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Zanardo ÉA, Dutra RL, Piazzon FB, Dias AT, Novo-Filho GM, Nascimento AM, Montenegro MM, Damasceno JG, Madia FAR, da Costa TVMM, Melaragno MI, Kim CA, Kulikowski LD. Cytogenomic assessment of the diagnosis of 93 patients with developmental delay and multiple congenital abnormalities: The Brazilian experience. Clinics (Sao Paulo) 2017; 72:526-537. [PMID: 29069255 PMCID: PMC5629705 DOI: 10.6061/clinics/2017(09)02] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 05/04/2017] [Indexed: 01/04/2023] Open
Abstract
OBJECTIVE The human genome contains several types of variations, such as copy number variations, that can generate specific clinical abnormalities. Different techniques are used to detect these changes, and obtaining an unequivocal diagnosis is important to understand the physiopathology of the diseases. The objective of this study was to assess the diagnostic capacity of multiplex ligation-dependent probe amplification and array techniques for etiologic diagnosis of syndromic patients. METHODS We analyzed 93 patients with developmental delay and multiple congenital abnormalities using multiplex ligation-dependent probe amplifications and arrays. RESULTS Multiplex ligation-dependent probe amplification using different kits revealed several changes in approximately 33.3% of patients. The use of arrays with different platforms showed an approximately 53.75% detection rate for at least one pathogenic change and a 46.25% detection rate for patients with benign changes. A concomitant assessment of the two techniques showed an approximately 97.8% rate of concordance, although the results were not the same in all cases. In contrast with the array results, the MLPA technique detected ∼70.6% of pathogenic changes. CONCLUSION The obtained results corroborated data reported in the literature, but the overall detection rate was higher than the rates previously reported, due in part to the criteria used to select patients. Although arrays are the most efficient tool for diagnosis, they are not always suitable as a first-line diagnostic approach because of their high cost for large-scale use in developing countries. Thus, clinical and laboratory interactions with skilled technicians are required to target patients for the most effective and beneficial molecular diagnosis.
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Affiliation(s)
- Évelin Aline Zanardo
- Laboratorio de Citogenomica, Departamento de Patologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, BR
- *Corresponding author. E-mail:
| | - Roberta Lelis Dutra
- Laboratorio de Citogenomica, Departamento de Patologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, BR
| | - Flavia Balbo Piazzon
- Laboratorio de Citogenomica, Departamento de Patologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, BR
| | - Alexandre Torchio Dias
- Laboratorio de Citogenomica, Departamento de Patologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, BR
| | - Gil Monteiro Novo-Filho
- Laboratorio de Citogenomica, Departamento de Patologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, BR
| | - Amom Mendes Nascimento
- Laboratorio de Citogenomica, Departamento de Patologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, BR
| | - Marília Moreira Montenegro
- Laboratorio de Citogenomica, Departamento de Patologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, BR
| | - Jullian Gabriel Damasceno
- Laboratorio de Citogenomica, Departamento de Patologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, BR
| | - Fabrícia Andreia Rosa Madia
- Laboratorio de Citogenomica, Departamento de Patologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, BR
| | | | - Maria Isabel Melaragno
- Departamento de Morfologia e Genetica, Universidade Federal de Sao Paulo, Sao Paulo, SP, BR
| | - Chong Ae Kim
- Unidade de Genetica, Departamento de Pediatria, Instituto da Crianca, Hospital das Clinicas HCFMUSP, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo, SP, BR
| | - Leslie Domenici Kulikowski
- Laboratorio de Citogenomica, Departamento de Patologia, Faculdade de Medicina FMUSP, Universidade de Sao Paulo, Sao Paulo, SP, BR
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Szczałuba K, Jakubiuk-Tomaszuk A, Kędzior M, Bernaciak J, Zdrodowska J, Kurzątkowski W, Radkowski M, Demkow U. Cytogenomic Evaluation of Children with Congenital Anomalies: Critical Implications for Diagnostic Testing and Genetic Counseling. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 912:11-9. [PMID: 26987321 DOI: 10.1007/5584_2016_234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Identification of submicroscopic chromosomal aberrations, as a cause of structural malformations, is currently performed by MLPA (multiplex ligation-dependent probe amplification) or array CGH (array comparative genomic hybridization) techniques. The aim of this study was the evaluation of diagnostic usefulness of MLPA and array CGH in patients with congenital malformations or abnormalities (at least one major or minor birth defect, including dysmorphism) with or without intellectual disability or developmental delay and the optimization of genetic counseling in the context of the results obtained. The MLPA and array CGH were performed in 91 patients diagnosed with developmental disorders and major or minor congenital anomalies. A total of 49 MLPA tests toward common microdeletion syndromes, 42 MLPA tests for subtelomeric regions of chromosomes, two tests for common aberrations in autism, and five array CGH tests were performed. Eight (9 %) patients were diagnosed with microdeletion MLPA, four (4 %) patients with subtelomeric MLPA, one (1 %) patient with autism MLPA. Further three (3 %) individuals had rearrangements diagnosed by array CGH. Altogether, chromosomal microaberrations were found in 16 patients (17 %). All the MLPA-detected rearrangements were found to be pathogenic, but none detected with array CGH could unequivocally be interpreted as pathogenic. In patients with congenital anomalies, the application of MLPA and array CGH techniques is efficient in detecting syndromic and unique microrearrangements. Consistent pre-MLPA test phenotyping leads to better post-test genetic counseling. Incomplete penetrance and unknown inheritance of detected variants are major issues in clinical interpretation of array CGH data.
