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Hu X, Baker EK, Johnson J, Balow S, Pena LDM, Conlin LK, Guan Q, Smolarek TA. Characterization of a rare mosaic unbalanced translocation of t(3;12) in a patient with neurodevelopmental disorders. Mol Cytogenet 2022; 15:10. [PMID: 35248119 PMCID: PMC8898488 DOI: 10.1186/s13039-022-00579-0] [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: 10/19/2021] [Accepted: 01/28/2022] [Indexed: 11/21/2022] Open
Abstract
Background Unbalanced translocations may be de novo or inherited from one parent carrying the balanced form and are usually present in all cells. Mosaic unbalanced translocations are extremely rare with a highly variable phenotype depending on the tissue distribution and level of mosaicism. Mosaicism for structural chromosomal abnormalities is clinically challenging for diagnosis and counseling due to the limitation of technical platforms and complex mechanisms, respectively. Here we report a case with a tremendously rare maternally-derived mosaic unbalanced translocation of t(3;12), and we illustrate the unreported complicated mechanism using single nucleotide polymorphism (SNP) array, fluorescence in situ hybridization (FISH), and chromosome analyses. Case presentation An 18-year-old female with a history of microcephaly, pervasive developmental disorder, intellectual disability, sensory integration disorder, gastroparesis, and hypotonia presented to our genetics clinic. She had negative karyotype by parental report but no other genetic testing performed previously. SNP microarray analysis revealed a complex genotype including 8.4 Mb terminal mosaic duplication on chromosome 3 (3p26.3->3p26.1) with the distal 5.7 Mb involving two parental haplotypes and the proximal 2.7 Mb involving three parental haplotypes, and a 6.1 Mb terminal mosaic deletion on chromosome 12 (12p13.33->12p13.31) with no evidence for a second haplotype. Adjacent to the mosaic deletion is an interstitial mosaic copy-neutral region of homozygosity (1.9 Mb, 12p13.31). The mother of this individual was confirmed by chromosome analysis and FISH that she carries a balanced translocation, t(3;12)(p26.1;p13.31). Conclusion Taken together, the proband, when at the stage of a zygote, likely carried the derivative chromosome 12 from this translocation, and a postzygotic mitotic recombination event occurred between the normal paternal chromosome 12 and maternal derivative chromosome 12 to “correct” the partial 3p trisomy and partial deletion of 12p. To the best of our knowledge, it is the first time to report the mechanism utilizing a combined cytogenetic and cytogenomic approach, and we believe it expands our knowledge of mosaic structural chromosomal disorders and provides new insight into clinical management and genetic counseling.
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Lopatkina ME, Ivanova SA, Lebedev IN. Estimation of the Prevalence and Parental Origin of Chromosomal Microdeletions and Microduplications Affecting the CNTN6 Gene in Patients with Neurodevelopmental Disorders and Healthy Individuals. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421070103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Gandawijaya J, Bamford RA, Burbach JPH, Oguro-Ando A. Cell Adhesion Molecules Involved in Neurodevelopmental Pathways Implicated in 3p-Deletion Syndrome and Autism Spectrum Disorder. Front Cell Neurosci 2021; 14:611379. [PMID: 33519384 PMCID: PMC7838543 DOI: 10.3389/fncel.2020.611379] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 12/15/2020] [Indexed: 01/06/2023] Open
Abstract
Autism spectrum disorder (ASD) is characterized by impaired social interaction, language delay and repetitive or restrictive behaviors. With increasing prevalence, ASD is currently estimated to affect 0.5–2.0% of the global population. However, its etiology remains unclear due to high genetic and phenotypic heterogeneity. Copy number variations (CNVs) are implicated in several forms of syndromic ASD and have been demonstrated to contribute toward ASD development by altering gene dosage and expression. Increasing evidence points toward the p-arm of chromosome 3 (chromosome 3p) as an ASD risk locus. Deletions occurring at chromosome 3p result in 3p-deletion syndrome (Del3p), a rare genetic disorder characterized by developmental delay, intellectual disability, facial dysmorphisms and often, ASD or ASD-associated behaviors. Therefore, we hypothesize that overlapping molecular mechanisms underlie the pathogenesis of Del3p and ASD. To investigate which genes encoded in chromosome 3p could contribute toward Del3p and ASD, we performed a comprehensive literature review and collated reports investigating the phenotypes of individuals with chromosome 3p CNVs. We observe that high frequencies of CNVs occur in the 3p26.3 region, the terminal cytoband of chromosome 3p. This suggests that CNVs disrupting genes encoded within the 3p26.3 region are likely to contribute toward the neurodevelopmental phenotypes observed in individuals affected by Del3p. The 3p26.3 region contains three consecutive genes encoding closely related neuronal immunoglobulin cell adhesion molecules (IgCAMs): Close Homolog of L1 (CHL1), Contactin-6 (CNTN6), and Contactin-4 (CNTN4). CNVs disrupting these neuronal IgCAMs may contribute toward ASD phenotypes as they have been associated with key roles in neurodevelopment. CHL1, CNTN6, and CNTN4 have been observed to promote neurogenesis and neuronal survival, and regulate neuritogenesis and synaptic function. Furthermore, there is evidence that these neuronal IgCAMs possess overlapping interactomes and participate in common signaling pathways regulating axon guidance. Notably, mouse models deficient for these neuronal IgCAMs do not display strong deficits in axonal migration or behavioral phenotypes, which is in contrast to the pronounced defects in neuritogenesis and axon guidance observed in vitro. This suggests that when CHL1, CNTN6, or CNTN4 function is disrupted by CNVs, other neuronal IgCAMs may suppress behavioral phenotypes by compensating for the loss of function.
