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Multiplex ligation dependent probe amplification - A useful, fast and cost-effective method for identification of small supernumerary marker chromosome in children with developmental delay and congenital heart defect. REV ROMANA MED LAB 2018. [DOI: 10.2478/rrlm-2018-0032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Abstract
Small supernumerary marker chromosome (sSMC) is a rare chromosomal abnormality and is detected in about 0.3% in cases with multiple congenital anomalies (MCA) and/or developmental delay. Different techniques for investigation of cases with MCA and/or developmental delay are available ranging from karyotyping to molecular cytogenetic technique and ultimately multiplex ligation dependent probe amplification (MLPA). Here we present a patient with multiple congenital anomalies for which classical cytogenetic technique was used as a first step in diagnosis and the results being confirmed by MLPA. The karyotype disclosed a sSMC considered to be a fragment of chromosome 22. The MLPA analysis using SALSA MLPA probemix P064-C2 Microdeletion Syndromes-1B confirmed the karyotype results, and according to the manufacturer’s recommendation we performed another confirmation analysis with MLPA probemix P311-B1 Congenital Heart Disease and MLPA probemix P250-B2 DiGeorge. We also suspected an Emanuel syndrome and performed another MLPA analysis with SALSA MLPA probemix P036-E3 Subtelomeres Mix 1 and probemix P070-B3 Subtelomeres Mix 2B for investigation of subtelomeric region that revealed a duplication of 11q25 region and the confirmation was performed using SALSA MLPA probemix P286-B2 Human Telomere-11.
In conclusion, we consider that MLPA is a valuable method for identification of sSMC in children with developmental delay and congenital anomalies. Genetic diagnosis using different molecular techniques, such as MLPA, for increasing accuracy in identification of chromosomal structural aberrations has an important role in clinical diagnosis and in genetic counselling and our case explain the importance of using a specific laboratory technique for each stage of diagnosis.
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2
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Teixeira WG, Marques FK, Freire MCM. Retrospective karyotype study in mentally retarded patients. Rev Assoc Med Bras (1992) 2016; 62:262-8. [PMID: 27310551 DOI: 10.1590/1806-9282.62.03.262] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 11/04/2014] [Indexed: 11/21/2022] Open
Abstract
OBJECTIVE To describe the chromosomal alterations in patients with mental retardation (MR) using G-banding karyotype analysis. METHOD A retrospective study of the results G-banding karyotype analysis of 369 patients investigated for MR was performed. Based on the structural rearrangements found, the authors searched all chromosomal regions related with breakpoints, and these were compared with the literature on MR and databases. RESULTS 338 (91.6%) normal cases, and 31 (8.4%) with some type of chromosomal abnormality were identified. Among the altered cases, 21 patients (67.8%) were identified with structural chromosomal alterations, nine (29%) with numerical alterations, and one (3.2%) with numerical and structural alterations. CONCLUSION Structural chromosomal abnormalities were observed more frequently in this study. G-banding karyotyping contributes to the investigation of the causes of MR, showing that this technique can be useful for initial screening of patients. However, higher resolution techniques such as array based comparative genomic hybridization (aCGH) and multiplex ligation-dependent probe amplification (MPLA) can detect submicroscopic alterations commonly associated with MR.
