de repeticiones de tripletes más frecuente en el gen ARX (1). Discusión: Se alcanzó el diagnóstico molecular en el 39% de los pacientes. Remarcamos la importancia de considerar variantes en mosaico, variantes en el número de copias y formas heredadas al momento de diseñar e interpretar los estudios moleculares, de tal forma de optimizar el diagnóstico y seguimiento de los pacientes con EED. Cabe destacar, que el 42% de las variantes detectadas fueron nuevas, ampliando nuestro conocimiento sobre las bases mole culares de las EED en población latino americana.

Variação de número de cópias no cromossomo 4: uma possível síndrome genética? / Number copies variation in chromosome 4: a possible genetic syndrome?

INTRODUÇÃO: Variantes de número de cópias (CNVs) são variações no número de cópias de uma região da sequência genômica, descrevendo deleções ou ganhos em relação a indivíduos controle. Podem ser comuns e de caráter benigno, de significado incerto ou variantes patogênicas. Para interpretação, classificação e avaliação de significado clínico, é realizado comparação dos resultados nas bases de dados do laboratório e análise da literatura científica. OBJETIVO: Relatar caso de adolescente com duplicação/triplicação no cromossomo 4 com déficit cognitivo e dismorfismo facial e discutir se essa CNV pode ser responsável pelos achados clínicos. RELATO DE CASO: Paciente de 15 anos, sexo feminino, levada ao ambulatório de Genética para investigação de possível síndrome genética. Pais consanguíneos (primos). Desde a infância apresenta estrabismo divergente, atraso no desenvolvimento neuropsicomotor com dificuldade de fala. Cursou com síndrome hipotônica com espasmos mioclônicos. Evoluiu com déficit cognitivo. A Ressonância magnética de encéfalo demonstrou comprometimento de hemisférios cerebelares e atrofia de ponte e mesencéfalo. Cariótipo normal (46, XX) e hibridização genômica comparativa baseada em microarranjos (a-CGH) revelou duplicação/ triplicação na região 4p 15.32p15.31, variante de significado incerto. CONCLUSÃO: Destaca-se a importância da investigação através de análises cromossômicas por microarranjos em pacientes com deficiência intelectual, síndrome do espectro do autismo e múltiplas malformações congênitas - isto para aprimoramento diagnóstico, cuidados médicos específicos e aconselhamento genético.

INTRODUCTION: Copy number variants (CNVs) are variations in the number of copies of a region of the genomic sequence, describing deletions or gains in relation to control individuals. They may be common and of benign nature, of uncertain meaning or pathogenic variants. For interpretation, classification and evaluation of clinical significance, a comparison of the results in the laboratory databases and analysis of the scientific literature is performed. OBJECTIVE: To report a case of adolescent with duplication / triplication on chromosome 4 with cognitive deficit and facial dysmorphism and to discuss whether this CNV can be responsible for the clinical findings. CASE REPORT: A 15-year-old female patient was taken to the Genetics outpatient clinic to investigate a possible genetic syndrome. Consanguineous parents. Since childhood, she has divergent strabismus, delayed neuropsychomotor development with speech difficulties. She developed with hypotonic syndrome with myoclonic spasms. She evolved with cognitive deficit. Magnetic resonance imaging of brain showed compromised cerebellar hemispheres and atrophy of the bridge and midbrain. Normal karyotype (46, XX) and comparative genomic hybridization based on microarrays (a-CGH) revealed duplication / triplication in the region 4p 15.32p15.31, variant of uncertain meaning. CONCLUSION: The importance of research through chromosomal analysis by microarray in patients with intellectual disability, autism spectrum syndrome and multiple congenital malformations is highlighted ­ this for diagnosis improvement, specific medical care and genetic counseling.

