Tracking the evolutionary pathways among Brazilian Lebiasina species (Teleostei: Lebiasinidae): a chromosomal and genomic comparative investigation

Despite several difficulties in chromosomal analyses of small-sized fishes, the cytogenetics of the Lebiasinidae was largely improved in the last years, showing differential patterns in the chromosomal evolution inside the family. In this context, it has been shown that genus Lebiasina preserves its karyotypic macrostructure, composed of 2n = 36 chromosomes, whereas the other genera generally present higher 2n. This study focused on the comparative cytogenetics of three Lebiasina species, one of them analyzed here for the first time, using conventional and molecular procedures. The results reinforced the differentiated evolutionary path of the genus Lebiasina while, at the same time, highlighted the genomic particularities that have accompanied the evolution of each species. In this sense, the repetitive components of the genome played a significant role in the differentiation of each species. It is also notable that L. minuta and L. melanoguttata, the two species that occur exclusively in the Brazilian territory, show greater chromosomal similarities to each other than to the trans-Andean sister species, L. bimaculata.(AU)

Apesar das dificuldades encontradas em se realizar análises cromossômicas em peixes de pequeno porte, os estudos citogenéticos em Lebiasinidae vêm crescendo nos últimos anos e demonstrando padrões diferenciados na evolução cromossômica entre os membros da família. Nesse contexto, o gênero Lebiasina tem mostrado preservar sua macroestrutura cariotípica, composta por 2n = 36 cromossomos, enquanto os demais gêneros geralmente apresentam 2n maiores. Este estudo tem como foco a citogenética comparativa de três espécies de Lebiasina, sendo uma delas analisada pela primeira vez aqui, através do emprego de técnicas convencionais e moleculares. Os resultados obtidos reforçam a trajetória evolutiva diferenciada do gênero Lebiasina, ao mesmo tempo em que evidenciam as particularidades genômicas que acompanham a evolução de cada uma das espécies. Neste contexto, os componentes repetitivos do genoma tiveram um papel importante na caracterização particular de cada uma das espécies. Também, é notável que L. minuta e L. melanoguttata, duas espécies que ocorrem exclusivamente no território brasileiro, apresentam maior proximidade citogenética entre elas do que com a espécie irmã transandina, L. bimaculata.(AU)

Prenatal diagnosis and genetic analysis of 9p24 microdeletion in six fetuses / 中华围产医学杂志

Objective:To investigate the prenatal diagnosis and genetic analysis of 9p24 microdeletion in six fetuses.Methods:Genetic data of six pregnant women with positive results of serological Down's syndrome screening at Henan Provincial People's Hospital from January 2018 to January 2020 were retrospectively collected and analyzed. Amniotic fluid and the parents' peripheral blood samples were subjected to G banding and array comparative genomic hybridization (aCGH) analysis. Detected copy number variation (CNV) were classified based on the American College of Medical Genetics and Genomics (ACMG) scoring standard.Results:Six fetuses showed no abnormalities in ultrasound during the second trimester as well as in karyotyping. A chromosome deletion of 1 019~6 001 kb at 9p24 was found in all six fetuses by aCGH, referring to disease-related genes DMRT1, SMARCA2, DOCK8, etc. The deletion of case 3 was inherited from the asymptomatic father, and the other fetal five were all de novo mutations. Cases 1, 2, 5, and 6 were pathogenic/likely pathogenic CNV carriers and cases 3 and 4 were CNV of unknown clinical significance carriers. After genetic counseling, cases 1, 2, 5, and 6 chose to terminate the pregnancies; cases 3 and 4 continued and gave birth to normal offspring. Conclusions:Fetuses with 9p24 microdeletion lack specific phenotypes before born. DMRT1 and SMARCA2 may be the key genes in this region.

Genetic analysis and prenatal diagnosis of intellectual disability caused by Xq25 microduplication in a pedigree / 中华围产医学杂志

Objective:To analyze the clinical and genetic characteristics of a 27-year-old male patient with intellectual disability and his pedigree to provide a reference for genetic counseling and prenatal diagnosis.Methods:G-banding and array comparative genomic hybridization (aCGH) were performed to analyze the karyotypes and genomic copy number variations of the proband (Ⅲ-1) and his family members. Based on the results, prenatal diagnosis was performed for one pregnant woman (Ⅲ-2) in the pedigree who is the sister of the proband.Results:All karyotyping were normal in the family members, while aCGH results showed a 1 533 kb microduplication in the Xq25 region of the proband, his mother (Ⅱ-3), his uncle (Ⅱ-2), and his sister (Ⅲ-2), which was confirmed to be pathogenic. The proband and his uncle presented with intellectual disability, bradylalia, and facial dysmorphism. In contrast, his mother and sister showed normal phenotypes. His sister's fetal karyotype and aCGH results were normal, and the pregnancy continued. A male baby (Ⅳ-1) was delivered vaginally at term and showed no physical or intellectual abnormalities during a 46-month follow-up.Conclusions:Xq25 microduplication might be the cause of intellectual disability in the proband. STAG2 is probably the essential gene in Xq25 region.

