1
|
Sivakumaran TA, Grebe TA. 15q26.3 deletions distal to IGF1R cause growth retardation, congenital heart defect and skeletal anomalies: Case report and review of literature. Am J Med Genet A 2023; 191:2392-2397. [PMID: 37434556 DOI: 10.1002/ajmg.a.63350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 06/23/2023] [Accepted: 06/28/2023] [Indexed: 07/13/2023]
Abstract
15q26 deletion is a rare genomic disorder characterized by intrauterine and postnatal growth retardation, microcephaly, intellectual disability, and congenital malformations. Here, we report a 4-month-old female with intrauterine growth retardation, short stature, pulmonary hypertension, atrial septal defect and congenital bowing of long bones of the legs. Chromosomal microarray analysis showed a de novo deletion of approximately 2.1 Mb at 15q26.3 region that does not include IGF1R. Our analysis of patients documented in the literature and the DECIPHER database with 15q26 deletions distal to IGF1R, including 10 patients with de novo pure deletions, allowed us to define the smallest region of overlap to 686 kb. This region includes ALDH1A3, LRRK1, CHSY1, SELENOS, SNRPA1, and PCSK6. We propose haploinsufficiency of one or more genes, besides IGF1R, within this region may contribute to the clinical findings in patients with 15q26.3 deletion.
Collapse
Affiliation(s)
- Theru A Sivakumaran
- Division of Pathology and Laboratory Medicine, Phoenix Children's Hospital, Phoenix, Arizona, USA
- Department of Child Health, University of Arizona College of Medicine-Phoenix, Phoenix, Arizona, USA
- Department of Pathology, University of Arizona College of Medicine-Phoenix, Phoenix, Arizona, USA
- Department of Pathology, Creighton University School of Medicine, Phoenix, Arizona, USA
| | - Theresa A Grebe
- Department of Child Health, University of Arizona College of Medicine-Phoenix, Phoenix, Arizona, USA
- Division of Genetics and Metabolism, Phoenix Children's Hospital, Phoenix, Arizona, USA
| |
Collapse
|
2
|
Genotype–Phenotype Correlations for Putative Haploinsufficient Genes in Deletions of 6q26-q27: Report of Eight Patients and Review of Literature. Glob Med Genet 2022; 9:166-174. [PMID: 35707784 PMCID: PMC9192176 DOI: 10.1055/s-0042-1743568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 01/11/2022] [Indexed: 11/06/2022] Open
Abstract
Background
Cytogenomic analyses have been used to detect pathogenic copy number variants. Patients with deletions at 6q26-q27 present variable clinical features. We reported clinical and cytogenomic findings of eight unrelated patients with a deletion of 6q26-q27. A systematic review of the literature found 28 patients with a deletion of 6q26-q27 from 2010 to 2020.
Results
For these 36 patients, the sex ratio showed equal occurrence between males and females; 29 patients (81%) had a terminal deletion and seven patients (19%) had a proximal or distal interstitial deletion. Of the 22 patients with parental studies, deletions of de novo, maternal, paternal, and bi-parental inheritance accounted for 64, 18, 14, and 4% of patients, respectively. The most common clinical findings were brain abnormalities (100%) in fetuses observed by ultrasonography followed by developmental delay and intellectual disability (81%), brain abnormalities (72%), facial dysmorphism (66%), hypotonia (63%), learning difficulty or language delay (50%), and seizures (47%) in pediatric and adult patients. Anti-epilepsy treatment showed the effect on controlling seizures in these patients. Cytogenomic mapping defined one proximal critical region at 6q26 containing the putative haploinsufficient gene
PRKN
and one distal critical region at 6q27 containing two haploinsufficient genes
DLL1
and
TBP
. Deletions involving the
PRKN
gene could associate with early-onset Parkinson disease and autism spectrum disorder; deletions involving the
DLL1
gene correlate with the 6q terminal deletion syndrome.
Conclusion
The genotype–phenotype correlations for putative haploinsufficient genes in deletions of 6q26-q27 provided evidence for precise diagnostic interpretation, genetic counseling, and clinical management of patients with a deletion of 6q26-q27.