Microarray-Based Genomic Analysis Identifies Germline and Somatic Copy Number Variants and Loss of Heterozygosity in Acute Myeloid Leukaemia

@#Introduction: Insights into molecular karyotyping using comparative genomic hybridization (CGH) and single nucleotide polymorphism (SNP) arrays enable the identification of copy number variations (CNVs) at a higher resolution and facilitate the detection of copy neutral loss of heterozygosity (CN-LOH) otherwise undetectable by conventional cytogenetics. The applicability of a customised CGH+SNP 180K DNA microarray in the diagnostic evaluation of Acute Myeloid Leukaemia (AML) in comparison with conventional karyotyping was assessed in this study. Methods: Paired tumour and germline post induction (remission sample obtained from the same patient after induction) DNA were used to delineate germline variants in 41 AML samples and compared with the karyotype findings. Results: After comparing the tumour versus germline DNA, a total of 55 imbalances (n 5-10 MB = 21, n 10-20 MB = 8 and n >20 MB = 26) were identified. Gains were most common in chromosome 4 (26.7%) whereas losses were most frequent in chromosome 7 (28.6%) and X (25.0%). CN-LOH was mostly seen in chromosome 4 (75.0%). Comparison between array CGH+SNP and karyotyping revealed 20 cases were in excellent agreement and 13 cases did not concord whereas in 15 cases finding could not be confirmed as no karyotypes available. Conclusion: The use of a combined array CGH+SNP in this study enabled the detection of somatic and germline CNVs and CN-LOHs in AML. Array CGH+SNP accurately determined chromosomal breakpoints compared to conventional cytogenetics in relation to presence of CNVs and CN-LOHs.

Application of chromosomal microarray technique in genetic analysis of patients with embryo development arrest / 实用医学杂志

Objective To investigate the value of chromosomal microarray technique in genetic analysis of patients with embryo development arrest. Methods A total number of 273 patients with embryo development arrest were recruited for the chromosomal microarray testing.Results 41.4% of the 273 patients were chromosomal abnormalities. Among which 61(22.34%)were numerical chromosomal abnormalities,43 were structural anoma-lies,including which 15.75% were terminal deletion or duplication and microdeletion or microduplication. And 9 (3.3%)were mosaicisms.Conclusions Chromosomal microarray technique is highly accurate and specific,which can offer more genetic information than conventional karyotyping. And chromosomal microarray technique can also facilitate estimation of recurrence risk of future pregnancies for patients with embryo development arrest.

Chromosomal microarrays testing in children with developmental disabilities and congenital anomalies / Análise cromossômica por microarray em crianças com deficiências de desenvolvimento e anomalias congênitas

OBJECTIVES: Clinical use of microarray-based techniques for the analysis of many developmental disorders has emerged during the last decade. Thus, chromosomal microarray has been positioned as a first-tier test. This study reports the first experience in a Chilean cohort. METHODS: Chilean patients with developmental disabilities and congenital anomalies were studied with a high-density microarray (CytoScan(tm) HD Array, Affymetrix, Inc., Santa Clara, CA, USA). Patients had previous cytogenetic studies with either a normal result or a poorly characterized anomaly. RESULTS: This study tested 40 patients selected by two or more criteria, including: major congenital anomalies, facial dysmorphism, developmental delay, and intellectual disability. Copy number variants (CNVs) were found in 72.5% of patients, while a pathogenic CNV was found in 25% of patients and a CNV of uncertain clinical significance was found in 2.5% of patients. CONCLUSION: Chromosomal microarray analysis is a useful and powerful tool for diagnosis of developmental diseases, by allowing accurate diagnosis, improving the diagnosis rate, and discovering new etiologies. The higher cost is a limitation for widespread use in this setting. .

OBJETIVO: O uso clínico de técnicas baseadas em microarrays para a análise de transtornos de desenvolvimento tem surgido durante a última década. Assim, o microarray cromossômico tem sido posicionado como um teste de primeiro nível clínico. Relatamos a primeira experiência em uma coorte chilena. MÉTODOS: Pacientes chilenos com atraso de desenvolvimento e anomalias congênitas foram estudados com um microarray de alta densidade (CytoScan(tm) HD Array, Affymetrix, Inc., Santa Clara, CA, EUA). Pacientes tiveram estudos citogenéticos anteriores, ou um resultado normal ou de uma anomalia não bem caracterizada. RESULTADOS: Foram analisados 40 pacientes selecionados por dois ou mais critérios, incluindo: anomalias congênitas maiores, dismorfismo facial, atraso de desenvolvimento e deficiência intelectual. Uma variante do número de cópia (CNV) foi encontrada em 72,5% dos pacientes, enquanto que uma CNV patogênica foi encontrada em 25% dos pacientes e uma CNV de significado clínico incerto foi encontrada em 2,5% dos pacientes. CONCLUSÕES: A análise cromossômica microarray é uma ferramenta útil e poderosa em transtornos de desenvolvimento, permite um diagnóstico preciso, melhora a taxa de diagnóstico e descobre novas etiologias. O custo mais elevado é uma limitação para um uso difundido em nossa realidade. .