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Affiliation(s)
- Krzysztof Szczałuba
- MedGen Medical Center, Warsaw, Poland.
- Medical Genetics Unit, Mastermed Medical Center, Białystok, Poland.
| | | | - Marta Kędzior
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | - Joanna Bernaciak
- Department of Medical Genetics, Institute of Mother and Child, Warsaw, Poland
| | | | | | - Marek Radkowski
- Department of Immunopathology of Infectious and Parasitic Diseases, Warsaw Medical University, Warsaw, Poland
| | - Urszula Demkow
- Department of Laboratory Diagnostics and Clinical Immunology of Developmental Age, Warsaw Medical University, Warsaw, Poland
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Screening for Subtelomeric Rearrangements in Thai Patients with Intellectual Disabilities Using FISH and Review of Literature on Subtelomeric FISH in 15,591 Cases with Intellectual Disabilities. GENETICS RESEARCH INTERNATIONAL 2016; 2016:9153740. [PMID: 27822388 PMCID: PMC5086359 DOI: 10.1155/2016/9153740] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 08/08/2016] [Accepted: 08/09/2016] [Indexed: 01/02/2023]
Abstract
We utilized fluorescence in situ hybridization (FISH) to screen for subtelomeric rearrangements in 82 Thai patients with unexplained intellectual disability (ID) and detected subtelomeric rearrangements in 5 patients. Here, we reported on a patient with der(20)t(X;20)(p22.3;q13.3) and a patient with der(3)t(X;3)(p22.3;p26.3). These rearrangements have never been described elsewhere. We also reported on a patient with der(10)t(7;10)(p22.3;q26.3), of which the same rearrangement had been reported in one literature. Well-recognized syndromes were detected in two separated patients, including 4p deletion syndrome and 1p36 deletion syndrome. All patients with subtelomeric rearrangements had both ID and multiple congenital anomalies (MCA) and/or dysmorphic features (DF), except the one with der(20)t(X;20), who had ID alone. By using FISH, the detection rate of subtelomeric rearrangements in patients with both ID and MCA/DF was 8.5%, compared to 2.9% of patients with only ID. Literature review found 28 studies on the detection of subtelomeric rearrangements by FISH in patients with ID. Combining data from these studies and our study, 15,591 patients were examined and 473 patients with subtelomeric rearrangements were determined. The frequency of subtelomeric rearrangements detected by FISH in patients with ID was 3%. Terminal deletions were found in 47.7%, while unbalanced derivative chromosomes were found in 47.9% of the rearrangements.
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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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Chen X, Li H, Mao Y, Xu X, Lv J, Zhou L, Lin X, Tang S. Subtelomeric multiplex ligation-dependent probe amplification as a supplement for rapid prenatal detection of fetal chromosomal aberrations. Mol Cytogenet 2014; 7:96. [PMID: 25506396 PMCID: PMC4265491 DOI: 10.1186/s13039-014-0096-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 11/28/2014] [Indexed: 12/18/2022] Open
Abstract
Background Pregnant women with high-risk indications are highly suspected of fetal chromosomal aberrations. To determine whether Multiplex Ligation-dependent Probe Amplification (MLPA) using subtelomeric probe mixes (P036-E2 and P070-B2) is a reliable method for rapid detection of fetal chromosomal aberrations. The subtelomeric MLPA probe mixes were used to evaluate 50 blood samples from healthy individuals. 168 amniocytes and 182 umbilical cord blood samples from high-risk fetuses were analyzed using the same subtelomeric MLPA probe sets. Karyotyping was also performed in all cases of high-risk pregnancies, and single nucleotide polymorphism array analysis was used to confirm submicroscopic and ambiguous results from MLPA/karyotyping. Results Subtelomeric MLPA analysis of normal samples showed normal result in all cases by use of P036-E2 probe mix, while P070-B2 probe mix gave normal results for all but one case. In one normal control case P070-B2 produced a duplicated signal of probe for 13q34. In the high-risk group, totally 44 chromosomal abnormalities were found by karyotyping and MLPA, including 23 aneuploidies and 21 rearrangements or mosaics. MLPA detected all 23 aneuploidies, 12 rearrangements and 1 mosaic. Importantly, MLPA revealed 4 chromosomal