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Cheng N, Wang Q, Shang Y, Xu Y, Huang K, Yang Z, Pan D, Xu W, Luo Y. Rapid and low-cost strategy for detecting genome-editing induced deletion: A single-copy case. Anal Chim Acta 2018; 1019:111-118. [DOI: 10.1016/j.aca.2018.02.060] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Revised: 02/12/2018] [Accepted: 02/19/2018] [Indexed: 12/27/2022]
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Verkerk AJMH, Zeidler S, Breedveld G, Overbeek L, Huigh D, Koster L, van der Linde H, de Esch C, Severijnen LA, de Vries BBA, Swagemakers SMA, Willemsen R, Hoogeboom AJM, van der Spek PJ, Oostra BA. CXorf56, a dendritic neuronal protein, identified as a new candidate gene for X-linked intellectual disability. Eur J Hum Genet 2018; 26:552-560. [PMID: 29374277 DOI: 10.1038/s41431-017-0051-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 11/20/2017] [Accepted: 11/23/2017] [Indexed: 11/09/2022] Open
Abstract
Intellectual disability (ID) comprises a large group of heterogeneous disorders, often without a known molecular cause. X-linked ID accounts for 5-10% of male ID cases. We investigated a large, three-generation family with mild ID and behavior problems in five males and one female, with a segregation suggestive for X-linked inheritance. Linkage analysis mapped a disease locus to a 7.6 Mb candidate region on the X-chromosome (LOD score 3.3). Whole-genome sequencing identified a 2 bp insertion in exon 2 of the chromosome X open reading frame 56 gene (CXorf56), resulting in a premature stop codon. This insertion was present in all intellectually impaired individuals and carrier females. Additionally, X-inactivation status showed skewed methylation patterns favoring the inactivation of the mutated allele in the unaffected carrier females. We demonstrate that the insertion leads to nonsense-mediated decay and that CXorf56 mRNA expression is reduced in the impaired males and female. In murine brain slices and primary hippocampal neuronal cultures, CXorf56 protein was present and localized in the nucleus, cell soma, dendrites, and dendritic spines. Although no other families have been identified with pathogenic variants in CXorf56, these results suggest that CXorf56 is the causative gene in this family, and thus a novel candidate gene for X-linked ID with behavior problems.
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Affiliation(s)
- Annemieke J M H Verkerk
- Department of Bioinformatics, Erasmus Medical Center, Rotterdam, The Netherlands. .,Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands.
| | - Shimriet Zeidler
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Guido Breedveld
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Lydia Overbeek
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Daphne Huigh
- Department of Bioinformatics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Linda Koster
- Department of Bioinformatics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Herma van der Linde
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Celine de Esch
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Lies-Anne Severijnen
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Bert B A de Vries
- Department of Human Genetics, Radboud Medical Center, Nijmegen, The Netherlands.,Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, The Netherlands
| | | | - Rob Willemsen
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Peter J van der Spek
- Department of Bioinformatics, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Ben A Oostra
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
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Sánchez JA, Henry O, Joda H, Solnestam B, Kvastad L, Johansson E, Akan P, Lundeberg J, Lladach N, Ramakrishnan D, Riley I, O'Sullivan C. Multiplex PCB-based electrochemical detection of cancer biomarkers using MLPA-barcode approach. Biosens Bioelectron 2016; 82:224-32. [DOI: 10.1016/j.bios.2016.04.018] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2015] [Revised: 03/15/2016] [Accepted: 04/06/2016] [Indexed: 11/15/2022]
