Array-Based Comparative Genomic Hybridization for the Genomewide Detection of Submicroscopic Chromosomal Abnormalities
Open accessAbstract
Microdeletions and microduplications, not visible by routine chromosome analysis, are a major cause of human malformation and mental retardation. Novel high-resolution, whole-genome technologies can improve the diagnostic detection rate of these small chromosomal abnormalities. Array-based comparative genomic hybridization allows such a high-resolution screening by hybridizing differentially labeled test and reference DNAs to arrays consisting of thousands of genomic clones. In this study, we tested the diagnostic capacity of this technology using approximately 3,500 flourescent in situ hybridization-verified clones selected to cover the genome with an average of 1 clone per megabase (Mb). The sensitivity and specificity of the technology were tested in normal-versus-normal control experiments and through the screening of patients with known microdeletion syndromes. Subsequently, a series of 20 cytogenetically normal patients with mental retardation and dysmorphisms suggestive of a chromosomal abnormality were analyzed. In this series, three microdeletions and two microduplications were identified and validated. Two of these genomic changes were identified also in one of the parents, indicating that these are large-scale genomic polymorphisms. Deletions and duplications as small as 1 Mb could be reliably detected by our approach. The percentage of false-positive results was reduced to a minimum by use of a dye-swap-replicate analysis, all but eliminating the need for laborious validation experiments and facilitating implementation in a routine diagnostic setting. This high-resolution assay will facilitate the identification of novel genes involved in human mental retardation and/or malformation syndromes and will provide insight into the flexibility and plasticity of the human genome.
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Microarray-based detection of structural variation and exome- and genome-wide sequencing have been pivotal for rare disease gene discovery, supported by in silico analysis and variant prioritization.
“Microarray-based detection of structural variation10 and exome-and genome-wide sequencing11,12 have been pivotal, bolstered by in silico analysis and prioritization of the discovered genetic variants.”
From A brief history of human disease genetics (2020) · cites this paper as [10]
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Development and validation of a CGH microarray for clinical cytogenetic diagnosis
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“F9 Hereditary neuropathy with liability to pressure ish del(17)(p12p12)(PMP22-) 5 5 0 Consistent”
BackgroundClinical Implementation of Chromosomal Microarray Analysis: Summary of 2513 Postnatal Cases
Lu, X., Shaw, C. A., Patel, A., Li, J., Cooper, M. L., Wells, W. R., Sullivan, C. M., Sahoo, T., Yatsenko, S. A., Bacino, C. A., et al. (2007) · PLoS ONE · doi:10.1371/journal.pone.0000327 · Cited by 248 · see citing works
“Using 1-Mb average coverage (3500 clones) BAC/PAC array analysis was shown to detect cryptic chromosomal imbalances in patients with idiopathic mental retardation and multiple congenital anomalies [12–14].”
BackgroundRosenberg, C., Knijnenburg, J., Bakker, E., Vianna‐Morgante, A. M., Sloos, W. C. R., Otto, P. A., Kriek, M., Hansson, K. B. M., Krepischi, A. C. V., Fiegler, H., et al. (2005) · Journal of Medical Genetics · doi:10.1136/jmg.2005.032268 · Cited by 236 · see citing works
Directly transmitted unbalanced chromosome abnormalities and euchromatic variants
Barber, J. C. K. (2005) · Journal of Medical Genetics · doi:10.1136/jmg.2004.026955 · Cited by 231 · see citing works
“148 149 Deletions, duplications, and copy number variation at the molecular level have been reviewed by Buckland, 193 and 1 Mb arrays are also providing evidence of large scale copy number variation.”