Collapse
|
3
|
Quach TT, Stratton HJ, Khanna R, Kolattukudy PE, Honnorat J, Meyer K, Duchemin AM. Intellectual disability: dendritic anomalies and emerging genetic perspectives. Acta Neuropathol 2021; 141:139-158. [PMID: 33226471 PMCID: PMC7855540 DOI: 10.1007/s00401-020-02244-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 11/04/2020] [Accepted: 11/05/2020] [Indexed: 12/12/2022]
Abstract
Intellectual disability (ID) corresponds to several neurodevelopmental disorders of heterogeneous origin in which cognitive deficits are commonly associated with abnormalities of dendrites and dendritic spines. These histological changes in the brain serve as a proxy for underlying deficits in neuronal network connectivity, mostly a result of genetic factors. Historically, chromosomal abnormalities have been reported by conventional karyotyping, targeted fluorescence in situ hybridization (FISH), and chromosomal microarray analysis. More recently, cytogenomic mapping, whole-exome sequencing, and bioinformatic mining have led to the identification of novel candidate genes, including genes involved in neuritogenesis, dendrite maintenance, and synaptic plasticity. Greater understanding of the roles of these putative ID genes and their functional interactions might boost investigations into determining the plausible link between cellular and behavioral alterations as well as the mechanisms contributing to the cognitive impairment observed in ID. Genetic data combined with histological abnormalities, clinical presentation, and transgenic animal models provide support for the primacy of dysregulation in dendrite structure and function as the basis for the cognitive deficits observed in ID. In this review, we highlight the importance of dendrite pathophysiology in the etiologies of four prototypical ID syndromes, namely Down Syndrome (DS), Rett Syndrome (RTT), Digeorge Syndrome (DGS) and Fragile X Syndrome (FXS). Clinical characteristics of ID have also been reported in individuals with deletions in the long arm of chromosome 10 (the q26.2/q26.3), a region containing the gene for the collapsin response mediator protein 3 (CRMP3), also known as dihydropyrimidinase-related protein-4 (DRP-4, DPYSL4), which is involved in dendritogenesis. Following a discussion of clinical and genetic findings in these syndromes and their preclinical animal models, we lionize CRMP3/DPYSL4 as a novel candidate gene for ID that may be ripe for therapeutic intervention.
Collapse
Affiliation(s)
- Tam T Quach
- Institute for Behavioral Medicine Research, Wexner Medical Center, The Ohio State University, Columbus, OH, 43210, USA
- INSERM U1217/CNRS, UMR5310, Université de Lyon, Université Claude Bernard Lyon 1, Lyon, France
| | | | - Rajesh Khanna
- Department of Pharmacology, University of Arizona, Tucson, AZ, 85724, USA
| | | | - Jérome Honnorat
- INSERM U1217/CNRS, UMR5310, Université de Lyon, Université Claude Bernard Lyon 1, Lyon, France
- French Reference Center on Paraneoplastic Neurological Syndromes and Autoimmune Encephalitis, Hospices Civils de Lyon, Lyon, France
- SynatAc Team, Institut NeuroMyoGène, Lyon, France
| | - Kathrin Meyer
- The Research Institute of Nationwide Children Hospital, Columbus, OH, 43205, USA
- Department of Pediatric, The Ohio State University, Columbus, OH, 43210, USA
| | - Anne-Marie Duchemin
- Department of Psychiatry and Behavioral Health, The Ohio State University, Columbus, OH, 43210, USA.