Fenotipo clínico mixto de deleción y duplicación de la región del síndrome de Sotos: microdeleción 5q35.2-q35.3 detectada por microarreglo de hibridación genómica comparativa / Mixed clinical phenotype of deletion and duplication of the Sotos syndrome region: 5q35.2-q35.3 microdeletion detected by CGH array

Resumen Introducción: El síndrome de Sotos es una enfermedad hereditaria caracterizada por el sobrecrecimiento prenatal y posnatal, con edad ósea avanzada, facies característica y retraso del desarrollo. Caso clínico: Se reporta el caso de un paciente con síndrome de Sotos y manifestaciones clínicas no descritas previamente, diagnosticado por microarreglos de hibridación genómica comparativa. Se detectó la duplicación de un gen y la deleción de 43 genes, entre los que se encuentran NSD1, gen asociado al síndrome de Sotos. La pérdida y la ganancia de estos otros genes pueden explicar las características atípicas en este paciente. Conclusiones: Por las características atípicas, el microarreglo de hibridación genómica comparativa fue una herramienta útil para el diagnóstico. Las alteraciones cromosómicas encontradas en este paciente demuestran la heterogeneidad clínica de las enfermedades genómicas.

Abstract Background: Sotos syndrome is an inherited disease characterized by pre- and postnatal overgrowth with advanced bone age, characteristic facies, and developmental delay. Case report: We report the case of a patient with Sotos syndrome and clinical manifestations not described previously, who was diagnosed comparative genomic hybridization arrangements (CGH array). The duplication of a gene and the deletion of 43 genes were identified, among which is the NSD1 gene, associated with Sotos syndrome. The gain and loss of these other genes may explain the atypical characteristics present in the patient. Conclusions: Due to its atypical characteristics, the CGH array was a useful tool for diagnosis. The chromosomal alterations found in this patient demonstrate the clinical heterogeneity of genomic diseases.

5p13. 2 Chromosomal duplication syndrome: case report and literature review / Síndrome de duplicação cromossômica 5p13. 2: relato de caso e revisão da literatura

Chromosome 5p13 duplication syndrome represents a contiguous gene syndrome involving duplication of several genes on chromosome 5p13. Some clinical phenotypes are related to it, such as: obsessive-compulsive behavior, small palpebral fissures, intellectual disability, global development delay and ocular hypertelorism. The exact mechanism behind these changes has not well known and further studies are needed for this purpose. Since it is a rare and uncommon clinical situation, the case report contributes to the knowledge of the disease and early diagnosis. This condition mainly affects the cognitive neuromuscular system. We describe an 8-year-old Brazilian patient with the duplication of chromosome 5p13.2, karyotype, whose neurodevelopmental evaluation presented cognitive impairment, severe language delay and atypical physical examination, with ocular hypertelorism, right auricular tags, congenital heart defect and long fingers. The patient was diagnosed by comparative genomic hybridization (CGH)-array revealing a 204Kb of DNA duplication. The exact mechanism behind these structural disorders is still unclear and further studies are needed for this purpose. Nevertheless, the diagnostic suspicion of this genetic alteration that, in general, presents late diagnosis, should be considered to enable better clinical support to the patients and family genetic counseling.

A síndrome da duplicação do cromossomo 5p13 representa uma síndrome genética contígua envolvendo a duplicação de vários genes contidos nesta região. Alguns fenótipos clínicos estão relacionados com ela, tais como: comportamento obsessivo compulsivo, fissuras palpebrais pequenas, déficit intelectual, atraso no desenvolvimento global e hipertelorismo ocular. Por ser uma situação clínica rara, o relato do caso contribui para a disseminação do conhecimento acerca da condição, assim como para seu diagnóstico precoce. Descrevemos uma paciente brasileira de oito anos com a duplicação do cromossomo 5p13.2, que na avaliação do neurodesenvolvimento apresentou comprometimento cognitivo, grave atraso da linguagem e dismorfismos como hipertelorismo ocular, apêndice auricular direito, sopro cardíaco, relacionado a defeito do septo ventricular, e dedos alongados. A paciente foi diagnosticada por meio da pesquisa molecular (CGH)-array com ganho de 204Kb de DNA. O mecanismo exato por trás dessas alterações estruturais ainda não está claro e são necessários mais estudos para este fim. Não obstante, a suspeita diagnóstica dessa alteração genética que, em geral, apresenta diagnóstico tardio, deve ser aventada para viabilizar melhor suporte clínico aos pacientes e aconselhamento genético familiar.

Genomic and transcriptomic characterization of the human glioblastoma cell line AHOL1

Cancer cell lines are widely used as in vitro models of tumorigenesis, facilitating fundamental discoveries in cancer biology and translational medicine. Currently, there are few options for glioblastoma (GBM) treatment and limited in vitro models with accurate genomic and transcriptomic characterization. Here, a detailed characterization of a new GBM cell line, namely AHOL1, was conducted in order to fully characterize its molecular composition based on its karyotype, copy number alteration (CNA), and transcriptome profiling, followed by the validation of key elements associated with GBM tumorigenesis. Large numbers of CNAs and differentially expressed genes (DEGs) were identified. CNAs were distributed throughout the genome, including gains at Xq11.1-q28, Xp22.33-p11.1, Xq21.1-q21.33, 4p15.1-p14, 8q23.2-q23.3 and losses at Yq11.21-q12, Yp11.31-p11.2, and 15q11.1-q11.2 positions. Nine druggable genes were identified, including HCRTR2, ETV1, PTPRD, PRKX, STS, RPS6KA6, ZFY, USP9Y, and KDM5D. By integrating DEGs and CNAs, we identified 57 overlapping genes enriched in fourteen pathways. Altered expression of several cancer-related candidates found in the DEGs-CNA dataset was confirmed by RT-qPCR. Taken together, this first comprehensive genomic and transcriptomic landscape of AHOL1 provides unique resources for further studies and identifies several druggable targets that may be useful for therapeutics and biologic and molecular investigation of GBM.