Association of FCGR3B gene copy number variations and lupus nephritis in Henan Han populations / 中华肾脏病杂志

Objective To evaluate the copy number variation of FCGR3B gene in Henan Han systemic lupus erythematosus (SLE) patients and healthy controls,and explore the association between FCGR3B gene copy number variants (CNVs) and lupus nephritis (LN) susceptibility in Henan Han population.Methods FCGR3B CNVs was investigated in 142 SLE patients with nephritis,187 SLE patients without nephritis and 328 healthy controls.A modified methodology based on competitive PCR named Multiplex AccuCopyTM Kit was used to detect FCGR3B copy number.Clinical and laboratory data were collected retrospectively from the medical record.Logistic regression analysis was used to determine the association of FCGR3B copy number variants with LN susceptibility.Rank correlation was used to determine the correlations between FCGE3B copy number variants and clinical phenotypes of LN.Results No significant difference was detected in the copy number variations of FCGR3B in different groups.Low copy number of FCGR3B was more commonly seen in patients with nephritis (P=0.042),and was a risk factor for LN (OR=2.059; 95％ CI:1.081-3.921; P=0.028).However,high copy number (＞ 2) had no effect on SLE patients without nephritis(OR=1.152; 95％CI:0.711-1.866; P=0.565) and LN patients (OR=0.838; 95％ CI:0.529-1.329; P=0.454).There were no associations between FCGR3B copy number variants and clinical phenotypes and immunologic characteristics of LN.Conclusion The low copy number of FCGR3B is a risk factor for LN in Henan Han population.

Comparison between single nucleotide polymorphism array and karyoty-ping in prenatal diagnosis in Down’ s screening abnormal pregnancy / 中国病理生理杂志

[ ABSTRACT] AIM:To evaluate the clinical application of single nucleotide polymorphism array ( SNP array) in prenatal diagnosis for screening the abnormality of women with Down’ s syndrome ( DS) .METHODS:The amniotic fluid samples ( n=312) collected by amniocentesis for the DS screening abnormality women were tested by karyotyping and SNP array analysis, respectively.The findings of karyotyping and SNP array analysis were compared.RESULTS:Two cases of trisomy 21 were identified by karyotyping and SNP array analysis, but SNP array analysis failed to identify 6 cases of chro-mosome balanced structural rearrangement.SNP detected 176 cases copy number variants ( CNVs) in 303 cases normal karyotype were detected by SNP, including 106 benign CNVs, 61 variants of unknown significance (VOUS), 9 de novo CNVs, and none of them was pathogenic.The distribution difference of CNVs in DS screening positive group and DS screening positive plus advanced maternal age group was not statistically significant ( P>0.05) .Furthermore, we reported 14 kinds of CNVs for the first time in population.CONCLUSION:SNP array can further assure chromosome microdupli-cation/microdeletion.In normal karyotype fetus of prenatal diagnosis, SNP can detect some clinical significant CNVs.

Microarray detection of the copy number variations in a patient with developmental delay / 临床儿科杂志

Objective To investigate the copy number variants of a developmental delay patient by applying single nucleotide polymorphisms array technique and to analyze the relationship between the clinical manifestation and copy number variants.Methods Single nucleotide polymorphisms array was used to detect genomic copy number variants in a child with development delay and her phenotypic normal parents.Results The patient had a 7. 9-Mb deletion at 8p23.3-p23.1 and a 27.4-Mb duplication at 8p23.1-p11.23, which were conifrmed as pathogenic copy number variants after comparative analysis with database.Conclusions Single nucleotide polymorphisms array could serve as a useful method to diagnose developmental delay patients and analyze pathogenesis.