| |
Collapse
|
4
|
Chai H, DiAdamo A, Grommisch B, Xu F, Zhou Q, Wen J, Mahoney M, Bale A, McGrath J, Spencer-Manzon M, Li P, Zhang H. A Retrospective Analysis of 10-Year Data Assessed the Diagnostic Accuracy and Efficacy of Cytogenomic Abnormalities in Current Prenatal and Pediatric Settings. Front Genet 2019; 10:1162. [PMID: 31850057 PMCID: PMC6902283 DOI: 10.3389/fgene.2019.01162] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Accepted: 10/23/2019] [Indexed: 01/01/2023] Open
Abstract
Background: Array comparative genomic hybridization (aCGH), karyotyping and fluorescence in situ hybridization (FISH) analyses have been used in a clinical cytogenetic laboratory. A systematic analysis on diagnostic findings of cytogenomic abnormalities in current prenatal and pediatric settings provides approaches for future improvement. Methods: A retrospective analysis was performed on abnormal findings by aCGH, karyotyping, and FISH from 3,608 prenatal cases and 4,509 pediatric cases during 2008–2017. The diagnostic accuracy was evaluated by comparing the abnormality detection rate (ADR) and the relative frequency (RF) of different types of cytogenomic abnormalities between prenatal and pediatric cases. A linear regression correlation between known prevalence and ADR of genomic disorders was used to extrapolate the prevalence of other genomic disorders. The diagnostic efficacy was estimated as percentage of detected abnormal cases by expected abnormal cases from served population. Results: The composite ADR for numerical chromosome abnormalities, structural chromosome abnormalities, recurrent genomic disorders, and sporadic pathogenic copy number variants (pCNVs) in prenatal cases were 13.03%, 1.77%, 1.69%, and 0.9%, respectively, and were 5.13%, 2.84%, 7.08%, and 2.69% in pediatric cases, respectively. The chromosomal abnormalities detected in prenatal cases (14.80%) were significantly higher than that of pediatric cases (7.97%) (p < 0.05), while the pCNVs detected in prenatal cases (2.59%) were significantly lower than that of pediatric cases (9.77%) (p < 0.05). The prevalence of recurrent genomic disorders and total pCNVs was estimated to be 1/396 and 1/291, respectively. Approximately, 29% and 35% of cytogenomic abnormalities expected from the population served were detected in current prenatal and pediatric diagnostic practice, respectively. Conclusion: For chromosomal abnormalities, effective detection of Down syndrome (DS) and Turner syndrome (TS) and under detection of sex chromosome numerical abnormalities in both prenatal and pediatric cases were noted. For pCNVs, under detection of pCNVs in prenatal cases and effective detection of DiGeorge syndrome (DGS) and variable efficacy in detecting other pCNVs in pediatric cases were noted. Extend aCGH analysis to more prenatal cases with fetal ultrasonographic anomalies, enhanced non-invasive prenatal (NIPT) testing screening for syndromic genomic disorders, and better clinical indications for pCNVs are approaches that could improve diagnostic yield of cytogenomic abnormalities.
Collapse
Affiliation(s)
- Hongyan Chai
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States
| | - Autumn DiAdamo
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States
| | - Brittany Grommisch
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States
| | - Fang Xu
- Prevention Genetics, Marshfield, WI, United States
| | - Qinghua Zhou
- The First Affiliated Hospital, Biomedical Translational Research Institute, Jinan University, Guangzhou, China
| | - Jiadi Wen
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States
| | - Maurice Mahoney
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States
| | - Allen Bale
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States
| | - James McGrath
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States
| | - Michele Spencer-Manzon
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States
| | - Peining Li
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States
| | - Hui Zhang
- Department of Genetics, Yale University School of Medicine, New Haven, CT, United States
| |
Collapse
|
5
|
Affiliation(s)
- Ivan Y. Iourov
- Yurov's Laboratory of Molecular Genetics and Cytogenomics of the Brain, Mental Health Research Center, Moscow 117152, Russian Federation
| |
Collapse
|
6
|
