1
|
Kriek M, Knijnenburg J, White SJ, Rosenberg C, den Dunnen JT, van Ommen GJB, Tanke HJ, Breuning MH, Szuhai K. Diagnosis of genetic abnormalities in developmentally delayed patients: a new strategy combining MLPA and array-CGH. Am J Med Genet A 2007; 143A:610-4. [PMID: 17318845 DOI: 10.1002/ajmg.a.31593] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Marjolein Kriek
- Center for Human and Clinical Genetics, Leiden University Medical Center, RC Leiden, The Netherlands.
| | | | | | | | | | | | | | | | | |
Collapse
|
2
|
Murthy SK, Nygren AOH, El Shakankiry HM, Schouten JP, Al Khayat AI, Ridha A, Al Ali MT. Detection of a novel familial deletion of four genes between BP1 and BP2 of the Prader-Willi/Angelman syndrome critical region by oligo-array CGH in a child with neurological disorder and speech impairment. Cytogenet Genome Res 2007; 116:135-40. [PMID: 17268193 DOI: 10.1159/000097433] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2006] [Accepted: 06/05/2006] [Indexed: 01/06/2023] Open
Abstract
Two common classes of deletions are described in the literature in individuals with Prader-Willi/Angelman syndrome (PWS/AS): one between breakpoint 1 (BP1) to BP3 and the other between BP2 to BP3 of the PWS/AS critical region on chromosome 15q11-->q13. We present here a novel observation of an approximately 253-kb deletion between BP1 and BP2 on 15q11.2, in a 3(1/2)-year-old boy, who was referred to us with a clinical suspicion of having Angelman syndrome and presenting with mental retardation, neurological disorder, developmental delay and speech impairment. Karyotype and FISH results were found to be normal. The microdeletion between BP1 and BP2 includes four genes - NIPA1, NIPA2, CYFIP1 and TUBGCP5 which was detected by a high-resolution oligonucleotide array-CGH that was further validated by a Multiplex Ligation-dependent Probe Amplification (MLPA) assay. The same deletion was observed in the father who presented with similar but relatively milder clinical features as compared to the affected son. Methylation studies by methylation-specific MLPA (MS-MLPA) of the SNRPN imprinting center (IC) showed a normal imprinting pattern, both in the patient and the father. To our knowledge a microdeletion limited only to the BP1-BP2 region has not yet been reported. The familial genetic alteration together with the striking clinical presentation in this study are interesting, but from our single case study it is difficult to suggest if the deletion is causative of some of the abnormal features or if it is a normal variant. The study however further strengthens the fact that genome-wide analysis by array CGH in individuals with developmental delay and mental retardation is very useful in detecting such hidden interstitial chromosomal rearrangements.
Collapse
Affiliation(s)
- S K Murthy
- Genetics Department, Al Wasl Hospital, DOHMS, Dubai, UAE.
| | | | | | | | | | | | | |
Collapse
|
3
|
Hwang KS, Pearson MA, Stankiewicz P, Lennon PA, Cooper ML, Wu J, Ou Z, Cai WW, Patel A, Cheung SW. Cryptic unbalanced translocation t(17;18)(p13.2;q22.3) identified by subtelomeric FISH and defined by array-based comparative genomic hybridization in a patient with mental retardation and dysmorphic features. Am J Med Genet A 2005; 137:88-93. [PMID: 16015583 DOI: 10.1002/ajmg.a.30858] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Molecular cytogenetics allows the identification of cryptic chromosome rearrangements, which is clinically useful in mentally retarded and/or dysmorphic individuals with normal results from conventional cytogenetics analysis. We report on a 3-year-old girl with mental retardation, growth deficiency, speech delay, and dysmorphic features including hypertelorism, upslanting palpebral fissures, midfacial hypoplasia, and posteriorly rotated ears. The G-banding analysis showed a 46,XX,t(3;8)(q26.2;p21.1)mat karyotype. However, her clinical features were suggestive of the 18q syndrome. Subtelomeric FISH analysis revealed a der(18) translocated material from chromosome 17. Array-based comparative genomic hybridization (array-CGH) with subtelomeric BAC and PAC clones confirmed the abnormality and refined the breakpoints to 18q22.3-qter and 17p13.2-pter (deletion of 8.5 Mb and duplication of 3.9 Mb, respectively). This case demonstrates the diagnostic utility of combining conventional cytogenetics with molecular chromosome analyses for the identification of subtle chromosome abnormalities.