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Multiplex ligation-dependent probe amplification workflow for the detection of submicroscopic chromosomal abnormalities in patients with developmental delay/intellectual disability. Mol Cytogenet 2013; 6:7. [PMID: 23383958 PMCID: PMC3599182 DOI: 10.1186/1755-8166-6-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 12/31/2012] [Indexed: 12/12/2022] Open
Abstract
Background Array based comparative genomic hybridization (arrayCGH) has been increasingly used as the method of choice for diagnosis of patients with unexplained developmental delay/intellectual disability (DD/ID) but is not universally available for the high throughput use in routine practice. The next-generation sequencing (NGS) techniques, emerging as a new tool in clinical diagnostics, are at present quite labour-intensive and expensive. Since multiplex ligation-dependent probe amplification (MLPA) is relatively fast, easily interpreted and cost-effective, it is still a method of choice for screening large cohorts of patients with DD/ID. Results We prospectively studied a cohort of 150 patients with DD/ID with or without dysmorphic features or additional congenital abnormalities. We used two distinct MLPA kits, SALSA P036 and P070, for subtelomere screening and MLPA kit SALSA P245 for the 21 common microdeletion syndromes. Subtelomere analysis was performed by both kits in all patients. All imbalances were verified by follow-up MLPA kits. The MLPA analysis revealed chromosome aberrations in 21 (14%) cases: 11 subtelomeric rearrangements and 10 microdeletions. Conclusions We have presented the results of the investigation of patients with DD/ID obtained by using a combination of the MLPA sets for subtelomere aberrations and microdeletion syndromes followed by the confirmation of the aberrant results by the region-specific MLPA kits. The use of two subtelomeric kits per patient and investigation of all aberrations by follow-up sets has reduced the rate of false positive and negative results and improved the diagnostic yield. The relatively low cost, simplicity and reliability makes MLPA an effective first-tier cytogenetic diagnostic test for screening large cohorts of DD/ID patients.
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Vandeweyer G, Van der Aa N, Reyniers E, Kooy RF. The contribution of CLIP2 haploinsufficiency to the clinical manifestations of the Williams-Beuren syndrome. Am J Hum Genet 2012; 90:1071-8. [PMID: 22608712 DOI: 10.1016/j.ajhg.2012.04.020] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Revised: 03/16/2012] [Accepted: 04/10/2012] [Indexed: 11/16/2022] Open
Abstract
Williams-Beuren syndrome is a rare contiguous gene syndrome, characterized by intellectual disability, facial dysmorphisms, connective-tissue abnormalities, cardiac defects, structural brain abnormalities, and transient infantile hypercalcemia. Genes lying telomeric to RFC2, including CLIP2, GTF2I and GTF2IRD1, are currently thought to be the most likely major contributors to the typical Williams syndrome cognitive profile, characterized by a better-than-expected auditory rote-memory ability, a relative sparing of language capabilities, and a severe visual-spatial constructive impairment. Atypical deletions in the region have helped to establish genotype-phenotype correlations. So far, however, hardly any deletions affecting only a single gene in the disease region have been described. We present here two healthy siblings with a pure, hemizygous deletion of CLIP2. A putative role in the cognitive and behavioral abnormalities seen in Williams-Beuren patients has been suggested for this gene on the basis of observations in a knock-out mouse model. The presented siblings did not show any of the clinical features associated with the syndrome. Cognitive testing showed an average IQ for both and no indication of the Williams syndrome cognitive profile. This shows that CLIP2 haploinsufficiency by itself does not lead to the physical or cognitive characteristics of the Williams-Beuren syndrome, nor does it lead to the Williams syndrome cognitive profile. Although contribution of CLIP2 to the phenotype cannot be excluded when it is deleted in combination with other genes, our results support the hypothesis that GTF2IRD1 and GTF2I are the main genes causing the cognitive defects associated with Williams-Beuren syndrome.