Cui C, Shu W, Li P. Fluorescence In situ Hybridization: Cell-Based Genetic Diagnostic and Research Applications. Front Cell Dev Biol 2016; 4:89. [PMID: 27656642 PMCID: PMC5011256 DOI: 10.3389/fcell.2016.00089] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Accepted: 08/11/2016] [Indexed: 12/14/2022] Open
Abstract
Fluorescence in situ hybridization (FISH) is a macromolecule recognition technology based on the complementary nature of DNA or DNA/RNA double strands. Selected DNA strands incorporated with fluorophore-coupled nucleotides can be used as probes to hybridize onto the complementary sequences in tested cells and tissues and then visualized through a fluorescence microscope or an imaging system. This technology was initially developed as a physical mapping tool to delineate genes within chromosomes. Its high analytical resolution to a single gene level and high sensitivity and specificity enabled an immediate application for genetic diagnosis of constitutional common aneuploidies, microdeletion/microduplication syndromes, and subtelomeric rearrangements. FISH tests using panels of gene-specific probes for somatic recurrent losses, gains, and translocations have been routinely applied for hematologic and solid tumors and are one of the fastest-growing areas in cancer diagnosis. FISH has also been used to detect infectious microbias and parasites like malaria in human blood cells. Recent advances in FISH technology involve various methods for improving probe labeling efficiency and the use of super resolution imaging systems for direct visualization of intra-nuclear chromosomal organization and profiling of RNA transcription in single cells. Cas9-mediated FISH (CASFISH) allowed in situ labeling of repetitive sequences and single-copy sequences without the disruption of nuclear genomic organization in fixed or living cells. Using oligopaint-FISH and super-resolution imaging enabled in situ visualization of chromosome haplotypes from differentially specified single-nucleotide polymorphism loci. Single molecule RNA FISH (smRNA-FISH) using combinatorial labeling or sequential barcoding by multiple round of hybridization were applied to measure mRNA expression of multiple genes within single cells. Research applications of these single molecule single cells DNA and RNA FISH techniques have visualized intra-nuclear genomic structure and sub-cellular transcriptional dynamics of many genes and revealed their functions in various biological processes.
Collapse
Affiliation(s)
- Chenghua Cui
- Laboratory of Clinical Cytogenetics, Department of Genetics, Yale School of MedicineNew Haven, CT, USA; Department of Pathology, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical SciencesTianjin, China
| | - Wei Shu
- Laboratory of Clinical Cytogenetics, Department of Genetics, Yale School of MedicineNew Haven, CT, USA; Department of Cell Biology and Genetics, Guangxi Medical UniversityNanning, China
| | - Peining Li
- Laboratory of Clinical Cytogenetics, Department of Genetics, Yale School of Medicine New Haven, CT, USA
| |
Collapse
|
7
|
Iourov IY, Vorsanova SG, Korostelev SA, Vasin KS, Zelenova MA, Kurinnaia OS, Yurov YB. [Structural variations of the genome in autistic spectrum disorders with intellectual disability]. Zh Nevrol Psikhiatr Im S S Korsakova 2016; 116:50-54. [PMID: 27500877 DOI: 10.17116/jnevro20161167150-54] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
AIM To analyze structural variations in the genome in children with autism and intellectual disability. MATERIAL AND METHODS Using high-resolution karyotyping (AffymetrixCytoScan HD Array) and original bioinformatic technology, 200 children with autism and intellectual disability were studied. RESULTS AND CONCLUSION Data on structural variations in the genome in children with autism and intellectual disability are provided. Causative genomic pathology (chromosome abnormalities and copy number variations - CNV) was determined in 97 cases (48.5%). Based on these RESULTS 24 candidate genes for autism with intellectual disability were selected. In 16 cases (8%), the chromosome mosaicism manifested as aneuploidy of whole autosomes and sex chromosomes (gonosomes) was identified. In 87 children (43.5%), there were genomic variations, which are characteristic of the so-called «grey zone» of genetic pathology in mental illnesses. Bioinformatic analysis showed that these genomic variations had a pleiotropic effect on the phenotype.