BackgroundFroyen, G., Corbett, M. A., Vandewalle, J., Järvelä, I. E., Lawrence, O., Meldrum, C. J., Bauters, M., Govaerts, K., Vandeleur, L., Esch, H. V., et al. (2008) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2007.11.002 · Cited by 223 · see citing works
Sagoo, G. S., Butterworth, A. S., Sanderson, S., Shaw-Smith, C. J., Higgins, J. P. T., & Burton, H. (2009) · Genetics in Medicine · doi:10.1097/gim.0b013e318194ee8f · Cited by 220 · see citing works
Gribble, S. M., Prigmore, E., Burford, D. C., Porter, K. M., Ng, B. L., Douglas, E. J., Fiegler, H., Carr, P., Kalaitzopoulos, D., Clegg, S., et al. (2005) · Journal of Medical Genetics · doi:10.1136/jmg.2004.024141 · Cited by 217 · see citing works
Copy number variations in neurodevelopmental disorders
Grayton, H. M., Fernandes, C., Rujescu, D., & Collier, D. A. (2012) · Progress in Neurobiology · doi:10.1016/j.pneurobio.2012.07.005 · Cited by 210 · see citing works
Schaeffer, A. J., Chung, J., Heretis, K., Wong, A., Ledbetter, D. H., & Martin, C. L. (2004) · The American Journal of Human Genetics · doi:10.1086/421250 · Cited by 207 · see citing works
Modena, P., Lualdi, E., Facchinetti, F., Veltman, J. A., Reid, J. F., Minardi, S. P., Janssen, I. M., Giangaspero, F., Forni, M., Finocchiaro, G., et al. (2006) · Journal of Clinical Oncology · doi:10.1200/jco.2006.06.3701 · Cited by 206 · see citing works
Self-citationSchoumans, J., Ruivenkamp, C., Holmberg, E., Kyllerman, M., Anderlid, B.-M., & Nordenskjöld, M. (2005) · Journal of Medical Genetics · doi:10.1136/jmg.2004.029637 · Cited by 205 · see citing works
Prenatal diagnosis of chromosomal abnormalities using array-based comparative genomic hybridization
Sahoo, T., Cheung, S. W., Ward, P. A., Darilek, S. A., Patel, A., del Gaudio, D., Kang, S. H. L., Lalani, S. R., Li, J., McAdoo, S. L., et al. (2006) · Genetics in Medicine · doi:10.1097/01.gim.0000245576.47154.63 · Cited by 204 · see citing works
COMPARATIVE GENOMIC HYBRIDIZATION
Pinkel, D., & Albertson, D. G. (2005) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev.genom.6.080604.162140 · Cited by 202 · see citing works
Molecular cytogenetic and rapid aneuploidy detection methods in prenatal diagnosis
Shaffer, L. G., & Bui, T. (2007) · American Journal of Medical Genetics Part C Seminars in Medical Genetics · doi:10.1002/ajmg.c.30114 · Cited by 201 · see citing works
“…with oligonucleotides [Lucito et al., 2003; Jobanputra et al., 2005; Friedman et al., 2006] or whole-genome tiling-path arrays utilizing BAC clones [Vissers et al., 2003; Ishkanian et al., 2004] can detect gains or losses of very short genomic segments (a few base pairs for oligonucleotide arrays…”
BackgroundThe array CGH and its clinical applications
Shinawi, M. S., & Cheung, S. W. (2008) · Drug Discovery Today · doi:10.1016/j.drudis.2008.06.007 · Cited by 200 · see citing works
Prenatal detection of unbalanced chromosomal rearrangements by array CGH
Rickman, L., Fiegler, H., Shaw-Smith, C., Nash, R., Cirigliano, V., Voglino, G., Ng, B. L., Scott, C., Whittaker, J., Adinolfí, M., et al. (2005) · Journal of Medical Genetics · doi:10.1136/jmg.2005.037648 · Cited by 200 · see citing works
Microarray‐based comparative genomic hybridization and its applications in human genetics
Oostlander, A., Meijer, G. A., & Ylstra, B. (2004) · Clinical Genetics · doi:10.1111/j.1399-0004.2004.00322.x · Cited by 198 · see citing works
“Array CGH can be used for the screening of known submicroscopic aberrations in human genetic diseases, as was described by the example of the PWS/AS, but this technique is also very suitable for the identification of yet unidentified abnormalities (29).”
BackgroundMethodInfluentialUse of targeted array‐based CGH for the clinical diagnosis of chromosomal imbalance: Is less more?
Bejjani, B. A., Saleki, R., Ballif, B. C., Rorem, E. A., Sundin, K., Theisen, A. P., Kashork, C. D., & Shaffer, L. G. (2005) · American Journal of Medical Genetics Part A · doi:10.1002/ajmg.a.30621 · Cited by 193 · see citing works
“…based upon previous reports in which 1.2 (log2 1.23¼ 0.3) and 0.8 (log2 0.81¼ 0.3) were selected as cut-off values based on experimental results of normal variation observed when two normal reference DNAs were co-hybridized to genomic microarrays [Hui et al., 2001; Vissers et al., 2003].”