translocations, 2 small supernumerary marker chromosomes (sSMCs), and 3 subtelomeric imbalances that were not well characterized or not detectable by karyotyping. However, MLPA showed negetive results for the remaining 8 rearrangements or mosaics, including 3 low mosaic aneuploidies, 1 inherited sSMC, and 4 paracentric inversions. Conclusions Results suggest that combined use of subtelomeric MLPA and karyotyping may be an alternative method for using karyotype analyses alone in rapid detection of aneuploidies, rearrangements, and sSMCs. Electronic supplementary material The online version of this article (doi:10.1186/s13039-014-0096-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xiangnan Chen
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Key Laboratory of Medical Genetics, Zhejiang, China
| | - Huanzheng Li
- Department of Genetics, Dingli Clinical Medical School, Wenzhou Medical University, Key Laboratory of Birth Defects, Wenzhou, Zhejiang 325000 China
| | - Yijian Mao
- Department of Genetics, Dingli Clinical Medical School, Wenzhou Medical University, Key Laboratory of Birth Defects, Wenzhou, Zhejiang 325000 China
| | - Xueqin Xu
- Department of Genetics, Dingli Clinical Medical School, Wenzhou Medical University, Key Laboratory of Birth Defects, Wenzhou, Zhejiang 325000 China
| | - Jiaojiao Lv
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Key Laboratory of Medical Genetics, Zhejiang, China
| | - Lili Zhou
- Department of Genetics, Dingli Clinical Medical School, Wenzhou Medical University, Key Laboratory of Birth Defects, Wenzhou, Zhejiang 325000 China
| | - Xiaoling Lin
- Department of Genetics, Dingli Clinical Medical School, Wenzhou Medical University, Key Laboratory of Birth Defects, Wenzhou, Zhejiang 325000 China
| | - Shaohua Tang
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Key Laboratory of Medical Genetics, Zhejiang, China ; Department of Genetics, Dingli Clinical Medical School, Wenzhou Medical University, Key Laboratory of Birth Defects, Wenzhou, Zhejiang 325000 China
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Behjati F, Ghasemi Firouzabadi S, Sajedi F, Kahrizi K, Najafi M, Ebrahimizade Ghasemlou B, Shafeghati Y, Behnia F, Mohammadi Arya AR, Karimi H, Hadipour F, Hadipour Z, Jamali P, Kariminejad R, Darvish H, Bahman I, Bagherizadeh E, Najmabadi H, Vameghi R. Identification of Chromosome Abnormalities in Subtelomeric Regions Using Multiplex Ligation Dependent Probe Amplification (MLPA) Technique in 100 Iranian Patients With Idiopathic Mental Retardation. IRANIAN RED CRESCENT MEDICAL JOURNAL 2014; 15:e8221. [PMID: 24693374 PMCID: PMC3950786 DOI: 10.5812/ircmj.8221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/09/2012] [Accepted: 06/14/2013] [Indexed: 11/16/2022]
Abstract
Background Mental retardation/Developmental delay (MR/DD) is present in 1 - 3% of the general
population (1, 2). MR is defined as a significant impairment of both cognitive (IQ <
70) and social adaptive functions, with onset before 18 years of age. Objectives The purpose was to determine the results of subtelomeric screening by the Multiplex
Ligation Dependent Probe Amplification (MLPA) Technique in 100 selected patients with
idiopathic mental retardation (IMR) in Iran. Materials and Methods A number of 100 patients with IMR, normal karyotypes and negative fragile-X and
metabolic tests were screened for subtelomeric abnormalities using MLPA technique. Results Nine of 100 patients showed subtelomeric abnormalities with at least one of the two
MLPA kits. Deletion in a single region was found in 3 patients, and in two different
subtelomeric regions in 1 patient. Duplication was only single and was present in 2
patients. Three patients were found to have both a deletion and duplication.MLPA testing
in the parental samples of 7 patients which was accessible showed that 4 patients were
de novo, 2 patients had inherited from a clinically normal mother, and one had inherited
from a clinically normal father. Screening with the two MLPA kits (SALSA P036 and SALSA
P070) proved abnormality in only five of the 9 patients. Conclusions So, the prevalence rate of abnormal subtelomeres using MLPA technique in patients with
idiopathic MR in our study was 5 - 9%, the higher limit referring to the positive
results of one of the two MLPA kits, and the lower limit representing the results of
positive double-checking with the two MLPA kits.