Collapse
Affiliation(s)
- I Yu Iourov
- Mental Health Research Center, Moscow, Russia; Veltishev Research and Clinical Institute for Pediatrics at the Pirogov Russian National Research Medical University, Moscow, Russia; Russian Medical Academy of Postgraduate Education, Moscow, Russia
| | - S G Vorsanova
- Mental Health Research Center, Moscow, Russia; Veltishev Research and Clinical Institute for Pediatrics at the Pirogov Russian National Research Medical University, Moscow, Russia; Moscow State University of Psychology and Education, Moscow, Russia
| | | | - K S Vasin
- Mental Health Research Center, Moscow, Russia; Veltishev Research and Clinical Institute for Pediatrics at the Pirogov Russian National Research Medical University, Moscow, Russia; Moscow State University of Psychology and Education, Moscow, Russia
| | - M A Zelenova
- Mental Health Research Center, Moscow, Russia; Veltishev Research and Clinical Institute for Pediatrics at the Pirogov Russian National Research Medical University, Moscow, Russia; Moscow State University of Psychology and Education, Moscow, Russia
| | - O S Kurinnaia
- Mental Health Research Center, Moscow, Russia; Veltishev Research and Clinical Institute for Pediatrics at the Pirogov Russian National Research Medical University, Moscow, Russia; Moscow State University of Psychology and Education, Moscow, Russia
| | - Yu B Yurov
- Mental Health Research Center, Moscow, Russia; Veltishev Research and Clinical Institute for Pediatrics at the Pirogov Russian National Research Medical University, Moscow, Russia; Moscow State University of Psychology and Education, Moscow, Russia
| |
Collapse
|
8
|
Spectrum of Cytogenomic Abnormalities Revealed by Array Comparative Genomic Hybridization on Products of Conception Culture Failure and Normal Karyotype Samples. J Genet Genomics 2016; 43:121-31. [PMID: 27020032 DOI: 10.1016/j.jgg.2016.02.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 02/04/2016] [Accepted: 02/07/2016] [Indexed: 12/18/2022]
Abstract
Approximately 30% of pregnancies after implantation end up in spontaneous abortions, and 50% of them are caused by chromosomal abnormalities. However, the spectrum of genomic copy number variants (CNVs) in products of conception (POC) and the underlying gene-dosage-sensitive mechanisms causing spontaneous abortions remain largely unknown. In this study, array comparative genomic hybridization (aCGH) analysis was performed as a salvage procedure for 128 POC culture failure (POC-CF) samples and as a supplemental procedure for 106 POC normal karyotype (POC-NK) samples. Chromosomal abnormalities were detected in 10% of POC-CF and pathogenic CNVs were detected in 3.9% of POC-CF and 5.7% of POC-NK samples. Compiled results from this study and relevant case series through a literature review demonstrated an abnormality detection rate (ADR) of 35% for chromosomal abnormalities in POC-CF samples, 3.7% for pathogenic CNVs in POC-CF samples, and 4.6% for pathogenic CNVs in POC-NK samples. Ingenuity Pathway Analysis (IPA) was performed on the genes from pathogenic CNVs found in POC samples. The denoted primary gene networks suggested that apoptosis and cell proliferation pathways are involved in miscarriage. In summary, a similar spectrum of cytogenomic abnormalities was observed in POC culture success and POC-CF samples. A threshold effect correlating the number of dosage-sensitive genes in a chromosome with the observed frequency of autosomal trisomy is proposed. A rationalized approach using firstly fluorescence in situ hybridization (FISH) testing with probes of chromosomes X/Y/18, 13/21, and 15/16/22 for common aneuploidies and polyploidies and secondly aCGH for other cytogenomic abnormalities is recommended for POC-CF samples.