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Affiliation(s)
- Wellcy Gonçalves Teixeira
- Instituto Hermes Pardini, Laboratory Specialist, Belo Horizonte MG , Brazil, MSc in General and Applied Biology - Laboratory Specialist at Instituto Hermes Pardini, Belo Horizonte, MG, Brazil
| | - Fabiana Kalina Marques
- Instituto Hermes Pardini, Belo Horizonte MG , Brazil, MSc in Genetics - Researcher at Instituto Hermes Pardini, Belo Horizonte, MG, Brazil
| | - Maíra Cristina Menezes Freire
- Instituto Hermes Pardini, Belo Horizonte MG , Brazil, PhD in Genetics - Researcher at Instituto Hermes Pardini, Belo Horizonte, MG, Brazil
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Santa María L, Faundes V, Curotto B, Morales P, Morales K, Aliaga S, Pugin Á, Alliende MA. Comparison of two subtelomeric assays for the screening of chromosomal rearrangements: analysis of 383 patients, literature review and further recommendations. J Appl Genet 2015; 57:63-9. [PMID: 26069167 DOI: 10.1007/s13353-015-0295-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 05/11/2015] [Accepted: 05/26/2015] [Indexed: 12/01/2022]
Abstract
Intellectual disability (ID) and global development delay (GDD) are caused by genetic factors such as subtelomeric rearrangements (SR) in 25 % of patients. There are several assays currently available to detect SR, but subtelomeric fluorescence in situ hybridisation (Subt-FISH) and subtelomeric multiplex ligation-dependent probe amplification (Subt-MLPA) have been the most frequently used. However, the diagnostic yield of each technique has not been compared. We reviewed the results of SR screening over a ten-year period in Chilean patients with ID/GDD using Subt-FISH and/or Subt-MLPA, compared the diagnostic yield of both tools and reviewed the corresponding literature. A total of 383 cases were included in this study, of which 53.8 % were males. The overall diagnostic yield was 8.9 % between both methods, but Subt-MLPA showed a higher performance than Subt-FISH (p = 0.002). A total of 4,181 patients with ID/GDD have been studied worldwide with Subt-MLPA and other subtelomeric assays, and 244 (5.84 %) had a pathogenic SR. It is estimated that Subt-MLPA may detect 92.6 % of the total cases with SR. The capacity of detecting tandem duplication and other critical regions, as well as the use of two MLPA kits, may explain the higher performance of this tool over Subt-FISH. Therefore, we recommend the use of this subtelomeric method as a cost-effective way to study ID/GDD patients.
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Affiliation(s)
- Lorena Santa María
- Laboratorio de Genética y Enfermedades Metabólicas, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Av. El Líbano 5524, Macul, Casilla 138-11, Santiago, Chile
| | - Víctor Faundes
- Laboratorio de Genética y Enfermedades Metabólicas, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Av. El Líbano 5524, Macul, Casilla 138-11, Santiago, Chile.
| | - Bianca Curotto
- Laboratorio de Genética y Enfermedades Metabólicas, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Av. El Líbano 5524, Macul, Casilla 138-11, Santiago, Chile
| | - Paulina Morales
- Laboratorio de Genética y Enfermedades Metabólicas, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Av. El Líbano 5524, Macul, Casilla 138-11, Santiago, Chile
| | - Karla Morales
- Laboratorio de Genética y Enfermedades Metabólicas, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Av. El Líbano 5524, Macul, Casilla 138-11, Santiago, Chile.,Escuela de Tecnología Médica, Facultad de Medicina, Universidad del Desarrollo, Santiago, Chile
| | - Solange Aliaga
- Laboratorio de Genética y Enfermedades Metabólicas, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Av. El Líbano 5524, Macul, Casilla 138-11, Santiago, Chile
| | - Ángela Pugin
- Laboratorio de Genética y Enfermedades Metabólicas, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Av. El Líbano 5524, Macul, Casilla 138-11, Santiago, Chile
| | - María Angélica Alliende
- Laboratorio de Genética y Enfermedades Metabólicas, Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Av. El Líbano 5524, Macul, Casilla 138-11, Santiago, Chile
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Szabó GP, Knegt AC, Ujfalusi A, Balogh E, Szabó T, Oláh É. Subtelomeric 6.7 Mb trisomy 10p and 5.6 Mb monosomy 21q detected by FISH and array-CGH in three related patients. Am J Med Genet A 2012; 158A:869-76. [PMID: 22407767 DOI: 10.1002/ajmg.a.35236] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2011] [Accepted: 12/30/2011] [Indexed: 11/12/2022]
Abstract
Cryptic subtelomeric chromosomal aberrations are responsible for 5-10% of moderate/severe and 1% of mild intellectual disability. Unbalanced subtelomeric chromosomal rearrangements result in variable phenotypes which seem to be highly influenced by both the size of the duplication/deletion and the chromosomes involved in the translocation. We report on three related patients with moderate intellectual disability, language delay, hypotonia, facial dysmorphism, cardiac anomalies, scoliosis, and kyphosis in whom a familial (maternal) unbalanced submicroscopic translocation was found by subtelomeric fluorescence in situ hybridization (FISH). This rearrangement resulted in a partial trisomy 10pter and partial monosomy 21qter. The karyotype was 46,XY.ish der(21)t(10;21)(p14;q22.2). Confirmation of a 6.7 Mb size distal duplication of the p15.3-14 region of chromosome 10 and a 5.6 Mb distal deletion of the q22.2-22.3 region of chromosome 21 was obtained by array-CGH. To our best knowledge, such a composition of subtelomeric unbalanced translocations has not yet been published. Detection of this aberration in successive pregnancies of carrier members of the family by prenatal FISH could prevent the recurrence of the disease. Furthermore, detection of the rearrangements and identification of genes located in the chromosomal regions involved might be of interest.
