1
|
Sun M, Zhang H, Li G, Guy CJ, Wang X, Lu X, Gong F, Lee J, Hassed S, Li S. Molecular characterization of 20 small supernumerary marker chromosome cases using array comparative genomic hybridization and fluorescence in situ hybridization. Sci Rep 2017; 7:10395. [PMID: 28871159 PMCID: PMC5583289 DOI: 10.1038/s41598-017-10466-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 08/10/2017] [Indexed: 12/25/2022] Open
Abstract
The variability of a small supernumerary marker chromosome (sSMC)-related phenotype is determined by the molecular component, the size, and shape of the marker chromosome. As fluorescence in situ hybridization has limitations regarding the resolution, efficiency, and accuracy. Recently, array comparative genomic hybridization (aCGH) was used for sSMC characterization. In this study, twenty cases with sSMCs were characterized by aCGH and FISH. Chromosomal origin of the marker chromosomes were successfully identified in seventeen of them. For the three cases with negative aCGH results, two of them were more likely due to that the sSMCs only contained centromere heterochromatin, whereas the reason for the remaining case with negative aCGH finding was uncertain. In order to establish a stronger genotype-phenotype correlation for clinical service in the future and avoid miss characterization, more sSMC cases were needed to be detailed characterized. This will help to clarify the variable clinical characteristics of sSMCs and provide additional information to aid clinical service and future research.
Collapse
Affiliation(s)
- Mingran Sun
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA.,Department of Hematology and Oncology, Anshan Hospital, the First Hospital of China Medical University, Anshan City, Liaoning, 114000, China.,Key Laboratory for Molecular Enzymology and Engineering, College of Life Sciences, Jilin University, Changchun City, Jilin, 130012, China
| | - Han Zhang
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA.,Center for Reproductive Medicine, Center for Prenatal Diagnosis, the First Hospital of Jilin University, Changchun City, Jilin, 130021, China
| | - Guiying Li
- Key Laboratory for Molecular Enzymology and Engineering, College of Life Sciences, Jilin University, Changchun City, Jilin, 130012, China
| | - Carrie J Guy
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Xianfu Wang
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Xianglan Lu
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Fangchao Gong
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA.,Department of Urology, the First Hospital of Jilin University, Changchun City, Jilin, 130000, China
| | - Jiyun Lee
- Department of Pathology, College of Medicine, Korea University, Seoul, 02841, Korea
| | - Susan Hassed
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA
| | - Shibo Li
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, 73104, USA.
| |
Collapse
|
2
|
Babameto-Laku A, Roko D, Vyshka G. Genetic Diagnosis of Chromosomal Congenital Anomalies in Albanian Pediatric Patients by Array CGH. Open Access Maced J Med Sci 2017; 5:587-591. [PMID: 28932296 PMCID: PMC5591585 DOI: 10.3889/oamjms.2017.147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 06/04/2017] [Accepted: 06/05/2017] [Indexed: 02/05/2023] Open
Abstract
AIM The aim of our study was to identify chromosomal imbalances by whole-genome microarray-based comparative genomic hybridization (array CGH) in DNA samples of children in which karyotype results cannot be obtained. The present paper describes the first Albanian experience of an array CGH application. MATERIAL AND METHODS The cohort included seven children with developmental delay or intellectual disability, facial dysmorphism and congenital anomalies according to clinical criteria, suggestive of chromosomal anomalies. The age range was from newborn to five years old. The cytogenetic analysis determined by a standard method of G-banding according to the International System for Human Cytogenetic Nomenclature (ISCN 2005) was performed for all our patients, while array CGH was performed on genomic DNA isolated from the blood of 7 cases. RESULTS Among the seven patients analysed with array CGH, three patients resulted in duplication and one deletion, one patient with a microdeletion and three patients with duplication. Array CGH facilitated the recognition of submicroscopic deletions and duplications as risk factors for genetic diagnosis in all our patients. CONCLUSIONS Our case series with congenital chromosomal anomalies confirms the high diagnostic value of the method, as suggested by previous studies. The technique must be available also in less developed countries, to significantly improve the genetic diagnosis of paediatric patients with developmental delay or intellectual disability, congenital anomalies and dysmorphic features. The identification of chromosomal abnormalities in these patients and the genetic counselling will provide family members with an explanation for their child's developmental disability or birth defect, allowing better information about recurrence risks, and permit the anticipation of certain medical problems that require intervention.