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Affiliation(s)
- Farkhondeh Behjati
- Genetics Research Center, University of Social Welfare and
Rehabilitation Sciences, Tehran, IR Iran
| | | | - Firoozeh Sajedi
- Pediatric Neurorehabilitation Research Center, University
of Social Welfare and Rehabilitation Sciences, Tehran, IR Iran
| | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and
Rehabilitation Sciences, Tehran, IR Iran
| | - Mostafa Najafi
- Genetics Research Center, University of Social Welfare and
Rehabilitation Sciences, Tehran, IR Iran
| | | | - Yousef Shafeghati
- Genetics Research Center, University of Social Welfare and
Rehabilitation Sciences, Tehran, IR Iran
- Sarem Cell Research Center, Sarem Hospital, Tehran, IR
Iran
| | - Fatemeh Behnia
- Department of Occupational Therapy, University of Social
Welfare and Rehabilitation Sciences, Tehran, IR Iran
| | | | | | | | - Zahra Hadipour
- Sarem Cell Research Center, Sarem Hospital, Tehran, IR
Iran
| | | | | | - Hossein Darvish
- Department of Medical Genetics, Shahid Beheshti University
of Medical Sciences, Tehran, IR Iran
| | - Ideh Bahman
- Genetics Research Center, University of Social Welfare and
Rehabilitation Sciences, Tehran, IR Iran
| | | | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and
Rehabilitation Sciences, Tehran, IR Iran
| | - Roshanak Vameghi
- Pediatric Neurorehabilitation Research Center, University
of Social Welfare and Rehabilitation Sciences, Tehran, IR Iran
- Corresponding author: Roshanak Vameghi, Pediatric
Neurorehabilitation Research Center, University of Social Welfare and Rehabilitation
Sciences, Tehran, IR Iran. Tel/Fax: +9821-22180099, E-mail:
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dos Santos SR, Freire-Maia DV. Absence of subtelomeric rearrangements in selected patients with mental retardation as assessed by multiprobe T FISH. J Negat Results Biomed 2012; 11:16. [PMID: 23259705 PMCID: PMC3546875 DOI: 10.1186/1477-5751-11-16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2012] [Accepted: 12/18/2012] [Indexed: 12/08/2022] Open
Abstract
Background Mental retardation (MR) is a heterogeneous condition that affects 2-3% of the general population and is a public health problem in developing countries. Chromosomal abnormalities are an important cause of MR and subtelomeric rearrangements (STR) have been reported in 4-35% of individuals with idiopathic MR or an unexplained developmental delay, depending on the screening tests and patient selection criteria used. Clinical checklists such as that suggested by de Vries et al. have been used to improve the predictive value of subtelomeric screening. Findings Fifteen patients (1–20 years old; five females and ten males) with moderate to severe MR from a genetics outpatient clinic of the Gaffrée and Guinle Teaching Hospital (HUGG) of the Federal University of Rio de Janeiro State (UNIRIO) were screened with Multiprobe T FISH after normal high resolution karyotyping. No subtelomeric rearrangements were detected even though the clinical score of the patients ranged from four to seven. Conclusion In developing countries, FISH-based techniques such as Multiprobe T FISH are still expensive. Although Multiprobe T FISH is a good tool for detecting STR, in this study it did not detect STR in patients with unexplained MR/developmental delay even though these patients had a marked chromosomal imbalance. Our findings also show that clinical scores are not reliable predictors of STR.
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Affiliation(s)
- Suely Rodrigues dos Santos
- Department of Genetics and Molecular Biology, Federal University of Rio de Janeiro State (DGBM-UNIRIO), Rio de Janeiro, RJ, Brazil.
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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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Valero MC, Martín Y, Hernández-Imaz E, Marina Hernández A, Meleán G, Valero AM, Javier Rodríguez-Álvarez F, Tellería D, Hernández-Chico C. A highly sensitive genetic protocol to detect NF1 mutations. J Mol Diagn 2011; 13:113-22. [PMID: 21354044 DOI: 10.1016/j.jmoldx.2010.09.002] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2010] [Revised: 08/02/2010] [Accepted: 09/21/2010] [Indexed: 12/30/2022] Open
Abstract
Neurofibromatosis type 1 (NF1) is a hereditary disorder caused by mutations in the NF1 gene. Detecting mutation in NF1 is hindered by the gene's large size, the lack of mutation hotspots, the presence of pseudogenes, and the wide variety of possible lesions. We developed a method for detecting germline mutations by combining an original RNA-based cDNA-PCR mutation detection method and denaturing high-performance liquid chromatography (DHPLC) with multiplex ligation-dependent probe amplification (MLPA). The protocol was validated in a cohort of 56 blood samples from NF1 patients who fulfilled NIH diagnostic criteria, identifying the germline mutation in 53 cases (95% sensitivity). The efficiency and reliability of this approach facilitated detection of different types of mutations, including single-base substitutions, deletions or insertions of one to several nucleotides, microdeletions, and changes in intragenic copy number. Because mutational screening for minor lesions was performed using cDNA and the characterization of mutated alleles was performed at both the RNA and genomic DNA level, the analysis provided insight into the nature of the different mutations and their effect on NF1 mRNA splicing. After validation, we implemented the protocol as a routine test. Here we present the overall unbiased spectrum of NF1 mutations identified in 93 patients in a cohort of 105. The results indicate that this protocol is a powerful new tool for the molecular diagnosis of NF1.
