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.

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.

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.

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 duplicación 7q11. 23: Primer caso descrito en América Latina / Chromosome 7q11. 23 duplication syndrome: First reported case in Latin America

El síndrome de duplicación 7q11.23 es una patología causada por la duplicación de una región del cromosoma 7 que comprende 26 genes. El primer caso descrito en la literatura fue reportado por Somerville et al., en el año 2005, quienes describieron un paciente con dolicocefalia, frente alta y estrecha, pestanas largas, nariz alta y ancha, filtrum corto, paladar ojival, maloclusión dental, retrognatia y retardo grave en el lenguaje. Presentamos una paciente colombiana con hallazgo de duplicación 7q11.23 mediante técnicas de hibridación genómica comparativa y hallazgos clínicos clásicos. Este es el primer caso comunicado en Colombia y en América Latina.

7q11.23 duplication syndrome is a disease caused by duplication of a region of chromosome 7 comprising 26 genes. The first case described in the literature was reported by Somerville et al. in 2005, who described a patient with dolichocephaly, high and narrow forehead, long eyelashes, high and wide nose, short philtrum, high arched palate, dental malocclusion, retrognathia, and severe language delay. We report the case of a Colombian patient with 7q11.23 duplication by comparative genomic hybridization techniques, and classical clinical findings, this being the first reported case in Colombia and Latin America.

A new mosaic der(18)t(1;18)(q32.1;q21.3) with developmental delay and facial dysmorphism / 소아과

We report the case of a 22-month-old boy with a new mosaic partial unbalanced translocation of 1q and 18q. The patient was referred to our Pediatric Department for developmental delay. He showed mild facial dysmorphism, physical growth retardation, a hearing disability, and had a history of patent ductus arteriosus. White matter abnormality on brain magnetic resonance images was also noted. His initial routine chromosomal analysis revealed a normal 46,XY karyotype. In a microarray-based comparative genomic hybridization (aCGH) analysis, subtle copy number changes in 1q32.1-q44 (copy gain) and 18q21.33-18q23 (copy loss) suggested an unbalanced translocation of t(1;18). Repeated chromosomal analysis revealed a low-level mosaic translocation karyotype of 46,XY,der(18)t(1;18)(q32.1;q21.3)[12]/46,XY[152]. Because his parents had normal karyotypes, his translocation was considered to be de novo. The abnormalities observed in aCGH were confirmed by metaphase fluorescent in situ hybridization. We report this patient as a new karyotype presenting developmental delay, facial dysmorphism, cerebral dysmyelination, and other abnormalities.

Prenatal diagnosis of chromosomal abnormalities using whole genome amplification / 实用医学杂志

Objective To evaluate the value of whole genome amplification (WGA) combined with array comparative genomic hybridization (aCGH) in prenatal diagnosis. Methods Array CGH were performed by the DNA of 18 prenatal specimens , which were amplified by WGA because of the low DNA yield. Result 3 of the 18 fetuses were 45, X0 and 9 of 15 fetuses with normal aCGH results showed healthy outcome. Conclusion It’ s feasible for prenatal diagnosis using WGA combined with aCGH which not only can shorten the reporting time but also keep the sensitivity and accuracy of detection.

Genomic characterization of some Iranian children with idiopathic mental retardation using array comparative genomic hybridization.

BACKGROUND: Mental retardation (MR) has a prevalence of 1‑3% and genetic causes are present in more than 50% of patients. Chromosomal abnormalities are one of the most common genetic causes of MR and are responsible for 4‑28% of mental retardation. However, the smallest loss or gain of material visible by standard cytogenetic is about 4 Mb and for smaller abnormalities, molecular cytogenetic techniques such as array comparative genomic hybridization (array CGH) should be used. It has been shown that 15‑25% of idiopathic MR (IMR) has submicroscopic rearrangements detectable by array CGH. In this project, the genomic abnormalities were investigated in 32 MR patients using this technique. MATERIALS AND METHODS: Patients with IMR with dysmorphism were investigated in this study. Karyotype analysis, fragile X and metabolic tests were first carried out on the patients. The copy number variation was then assessed in a total of 32 patients with normal results for the mentioned tests using whole genome oligo array CGH. Multiple ligation probe amplification was carried out as a confirmation test. RESULTS: In total, 19% of the patients showed genomic abnormalities. This is reduced to 12.5% once the two patients with abnormal karyotypes (upon re‑evaluation) are removed. CONCLUSION: The array CGH technique increased the detection rate of genomic imbalances in our patients by 12.5%. It is an accurate and reliable method for the determination of genomic imbalances in patients with IMR and dysmorphism.