MethodInfluentialMicroarray‐based CGH detects chromosomal mosaicism not revealed by conventional cytogenetics
Cheung, S. W., Shaw, C. A., Scott, D. A., Patel, A., Sahoo, T., Bacino, C. A., Pursley, A. N., Li, J., Erickson, R. P., Gropman, A. L., et al. (2007) · American Journal of Medical Genetics Part A · doi:10.1002/ajmg.a.31740 · Cited by 190 · see citing works
“The multiplex nature of aCGH is comparable to hundreds or to thousands of single locus FISH tests, which makes it highly efficient and cost effective [Vissers et al., 2003; Shaw-Smith et al., 2004; Menten et al., 2006].”
MethodWang, N. J., Liu, D., Parokonny, A. S., & Schanen, N. C. (2004) · The American Journal of Human Genetics · doi:10.1086/422854 · Cited by 180 · see citing works
“…comparative genomic hybridization (array CGH) has been used elsewhere to scan for genomic abnormalities at a 1-Mb resolution level, as well as at higher resolutions, for a single chromosome or smaller genomic region (Bruder et al. 2001; Hodgson et al. 2001; Vissers et al. 2003; Yu et al. 2003).”
MethodFroyen, G., Esch, H. V., Bauters, M., Hollanders, K., Frints, S. G. M., Vermeesch, J. R., Devriendt, K., Fryns, J., & Marynen, P. (2007) · Human Mutation · doi:10.1002/humu.20564 · Cited by 177 · see citing works
“…with MR, array-CGH screening for anomalies has been reported using subtelomeric arrays [Veltman et al., 2002], 1-Mb resolution full genome arrays [Vissers et al., 2003; ShawSmith et al., 2004; Schoumans et al., 2004; Menten et al., 2006], region- or topic-specific arrays [Van Buggenhout et al.,…”
MethodGuidelines for molecular karyotyping in constitutional genetic diagnosis
Vermeesch, J. R., Fiegler, H., de Leeuw, N., Szuhai, K., Schoumans, J., Ciccone, R., Speleman, F., Rauch, A. M., Clayton‐Smith, J., van Ravenswaaij‐Arts, C. M. A., et al. (2007) · European Journal of Human Genetics · doi:10.1038/sj.ejhg.5201896 · Cited by 175 · see citing works
Swinkels, M. E. M., Simons, A., Smeets, D., Vissers, L. E. L. M., Veltman, J. A., Pfundt, R., Vries, B. B. A. D., Faas, B. H. W., Schrander-Stumpel, C. T. R. M., McCann, E., et al. (2008) · American Journal of Medical Genetics Part A · doi:10.1002/ajmg.a.32310 · Cited by 170 · see citing works
“Deletion breakpoints were precisely mapped using a combination of cytogenetic and molecular techniques, including fluorescence in situ hybridization (FISH) and array-based comparative genomic hybridization (array CGH) [Vissers et al., 2003; de Vries et al., 2005].”
MethodSelf-citationA decade of structural variants: description, history and methods to detect structural variation
Escaramís, G., Docampo, E., & Rabionet, R. (2015) · Briefings in Functional Genomics · doi:10.1093/bfgp/elv014 · Cited by 170 · see citing works
“genomic hybridization (array-CGH) [9] and ROMA [10], it was finally possible to perform finer analysis of genome structural variation.”
MethodIdentification of disease genes by whole genome CGH arrays
Vissers, L. E. L. M., Veltman, J. A., van Kessel, A. G., & Brunner, H. G. (2005) · Human Molecular Genetics · doi:10.1093/hmg/ddi268 · Cited by 167 · see citing works
“High-density BAC arrays have recently been constructed with the aim to perform genome-wide copy number analyses, initially with a resolution of one clone per megabase (48,49) and now with a tiling resolution of approximately one clone per 100 kb (50).”