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Affiliation(s)
- María Carmen Valero
- Molecular Genetics Unit, University Hospital Ramón y Cajal, Institute of Health Research, IRYCIS, Madrid, Spain
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Cáceres A, Armengol L, Villatoro S, González JR. MLPAstats: an R GUI package for the integrated analysis of copy number alterations using MLPA data. BMC Bioinformatics 2011; 12:147. [PMID: 21682923 PMCID: PMC3118163 DOI: 10.1186/1471-2105-12-147] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Accepted: 05/11/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Multiplex-Dependent Probe Amplification (MLPA) is a cost-effective experimental method for candidate gene studies, aimed at the identification of copy number alterations. The analysis of such genetic variants, from electropherogram peak intensities, involves two main stages. First, peak normalization for each probe is required to remove the contribution of probe size to peak intensity. Second, the statistical significance of peak alteration between case and control samples is estimated. A number of methods have been proposed in each step with varying levels of complexity and precision. However, there is no single framework from which the results of each method and possible combinations at each step can be assessed. RESULTS We present MLPAstats, an R package designed to integrate the methods for exploring different analysis scenarios in a reliable way. A GUI has been developed to allow researchers to find their optimal analysis strategy. CONCLUSIONS MLPAstats is an analysis tool that promotes the use of cost-effective MLPA suitable for candidate gene studies. Its R implementation allows future methods to be easily incorporated, while its GUI will facilitate its use by non-expert analysts. A vignette describing a set-by-step tutorial is also available with the package.
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Affiliation(s)
- Alejandro Cáceres
- Center for Research in Environmental Epidemiology, Doctor Aiguader 88, Barcelona 08003, Spain.
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12
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Lincoln-de-Carvalho CR, Vicente FMP, Vieira TAP, de Mello MP, Marques-de-Faria AP. A de novo cryptic 5p deletion and 9p duplication detected by subtelomeric MLPA in a boy with cri du chat syndrome. Am J Med Genet A 2011; 155A:450-4. [PMID: 21271672 DOI: 10.1002/ajmg.a.33458] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Carolina R Lincoln-de-Carvalho
- Department of Medical Genetics, School of Medical Sciences, State University of Campinas (UNICAMP), Campinas, SP, Brazil
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Comprehensive copy number variant (CNV) analysis of neuronal pathways genes in psychiatric disorders identifies rare variants within patients. J Psychiatr Res 2010; 44:971-8. [PMID: 20398908 DOI: 10.1016/j.jpsychires.2010.03.007] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2010] [Revised: 03/12/2010] [Accepted: 03/16/2010] [Indexed: 01/11/2023]
Abstract
BACKGROUND Copy number variations (CNV) have become an important source of human genome variability noteworthy to consider when studying genetic susceptibility to complex diseases. As recent studies have found evidences for the potential involvement of CNVs in psychiatric disorders, we have studied the dosage effect of structural genome variants as a possible susceptibility factor for different psychiatric disorders in a candidate gene approach. METHODS After selection of 68 psychiatric disorders' candidate genes overlapping with CNVs, MLPA assays were designed to determine changes in copy number of these genes. The studied sample consisted of 724 patients with psychiatric disorders (accounting for anxiety disorders, mood disorders, eating disorders and schizophrenia) and 341 control individuals. RESULTS CNVs were detected in 30 out of the 68 genes screened, indicating that a considerable proportion of neuronal pathways genes contain CNVs. When testing the overall burden of rare structural genomic variants in the different psychiatric disorders compared to control individuals, there was no statistically significant difference in the total amount of gains and losses. However, 14 out of the 30 changes were only found in psychiatric disorder patients but not in control individuals. These genes include GRM7, previously associated to major depression disorder and bipolar disorder, SLC6A13, in anxiety disorders, and S100B, SSTR5 and COMT in schizophrenia. CONCLUSIONS Although we have not been able to found a clear association between the studied CNVs and psychiatric disorders, the rare variants found only within the patients could account for a step further towards understanding the pathophysiology of psychiatric disorders.
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Hila L, Tébourbi H, Abeid L, Rejeb I, Chaabouni H. Subtelomeric microduplications in three sisters with moderate mental retardation. Biochem Genet 2010; 48:909-14. [PMID: 20811773 DOI: 10.1007/s10528-010-9371-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2008] [Accepted: 04/26/2010] [Indexed: 11/26/2022]
Abstract
Copy number changes of subtelomeric regions are a common cause of mental retardation, occurring in approximately 5% of mentally retarded patients. New molecular techniques allow the identification of subtelomeric microduplications. We report a Tunisian family of three sisters with moderate mental retardation, facial dysmorphism, cardiopathy, and bilateral clinodactyly of the third and fourth toes, explored by MLPA, showing the same associated microduplications, 15q and Xq, without a concurrent deletion.