MICrocephaly, disproportionate pontine and cerebellar hypoplasia syndrome: A clinico-radiologic phenotype linked to calcium/calmodulin-dependent serine protein kinase gene mutation.

MICrocephaly, disproportionate pontine and cerebellar hypoplasia (MICPCH) syndrome, a rare X-linked disorder, generally seen in girls, is characterized by neurodevelopmental delay, microcephaly, and disproportionate pontine and cerebellar hypoplasia. It is caused by inactivating calcium/calmodulin-dependent serine protein kinase (CASK) gene mutations. We report a 2-year-old girl with severe neurodevelopmental delay, microcephaly, minimal pontine hypoplasia, cerebellar hypoplasia, and normal looking corpus callosum, with whom the conventional cytogenetic studies turned out to be normal, and an array-comparative genomic hybridization (a-CGH) analysis showed CASK gene duplication at Xp11.4. Our case highlights the importance of using clinico-radiologic phenotype to guide genetic investigation and it also confirms the role of a-CGH analysis in establishing the genetic diagnosis of MICPCH syndrome, when conventional cytogenetic studies are inconclusive.

Clinical diagnosis and mutation analysis of a Chinese boy with Phelan-McDermid syndrome / 中华实用儿科临床杂志

Objective To explore the clinical features and genetic diagnosis analysis of a Chinese boy with unexplained overgrowth and developmental delay.Methods The clinical symptoms of the boy were described,and performed routine G-banding was performed to analyze the karyotype of the patient,and multiplex ligation-dependent probe amplification (MLPA) was used to detect the copy number variation (CNVs) in the 22q13 region,and array-comparative genomic hybridization(array CGH) was used to detect all chromosome abnormally,then fluorescence in situ hybridization(FISH) confirmed the result.Results 1.The boy was 1.5 years old and complained about accelerated growth,global developmental delay,severely delayed speech ability and peculiar facial features.2.Routine karyotype analysis showed a karyotype of 46,XY.MLPA found terminal deletion with breakpoints within the SHANK3 gene and ACR gene,RABL2B gene,and array CGH finely mapped the deletion on 22q13,furthermore FISH confirmed the micro deletion.Conclusions Combining the clinical manifestations and effective examination of 22q13 deletion,the boy got a reliable diagnosis of Phelan-McDermid syndrome;as array CGH can be useful to screen CNVs of all chromosome,so MLPA should be applied to some special CNVs.

A case of isodicentric chromosome 15 presented with epilepsy and developmental delay / 소아과

We report a case of isodicentric chromosome 15 (idic(15) chromosome), the presence of which resulted in uncontrolled seizures, including epileptic spasms, tonic seizures, and global developmental delay. A 10-month-old female infant was referred to our pediatric neurology clinic because of uncontrolled seizures and global developmental delay. She had generalized tonic-clonic seizures since 7 months of age. At referral, she could not control her head and presented with generalized hypotonia. Her brain magnetic resonance imaging scans and metabolic evaluation results were normal. Routine karyotyping indicated the presence of a supernumerary marker chromosome of unknown origin (47, XX +mar). An array-comparative genomic hybridization (CGH) analysis revealed amplification from 15q11.1 to 15q13.1. Subsequent fluorescence in situ hybridization analysis confirmed a idic(15) chromosome. Array-CGH analysis has the advantage in determining the unknown origin of a supernumerary marker chromosome, and could be a useful method for the genetic diagnosis of epilepsy syndromes associated with various chromosomal aberrations.