BackgroundMethodSelf-citationKoolen, D. A., Nillesen, W. M., Versteeg, M. H. A., Merkx, G. F. M., Knoers, N. V. A. M., Kets, M., Vermeer, S., van Ravenswaaij‐Arts, C. M. A., de Kovel, C. G. F., Brunner, H. G., et al. (2004) · Journal of Medical Genetics · doi:10.1136/jmg.2004.023671 · Cited by 161 · see citing works
Self-citationBaldwin, E. L., Lee, J.-Y., Blake, D. M., Bunke, B. P., Alexander, C. R., Kogan, A. L., Ledbetter, D. H., & Martin, C. L. (2008) · Genetics in Medicine · doi:10.1097/gim.0b013e318177015c · Cited by 159 · see citing works
Vissers, L. E. L. M., Vries, B. B. A. D., & Veltman, J. A. (2009) · Journal of Medical Genetics · doi:10.1136/jmg.2009.072942 · Cited by 156 · see citing works
Self-citationGenomic microarrays in mental retardation: A practical workflow for diagnostic applications
Koolen, D. A., Pfundt, R., de Leeuw, N., Hehir‐Kwa, J. Y., Nillesen, W. M., Neefs, I., Scheltinga, I., Sistermans, E. A., Smeets, D., Brunner, H. G., et al. (2008) · Human Mutation · doi:10.1002/humu.20883 · Cited by 154 · see citing works
“…almost all studies to compare the CNVs obtained, to collections of CNVs identified in unaffected control individuals, apart from the few studies that were published prior to the publication of widespread copy number variation in healthy individuals [Vissers et al., 2003; Shaw-Smith et al., 2004].”
BackgroundResultInfluentialSelf-citationMolecular Karyotyping: Array CGH Quality Criteria for Constitutional Genetic Diagnosis
Vermeesch, J. R., Melotte, C., Froyen, G., Vooren, S. V., Dutta, B., Maas, N. M. C., Vermeulen, S. J. T., Menten, B., Speleman, F., Moor, B. D., et al. (2005) · Journal of Histochemistry & Cytochemistry · doi:10.1369/jhc.4a6436.2005 · Cited by 154 · see citing works
“…far that use array CGH for the detection of constitutional chromosomal imbalances lack uniformity in addressing the quality of an array and identifying appropriate threshold values (Snijders et al. 2001; Vissers et al. 2003; Schaeffer et al. 2004; Schoumans et al. 2004; Shaw-Smith et al. 2004).”
BackgroundGenomic disorders 20 years on—mechanisms for clinical manifestations
Harel, T., & Lupski, J. R. (2017) · Clinical Genetics · doi:10.1111/cge.13146 · Cited by 142 · see citing works
“CMA was first introduced to the clinical diagnostic field in 2004, with arrays that contained bacterial artificial chromosome (BAC) clones corresponding to known clinically relevant microdeletion genomic intervals.(24) Rapid human genome advancements led to replacement of BAC clones with oligonucleotide sequences in t…”
MethodBuysse, K., Chiaie, B. D., Coster, R. V., Loeys, B., Paepe, A. D., Mortier, G. R., Speleman, F., & Menten, B. (2009) · European Journal of Medical Genetics · doi:10.1016/j.ejmg.2009.09.002 · Cited by 142 · see citing works
Medical applications of array CGH and the transformation of clinical cytogenetics
Shaffer, L. G., & Bejjani, B. A. (2006) · Cytogenetic and Genome Research · doi:10.1159/000095928 · Cited by 141 · see citing works
“Shaw-Smith et al. (2004) reported the study of 50 patients with learning disabilities and dysmorphic features using a genome-wide array with an average coverage similar to that of Vissers et al. (2003).”
BackgroundMethodInfluentialDhami, P., Coffey, A. J., Abbs, S. J., Vermeesch, J. R., Dumanski, J. P., Woodward, K. J., Andrews, R., Langford, C., & Vetrie, D. L. P. (2005) · The American Journal of Human Genetics · doi:10.1086/429588 · Cited by 143 · see citing works
“…measure from single copy-number losses or gains to high copy-number amplifications, as well as sufficient resolution and scalability for complete genomewide scans (Snijders et al. 2001; Fiegler et al. 2003; Vissers et al. 2003; Iafrate et al. 2004; Inazawa et al. 2004; Ishkanian et al. 2004).”
BackgroundA cytogeneticist's perspective on genomic microarrays
Shaffer, L. G. (2004) · Human Reproduction Update · doi:10.1093/humupd/dmh022 · Cited by 135 · see citing works
“With the development of microarrays that contain loci selected from the entire genome (Snijders et al., 2001; Vissers et al., 2003), much interest has been generated in providing this format for cytogenetic diagnosis.”