Unexpected detection of Duchenne muscular dystrophy gene mutation by array comparative genomic hybridization in prenatal diagnosis: a retrospective analysis / 中华围产医学杂志

Objective:To explore the accuracy of array comparative genomic hybridization(aCGH) in the unexpected detection of Duchenne muscular dystrophy ( DMD) gene duplication/deletion in prenatal diagnosis. Methods:A retrospective analysis was performed on 31 cases with DMD gene duplication/deletion detected by aCGH among 5 025 prenatal diagnosis samples without family history of DMD in Henan Provincial People's Hospital from July 2018 to December 2019. The multiplex ligation-dependent probe amplification (MLPA) method was used to verify the above results. The American College of Medical Genetics and Genomics (ACMG) guideline was referred for pathogenicity analysis of the detected duplicates/deletions. Descriptive analysis was adopted in analysis. Results:The total unexpected DMD gene duplication/deletion rate was 0.62% (31/5 025), among which 25 cases were with microduplication/microdeletion ≤ 200 kb and six were >200 kb; there were 24 cases of deletion, seven cases of duplication; exon or intron duplication/deletion were accounted for 19 and 12 cases, respectively. According to the five classification standards of ACMG guideline, there were 17 cases with pathogenic variants and 14 cases with uncertain pathogenicity/likely benign variants. Of the 19 with exon mutations, 17 cases were DMD intragenic variants, and two cases involved variants in and outside DMD gene, which were verified by MLPA whose results were all positive. Conclusions:The duplication/deletion of exon region of DMD gene detected by aCGH technique is accurate and reliable, which plays an important role in the diagnosis of DMD. For these cases involved both internal and external regions of DMD gene, aCGH can identify the upstream and downstream breaking points of DMD gene, thus providing the basis for ACMG grading.

Presencia de duplicación 2p25.3 y síndrome de microdeleción 2q37.3 en un mismo individuo / Presence of 2p25.3 Duplication and 2q37.3 Microdeletion Syndrome in the Same Individual / Presença de duplicação 2p25.3 e síndrome da microdeleção 2p25.3 no mesmo indivíduo

Resumen: El estudio del cromosoma 2 en los seres humanos ha permitido reconocer que su alteración, basada en una localización específica, puede conducir a diversas enfermedades asociadas. Mediante la identificación fenotípica, sustentada en el estudio molecular de hibridación genómica comparativa y un estudio bioinformático posterior, se detectó la presencia de una duplicación patogénica en la región cromosómica 2p25.3p24.3, relacionada con la afección de 36 genes. Adicionalmente, se identificó una deleción patogénica en la citobanda 2q37.3, relacionada con la afección de 36 genes. El análisis bioinformático demostró interacciones entre genes que explican características sintomatológicas. Esta es la primera vez que se presentan estas dos variantes en un mismo individuo. Ambas alteraciones se han asociado con retraso psicomotor moderado, autismo, neurohipófisis ectópica, aracnodactilia, cardiopatía congénita y alteraciones cardiovasculares. Se ha propuesto que la mutación HDAC4 es la causante de la mayoría de las características del síndrome de microdeleción 2q37. El fenotipo clínico heterogéneo es el resultado del reordenamiento cromosómico encontrado, lo cual permite describir, interpretar y dar un tratamiento oportuno y dirigido a la paciente y la respectiva conserjería genética familiar. Finalmente, esta es la primera vez que se reporta este tipo específico de reordenamiento cromosómico.

Abstract: The study of chromosome 2 in humans has allowed recognizing that its alteration, based on a specific location, can lead to various associated diseases. Through the phenotypic identification, supported by comparative genomic hybridization and subsequent bioinformatic analysis, the presence of a pathogenic duplication was detected in the chromosomal region 2p25.3p24.3 affecting 36 genes. Additionally, a pathogenic deletion was identified in cytoband 2q37.3 affecting 36 genes. The bioinformatic analysis showed interactions among genes that explain symptomatic characteristics. This is the first time that these two variants are present in the same individual. Both disorders have been associated with moderate psychomotor retardation, autism, ectopic neurohypophysis, arachnodactyly, congenital heart disease, and cardiovascular disorders. The hdac4 mutation has been suggested to cause most of the features of 2q37 microdeletion syndrome. The heterogeneous clinical phenotype derives from the chromosomal rearrangement found, which allows describing, interpreting, and providing the patient with timely targeted treatment and the respective family genetic counseling. Finally, this specific type of chromosomal rearrangement has been reported for the first time.