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Affiliation(s)
- Lamia Hila
- Faculté de Médecine de Tunis, Laboratoire de Génétique Humaine, Tunisia.
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Use of Multiplex Ligation-Dependent Probe Amplification (MLPA) in screening of subtelomeric regions in children with idiopathic mental retardation. Indian J Pediatr 2009; 76:1027-31. [PMID: 19907935 DOI: 10.1007/s12098-009-0218-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/16/2009] [Accepted: 04/09/2009] [Indexed: 10/20/2022]
Abstract
OBJECTIVE To detect subtelomeric copy number variations (deletions and duplications) using Multiplex Ligation-Dependent Probe Amplification (MLPA) technique in children with idiopathic mental retardation. METHODS All children presenting to the genetics out-patient department for evaluation of mental retardation or developmental delay over a period of two years, for whom no identifiable cause could be found by clinical evaluation, karyotyping, neuroimaging and other relevant investigations. RESULTS In the present study, two cases deletions and one case of duplication were detected amongst 65 cases with idiopathic mental retardation/ global developmental delay. The overall detection rate is 4.6%. The detection rate is higher (13%) in children with facial dysmorphism. CONCLUSION MLPA for subtelomeric regions is recommended for evaluation of children with idiopathic mental retardation/ global developmental delay were included in the study.
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MLPA subtelomere analysis in Tunisian mentally retarded patients. Biochem Genet 2009; 47:727-33. [PMID: 19590834 DOI: 10.1007/s10528-009-9271-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2008] [Accepted: 06/24/2009] [Indexed: 12/08/2022]
Abstract
Subtelomeric rearrangements significantly contribute to idiopathic mental retardation and result in several mental retardation syndromes; however, most subtelomeric defects lack a characteristic phenotype. Thirty patients with unexplained mental retardation, a normal R banded karyotype at the 550 band, and no clinically recognizable syndrome were screened by Multiplex ligation-dependent probe amplification (MLPA). Four anomalies were identified: deletion 17q, duplications (4q), and associated duplications 15q and Xq. This duplication was found in two sisters of the proband. Anomalies were unidentified by the conventional technique. The prevalence of subtelomeric imbalances in our cohort of moderate to severe mental retardation is around 13% and is consistent with the literature. The sensitivity of the MLPA technique was characterized on cytogenetically verified positive and negative controls. MLPA is a fast, reliable, and relatively inexpensive technique to detect subtelomeric rearrangement in comparison with the fluorescence in situ hybridization (FISH) technique.
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17
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Auber B, Bruemmer V, Zoll B, Burfeind P, Boehm D, Liehr T, Brockmann K, Wilichowski E, Argyriou L, Bartels I. Identification of subtelomeric genomic imbalances and breakpoint mapping with quantitative PCR in 296 individuals with congenital defects and/or mental retardation. Mol Cytogenet 2009; 2:10. [PMID: 19284615 PMCID: PMC2660352 DOI: 10.1186/1755-8166-2-10] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2009] [Accepted: 03/12/2009] [Indexed: 01/04/2023] Open
Abstract
Background Submicroscopic imbalances in the subtelomeric regions of the chromosomes are considered to play an important role in the aetiology of mental retardation (MR). The aim of the study was to evaluate a quantitative PCR (qPCR) protocol established by Boehm et al. (2004) in the clinical routine of subtelomeric testing. Results 296 patients with MR and a normal karyotype (500–550 bands) were screened for subtelomeric imbalances by using qPCR combined with SYBR green detection. In total, 17 patients (5.8%) with 20 subtelomeric imbalances were identified. Six of the aberrations (2%) were classified as causative for the symptoms, because they occurred either de novo in the patients (5 cases) or the aberration were be detected in the patient and an equally affected parent (1 case). The extent of the deletions ranged from 1.8 to approximately 10 Mb, duplications were 1.8 to approximately 5 Mb in size. In 6 patients, the copy number variations (CNVs) were rated as benign polymorphisms, and the clinical relevance of these CNVs remains unclear in 5 patients (1.7%). Therefore, the overall frequency of clinically relevant imbalances ranges between 2% and 3.7% in our cohort. Conclusion This study illustrates that the qPCR/SYBR green technique represents a rapid and versatile method for the detection of subtelomeric imbalances and the option to map the breakpoint. Thus, this technique is highly suitable for genotype/phenotype studies in patients with MR/developmental delay and/or congenital defects.
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Affiliation(s)
- Bernd Auber
- Institute of Human Genetics, Georg August University, Göttingen, Germany.