Sex-dependent differences in DNA copy number alterations in hepatocellular carcinoma / 第二军医大学学报

Objective To identify the sex-related DNA copy number alterations (CNA) in hepatocellular carcinoma (HCC). Methods High-resolution array comparative genomic hybridization Carray- CGH) was used to examine 17 female and 46 male HCCs. Two-tailed Fisher's exact test or χ2 test was used to compare the differences in CNA between females and males. Results The overall frequencies and patterns of CNA in female and male cases were similar. However, female HCC tumors presented more copy number gains compared to male on lq21. 3-q22(76. 5% vs 37. 0%, P = 0. 009), llqll(35. 3% vs 0. 0%, P = 0. 000 2) and 19ql3. 31-ql3. 32(23. 5% vs 0. 0%, P = 0. 004), and more loss on 16pll. 2(35. 3% vs 6. 5%, P = 0. 009). Relative to females, male cases had more copy number loss on llqll(63. 0% vs 17. 6%, P = 0. 002). Further analyses showed that llqll gain was correlated with 19ql3. 31-ql3. 32 gain(P = 0. 042) and 16pll. 2 loss(P = 0. 033), while lq21. 3-q22 gain was correlated with 19ql3. 31-ql3. 32 gain(P = 0. 046). Conclusion Our findings suggest that CNA may play an important role in sex-related difference in HCC development.

14q32.33 Deletion Identified by array-CGH in a 5-year old-girl with Seizure

Deletions of 14q including band 14q32.33 are uncommon. Patients with terminal deletions of chromosome 14 usually share a number of clinical features. By molecular techniques (array comparative genomic hybridization (CGH) and fluorescence in situ hybridization (FISH), we identified a young girl with 0.3 Mb terminal 14q32.33 deletion. Review of the nine cases with pure terminal 14q32.3 deletions described to date documented that our observation is the smallest terminal 14q deletion ever reported. The phenotype of our patient is much less severe than the phenotypes of the patients reported previously. We report our experience in examining the clinical, behavioral, and cognitive findings in a 5-year-old girl studied with chromosomal microarray hybridization and reviewed previously reported patients with 14q32 deletions.

An update of preimplantation genetic diagnosis in gene diseases, chromosomal translocation, and aneuploidy screening / 대한생식의학회지

Preimplantation genetic diagnosis (PGD) is gradually widely used in prevention of gene diseases and chromosomal abnormalities. Much improvement has been achieved in biopsy technique and molecular diagnosis. Blastocyst biopsy can increase diagnostic accuracy and reduce allele dropout. It is cost-effective and currently plays an important role. Whole genome amplification permits subsequent individual detection of multiple gene loci and screening all 23 pairs of chromosomes. For PGD of chromosomal translocation, fluorescence in-situ hybridization (FISH) is traditionally used, but with technical difficulty. Array comparative genomic hybridization (CGH) can detect translocation and 23 pairs of chromosomes that may replace FISH. Single nucleotide polymorphisms array with haplotyping can further distinguish between normal chromosomes and balanced translocation. PGD may shorten time to conceive and reduce miscarriage for patients with chromosomal translocation. PGD has a potential value for mitochondrial diseases. Preimplantation genetic haplotyping has been applied for unknown mutation sites of single gene disease. Preimplantation genetic screening (PGS) using limited FISH probes in the cleavage-stage embryo did not increase live birth rates for patients with advanced maternal age, unexplained recurrent abortions, and repeated implantation failure. Polar body and blastocyst biopsy may circumvent the problem of mosaicism. PGS using blastocyst biopsy and array CGH is encouraging and merit further studies. Cryopreservation of biopsied blastocysts instead of fresh transfer permits sufficient time for transportation and genetic analysis. Cryopreservation of embryos may avoid ovarian hyperstimulation syndrome and possible suboptimal endometrium.

Deoxyribonucleic Acid Copy Number Aberrations in Vasospastic Angina Patients Using an Array Comparative Genomic Hybridization

BACKGROUND AND OBJECTIVES: Vasospastic angina (VA) is a specific type of coronary artery disease and develops as a result of coronary artery spasm. Recently, a few studies have revealed that VA caused by coronary artery spasm is related to genetic traits. The objective of this study was to use the recently developed technique of array comparative genomic hybridization (CGH) to screen the genetic aberrations of VA. SUBJECTS AND METHODS: To identify candidate genes that might be causally involved in the pathogenesis of VA, genomic deoxyribonucleic acids were extracted from whole blood of 28 patients with VA who presented at Department of Cardiology at Seoul St. Mary's Hospital, Seoul, Korea. The copy number profiles of these patients was then analyzed using array CGH and reverse transcriptase (RT) quantitative polymerase chain reaction (PCR). RESULTS: Array CGH revealed gains in 31 different regions, with losses in the 4q35.2, 7q22.1, 10q26.3, 15q11.2, 16p13.11, 17p11.2 and 19q13.3 regions (more than 32% aberration in these regions). Several loci were found to be frequently including gains of 5p and 11q (50% of samples). The most common losses were found in 7q (54% of samples). Copy number aberrations in chromosomal regions were detected and corresponding genes were confirmed by RT quantitative PCR. The fold change levels were highest in the CTDP1 (18q23), HDAC10 (22q13.33), KCNQ1 (11p15.5-p15.4), NINJ2 (12p13.33), NOTCH2 (1p12-p11.2), PCSK6 (15q26.3), SDHA (5p15.33), and MUC17 (7q22.1) genes. CONCLUSION: Many candidate chromosomal regions that might be related to the pathogenesis of VA were detected by array CGH and should be systematically investigated to establish the causative and specific genes for VA.