Resumo: O estudo do cromossomo 2 em seres humanos nos permitiu reconhecer que sua alteração, com base em uma localização específica, pode levar a diversas doenças associadas. Por meio da identificação fenotípica, apoiada no estudo molecular da hibridação genômica comparativa e em um estudo bioinformático posterior, foi detectada a presença de uma duplicação patogénica na região cromossômica 2p25.3p24.3, relacionada a 36 genes afetados. Além disso, uma deleção patogénica foi identificada na citobanda 2q37.3, relacionada a 36 genes afetados. A análise bioinformática mostrou interações entre genes que explicam características sintomáticas. É a primeira vez que essas duas variantes são apresentadas no mesmo indivíduo. Ambos os distúrbios tém sido associados a retardo psicomotor moderado, autismo, neuro-hipófise ectópica, aracnodactilia, doenças cardíacas congénitas e distúrbios cardiovasculares. Propõe-se que a mutação hdac4 é a causa da maioria das características da síndrome de microdeleção 2q37. O fenótipo clínico heterogéneo é o resultado do rearranjo cromossômico encontrado, que permite descrever, interpretar e oferecer um tratamento oportuno direcionado ao paciente e ao respectivo aconselhamento genético familiar. Finalmente, também é a primeira vez que esse tipo específico de rearranjo cromossômico é relatado.

Williams–Beuren syndrome in Mexican patients confirmed by FISH and assessed by aCGH

Williams–Beuren syndrome (WBS) has a prevalence of 1/7500–20000 live births and results principally from a de novo deletion in 7q11.23 with a length of 1.5 Mb or 1.8 Mb. This study aimed to determine the frequency of 7q11.23 deletion, size of the segment lost, and involved genes in 47 patients with a clinical diagnosis of WBS and analysed by fluorescence in situ hybridization (FISH); among them, 31 had the expected deletion. Micro-array comparative genomic hybridization (aCGH) confirmed the loss in all 18 positive-patients tested: 14 patients had a 1.5 Mb deletion with the same breakpoints at 7q11.23 (hg19: 72726578–74139390) and comprising 24 coding genes from TRIM50 to GTF2I. Four patients showed an atypical deletion: two had a 1.6Mb loss encompassing 27 coding genes, from NSUN5 to GTF2IRD2; another had a 1.7 Mb deletion involving 27 coding genes, from POM121 to GTF2I; the remaining patient presented a deletion of 1.2 Mb that included 21 coding genes from POM121 to LIMK1. aCGH confirmed the lack of deletion in 5/16 negative-patients by FISH. All 47 patients had the characteristic facial phenotype of WBS and 45 of 47 had the typical behavioural and developmental abnormalities. Our observations further confirm that patients with a classical deletion present a typical WBS phenotype, whereas those with a high (criteria of the American Association of Pediatrics, APP) clinical scorebut lacking the expected deletion may harbour an ELN point mutation. Overall, the concomitant CNVs appeared to be incidental findings.

Identification of ATP7B gene variant by combined use of Sanger sequencing, array CGH and quantitative PCR / 中华医学遗传学杂志

Objective@#To identify the type and origin of ATP7B gene mutation in a family affected with Wilson disease by combined use of multiple methods.@*Methods@#Peripheral blood samples were collected from the proband, her parents and her brother. Sanger sequencing were used to detect point mutation and small deletion/insertion of the 21 exons and flanking sequences of the ATP7B gene in all family members. Array-based comparative genomic hybridization (aCGH) was performed to identify copy number variations (CNVs) of the ATP7B gene in the proband. The result was validated by quantitative PCR (qPCR) in other 3 members.@*Results@#Sanger sequencing indicated that the proband carried a heterozygous variation c. 2668G>A (p.V890M) derived from her mother. In addition, 5 common SNPs were detected in her mother, three of which were also identified in her father and brother. The 5 SNPs in the proband were of the wide type. aCGH analysis demonstrated that the proband was heterozygous for a 4 kb deletion, which encompassed exons 2 and 3 of the ATP7B gene and 2 SNPs. qPCR showed that the copy number in her father and brother was about half of the control, indicating heterozygous loss of exons 2 and 3.@*Conclusion@#The combined Sanger sequencing, array CGH and qPCR has identified a novel CNV involving the ATP7B gene. The strategy can improve the diagnostic rate for hereditary or rare diseases.

Effects of Copy Number Variations on Developmental Aspects of Children With Delayed Development

OBJECTIVE: To determine effects of copy number variations (CNV) on developmental aspects of children suspected of having delayed development. METHODS: A retrospective chart review was done for 65 children who underwent array-comparative genomic hybridization after visiting physical medicine & rehabilitation department of outpatient clinic with delayed development as chief complaints. Children were evaluated with Denver Developmental Screening Test II (DDST-II), Sequenced Language Scale for Infants (SELSI), or Preschool Receptive-Expressive Language Scale (PRES). A Mann-Whitney U test was conducted to determine statistical differences of developmental quotient (DQ), receptive language quotient (RLQ), and expressive language quotient (ELQ) between children with CNV (CNV(+) group, n=16) and children without CNV (CNV(–) group, n=37). RESULTS: Of these subjects, the average age was 35.1 months (mean age, 35.1±24.2 months). Sixteen (30.2%) patients had copy number variations. In the CNV(+) group, 14 children underwent DDST-II. In the CNV(–) group, 29 children underwent DDST-II. Among variables, gross motor scale was significantly (p=0.038) lower in the CNV(+) group compared with the CNV(–) group. In the CNV(+) group, 5 children underwent either SELSI or PRES. In the CNV(–) group, 27 children underwent above language assessment examination. Both RLQ and ELQ were similar between the two groups. CONCLUSION: The gross motor domain in DQ was significantly lower in children with CNV compared to that in children without CNV. This result suggests that additional genetic factors contribute to this variability. Active detection of genomic imbalance could play a vital role when prominent gross motor delay is presented in children with delayed development.