Collapse
MESH Headings
- Abnormalities, Multiple/genetics
- Abnormalities, Multiple/pathology
- Child, Preschool
- Chromosome Banding
- Chromosomes, Human, Pair 17/genetics
- Chromosomes, Human, Pair 18/genetics
- Face/abnormalities
- Female
- Genome, Human
- Humans
- In Situ Hybridization, Fluorescence/methods
- Intellectual Disability/pathology
- Karyotyping
- Nucleic Acid Hybridization/methods
- Syndrome
- Telomere/genetics
- Translocation, Genetic
Collapse
Affiliation(s)
- Kwei Shuai Hwang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
4
|
Miyagi M, Humphry M, Ma ZY, Lambrides CJ, Bateson M, Liu CJ. Construction of bacterial artificial chromosome libraries and their application in developing PCR-based markers closely linked to a major locus conditioning bruchid resistance in mungbean (Vigna radiata L. Wilczek). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2004; 110:151-6. [PMID: 15490104 DOI: 10.1007/s00122-004-1821-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2004] [Accepted: 09/12/2004] [Indexed: 05/03/2023]
Abstract
Bacterial artificial chromosome (BAC) libraries have been widely used in different aspects of genome research. In this paper we report the construction of the first mungbean (Vigna radiata L. Wilczek) BAC libraries. These BAC clones were obtained from two ligations and represent an estimated 3.5 genome equivalents. This correlated well with the screening of nine random single-copy restriction fragment length polymorphism probes, which detected on average three BACs each. These mungbean clones were successfully used in the development of two PCR-based markers linked closely with a major locus conditioning bruchid (Callosobruchus chinesis) resistance. These markers will be invaluable in facilitating the introgression of bruchid resistance into breeding programmes as well as the further characterisation of the resistance locus.
Collapse
Affiliation(s)
- M Miyagi
- CSIRO Plant Industry, Queensland Bioscience Precinct, 306 Carmody Road, Brisbane, QLD 4067, Australia
| | | | | | | | | | | |
Collapse
|
5
|
Souter VL, Glass IA, Chapman DB, Raff ML, Parisi MA, Opheim KE, Disteche CM. Multiple fetal anomalies associated with subtle subtelomeric chromosomal rearrangements. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2003; 21:609-615. [PMID: 12808681 DOI: 10.1002/uog.112] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We report two cases of multiple fetal anomalies detected by prenatal ultrasound and associated with subtle subtelomeric chromosomal rearrangements. The first case presented at 25 weeks of gestation with an enlarged cisterna magna and ventriculomegaly. Karyotyping of amniocytes showed a subtle terminal abnormality of chromosome 6q. Thereafter, screening of all unique chromosomal subtelomeric regions using a panel of telomere-specific, fluorescence in situ hybridization (FISH) probes revealed an unbalanced reciprocal translocation between 6q and 17p [46,XX.ish der(6)t(6;17)(q25.3;p13)(TelVysion6q-;TelVysion17p+)]. The second case presented at 25 weeks of gestation with tetralogy of Fallot and at 34 weeks of gestation had additional ultrasound findings of an arachnoid cyst and intrauterine growth restriction. Postnatal karyotyping of peripheral blood was performed and appeared normal. However, a cryptic deletion of the subtelomeric region of the long arm of chromosome 14 was identified when the infant's blood sample was used as a control for an oncology FISH probe. Thereafter, screening of all unique chromosomal subtelomeric regions using a panel of telomere-specific FISH probes revealed an unbalanced reciprocal translocation of chromosomes 14q and 20p [46,XY.ish der(14)t(14;20)(q32.3;p13)(IGH-, D14S308-,TelVysion20p+)mat]. These two cases add to a growing number of reports of cryptic subtelomeric chromosomal rearrangements associated with congenital anomalies. This is the first report of multiple, simultaneous FISH screening of the subtelomeric regions in amniotic fluid and has demonstrated the technical feasibility of this technique in the prenatal period.