Collapse
Affiliation(s)
- Anila Babameto-Laku
- Service of Medical Genetics, University Hospital Center “Mother Theresa”, Faculty of Medicine, Tirana, Albania
| | - Dorina Roko
- Service of Medical Genetics, University Hospital Center “Mother Theresa”, Faculty of Medicine, Tirana, Albania
| | - Gentian Vyshka
- Biomedical and Experimental Department, Faculty of Medicine, University of Medicine in Tirana, Tirana, Albania
- Correspondence: Gentian Vyshka. Biomedical and Experimental Department, Faculty of Medicine, the University of Medicine in Tirana, Tirana, Albania. E-mail:
| |
Collapse
|
3
|
Liu D, Wang H, Schwender H, Marazita ML, Wang Z, Yuan Y, Wang P, Liang KY, Wu-Chou YH, Wang M, Shi B, Zhu H, Wu T, Beaty TH. Gene-gene interaction of single nucleotide polymorphisms in 16p13.3 may contribute to the risk of non-syndromic cleft lip with or without cleft palate in Chinese case-parent trios. Am J Med Genet A 2017; 173:1489-1494. [PMID: 28402597 DOI: 10.1002/ajmg.a.38190] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 12/13/2016] [Accepted: 02/01/2017] [Indexed: 11/07/2022]
Abstract
Non-syndromic cleft lip with or without cleft palate (NSCL/P) is a common birth defect with a complex and heterogeneous etiology. A recent genome-wide association study (GWAS) among Chinese populations has identified a new region at 16p13.3 as being associated with NSCL/P, which requires further replication. Here, we attempted to replicate and further clarify the genetic association between this region and NSCL/P, as well as testing for potential gene-gene (G × G) and gene-environment (G × E) interactions. We conducted transmission disequilibrium tests on 69 single nucleotide polymorphisms (SNPs) mapping to 16p13.3 among 806 Chinese case-parent trios ascertained through an international consortium where a GWAS of oral clefts was conducted. G × G, as well as G × E interactions involving maternal environmental tobacco smoke (ETS) and multivitamin supplementation, were explored using conditional logistic regression model. We applied Cordell's method as implemented in the R package TRIO to test for possible interactions. While no SNPs showed evidence of linkage and association with NSCL/P after Bonferroni correction, we found signals of G × G interactions between SNPs in 16p13.3. Nine pairs of SNP-SNP interactions attained significance after Bonferroni correction, among which the most significant interaction was found between rs2072346 (ADCY9) and rs11646137 (intergenic region, P = 7.2 × 10-5 ). Linkage disequilibrium (LD) analysis revealed only low level of LD between these SNPs. This study failed to confirm the significant association between SNPs within 16p13.3 and the risk of NSCL/P, but underlined the importance of taking into account potential G × G interactions for the genetic association analysis of NSCL/P.