Karyotype ana1ysis of small supernumerary marker chromosome in 20 486 samples for prenatal diagnosis / 中华围产医学杂志

Objective To investigate the detection rate,clinical indications and pregnancy outcomes of pregnancies with prenatally diagnosed small supernumerary marker chromosome (sSMC) to provide a theoretical foundation for prenatal diagnosis and genetic counseling of sSMC.Methods This study retrospectively analyzed the clinical data of 20541 cases who underwent prenatal diagnosis at the Prenatal Diagnostic Center in the Department of Obstetrics and Gynecology in Peking University First Hospital from January 2007 to May 2018.The detection rate,diagnostic indications and pregnancy outcomes of the cases with sSMC were analyzed after cell culture and karyotyping.Array comparative genomic hybridization (aCGH) was used to analyze the origin of fetal abnormal chromosome in some cases.Results Prenatal diagnostic samples of 20486 cases were successfully cultured,among which 20 (sSMC) were detected giving an detection rate of 0.98‰,while the figures in samples obtained through chorionic villus sampling,amniocentesis and umbilical cord blood sampling were 2.20 ‰ (2/910),0.74 ‰ (14/18824) and 5.32 ‰ (4/752),respectively.Twelve cases of mosaic karyotype were also found.In gravidas for prenatal diagnosis indicated by maternal or paternal chromosomal abnormality,fetal structural anomalies on ultrasonography,adverse pregnant history,advanced maternal age and high risk of Down's syndrome,the detection rates of sSMC were 10.42 ‰ (1/96),2.65 ‰ (4/1507),1.89 ‰ (5/2 643),0.83‰ (8/9 624) and 0.49‰ (2/4013),respectively.Eleven cases were further analyzed with aCGH,four of which showed pathogenic copy number variants involving 2q11.1-q12.1,2p12-p11.1 and 2q11.1-q12.1,7q 11.21-q 11.23 and 15q11.1-q 13.3 dup1ications and terminated the pregnancies.Seven cases carried nonpathogenic marker chromosomes,of which one terminated the pregnancy,while the other six continued to fullterm with uneventful outcomes until follow-ups.Conclusions sSMC is hard to detect in prenatal diagnosis,but maternal or paternal chromosomal abnormalities,fetal structural anomalies on ultrasonography and adverse pregnancy and childbirth history are strong indications.Cytogenetics and molecular diagnosis combined can clarify the character,origin and pathogenicity of sSMC,and is of great clinical importance in prenatal genetic counseling and maternal decision making.

Prenatal chromosomal microarray analysis of fetus with increased nuchal translucency

Nuchal translucency is an important indicator of an aneuploid fetus in prenatal diagnostics. Previously, only the presence of aneuploid could be confirmed by conventional karyotyping of fetuses with thick nuchal translucency. With the development of genetic diagnostic techniques, however, it has been reported that subtle variations not detectable by conventional karyotyping might occur in cases of pathologic clinical syndrome in euploid fetuses. One of the newer, high-resolution genetic methods in the prenatal setting is chromosomal microarray. The possible association between nuchal translucency thickness with normal karyotype and submicroscopic chromosomal abnormalities detectable by microarray has been studied. How and when to apply microarray in clinical practice, however, is still debated. This article reviews the current studies on the clinical application of microarray in cases of increased nuchal translucency with normal karyotype for prenatal diagnosis.

Array Comparative Genomic Hybridization as the First-line Investigation for Neonates with Congenital Heart Disease: Experience in a Single Tertiary Center

BACKGROUND AND OBJECTIVES: The purpose of the present study was to investigate the advantages and disadvantages of verifying genetic abnormalities using array comparative genomic hybridization (a-CGH) immediately after diagnosis of congenital heart disease (CHD). METHODS: Among neonates under the age of 28 days who underwent echocardiography from January 1, 2014 to April 30, 2016, neonates whose chromosomal and genomic abnormalities were tested using a-CGH in cases of an abnormal finding on echocardiography were enrolled. RESULTS: Of the 166 patients diagnosed with CHD, 81 underwent a-CGH and 11 patients (11/81, 13.5%) had abnormal findings on a-CGH. 22q11.2 deletion syndrome was the most common (4/11, 36.4%). On the first a-CGH, 4 patients were negative (4/81, 5%). Three of them were finally diagnosed with Williams syndrome using fluorescent in situ hybridization (FISH), 1 patient was diagnosed with Noonan syndrome through exome sequencing. All of them exhibited diffuse pulmonary artery branch hypoplasia, as well as increased velocity of blood flow, on repeated echocardiography. Five patients started rehabilitation therapy at mean 6 months old age in outpatient clinics and epilepsy was diagnosed in 2 patients. Parents of 2 patients (22q11.2 deletion syndrome and Patau syndrome) refused treatment due to the anticipated prognosis. CONCLUSIONS: Screening tests for genetic abnormalities using a-CGH in neonates with CHD has the advantage of early diagnosis of genetic abnormality during the neonatal period in which there is no obvious symptom of genetic abnormality. However, there are disadvantages that some genetic abnormalities cannot be identified on a-CGH.