Collapse
|
9
|
Meng J, Matarese C, Crivello J, Wilcox K, Wang D, DiAdamo A, Xu F, Li P. Changes in and Efficacies of Indications for Invasive Prenatal Diagnosis of Cytogenomic Abnormalities: 13 Years of Experience in a Single Center. Med Sci Monit 2015; 21:1942-8. [PMID: 26143093 PMCID: PMC4497468 DOI: 10.12659/msm.893870] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Background Because the future application of cell-free fetal DNA screening is expected to dramatically improve the diagnostic yield and reduce unnecessary invasive procedures, it is time to summarize the indications of invasive prenatal diagnosis. This retrospective study was performed to evaluate the changes and efficacies of indications of invasive procedures for detecting cytogenomic abnormalities from 2000 to 2012. Material/Methods From our regional obstetric unit, 7818 invasive procedures were referred by indications of advance maternal age (AMA), abnormal ultrasound findings (aUS), abnormal maternal serum screening (aMSS), and family history (FH). Chromosome, fluorescence in situ hybridization (FISH), and array comparative genomic hybridization (aCGH) analyses were performed on chorionic villus sampling (CVS) and amniotic fluid (AF) specimens at the Yale Cytogenetics Laboratory. The abnormal findings from single or combined indications were compared to evaluate the diagnostic yield. Results The annual caseload declined by 57.2% but the diagnostic yield increased from 7.2% to 13.4%. Chromosomal and genomic abnormalities were detected in 752 cases (9.6%, 752/7818) and 12 cases (4%, 12/303), respectively. Significantly decreased AMA referrals and increased aUS and aMSS referrals were noted. The top 3 indications by diagnostic yield were AMA/aUS (51.4% for CVS, 24.2% for AF), aUS (34.7% for CVS, 14.5% for AF), and AMA/aMSS (17.8% for CVS, 9.9% for AF). Conclusions Over a period of 13 years, the indication of aMSS and aUS were increasing while AMA was decreasing for prenatal diagnosis of cytogenomic abnormalities, and there was a continuous trend of reduced invasive procedures. Prenatal evaluation using AMA/aUS was the most effective in detecting chromosomal abnormalities, but better indications for genomic abnormalities are needed.
Collapse
Affiliation(s)
- Jinlai Meng
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Chelsea Matarese
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Julianna Crivello
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Katherine Wilcox
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Dongmei Wang
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Autumn DiAdamo
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Fang Xu
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - Peining Li
- Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| |
Collapse
|
10
|
Iourov IY, Vorsanova SG, Yurov YB. In silico molecular cytogenetics: a bioinformatic approach to prioritization of candidate genes and copy number variations for basic and clinical genome research. Mol Cytogenet 2014; 7:98. [PMID: 25525469 PMCID: PMC4269961 DOI: 10.1186/s13039-014-0098-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Accepted: 12/02/2014] [Indexed: 01/08/2023] Open
Abstract
Background The availability of multiple in silico tools for prioritizing genetic variants widens the possibilities for converting genomic data into biological knowledge. However, in molecular cytogenetics, bioinformatic analyses are generally limited to result visualization or database mining for finding similar cytogenetic data. Obviously, the potential of bioinformatics might go beyond these applications. On the other hand, the requirements for performing successful in silico analyses (i.e. deep knowledge of computer science, statistics etc.) can hinder the implementation of bioinformatics in clinical and basic molecular cytogenetic research. Here, we propose a bioinformatic approach to prioritization of genomic variations that is able to solve these problems. Results Selecting gene expression as an initial criterion, we have proposed a bioinformatic approach combining filtering and ranking prioritization strategies, which includes analyzing metabolome and interactome data on proteins encoded by candidate genes. To finalize the prioritization of genetic variants, genomic, epigenomic, interactomic and metabolomic data fusion has been made. Structural abnormalities and aneuploidy revealed by array CGH and FISH have been evaluated to test the approach through determining genotype-phenotype correlations, which have been found similar to those of previous studies. Additionally, we have been able to prioritize copy number variations (CNV) (i.e. differentiate between benign CNV and CNV with phenotypic outcome). Finally, the approach has been applied to prioritize genetic variants in cases of somatic mosaicism (including tissue-specific mosaicism). Conclusions In order to provide for an in silico evaluation of molecular cytogenetic data, we have proposed a bioinformatic approach to prioritization of candidate genes and CNV. While having the disadvantage of possible unavailability of gene expression data or lack of expression variability between genes of interest, the approach provides several advantages. These are (i) the versatility due to independence from specific databases/tools or software, (ii) relative algorithm simplicity (possibility to avoid sophisticated computational/statistical methodology) and (iii) applicability to molecular cytogenetic data because of the chromosome-centric nature. In conclusion, the approach is able to become useful for increasing the yield of molecular cytogenetic techniques.