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Affiliation(s)
- Josan Gandawijaya
- University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - Rosemary A Bamford
- University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
| | - J Peter H Burbach
- Department of Translational Neuroscience, Brain Center Rudolf Magnus, University Medical Center Utrecht and Utrecht University, Utrecht, Netherlands
| | - Asami Oguro-Ando
- University of Exeter Medical School, University of Exeter, Exeter, United Kingdom
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Garcia SL, Lauritsen J, Zhang Z, Bandak M, Dalgaard MD, Nielsen RL, Daugaard G, Gupta R. Prediction of Nephrotoxicity Associated With Cisplatin-Based Chemotherapy in Testicular Cancer Patients. JNCI Cancer Spectr 2020; 4:pkaa032. [PMID: 32617516 PMCID: PMC7315098 DOI: 10.1093/jncics/pkaa032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Background Cisplatin-based chemotherapy may induce nephrotoxicity. This study presents a random forest predictive model that identifies testicular cancer patients at risk of nephrotoxicity before treatment. Methods Clinical data and DNA from saliva samples were collected for 433 patients. These were genotyped on Illumina HumanOmniExpressExome-8 v1.2 (964 193 markers). Clinical and genomics-based random forest models generated a risk score for each individual to develop nephrotoxicity defined as a 20% drop in isotopic glomerular filtration rate during chemotherapy. The area under the receiver operating characteristic curve was the primary measure to evaluate models. Sensitivity, specificity, and positive and negative predictive values were used to discuss model clinical utility. Results Of 433 patients assessed in this study, 26.8% developed nephrotoxicity after bleomycin-etoposide-cisplatin treatment. Genomic markers found to be associated with nephrotoxicity were located at NAT1, NAT2, and the intergenic region of CNTN6 and CNTN4. These, in addition to previously associated markers located at ERCC1, ERCC2, and SLC22A2, were found to improve predictions in a clinical feature–trained random forest model. Using only clinical data for training the model, an area under the receiver operating characteristic curve of 0.635 (95% confidence interval [CI] = 0.629 to 0.640) was obtained. Retraining the classifier by adding genomics markers increased performance to 0.731 (95% CI = 0.726 to 0.736) and 0.692 (95% CI = 0.688 to 0.696) on the holdout set. Conclusions A clinical and genomics-based machine learning algorithm improved the ability to identify patients at risk of nephrotoxicity compared with using clinical variables alone. Novel genetics associations with cisplatin-induced nephrotoxicity were found for NAT1, NAT2, CNTN6, and CNTN4 that require replication in larger studies before application to clinical practice.
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Affiliation(s)
- Sara L Garcia
- Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Jakob Lauritsen
- Department of Oncology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Zeyu Zhang
- Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, Denmark.,Key Laboratory of Genetic Network Biology, Institute of Genetics and Developmental Biology, University of Chinese Academy of Sciences, Beijing, China
| | - Mikkel Bandak
- Department of Oncology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Marlene D Dalgaard
- Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Rikke L Nielsen
- Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, Denmark.,Sino-Danish Center for Education and Research, Eastern Yanqihu campus, University of Chinese Academy of Sciences, Beijing, China
| | - Gedske Daugaard
- Department of Oncology, Copenhagen University Hospital, Copenhagen, Denmark
| | - Ramneek Gupta
- Department of Health Technology, Technical University of Denmark, Kgs. Lyngby, Denmark
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The Reeler Mouse: A Translational Model of Human Neurological Conditions, or Simply a Good Tool for Better Understanding Neurodevelopment? J Clin Med 2019; 8:jcm8122088. [PMID: 31805691 PMCID: PMC6947477 DOI: 10.3390/jcm8122088] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 11/26/2019] [Accepted: 11/28/2019] [Indexed: 12/25/2022] Open
Abstract
The first description of the Reeler mutation in mouse dates to more than fifty years ago, and later, its causative gene (reln) was discovered in mouse, and its human orthologue (RELN) was demonstrated to be causative of lissencephaly 2 (LIS2) and about 20% of the cases of autosomal-dominant lateral temporal epilepsy (ADLTE). In both human and mice, the gene encodes for a glycoprotein referred to as reelin (Reln) that plays a primary function in neuronal migration during development and synaptic stabilization in adulthood. Besides LIS2 and ADLTE, RELN and/or other genes coding for the proteins of the Reln intracellular cascade have been associated substantially to other conditions such as spinocerebellar ataxia type 7 and 37, VLDLR-associated cerebellar hypoplasia, PAFAH1B1-associated lissencephaly, autism, and schizophrenia. According to their modalities of inheritances and with significant differences among each other, these neuropsychiatric disorders can be modeled in the homozygous (reln−/−) or heterozygous (reln+/−) Reeler mouse. The worth of these mice as translational models is discussed, with focus on their construct and face validity. Description of face validity, i.e., the resemblance of phenotypes between the two species, centers onto the histological, neurochemical, and functional observations in the cerebral cortex, hippocampus, and cerebellum of Reeler mice and their human counterparts.