BackgroundMethodInfluentialMefford, H. C., Cooper, G. M., Zerr, T., Smith, J. D., Baker, C., Shafer, N., Thorland, E. C., Skinner, C., Schwartz, C. E., Nickerson, D. A., et al. (2009) · Genome Research · doi:10.1101/gr.094987.109 · Cited by 132 · see citing works
“This is particularly true for neurocognitive disorders like intellectual disability (ID), autism, and schizophrenia (Christian et al. 2008; de Vries et al. 2005; Friedman et al. 2006; International Schizophrenia Consortium 2008; Kirov et al. 2009; Kumar et al. 2008; Marshall et al. 2008; Rosenberg et al. 2006; Sebat e…”
BackgroundWagenstaller, J., Spranger, S., Lorenz‐Depiereux, B., Kazmierczak, B., Nathrath, M., Wahl, D., Heye, B., Gläser, D., Liebscher, V., Meitinger, T., et al. (2007) · The American Journal of Human Genetics · doi:10.1086/521274 · Cited by 132 · see citing works
Rajcan‐Separovic, E., Harvard, C., Liu, X., McGillivray, B. C., Hall, J. G., Qiao, Y., Hurlburt, J., Hildebrand, J., Mickelson, E. C. R., Holden, J. J. A., et al. (2006) · Journal of Medical Genetics · doi:10.1136/jmg.2006.045013 · Cited by 130 · see citing works
Feenstra, I., Vissers, L. E. L. M., Orsel, M., van Kessel, A. G., Brunner, H. G., Veltman, J. A., & van Ravenswaaij‐Arts, C. M. A. (2007) · American Journal of Medical Genetics Part A · doi:10.1002/ajmg.a.31850 · Cited by 130 · see citing works
“Array CGH was performed essentially as described before, with minor modifications [Vissers et al., 2003; de Vries et al., 2005].”
BackgroundMethodSelf-citationKrepischi, A. C. V., Vianna‐Morgante, A. M., Jehee, F. S., Passos‐Bueno, M. R., Knijnenburg, J., Szuhai, K., Sloos, W. C. R., Mazzeu, J. F., Kok, F., Cheroki, C., et al. (2006) · Cytogenetic and Genome Research · doi:10.1159/000095922 · Cited by 126 · see citing works
“Because of the limited number of patients initially described ( 400) (Vissers et al., 2003; Shaw-Smith et al., 2004; Schoumans et al., 2005; Tyson et al., 2005; Menten et al., 2006; Rosenberg et al., 2006), copy number alterations detected by array-CGH appeared to be distributed randomly across the…”
BackgroundInfluentialFeenstra, I., Fang, J., Koolen, D. A., Siezen, A., Evans, C. R., Winter, R. M., Lees, M. M., Riegel, M., Vries, B. B. A. D., van Ravenswaaij‐Arts, C. M. A., et al. (2005) · European Journal of Medical Genetics · doi:10.1016/j.ejmg.2005.10.131 · Cited by 124 · see citing works
“Moreover, the number of more or less unique chromosomal aberrations that are identified is rapidly increasing due to the development of new molecular and cytogenetic techniques such as multiplex ligation-dependent probe amplification (MPLA), multiplex amplifiable probe hybridisation (MAPH) and array-based comparative…”
BackgroundMolecular karyotyping using an SNP array for genomewide genotyping
Rauch, A. M., Rüschendorf, F., Huang, J., Trautmann, U., Becker, C., Thiel, C. T., Jones, K. W., Reis, A., & Nürnberg, P. (2004) · Journal of Medical Genetics · doi:10.1136/jmg.2004.022855 · Cited by 122 · see citing works
Lockwood, W. W., Chari, R., Chi, B., & Lam, W. L. (2005) · European Journal of Human Genetics · doi:10.1038/sj.ejhg.5201531 · Cited by 120 · see citing works
Hoyer, J., Dreweke, A., Becker, C., Göhring, I., Thiel, C. T., Peippo, M. M., Rauch, R., Hofbeck, M., Trautmann, U., Zweier, C., et al. (2007) · Journal of Medical Genetics · doi:10.1136/jmg.2007.050914 · Cited by 120 · see citing works
Roversi, G., Pfundt, R., Moroni, R. F., Magnani, I., van Reijmersdal, S. V., Pollo, B., Straatman, H., Larizza, L., & Schoenmakers, E. (2005) · Oncogene · doi:10.1038/sj.onc.1209177 · Cited by 118 · see citing works
“These boundaries were arbitrarily set by examining the results of the normal versus normal hybridizations and supported by the results of previously published work (Veltman et al., 2003a, b; Vissers et al., 2003).”