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Affiliation(s)
- Gabriella P Szabó
- Pediatrics Institute, University of Debrecen, Medical and Health Science Center, Debrecen, Hungary.
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5
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Rafati M, Ghadirzadeh MR, Heshmati Y, Adibi H, Keihanidoust Z, Eshraghian MR, Dastan J, Hoseini A, Purhoseini M, Ghaffari SR. "Familial" versus "sporadic" intellectual disability: contribution of subtelomeric rearrangements. Mol Cytogenet 2012; 5:4. [PMID: 22260313 PMCID: PMC3284400 DOI: 10.1186/1755-8166-5-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Accepted: 01/19/2012] [Indexed: 01/05/2023] Open
Abstract
Background Cryptic subtelomeric rearrangements have been proposed as a significant cause of sporadic intellectual disability (ID) but the role of such aberrations in familial ID has not yet been studied. As positive family history of ID had been proposed as an important and significant predicting factor of subtelomeric rearrangements, it was assumed that the contribution of subtelomeric aberrations in familial ID would be much more than the sporadic ones. Three hundred and twenty two patients from 102 unrelated families with more than two ID patients in the first degree relatives have been investigated. Assessment of subtelomeric rearrangements were carried out using Multiplex Ligation-Dependent Probe Amplification (MLPA) technique. Detected aberrations were then confirmed by Fluorescence in Situ Hybridization (FISH) method. Results Among the families studied, 27.4% had 4-12, 36.3% had 3 and 36.3% had 2 affected individuals in the first degree relatives. One unbalanced translocation and 4 polymorphic changes were detected. The prevalence of clinically significant subtelomeric rearrangements was 0.98%. Conclusion This is the first investigation of subtelomeric aberrations in a large sample set of familial ID patients. Our results show that the contribution of subtelomeric rearrangements to familial ID is not as much as what had been determined for sporadic ones in the literature. Moreover, this study shows that the positive family history by alone, cannot be the most important and determining indicator of subtelomeric aberrations while it would be a good predicting factor when associated with dysmorphism or congenital malformations. These findings propose that other cryptic chromosomal abnormalities or even single gene disorders may be the main cause of familial ID rather than subtelomeric aberrations.
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Affiliation(s)
- Maryam Rafati
- Department of Medical Genetics, Tehran University of Medical Sciences, Tehran, Iran.
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Lee JY, Cho YH, Hallford G. Delineation of subtelomeric deletion of the long arm of chromosome 6. Ann Hum Genet 2011; 75:755-64. [PMID: 21950800 DOI: 10.1111/j.1469-1809.2011.00675.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Pure subtelomeric deletion of the long arm of chromosome 6 is rare. The frequency of this deletion accounts for approximately 0.05% of subjects with intellectual disability and developmental delay with or without dysmorphic features. Common phenotypes associated with this deletion include intellectual disability, developmental delay, dysmorphic features, seizure, hypotonia, microcephaly and hypoplasia of the corpus callosum. The smallest overlapped region is approximately 0.4 Mb, and contains three known genes. Of these genes, TBP has been considered as a plausible candidate gene for the phenotype in patients with a subtelomeric 6q deletion. Analysis of the breakpoints in 14 cases revealed a potential common breakpoint interval 8.0-9.0 Mb from the chromosome 6q terminus where the FRA6E fragile site exists and the PARK2 gene is located. This suggests that breakage at the FRA6E fragile site may be the mechanism behind chromosome 6q subtelomeric deletion in some of the cases.