Síndrome de Cohen diagnosticado con hibridación genómica comparativa por microarreglos / Cohen syndrome diagnosed using microarray comparative genomic hybridization / Síndrome de Cohen diagnosticado com hibridação genômica comparativa por microarranjos

RESUMEN El síndrome de Cohen (SC) es una enfermedad genética rara, con herencia autosómica recesiva. Se origina por daños en el gen VPS13B, locus 8q22-q23. El fenotipo característico consiste en discapacidad intelectual, microcefalia, facies dismórfica, anormalidades oftalmológicas, obesidad central e hipotonía. Solo se han publicado aproximadamente 150 casos, la mayoría de origen finlandés. Reportamos el caso de un preescolar con talla baja, craneosinostosis, facies dismórfica, hipotonía y retraso del desarrollo psicomotor a quien se le diagnosticó SC por medio de Hibridación Genómica Comparativa por microarreglos (HGCm), que mostró una deleción en homocigosis de 0.153 Mb en 8q22.2 incluyendo el gen VPS13B, OMIM #216550. Con esta publicación contribuimos al conocimiento epidemiológico de un síndrome genético infrecuente, y mostramos el aporte de la HGCm al diagnóstico etiológico de pacientes con discapacidad intelectual inexplicada, retardo del desarrollo psicomotor, problemas del lenguaje, autismo y anomalías congénitas múltiples.

SUMMARY Cohen syndrome (CS) is an uncommon autosomal recessive genetic disorder attributed to damage on VPS13B gene, locus 8q22-q23. Characteristic phenotype consists of intelectual disability, microcephaly, facial dysmorphism, ophthalmic abnormalities, truncal obesity and hipotony. Worldwide, around 150 cases have been published, mostly in Finish patients. We report the case of a 3 year-old male, with short height, craniosynostosis, facial dysmorphism, hipotony, and developmental delay. He was diagnosed with Cohen syndrome using Microarray Comparative Genomic Hibridization (aCGH) that showed homozygous deletion of 0.153 Mb on 8q22.2 including VPS13B gene, OMIM #216550. With this report we contribute to enlarge epidemiological databases on an uncommon genetic disorder. Besides, we illustrate on the contribution of aCGH to the etiological diagnosis of patients with unexplained intellectual disability, delayed psychomotor development, language difficulties, autism and multiple congenital anomalies.

RESUMO A síndrome de Cohen (SC) é uma doenças genética rara, com herança autossômica recessiva. Se origina por danos no gene VPS13B, locus 8q22-q23. O fenótipo característico consiste em deficiência intelectual, microcefalia, faces dismórfica, anormalidades oftalmológicas, obesidade central e hipotonia. Só se há publicado aproximadamente 150 casos, a maioria de origem finlandês. Reportamos o caso de um pré-escolar com estatura baixa, craniossinostose, faces dismórfica, hipotonia e retraso do desenvolvimento psicomotor a quem se lhe diagnosticou SC por meio de Hibridação Genômica Comparativa por microarranjos (HGCm), que mostrou uma deleção em homozigoto de 0.153 Mb em 8q22.2 incluindo o gene VPS13B, OMIM #216550. Com esta publicação contribuímos ao conhecimento epidemiológico de uma síndrome genética infrequente, e mostramos o aporte da HGCm ao diagnóstico etiológico de pacientes com deficiência intelectual inexplicada, atraso do desenvolvimento psicomotor, problemas da linguagem, autismo e anomalias congénitas múltiplas.

Preimplantation genetic diagnosis associated to Duchenne muscular dystrophy / Diagnóstico genético pré-implantacional associado à distrofia muscular de Duchenne

ABSTRACT Duchenne muscular dystrophy is the most common muscle disease found in male children. Currently, there is no effective therapy available for Duchenne muscular dystrophy patients. Therefore, it is essential to make a prenatal diagnosis and provide genetic counseling to reduce the birth of such boys. We report a case of preimplantation genetic diagnosis associated with Duchenne muscular dystrophy. The couple E.P.R., 38-year-old, symptomatic patient heterozygous for a 2 to 47 exon deletion mutation in DMD gene and G.T.S., 39-year-old, sought genetic counseling about preimplantation genetic diagnosis process. They have had a 6-year-old son who died due to Duchenne muscular dystrophy complications. The couple underwent four cycles of intracytoplasmic sperm injection (ICSI) and eight embryos biopsies were analyzed by polymerase chain reaction (PCR) for specific mutation analysis, followed by microarray-based comparative genomic hybridisation (array CGH) for aneuploidy analysis. Preimplantation genetic diagnosis revealed that two embryos had inherited the maternal DMD gene mutation, one embryo had a chromosomal alteration and five embryos were normal. One blastocyst was transferred and resulted in successful pregnancy. The other embryos remain vitrified. We concluded that embryo analysis using associated techniques of PCR and array CGH seems to be safe for embryo selection in cases of X-linked disorders, such as Duchenne muscular dystrophy.