Collapse
Affiliation(s)
- V L Souter
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98105-0371, USA.
| | | | | | | | | | | | | |
Collapse
|
6
|
Abstract
Prenatal chromosome diagnosis has been a rapidly changing field over the past 10 years for both sampling methodologies and molecular techniques to complement chromosome analysis. This review summarizes current techniques used by the clinician and their risks, and selected aspects of cytogenetic and molecular techniques used by the laboratories. Within the next 3 to 5 years, DNA techniques are expected to complement, and potentially replace, aspects of current cytogenetic and FISH techniques, and provide more detailed information on the genetic status of the fetus.
Collapse
Affiliation(s)
- Alan E Donnenfeld
- Genzyme Genetics, Department of Obstetrics and Gynecology, Drexel University College of Medicine, 819 Locust Street, Philadelphia, PA 19107, USA.
| | | |
Collapse
|
7
|
Xu J, Chen Z. Advances in molecular cytogenetics for the evaluation of mental retardation. AMERICAN JOURNAL OF MEDICAL GENETICS. PART C, SEMINARS IN MEDICAL GENETICS 2003; 117C:15-24. [PMID: 12561054 DOI: 10.1002/ajmg.c.10016] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
Recent years have witnessed rapid advances in molecular cytogenetics and its impact in studying mental retardation (MR). We review new molecular cytogenetic methods, including interphase fluorescence in situ hyrbridization (FISH), comparative genomic hybridization (CGH), multicolor karyotyping, telomere FISH, primed in situ labeling (PRINS), genotyping, microdissection, and microarray for the evaluation of MR. These new methods are very useful in two major aspects: further characterization of chromosome abnormalities as detected with routine banding analysis, including additions, duplications, deletions, translocations, markers, or complex aberrations; and screening for "hidden" chromosome aberrations in patients with an apparently normal karyotype. These new methods have great diagnostic potential in prenatal, postnatal, and preimplantational settings. Although powerful, at this point, they are primarily research tools in nature. It is essential that these new methods be used in conjunction with standard methods in order to maximize obtainable information for better management of patients with MR.
Collapse
Affiliation(s)
- Jie Xu
- McMaster University Medical Center 3N14, 1200 Main Street W., Hamilton, Ontario L8S 4J9, Canada.
| | | |
Collapse
|
8
|
Affiliation(s)
- Laird Jackson
- Department of Obstetrics and Gynecology, MCP Hahnemann University, Philadelphia, Pennsylvania 19107, USA.
| |
Collapse
|
9
|
Veltman JA, Schoenmakers EFPM, Eussen BH, Janssen I, Merkx G, van Cleef B, van Ravenswaaij CM, Brunner HG, Smeets D, van Kessel AG. High-throughput analysis of subtelomeric chromosome rearrangements by use of array-based comparative genomic hybridization. Am J Hum Genet 2002; 70:1269-76. [PMID: 11951177 PMCID: PMC447601 DOI: 10.1086/340426] [Citation(s) in RCA: 160] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2001] [Accepted: 02/25/2002] [Indexed: 12/08/2022] Open
Abstract
Telomeric chromosome rearrangements may cause mental retardation, congenital anomalies, and miscarriages. Automated detection of subtle deletions or duplications involving telomeres is essential for high-throughput diagnosis, but impossible when conventional cytogenetic methods are used. Array-based comparative genomic hybridization (CGH) allows high-resolution screening of copy number abnormalities by hybridizing differentially labeled test and reference genomes to arrays of robotically spotted clones. To assess the applicability of this technique in the diagnosis of (sub)telomeric imbalances, we here describe a blinded study, in which DNA from 20 patients with known cytogenetic abnormalities involving one or more telomeres was hybridized to an array containing a validated set of human-chromosome-specific (sub)telomere probes. Single-copy-number gains and losses were accurately detected on these arrays, and an excellent concordance between the original cytogenetic diagnosis and the array-based CGH diagnosis was obtained by use of a single hybridization. In addition to the previously identified cytogenetic changes, array-based CGH revealed additional telomere rearrangements in 3 of the 20 patients studied. The robustness and simplicity of this array-based telomere copy-number screening make it highly suited for introduction into the clinic as a rapid and sensitive automated diagnostic procedure.