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Affiliation(s)
- Ji-Yun Lee
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA.
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7
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P. Szabó G, Bessenyei B, Balogh E, Ujfalusi A, Szakszon K, Oláh É. Detection of subtelomeric chromosomal rearrangements in idiopathic mental retardation. Orv Hetil 2010; 151:1091-8. [DOI: 10.1556/oh.2010.28911] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
A kromoszómák szubtelomerikus régiói génben gazdag területek, átrendeződésük hagyományos kromoszómaanalízissel nem detektálható. Mivel a mentális retardációk közel 7%-áért felelősek, kimutatásuk diagnosztikai szempontból jelentős, és lehetőséget nyújt az ismétlődés megakadályozására is. A kimutatásukra alkalmas módszerek egyike a szubtelomerikus fluoreszcencia in situ hibridizáció. Ötvenkilenc idiopathiás mentálisan retardált beteg közül 35 közepes/súlyos értelmi fogyatékost választottunk ki a nemzetközi irodalomban ajánlott kritériumok alapján. Közülük 6 beteg esetében mutattunk ki szubtelomerikus aberrációt, 5 familiáris (két család), egy
de novo
esetnek bizonyult. Huszonkilenc betegben szubtelomerikus kromoszómaátrendeződést nem igazoltunk. A 6 beteg közül kettőben 8pter deléciót és 12pter duplikációt, háromban 21qter deléciót és 10pter duplikációt azonosítottunk kiegyensúlyozatlan transzlokáció formájában. Egy betegnél
de novo
keletkezett 3qter deléciót detektáltunk. Az eltérések eredetének tisztázása során 12 egészséges családtag közül öt bizonyult kiegyensúlyozott transzlokációhordozónak. Az irodalmi adatokkal összhangban megállapítottuk, hogy a fenotípust a deléció és a duplikáció mérete, valamint transzlokációk esetén az érintett partner kromoszómák együttesen határozzák meg.
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Affiliation(s)
- Gabriella P. Szabó
- 1 Debreceni Egyetem Orvos- és Egészségtudományi Centrum Gyermekgyógyászati Intézet, Klinikai Genetikai Központ Debrecen Nagyerdei krt. 98. 4032
| | - Beáta Bessenyei
- 1 Debreceni Egyetem Orvos- és Egészségtudományi Centrum Gyermekgyógyászati Intézet, Klinikai Genetikai Központ Debrecen Nagyerdei krt. 98. 4032
| | - Erzsébet Balogh
- 1 Debreceni Egyetem Orvos- és Egészségtudományi Centrum Gyermekgyógyászati Intézet, Klinikai Genetikai Központ Debrecen Nagyerdei krt. 98. 4032
| | - Anikó Ujfalusi
- 1 Debreceni Egyetem Orvos- és Egészségtudományi Centrum Gyermekgyógyászati Intézet, Klinikai Genetikai Központ Debrecen Nagyerdei krt. 98. 4032
| | - Katalin Szakszon
- 1 Debreceni Egyetem Orvos- és Egészségtudományi Centrum Gyermekgyógyászati Intézet, Klinikai Genetikai Központ Debrecen Nagyerdei krt. 98. 4032
| | - Éva Oláh
- 1 Debreceni Egyetem Orvos- és Egészségtudományi Centrum Gyermekgyógyászati Intézet, Klinikai Genetikai Központ Debrecen Nagyerdei krt. 98. 4032
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8
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Lam ACF, Lai KKS, Chau ATC, Lo IFM, Lam STS. Subtelomeric 1q deletion syndrome causing patella hypoplasia and limb deformities, features overlapping with genitopatellar syndrome. Clin Genet 2009; 76:102-7. [PMID: 19500117 DOI: 10.1111/j.1399-0004.2008.01121.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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9
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Belligni EF, Biamino E, Molinatto C, Messa J, Pierluigi M, Faravelli F, Zuffardi O, Ferrero GB, Silengo MC. Subtelomeric FISH analysis in 76 patients with syndromic developmental delay/intellectual disability. Ital J Pediatr 2009; 35:9. [PMID: 19490664 PMCID: PMC2687548 DOI: 10.1186/1824-7288-35-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2008] [Accepted: 04/27/2009] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Intellectual disability affects approximately 1 to 3% of the general population. The etiology is still poorly understood and it is estimated that one-half of the cases are due to genetic factors. Cryptic subtelomeric aberrations have been found in roughly 5 to 7% of all cases. METHODS We performed a subtelomeric FISH analysis on 76 unrelated children with normal standard karyotype ascertained by developmental delay or intellectual disability, associated with congenital malformations, and/or facial dysmorphisms. RESULTS Ten cryptic chromosomal anomalies have been identified in the whole cohort (13,16%), 8 in the group of patients characterized by developmental delay or intellectual disability associated with congenital malformations and facial dysmorphisms, 2 in patients with developmental delay or intellectual disability and facial dysmorphisms only. CONCLUSION We demonstrate that a careful clinical examination is a very useful tool for pre-selection of patients for genomic analysis, clearly enhancing the chromosomal anomaly detection rate. Clinical features of most of these patients are consistent with the corresponding emerging chromosome phenotypes, pointing out these new clinical syndromes associated with specific genomic imbalances.