Collapse
Affiliation(s)
- Ivan Y Iourov
- Mental Health Research Center, Russian Academy of Medical Sciences, 117152 Moscow, Russia ; Russian National Research Medical University named after N.I. Pirogov, Separated Structural Unit "Clinical Research Institute of Pediatrics", Ministry of Health of Russian Federation, 125412 Moscow, Russia ; Department of Medical Genetics, Russian Medical Academy of Postgraduate Education, Moscow, 123995 Russia
| | - Svetlana G Vorsanova
- Mental Health Research Center, Russian Academy of Medical Sciences, 117152 Moscow, Russia ; Russian National Research Medical University named after N.I. Pirogov, Separated Structural Unit "Clinical Research Institute of Pediatrics", Ministry of Health of Russian Federation, 125412 Moscow, Russia
| | - Yuri B Yurov
- Mental Health Research Center, Russian Academy of Medical Sciences, 117152 Moscow, Russia ; Russian National Research Medical University named after N.I. Pirogov, Separated Structural Unit "Clinical Research Institute of Pediatrics", Ministry of Health of Russian Federation, 125412 Moscow, Russia
| |
Collapse
|
11
|
Xu Z, Geng Q, Luo F, Xu F, Li P, Xie J. Multiplex ligation-dependent probe amplification and array comparative genomic hybridization analyses for prenatal diagnosis of cytogenomic abnormalities. Mol Cytogenet 2014; 7:84. [PMID: 25530804 PMCID: PMC4271441 DOI: 10.1186/s13039-014-0084-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2014] [Accepted: 11/03/2014] [Indexed: 08/19/2023] Open
Abstract
Background The aims of this study were to evaluate the clinical utility of multiplex ligation-dependent probe amplification (MLPA) and array comparative genomic hybridization (aCGH) analyses on prenatal cases and to review prenatal ultrasound findings of cytogenomic syndromes. Results Of the 54 prenatal cases analyzed, cytogenomic abnormalities were characterized in 14 cases. In four fetuses with abnormal ultrasound findings, a 40.701 Mb duplication of 8q22.3-q24.3 and a 23.839 Mb deletion of 7q33-q36.3 derived from a paternal balanced translocation, a de novo 13.062 Mb deletion of 11q24.1-q25 for Jacobsen syndrome, a de novo 19.971 Mb deletion of 7q11.23-q21.3 for type 1 split-hand/foot malformation (SHFM1), and a de novo 28.909 Mb duplication of 3q21.1-q25.1 were detected. A 699.8 Kb deletion at 5p15.33 for Cri du Chat syndrome was confirmed in a fetus with abnormal MLPA result. A fetus with abnormal maternal screening was detected with a de novo distal 1.747 Mb duplication at 2q37.1-q37.2 and a 6.664 Mb deletion at 2q37.2-q37.3. Of the eight cases referred by history of spontaneous abortions, derivative chromosomes 11 from paternal carriers of a balanced 8q/11q and a 10q/11q translocation were noted in two cases, simple aneuploids of trisomy 2 and trisomy 21 were seen in three cases, and compound aneuploids of two or three chromosomes were found in three cases. Post-test genetic counseling was performed with detailed genomic information and well characterized postnatal syndromic features. Conclusions These results demonstrated that coupling MLPA screening and aCGH analysis are a cost-effective approach to detect cytogenomic abnormalities in a prenatal setting. The aCGH analysis provided not only genomic maps of breakpoints and gene content of imbalanced regions but also better inference of related phenotypes for genetic counseling. Prenatal ultrasound findings reported in the literature for Jacobsen syndrome, SHFM and Cri du Chat syndrome were summarized for use as diagnostic references.
Collapse
Affiliation(s)
- Zhiyong Xu
- Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, Guangdong China
| | - Qian Geng
- Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, Guangdong China
| | - Fuwei Luo
- Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, Guangdong China
| | - Fang Xu
- Department of Genetics, Yale University School of Medicine, New Haven, CT USA
| | - Peining Li
- Department of Genetics, Yale University School of Medicine, New Haven, CT USA
| | - Jiansheng Xie
- Shenzhen Maternity and Child Healthcare Hospital, Shenzhen, Guangdong China
| |
Collapse
|