RESUMO A distrofia muscular de Duchenne é a doença muscular mais comum observadas em crianças do sexo masculino. Atualmente, não há terapia eficaz disponível para distrofia muscular de Duchenne, portanto, é essencial o diagnóstico pré-natal e o aconselhamento genético para reduzir o nascimento desses meninos. Relatamos um caso de diagnóstico genético pré-implantação associado à distrofia muscular de Duchenne. O casal E.P.R., 38 anos, heterozigota, sintomática para uma mutação de deleção dos éxons 2 a 47 no gene DMD e G.T.S., 39 anos, buscaram aconselhamento genético sobre o processo de diagnóstico genético pré-implantação. O casal relatou que tiveram um filho de 6 anos que morreu devido a complicações da distrofia muscular de Duchenne. Os pacientes realizaram quatro ciclos de injeção intracitoplásmica de espermatozoides (ICSI) e oito biópsias de embriões foram analisadas por reação em cadeia da polimerase (PCR) para análise de mutação específica, seguida hibridação genômica comparativa baseada em microarranjos ( array CGH) para a pesquisa de aneuploidias. O diagnóstico genético pré-implantação revelou que dois embriões haviam herdado a mutação materna no gene DMD , um embrião tinha uma alteração cromossômica e cinco embriões eram normais. Um blastocisto foi transferido e resultou em gravidez bem sucedida. Os outros embriões permanecem vitrificados. Concluímos que a análise de embriões utilizando técnicas associadas de PCR e CGH array mostrou-se segura para a seleção de embriões em casos de doenças ligadas ao X, como a distrofia muscular de Duchenne.

Genomic imbalances in syndromic congenital heart disease / Desequilíbrios genômicos na cardiopatia congênita sindrômica

Abstract Objective: To identify pathogenic genomic imbalances in patients presenting congenital heart disease (CHD) with extra cardiac anomalies and exclusion of 22q11.2 deletion syndrome (22q11.2 DS). Methods: 78 patients negative for the 22q11.2 deletion, previously screened by fluorescence in situ hybridization (FISH) and/or multiplex ligation probe amplification (MLPA) were tested by chromosomal microarray analysis (CMA). Results: Clinically significant copy number variations (CNVs ≥300 kb) were identified in 10% (8/78) of cases. In addition, potentially relevant CNVs were detected in two cases (993 kb duplication in 15q21.1 and 706 kb duplication in 2p22.3). Genes inside the CNV regions found in this study, such as IRX4, BMPR1A, SORBS2, ID2, ROCK2, E2F6, GATA4, SOX7, SEMAD6D, FBN1, and LTPB1 are known to participate in cardiac development and could be candidate genes for CHD. Conclusion: These data showed that patients presenting CHD with extra cardiac anomalies and exclusion of 22q11.2 DS should be investigated by CMA. The present study emphasizes the possible role of CNVs in CHD.

Resumo Objetivo: Identificar desequilíbrios genômicos patogênicos em pacientes que apresentam cardiopatias congênitas (CC) e anomalias extracardíacas e exclusão da síndrome de deleção 22q11.2 (SD22q11.2). Métodos: Foram avaliados por microarray cromossômico (CMA) 78 pacientes negativos para a deleção 22q11.2, previamente testados por hibridação in situ com fluorescência (FISH) e/ou amplificação de múltiplas sondas dependentes de ligação (MLPA). Resultados: Foram identificadas variações do número de cópias de DNA (CNVs) clinicamente significativas (≥ 300 kb) em 10% (8/78) dos casos, além de CNVs potencialmente relevantes em dois casos (duplicação de 993 kb em 15q21.1 e duplicação de 706 kb em 2p22.3). Genes envolvidos como IRX4, BMPR1A, SORBS2, ID2, ROCK2, E2F6, GATA4, SOX7, SEMAD6D, FBN1 e LTPB1 são conhecidos por atuar no desenvolvimento cardíaco e podem ser genes candidatos a CC. Conclusão: Esses dados mostram que pacientes que apresentam CC, com anomalias extracardíacas e exclusão da SD22q11.2, devem ser investigados por CMA. Ainda, este estudo enfatiza a possível função das CNVs nas CC.

Cri-du-chat syndrome diagnosed in a 21-year-old woman by means of comparative genomic hybridization / Síndrome de cri du chat diagnosticado en mujer de 21 años por hibridación genómica comparativa

Abstract The cri-du-chat syndrome is caused by a deletion on the short arm of chromosome number 5. The size of genetic material loss varies from the 5p15.2 region only to the whole arm. Prevalence rates range between 1:15000 and 1:50000 live births. Diagnosis is suspected on infants with a high-pitched (cat-like) cry, facial dysmorfism, hypotonia and delayed psychomotor development. In adults, phenotypic findings are less specific. It is confirmed through high-resolution G-banding karyotype, fluorescent in situ hybridization or microarray-based comparative genomic hybridization (a-CGH). The following is the case report of a 21-year-old female patient with severe mental retardation and trichotillomania, who does not control sphincters and does not bathe or eat by herself. Her communication is based only on sounds and dysmorphic facies. The G-band karyotype reported is 46, XX. a-CGH shows 18.583Mb interstitial microdeletion in 5p15.33p14.3, including the cri-du-chat critical region. In children or adults with unexplained mental retardation and normal karyotype results (like this case), an a-CGH should be performed to make an etiological diagnosis, establish the prognosis, order additional medical tests and specific treatments, and offer appropriate genetic counseling.