Miller-Dieker Syndrome with der(17)t(12;17)(q24.33;p13.3)pat Presenting with a Potential Risk of Mis-identification as a de novo Submicroscopic Deletion of 17p13.3 / 대한진단검사의학회지

Miller-Dieker syndrome involves a severe type of lissencephaly, which is caused by defects in the lissencephaly gene (LIS1). We report the case of a female infant with der(17)t(12;17)(q24.33;p13.3)pat caused by an unbalanced segregation of the parental balanced translocation of 17p with other chromosomes. The proband presented with facial dysmorphism, arthrogryposis, and intrauterine growth retardation. Most cases of Miller-Dieker syndrome have a de novo deletion involving 17p13.3. When Miller-Dieker syndrome is caused by an unbalanced translocation, mild-to-severe phenotypes occur according to the extension of the involved partner chromosome. However, a pure partial monosomy derived from a paternal balanced translocation is relatively rare. In this case, the submicroscopic cryptic deletion in the proband was initially elucidated by FISH, and karyotype analysis did not reveal additional chromosome abnormalities such as translocation. However, a family history of recurrent pregnancy abnormalities strongly suggested familial translocation. Sequential G-banding and FISH analysis of the father's chromosomes showed that the segment of 17p13.3-->pter was attached to the 12qter. Thus, we report a case that showed resemblance to the findings in cases of a nearly pure 17p deletion, derived from t(12;17), and delineated by whole genome array comparative genomic hybridization (CGH). If such cases are incorrectly diagnosed as Miller-Dieker syndrome caused by de novo 17p13.3 deletion, the resultant improper genetic counseling may make it difficult to exactly predict the potential risk of recurrent lissencephaly for successive pregnancies.

Cri-du-chat Syndrome: Application of Array CGH in Diagnostic Evaluation

The human genome contains many submicroscopic copy number variations which includes deletions, duplications and insertions. Although conventional karyotyping remains an important diagnostic tool in evaluating a dysmorphic patient with mental retardation, molecular diagnostic technology such as array comparative genomic hybridization (aCGH) has proven to be sensitive and reliable in detecting these submicroscopic anomalies. A 3 month-old infant with dysmorphic facies, microcephaly and global developmental delay was referred for genetic evaluation. Preliminary karyotyping which was confounded by the quality of metaphase spread was normal; however, aCGH detected a 30.6Mb deletion from 5p15.33-p13.3. This case illustrates the usefulness of aCGH as an adjunctive investigative tool for detecting chromosomal imbalances.

A Case of Partial Trisomy 15q25.3-qter / 대한진단검사의학회지

A 15q25-qter partial trisomy characterized by pre or postnatal overgrowth, tall stature, macrocephaly and craniosynostosis has rarely been reported. The cause of overgrowth has been thought to be the triplication of the insulin-like growth factor 1 receptor (IGF1R) gene located on the 15q26.3. We report a patient with partial trisomy 15q25.3-qter showing mental retardation, developmental delay, macrocephaly, long narrow face, ptosis, high palate arch, scoliosis, clinodactyly and overgrowth. Additional material located on terminal 2q was found in karyotyping analysis. In bacterial artificial chromosome (BAC) clone-based-array comparative genomic hybridization (aCGH) analysis, a gain of 31 clones on 15q25.3-qter and a loss of 2 clones on 2q37.3 were observed. An extra copy of IGF1R gene was observed on derivative chromosome 2 in FISH analysis. In conclusion, the patient was diagnosed to have de novo 46,XX,der(2)t(2;15)(q37.3;q25.3) chromosome complement. Adequate genetic counseling and regular follow-ups would be needed for the patient.

Current Status and Future Clinical Applications of Array.based Comparative Genomic Hybridization

No abstract available.