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Affiliation(s)
- Geert Vandeweyer
- Department of Medical Genetics, University Hospital of Antwerp, University of Antwerp, Edegem, Belgium
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Stuppia L, Antonucci I, Palka G, Gatta V. Use of the MLPA assay in the molecular diagnosis of gene copy number alterations in human genetic diseases. Int J Mol Sci 2012; 13:3245-3276. [PMID: 22489151 PMCID: PMC3317712 DOI: 10.3390/ijms13033245] [Citation(s) in RCA: 156] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Revised: 02/28/2012] [Accepted: 02/29/2012] [Indexed: 11/16/2022] Open
Abstract
Multiplex Ligation-dependent Probe Amplification (MLPA) assay is a recently developed technique able to evidence variations in the copy number of several human genes. Due to this ability, MLPA can be used in the molecular diagnosis of several genetic diseases whose pathogenesis is related to the presence of deletions or duplications of specific genes. Moreover, MLPA assay can also be used in the molecular diagnosis of genetic diseases characterized by the presence of abnormal DNA methylation. Due to the large number of genes that can be analyzed by a single technique, MLPA assay represents the gold standard for molecular analysis of all pathologies derived from the presence of gene copy number variation. In this review, the main applications of the MLPA technique for the molecular diagnosis of human diseases are described.
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Affiliation(s)
- Liborio Stuppia
- Department of Oral Sciences, Nano and Biotechnologies, “G. d’Annunzio” University, Via dei Vestini 31, 66013 Chieti, Italy; E-Mails: (I.A.); (G.P.); (V.G.)
| | - Ivana Antonucci
- Department of Oral Sciences, Nano and Biotechnologies, “G. d’Annunzio” University, Via dei Vestini 31, 66013 Chieti, Italy; E-Mails: (I.A.); (G.P.); (V.G.)
| | - Giandomenico Palka
- Department of Oral Sciences, Nano and Biotechnologies, “G. d’Annunzio” University, Via dei Vestini 31, 66013 Chieti, Italy; E-Mails: (I.A.); (G.P.); (V.G.)
| | - Valentina Gatta
- Department of Oral Sciences, Nano and Biotechnologies, “G. d’Annunzio” University, Via dei Vestini 31, 66013 Chieti, Italy; E-Mails: (I.A.); (G.P.); (V.G.)
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Hochstenbach R, Buizer-Voskamp JE, Vorstman JAS, Ophoff RA. Genome arrays for the detection of copy number variations in idiopathic mental retardation, idiopathic generalized epilepsy and neuropsychiatric disorders: lessons for diagnostic workflow and research. Cytogenet Genome Res 2011; 135:174-202. [PMID: 22056632 DOI: 10.1159/000332928] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022] Open
Abstract
We review the contributions and limitations of genome-wide array-based identification of copy number variants (CNVs) in the clinical diagnostic evaluation of patients with mental retardation (MR) and other brain-related disorders. In unselected MR referrals a causative genomic gain or loss is detected in 14-18% of cases. Usually, such CNVs arise de novo, are not found in healthy subjects, and have a major impact on the phenotype by altering the dosage of multiple genes. This high diagnostic yield justifies array-based segmental aneuploidy screening as the initial genetic test in these patients. This also pertains to patients with autism (expected yield about 5-10% in nonsyndromic and 10-20% in syndromic patients) and schizophrenia (at least 5% yield). CNV studies in idiopathic generalized epilepsy, attention-deficit hyperactivity disorder, major depressive disorder and Tourette syndrome indicate that patients have, on average, a larger CNV burden as compared to controls. Collectively, the CNV studies suggest that a wide spectrum of disease-susceptibility variants exists, most of which are rare (<0.1%) and of variable and usually small effect. Notwithstanding, a rare CNV can have a major impact on the phenotype. Exome sequencing in MR and autism patients revealed de novo mutations in protein coding genes in 60 and 20% of cases, respectively. Therefore, it is likely that arrays will be supplanted by next-generation sequencing methods as the initial and perhaps ultimate diagnostic tool in patients with brain-related disorders, revealing both CNVs and mutations in a single test.
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Affiliation(s)
- R Hochstenbach
- Division of Biomedical Genetics, Department of Medical Genetics, University Medical Centre Utrecht, Utrecht, The Netherlands.
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