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Affiliation(s)
- Elga F Belligni
- Dipartimento di Scienze Pediatriche, University of Torino, Torino, Italy
| | - Elisa Biamino
- Dipartimento di Scienze Pediatriche, University of Torino, Torino, Italy
| | - Cristina Molinatto
- Dipartimento di Scienze Pediatriche, University of Torino, Torino, Italy
| | - Jole Messa
- Dipartimento di Biologia Generale e Genetica Medica, University of Pavia, Pavia, Italy
| | | | | | - Orsetta Zuffardi
- Dipartimento di Biologia Generale e Genetica Medica, University of Pavia, Pavia, Italy
| | - Giovanni B Ferrero
- Dipartimento di Scienze Pediatriche, University of Torino, Torino, Italy
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Fisch GS, Battaglia A, Parrini B, Youngblom J, Simensen R. Cognitive-behavioral features of children with Wolf-Hirschhorn syndrome: Preliminary report of 12 cases. AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS 2008; 148C:252-6. [DOI: 10.1002/ajmg.c.30185] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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11
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Gouas L, Goumy C, Véronèse L, Tchirkov A, Vago P. Gene dosage methods as diagnostic tools for the identification of chromosome abnormalities. ACTA ACUST UNITED AC 2008; 56:345-53. [DOI: 10.1016/j.patbio.2008.03.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2008] [Accepted: 03/14/2008] [Indexed: 10/22/2022]
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Prospective screening of patients with unexplained mental retardation using subtelomeric MLPA strongly increases the detection rate of cryptic unbalanced chromosomal rearrangements. Eur J Med Genet 2007; 51:93-105. [PMID: 18032123 DOI: 10.1016/j.ejmg.2007.10.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2007] [Accepted: 10/08/2007] [Indexed: 12/08/2022]
Abstract
This study was designed to increase the diagnostic detection rate for subtelomeric unbalanced chromosomal rearrangements (UCRs) that are believed to cause 3-5% of all cases of mental retardation (MR), but often remain undetected by routine karyotyping because of limited resolution in light microscopy. Increased detection of such cryptic UCRs may be achieved by CGH- or SNP-array technology adapted for genome wide screening but these techniques are labor-intensive and expensive. We have implemented subtelomeric Multiplex Ligation-dependant Probe Amplification (MLPA), a relatively low cost and technically uncomplicated molecular approach, as a high throughput prospective screening tool for UCRs in MR patients. We prospectively studied a cohort of 466 MR patients and detected 53 aberrant MLPA signals. After exclusion of false-positives, potential familial polymorphisms and of non-cryptic UCRs also found in routine chromosome analysis, 18 cases or 3.9% of total could be confirmed as true cryptic subtelomeric UCRs. These were 6 terminal deletions, 8 unbalanced translocations, 3 Prader-Willi deletions and 1 subtelomeric interstitial deletion. This result increases our laboratory's detection rate in this patient cohort from 8.3% (without MLPA) to 12.2% (with MLPA), representing a 47% improvement. This study demonstrates that when applying MLPA in a routine cytogenetic diagnostic setting, a major increase of the diagnostic yield can be achieved.