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Repnikova EA, Lyalin DA, McDonald K, Astbury C, Hansen-Kiss E, Cooley LD, Pfau R, Herman GE, Pyatt RE, Hickey SE. CNTN6 copy number variations: Uncertain clinical significance in individuals with neurodevelopmental disorders. Eur J Med Genet 2019; 63:103636. [PMID: 30836150 DOI: 10.1016/j.ejmg.2019.02.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 02/12/2019] [Accepted: 02/24/2019] [Indexed: 11/26/2022]
Abstract
Copy number variations (CNVs) of the CNTN6 gene - a member of the contactin gene superfamily - have been previously proposed to have an association with neurodevelopmental and autism spectrum disorders. However, no functional evidence has been provided to date and phenotypically normal and mildly affected carriers complicate the interpretation of this aberration. In view of conflicting reports on the pathogenicity of CNVs involving CNTN6 and association with different phenotypes, we, independently, evaluated clinical features of nineteen patients with detected CNV of CNTN6 as part of their clinical microarray analysis at Children's Mercy and Nationwide Children's Hospitals for the period of 2008-2015. The clinical presentations of these patients were variable making it difficult to establish genotype-phenotype correlations. CNVs were inherited in six patients. For thirteen patients, inheritance pattern was not established due to unavailability of parental samples for testing. In three cases CNV was inherited from a healthy parent and in three cases from a parent with neurodevelopmental symptoms. Of the nineteen patients, four had a separate genetic abberation in addition to CNV of the CNTN6 that could independently explain their respective phenotypes. Separately, CNTN6 sequencing was performed on an autism spectrum disorder (ASD) research cohort of 94 children from 80 unrelated families. We found no difference in frequency of rare coding variants between the cohort of patients and controls. We conclude that CNVs involving CNTN6 alone seem to be most likely a neutral variant or a possible modifier rather than a disease-causing variant. Patients with CNVs encompassing CNTN6 could benefit from additional genetic testing since a clinical diagnosis due to a CNV of CNTN6 alone is still questionable.
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Affiliation(s)
- Elena A Repnikova
- The Division of Clinical Genetics and Genomics Laboratories, Children's Mercy Hospital Kansas City, Kansas City, MO, 64108 USA; University Missouri-Kansas City School of Medicine, Kansas City, MO, 64108, USA.
| | - Dmitry A Lyalin
- The Division of Clinical Genetics and Genomics Laboratories, Children's Mercy Hospital Kansas City, Kansas City, MO, 64108 USA
| | - Kimberly McDonald
- Department of Pediatrics, Nationwide Children's Hospital, Columbus, OH, 43205, USA
| | - Caroline Astbury
- Cytogenetics and Molecular Genetics Laboratory, Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH, 43205, USA
| | - Emily Hansen-Kiss
- Department of Pediatrics, Nationwide Children's Hospital, Columbus, OH, 43205, USA; Center for Molecular and Human Genetics, The Research Institute at Nationwide Children's Hospital, Columbus, OH, 43205, USA
| | - Linda D Cooley
- The Division of Clinical Genetics and Genomics Laboratories, Children's Mercy Hospital Kansas City, Kansas City, MO, 64108 USA; University Missouri-Kansas City School of Medicine, Kansas City, MO, 64108, USA
| | - Ruthann Pfau
- Cytogenetics and Molecular Genetics Laboratory, Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH, 43205, USA; The Ohio State University College of Medicine, Columbus, OH, 43210, USA
| | - Gail E Herman
- Department of Pediatrics, Nationwide Children's Hospital, Columbus, OH, 43205, USA; Center for Molecular and Human Genetics, The Research Institute at Nationwide Children's Hospital, Columbus, OH, 43205, USA; The Ohio State University College of Medicine, Columbus, OH, 43210, USA
| | - Robert E Pyatt
- Cytogenetics and Molecular Genetics Laboratory, Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH, 43205, USA
| | - Scott E Hickey
- Department of Pediatrics, Nationwide Children's Hospital, Columbus, OH, 43205, USA; The Ohio State University College of Medicine, Columbus, OH, 43210, USA.
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