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18
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Terefework Z, Pham CL, Prosperi AC, Entius MM, Errami A, van Spanning RJM, Zaura E, Ten Cate JM, Crielaard W. MLPA diagnostics of complex microbial communities: relative quantification of bacterial species in oral biofilms. J Microbiol Methods 2008; 75:558-65. [PMID: 18824042 DOI: 10.1016/j.mimet.2008.08.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2008] [Revised: 08/01/2008] [Accepted: 08/29/2008] [Indexed: 11/27/2022]
Abstract
A multitude of molecular methods are currently used for identification and characterization of oral biofilms or for community profiling. However, multiplex PCR techniques that are able to routinely identify several species in a single assay are not available. Multiplex Ligation-dependent Probe Amplification (MLPA) identifies up to 45 unique fragments in a single tube PCR. Here we report a novel use of MLPA in the relative quantification of targeted microorganisms in a community of oral microbiota. We designed 9 species specific probes for: Actinomyces gerencseriae, Actinomyces naeslundii, Actinomyces odontolyticus, Candida albicans, Lactobacillus acidophilus, Rothia dentocariosa, Streptococcus mutans, Streptococcus sanguinis and Veillonella parvula; and genus specific probes for selected oral Streptococci and Lactobacilli based on their 16S rDNA sequences. MLPA analysis of DNA pooled from the strains showed the expected specific MLPA products. Relative quantification of a serial dilution of equimolar DNA showed that as little as 10 pg templates can be detected with clearly discernible signals. Moreover, a 2 to 7% divergence in relative signal ratio of amplified probes observed from normalized peak area values suggests MLPA can be a cheaper alternative to using qPCR for quantification. We observed 2 to 6 fold fluctuations in signal intensities of MLPA products in DNAs isolated from multispecies biofilms grown in various media for various culture times. Furthermore, MLPA analyses of DNA isolated from saliva obtained from different donors gave a varying number and intensity of signals. This clearly shows the usefulness of MLPA in a quantitative description of microbial shifts.
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Affiliation(s)
- Zewdu Terefework
- Department of Cariology, Endodontology, Pedodontology, Academic Centre for Dentistry Amsterdam, University of Amsterdam and VU University Amsterdam, The Netherlands.
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19
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González JR, Carrasco JL, Armengol L, Villatoro S, Jover L, Yasui Y, Estivill X. Probe-specific mixed-model approach to detect copy number differences using multiplex ligation-dependent probe amplification (MLPA). BMC Bioinformatics 2008; 9:261. [PMID: 18522760 PMCID: PMC2492880 DOI: 10.1186/1471-2105-9-261] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2008] [Accepted: 06/04/2008] [Indexed: 11/10/2022] Open
Abstract
Background MLPA method is a potentially useful semi-quantitative method to detect copy number alterations in targeted regions. In this paper, we propose a method for the normalization procedure based on a non-linear mixed-model, as well as a new approach for determining the statistical significance of altered probes based on linear mixed-model. This method establishes a threshold by using different tolerance intervals that accommodates the specific random error variability observed in each test sample. Results Through simulation studies we have shown that our proposed method outperforms two existing methods that are based on simple threshold rules or iterative regression. We have illustrated the method using a controlled MLPA assay in which targeted regions are variable in copy number in individuals suffering from different disorders such as Prader-Willi, DiGeorge or Autism showing the best performace. Conclusion Using the proposed mixed-model, we are able to determine thresholds to decide whether a region is altered. These threholds are specific for each individual, incorporating experimental variability, resulting in improved sensitivity and specificity as the examples with real data have revealed.
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Affiliation(s)
- Juan R González
- Center for research in environmental epidemiology (CREAL), Barcelona, Spain.
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Joshi VA, Mancini-DiNardo D, Funke BH. Selection of a platform for mutation detection. ACTA ACUST UNITED AC 2008; Chapter 7:Unit 7.15. [PMID: 18428425 DOI: 10.1002/0471142905.hg0715s56] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
New mutation detection technologies must keep pace by becoming more cost-effective while offering improved technical sensitivity and higher throughput capacity. In recent years, the number of mutation detection platforms available to the clinical researcher has grown to a point where it is difficult to keep track of all available options as well as their benefits and pitfalls. This unit provides an entry point for a variety of researchers who wish to analyze samples for known or novel mutations and need to determine which platform is most suited for their particular needs. A practical guide is provided in this unit, including a brief overview, information on assay parameters, design and cost considerations, as well as platform flexibility and scalability of the assay. Although the focus here is on applications involving human disease, many of these platforms can be easily adapted to the study of other organisms.