Collapse
Affiliation(s)
- Joris A Veltman
- Department of Human Genetics, University Medical Center Nijmegen, Nijmegen, The Netherlands.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
10
|
Abstract
An increasing number of human diseases are recognized to result from recurrent DNA rearrangements involving unstable genomic regions. These are termed genomic disorders, in which the clinical phenotype is a consequence of abnormal dosage of gene(s) located within the rearranged genomic fragments. Both inter- and intrachromosomal rearrangements are facilitated by the presence of region-specific low-copy repeats (LCRs) and result from nonallelic homologous recombination (NAHR) between paralogous genomic segments. LCRs usually span approximately 10-400 kb of genomic DNA, share >or= 97% sequence identity, and provide the substrates for homologous recombination, thus predisposing the region to rearrangements. Moreover, it has been suggested that higher order genomic architecture involving LCRs plays a significant role in karyotypic evolution accompanying primate speciation.
Collapse
Affiliation(s)
- Paweł Stankiewicz
- Dept Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030-3498, USA
| | | |
Collapse
|
11
|
Lee C, Lemyre E, Miron PM, Morton CC. Multicolor fluorescence in situ hybridization in clinical cytogenetic diagnostics. Curr Opin Pediatr 2001; 13:550-5. [PMID: 11753105 DOI: 10.1097/00008480-200112000-00010] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Multicolor fluorescence in situ hybridization is a technology that has vastly expanded the diagnostic repertoire of the clinical cytogenetics laboratory. The limitations of conventional chromosome banding analysis can often be overcome by the high sensitivity and specificity of multicolor fluorescence in situ hybridization tests. This article reviews the latest multicolor fluorescence in situ hybridization tests (including multiplex fluorescence in situ hybridization, spectral karyotyping, cross-species color banding, and comparative genomic hybridization) that are currently limited to a few select clinical cytogenetic laboratories, but may soon have more dominant roles in clinical cytogenetic practice.
Collapse
Affiliation(s)
- C Lee
- Department of Pathology, Brigham and Women's Hospital, Boston Massachusetts, USA.
| | | | | | | |
Collapse
|
12
|
Fauth C, Speicher MR. Classifying by colors: FISH-based genome analysis. CYTOGENETICS AND CELL GENETICS 2001; 93:1-10. [PMID: 11474168 DOI: 10.1159/000056937] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
In recent years a fascinating evolution of different multicolor fluorescence in situ hybridization (FISH) technologies could be witnessed. The various approaches to cohybridize multiple DNA probes in different colors opened new avenues for FISH-based automated karyotyping or the simultaneous analysis of multiple defined regions within the genome. These developments had a remarkable impact on microscopy design and the usage of highly sensitive area imagers. In addition, they led to the introduction of new fluorochromes with appropriate filter combinations, refinements of hybridization protocols, novel probe sets, and innovative software for automated chromosome analysis. This paper attempts to summarize the various multicolor approaches and discusses the application of the individual technologies.
Collapse
Affiliation(s)
- C Fauth
- Institut für Anthropologie und Humangenetik, Ludwig-Maximilians-Universität München, Goethestrasse 31, D-80336 Münich, Germany
| | | |
Collapse
|
13
|
Affiliation(s)
- D Baralle
- Department of Medical Genetics, Addenbrookes Hospital, CB2 5AQ, Cambridge, UK.
| |
Collapse
|
14
|
|