Collapse
Affiliation(s)
- Dongjing Liu
- School of Public Health, Peking University, Beijing, China
| | - Hong Wang
- School of Public Health, Peking University, Beijing, China
| | - Holger Schwender
- Mathematical Institute, Heinrich Heine University Duesseldorf, Duesseldorf, Germany
| | - Mary L Marazita
- Center for Craniofacial and Dental Genetics, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Zhuqing Wang
- School of Public Health, Peking University, Beijing, China
| | - Yuan Yuan
- School of Public Health, Peking University, Beijing, China
| | - Ping Wang
- Beijing Center for Disease Prevention and Control, Beijing, China
| | | | | | - Mengying Wang
- School of Public Health, Peking University, Beijing, China
| | - Bing Shi
- State Key Laboratory of Oral Disease, West China College of Stomatology, Sichuan University, Chengdu, China
| | - Hongping Zhu
- School of Stomatology, Peking University, Beijing, China
| | - Tao Wu
- School of Public Health, Peking University, Beijing, China.,Key Laboratory of Reproductive Health, Ministry of Health, Beijing, China
| | - Terri H Beaty
- School of Public Health, Johns Hopkins University, Baltimore, Maryland
| |
Collapse
|
4
|
Gomez-Ospina N, Bernstein JA. Clinical, cytogenetic, and molecular outcomes in a series of 66 patients with Pierre Robin sequence and literature review: 22q11.2 deletion is less common than other chromosomal anomalies. Am J Med Genet A 2016; 170A:870-80. [PMID: 26756138 DOI: 10.1002/ajmg.a.37538] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Accepted: 12/17/2015] [Indexed: 01/01/2023]
Abstract
Pierre Robin sequence (PRS) is an important craniofacial anomaly that can be seen as an isolated finding or manifestation of multiple syndromes. 22q11.2 deletion and Stickler syndrome are cited as the two most common conditions associated with PRS, but their frequencies are debated. We performed a retrospective study of 66 patients with PRS and reviewed their genetic testing, diagnoses, and clinical findings. The case series is complemented by a comprehensive literature review of the nature and frequency of genetic diagnosis in PRS. In our cohort 65% of patients had associated anomalies; of these, a genetic diagnosis was established in 56%. Stickler syndrome was the most common diagnosis, comprising approximately 11% of all cases, followed by Treacher Collins syndrome (9%). The frequency of 22q11.2 deletion was 1.5%. Chromosome arrays, performed for 72% of idiopathic PRS with associated anomalies, revealed two cases of 18q22→qter deletion, a region not previously reported in association with PRS. A review of the cytogenetic anomalies identified in this population supports an association between the 4q33-qter, 17q24.3, 2q33.1, and 11q23 chromosomal loci and PRS. We found a low frequency of 22q11.2 deletion in PRS, suggesting it is less commonly implicated in this malformation. Our data also indicate a higher frequency of cytogenetic anomalies in PRS patients with associated anomalies, and a potential new link with the 18q22→qter locus. The present findings underscore the utility of chromosomal microarrays in cases of PRS with associated anomalies and suggest that delaying testing for apparently isolated cases should be considered.
Collapse
|
5
|
A prenatally ascertained de novo terminal deletion of chromosomal bands 1q43q44 associated with multiple congenital abnormalities in a female fetus. Case Rep Genet 2015; 2015:517678. [PMID: 25722899 PMCID: PMC4334433 DOI: 10.1155/2015/517678] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 12/22/2014] [Accepted: 01/13/2015] [Indexed: 11/17/2022] Open
Abstract
Terminal deletions in the long arm of chromosome 1 result in a postnatally recognizable disorder described as 1q43q44 deletion syndrome. The size of the deletions and the resulting phenotype varies among patients. However, some features are common among patients as the chromosomal regions included in the deletions. In the present case, ultrasonography at 22 weeks of gestation revealed choroid plexus cysts (CPCs) and a single umbilical artery (SUA) and therefore amniocentesis was performed. Chromosomal analysis revealed a possible terminal deletion in 1q and high resolution array CGH confirmed the terminal 1q43q44 deletion and estimated the size to be approximately 8 Mb. Following termination of pregnancy, performance of fetopsy allowed further clinical characterization. We report here a prenatal case with the smallest pure terminal 1q43q44 deletion, that has been molecularly and phenotypically characterized. In addition, to our knowledge this is the first prenatal case reported with 1q13q44 terminal deletion and Pierre-Robin sequence (PRS). Our findings combined with review data from the literature show the complexity of the genetic basis of the associated syndrome.
Collapse
|