Resumen El síndrome de cri du chat o del maullido de gato es causado por una deleción en el brazo corto del cromosoma 5; el tamaño de la pérdida de material genético varía desde solo la región 5p15.2 hasta el brazo entero. La prevalencia va desde 1 por 15 000 habitantes hasta 1 por 50 000 habitantes. Su diagnóstico se puede confirmar con cariotipo con bandas G de alta resolución, hibridación fluorescente in situ o hibridación genómica comparativa por microarreglos (HGCm); este se sospecha en infantes con un llanto similar al maullido de un gato, fascies dismórficas, hipotonía y retardo del desarrollo psicomotor; sin embargo, en los adultos afectados los hallazgos fenotípicos son menos específicos. Se presenta el caso de una mujer de 21 años con retardo mental severo y tricotilomanía, que no controla esfínteres y no se baña ni come sola; solo emite ruidos y tiene facies dismórficas. El cariotipo de bandas G es reportado 46, XX y la HGCm muestra microdeleción de 18.583Mb en 5p15.33p14.3, incluyendo región crítica de cri du chat. En pacientes de este tipo se debe realizar HGCm para hacer un diagnóstico etiológico, establecer un pronóstico, ordenar pruebas médicas adicionales y tratamientos específicos y realizar la adecuada asesoría genética.

Microarreglos cromosómicos en 236 pacientes chilenos con trastornos del neurodesarrollo y anomalías congénitas / Microarrays in 236 patients with neurodevelopmental disorders and congenital abnormalities

Background: In 20% of neurodevelopmental disorders (NDD) and congenital abnormalities (CA) the cause would be a genomic imbalance detectable only by chromosomal microarrays (CMA). Aim: To analyze the results of CMA performed at the INTA Laboratory of Molecular Cytogenetics, during a period of four years in patients with NDD or CA. Material and Methods: Retrospective study that included all CMA reports of Chilean patients. Age, sex, clinical diagnosis and origin were analyzed, as well as the characteristics of the finding. The percentage of cases diagnosed by CMA was calculated considering all patients with pathogenic (PV) or probably pathogenic variants (VLP). Finally, we studied the association between patients' characteristics and a positive CMA outcome. Results: A total of 236 reports were analyzed. The median age was 5.41 (range 2.25-9.33) years, and 59% were men. Ninety chromosomal imbalances were found, which corresponded mainly to deletions (53.3%), with a median size of 1.662 (range 0.553-6.673) Megabases. The diagnostic rate of CMA in Chilean patients from all over the country was 19.2%. There was a close relationship between the patient's sex and the detection of VLP/VP (p = 0.034). Conclusions: Our diagnostic rate and the association between female sex and a higher percentage of diagnosed cases are concordant with other international studies. Therefore, CMA is a valid diagnostic tool in the Chilean population.

Analysis of clinical outcomes of different embryo stage biopsy in array comparative genomic hybridization based preimplantation genetic diagnosis and screening / 中华妇产科杂志

Objective To evaluate the efficiency of the application of array comparative genomic hybridization (array-CGH) in preimplantation genetic diagnosis or screening (PGD/PGS), and compare the clinical outcomes of different stage embryo biopsy. Methods The outcomes of 381 PGD/PGS cycles referred in the First Affiliated Hospital of Nanjing Medical University from July 2011 to August 2015 were retrospectively analyzed. There were 320 PGD cycles with 156 cleavage-stage-biopsy cycles and 164 trophectoderm-biopsy cycles, 61 PGS cycles with 23 cleavage-stage-biopsy cycles and 38 trophectoderm-biopsy cycles.Chromosomal analysis was performed by array-CGH technology combined with whole genome amplification.Single embryo transfer was performed in all transfer cycles.Live birth rate was calculated as the main clinical outcomes. Results The embryo diagnosis rate of PGD/PGS by array-CGH were 96.9%-99.1%. In PGD biopsy cycles, the live birth rate per embryo transfer cycle and live birth rate per embryo biopsy cycle were 50.0%(58/116) and 37.2%(58/156) in cleavage-stage-biopsy group, 67.5%(85/126) and 51.8%(85/164) in trophectoderm-biopsy group (both P<0.01). In PGS biopsy cycles, the live birth rate per embryo transfer cycle and live birth rate per embryo biopsy cycle were the same as 34.8%(8/23) in cleavage-stage-biopsy group, the same as 42.1%(16/38) in trophectoderm-biopsy group (both P>0.05). Conclusions High diagnosis rate and idea live birth rate are achieved in PGD/PGS cycles based on array-CGH technology.The live birth rate of trophectoderm-biopsy group is significantly higher than that of cleavage-stage-biopsy group in PGD cycles;the efficiency of trophectoderm-biopsy is better.