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Affiliation(s)
- Victoria A Joshi
- Harvard Medical School-Partners Healthcare Center for Genetics and Genomics, Cambridge, Massachusetts, USA
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Chou LS, Lyon E, Mao R. Molecular diagnosis utility of multiplex ligation-dependent probe amplification. ACTA ACUST UNITED AC 2008; 2:373-85. [DOI: 10.1517/17530059.2.4.373] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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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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Huang JS, Huang CJ, Chen SK, Chien CC, Chen CW, Lin CM. Associations between VHL genotype and clinical phenotype in familial von Hippel-Lindau disease. Eur J Clin Invest 2007; 37:492-500. [PMID: 17537157 DOI: 10.1111/j.1365-2362.2007.01806.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BACKGROUND Von Hippel-Lindau (VHL) disease is an autosomal dominant hereditary disorder associated with tumours and cysts in the central nervous system (CNS) and other visceral organs. Germline mutations in the VHL gene on chromosome 3p25-26 are considered the cause of this disease. MATERIALS AND METHODS We studied six patients with VHL disease and their relatives. Loss of heterozygosity (LOH) was determined by five flanking microsatellite polymorphic markers in the VHL locus. Multiplex ligation-dependent probe amplification (MLPA) and quantitative real-time polymerase chain reaction (qPCR) amplification were used to detect the genomic deletions. Single-strand conformation polymorphism (SSCP) analysis was applied to test for sequence variations. RESULTS Three germline deletions in the VHL gene (142.9, 53.3 and 3.3 kb) were found by MLPA. These deletions were defined clearly by qPCR analyses. The142.9 kb germline deletion was significantly associated with patients with CNS haemangioblastomas (P < 0.01 by Fisher's exact test), and one missense mutation (Gln209Arg) was detected from a patient with a pancreatic cyst in the same family. LOH was also detected from a patient with bilateral renal cell carcinomas. CONCLUSION Diverse genetic conditions are associated with the clinical manifestations of VHL disease. Genomic deletions that can be detected by MLPA or qPCR are major causes for this syndrome. Missense mutations and LOH accompanying the disease lead to complex clinical symptoms and genotypic determination can facilitate a clinical diagnosis because of their strong association.
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Affiliation(s)
- J S Huang
- Department of Neurosurgery, Cathay General Hospital, Taipei, Taiwan
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Holtkamp N, Ziegenhagen N, Malzer E, Hartmann C, Giese A, von Deimling A. Characterization of the amplicon on chromosomal segment 4q12 in glioblastoma multiforme. Neuro Oncol 2007; 9:291-7. [PMID: 17504929 PMCID: PMC1907422 DOI: 10.1215/15228517-2007-009] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
A subset of glioblastomas (GBMs) carry gene amplifications on chromosomal segment 4q12. To characterize this amplicon in detail, we analyzed a set of 100 samples consisting of 65 GBMs, 10 WHO grade III astrocytomas, 12 oligodendrogliomas, and 13 glioma cell cultures. We applied multiplex ligation-dependent probe amplification to determine the gene dosage of PDGFRA, KIT, and KDR and the flanking genes USP46, RASL11B, LNX1, CHIC2, SEC3L1, and IGFBP7. The amplicon was highly variable in size and copy number and extended over a region of up to 5 Mb. Amplifications on 4q12 were observed in 15% of GBMs and 23% of GBM cell cultures but not in 22 other gliomas. We analyzed transcription and translation of some genes within this amplicon. Gene amplification generally correlated with high transcript levels but did not necessarily result in increased protein levels. However, we detected frequent expression of proteins encoded by PDGFRA, KIT, and KDR in GBMs and GBM cell cultures independent of the amplification status. Future treatment of GBM patients may include drugs targeting multiple kinases that are encoded by genes on chromosomal segment 4q12.
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Affiliation(s)
| | | | | | | | | | - Andreas von Deimling
- Address correspondence to Andreas von Deimling, Department of Neuropathology, Ruprecht-Karls-Universität, Im Neuenheimer Feld 220, 69120 Heidelberg, Germany (
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Lugtenberg D, JC Hamel B, van Bokhoven H, PM de Brouwer A. Strategies for present and future mental retardation diagnosis. FUTURE NEUROLOGY 2006. [DOI: 10.2217/14796708.1.6.775] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mental retardation (MR) is a highly heterogeneous condition with a prevalence of 1–3% in the general population. The psychosocial burden on families with mentally handicapped children is extensive. In addition, the accompanying expenses with mental handicaps are considerable. In this review a comprehensive strategy to systematically identify the causative genetic defect in patients with mental retardation is proposed. This strategy is a combination of routinely used and recently developed approaches, such as direct DNA sequencing, single nucleotide polymorphism arrays and expression profiling, to establish a molecular diagnosis in MR patients. Finally, it will be described how these mutations can be studied in different model systems, which can eventually be used to elucidate the neurobiological basis of MR and to facilitate possible therapeutic intervention.
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Affiliation(s)
- Dorien Lugtenberg
- Radboud University, Department of Human Genetics, Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Ben JC Hamel
- Radboud University, Department of Human Genetics, Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Hans van Bokhoven
- Radboud University, Department of Human Genetics, Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Arjan PM de Brouwer
- Radboud University, Department of Human Genetics, Nijmegen Medical Centre, PO Box 9101, 6500 HB Nijmegen, The Netherlands
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