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13
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Ahn JW, Mackie Ogilvie C, Welch A, Thomas H, Madula R, Hills A, Donaghue C, Mann K. Detection of subtelomere imbalance using MLPA: validation, development of an analysis protocol, and application in a diagnostic centre. BMC MEDICAL GENETICS 2007; 8:9. [PMID: 17338807 PMCID: PMC1831468 DOI: 10.1186/1471-2350-8-9] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2006] [Accepted: 03/05/2007] [Indexed: 12/08/2022]
Abstract
BACKGROUND Commercial MLPA kits (MRC-Holland) are available for detecting imbalance at the subtelomere regions of chromosomes; each kit consists of one probe for each subtelomere. METHODS For validation of the kits, 208 patients were tested, of which 128 were known to be abnormal, corresponding to 8528 genomic regions overall. Validation samples included those with trisomy 13, 18 and 21, microscopically visible terminal deletions and duplications, sex chromosome abnormalities and submicroscopic abnormalities identified by multiprobe FISH. A robust and sensitive analysis system was developed to allow accurate interpretation of single probe results, which is essential as breakpoints may occur between MLPA probes. RESULTS The validation results showed that MLPA is a highly efficient technique for medium-throughput screening for subtelomere imbalance, with 95% confidence intervals for positive and negative predictive accuracies of 0.951-0.996 and 0.9996-1 respectively. A diagnostic testing strategy was established for subtelomere MLPA and any subsequent follow-up tests that may be required. The efficacy of this approach was demonstrated during 15 months of diagnostic testing when 455 patients were tested and 27 (5.9%) abnormal cases were detected. CONCLUSION The development of a robust, medium-throughput analysis system for the interpretation of results from subtelomere assays will be of benefit to other Centres wishing to implement such an MLPA-based service.
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Affiliation(s)
- Joo Wook Ahn
- Cytogenetics Department, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | | | - Alysia Welch
- Cytogenetics Department, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Helen Thomas
- Cytogenetics Department, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Rajiv Madula
- Department of Medical and Molecular Genetics, King's College London School of Medicine, Guy's Hospital, London, UK
| | - Alison Hills
- Cytogenetics Department, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Celia Donaghue
- Cytogenetics Department, Guy's and St Thomas' NHS Foundation Trust, London, UK
| | - Kathy Mann
- Cytogenetics Department, Guy's and St Thomas' NHS Foundation Trust, London, UK
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Girirajan S, Mendoza-Londono R, Vlangos CN, Dupuis L, Nowak NJ, Bunyan DJ, Hatchwell E, Elsea SH. Smith–Magenis syndrome and moyamoya disease in a patient with del(17)(p11.2p13.1). Am J Med Genet A 2007; 143A:999-1008. [PMID: 17431895 DOI: 10.1002/ajmg.a.31689] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Chromosomal rearrangements causing microdeletions and microduplications are a major cause of congenital malformation and mental retardation. Because they are not visible by routine chromosome analysis, high resolution whole-genome technologies are required for the detection and diagnosis of small chromosomal abnormalities. Recently, array-comparative genomic hybridization (aCGH) and multiplex ligation-dependent probe amplification (MLPA) have been useful tools for the identification and mapping of deletions and duplications at higher resolution and throughput. Smith-Magenis syndrome (SMS) is a multiple congenital anomalies/mental retardation syndrome caused by deletion or mutation of the retinoic acid induced 1 (RAI1) gene and is often associated with a chromosome 17p11.2 deletion. We report here on the clinical and molecular analysis of a 10-year-old girl with SMS and moyamoya disease (occlusion of the circle of Willis). We have employed a combination of aCGH, FISH, and MLPA to characterize an approximately 6.3 Mb deletion spanning chromosome region 17p11.2-p13.1 in this patient, with the proximal breakpoint within the RAI1 gene. Further, investigation of the genomic architecture at the breakpoint intervals of this large deletion documented the presence of palindromic repeat elements that could potentially form recombination substrates leading to unequal crossover.
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Affiliation(s)
- Santhosh Girirajan
- Department of Human Genetics, Medical College of Virginia Campus, Virginia Commonwealth University, Richmond, VA 23298, USA
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