MethodResultSelf-citationDetection of Clinically Relevant Copy Number Variants with Whole-Exome Sequencing
de Ligt, J., Boone, P. M., Pfundt, R., Vissers, L. E. L. M., Richmond, T., Geoghegan, J. M., O'Moore, K., de Leeuw, N., Shaw, C. J., Brunner, H. G., et al. (2013) · Human Mutation · doi:10.1002/humu.22387 · Cited by 115 · see citing works
Self-citationHochstenbach, R., Buizer‐Voskamp, J. E., Vorstman, J. A. S., & Ophoff, R. A. (2011) · Cytogenetic and Genome Research · doi:10.1159/000332928 · Cited by 110 · see citing works
ten Berg, K., van Hasselt, P. M., Eleveld, M. J., van der Wijst, S. E., Hol, F. A., Vroede, M. D., Beemer, F. A., Hochstenbach, P. F. R., & Poot, M. (2007) · European Journal of Human Genetics · doi:10.1038/sj.ejhg.5201899 · Cited by 111 · see citing works
Treff, N. R., Tao, X., Schillings, W. J., Bergh, P. A., Scott, R. T., & Levy, B. (2011) · Fertility and Sterility · doi:10.1016/j.fertnstert.2011.04.038 · Cited by 111 · see citing works
Exome sequencing and whole genome sequencing for the detection of copy number variation
Hehir‐Kwa, J. Y., Pfundt, R., & Veltman, J. A. (2015) · Expert Review of Molecular Diagnostics · doi:10.1586/14737159.2015.1053467 · Cited by 109 · see citing works
“Although the clinical proof of principal of this array technology for neurodevelopmental disorders was already shown in 2003 [96,97], the first larger studies and consensus statements were published several years later in 2010 [5].”
ResultSelf-citationFiorentino, F., Caiazzo, F., Napolitano, S., Spizzichino, L., Bono, S., Sessa, M., Nuccitelli, A., Biricik, A., Gordon, A. T., Rizzo, G., et al. (2011) · Prenatal Diagnosis · doi:10.1002/pd.2884 · Cited by 109 · see citing works
Tyson, C., Harvard, C., Locker, R., Friedman, J. M., Langlois, S., Lewis, M. E. S., Allen, M. I. V., Somerville, M. J., Arbour, L. T., Clarke, L. A., et al. (2005) · American Journal of Medical Genetics Part A · doi:10.1002/ajmg.a.31015 · Cited by 107 · see citing works
“…has provided the opportunity to screen the whole genome for submicroscopic gains and losses [Pinkel et al., 1998; Albertson and Pinkel, 2003; Vissers et al., 2003; Shaw-Smith et al., 2004, for review see Oostlander et al., 2004; Salman et al., 2004; Shaffer and Bejjani, 2004; Smeets, 2004]…”
BackgroundThe impact of chromosomal rearrangements on regulation of gene expression
Harewood, L., & Fraser, P. (2014) · Human Molecular Genetics · doi:10.1093/hmg/ddu278 · Cited by 100 · see citing works
“Large cytogenetically visible rearrangements have been associated with numerous different syndromes, and the advent of technologies, such as comparative genomic hybridization (CGH) in the early 1990s (47) and later array-based CGH (48,49), allowed the discovery of further cytogenetically cryptic deletions and duplicat…”
BackgroundKoochek, M., Harvard, C., Hildebrand, M., Allen, M. I. V., Wingert, H., Mickelson, E. C. R., Holden, J., Rajcan‐Separovic, E., & Lewis, M. E. S. (2006) · Clinical Genetics · doi:10.1111/j.1399-0004.2005.00560.x · Cited by 101 · see citing works
“Whole genome array-CGH screening has been shown to be useful in identifying cryptic chromosomal rearrangements in individuals presenting with intellectual disabilities and normal karyotypes (23, 24, 25) and can identify cryptic imbalances in individuals with apparently balanced rearrangements and autism (10).”
BackgroundIntellectual disability genomics: current state, pitfalls and future challenges
Maia, N., Sá, M. J. N., Pires, M. M., de Brouwer, A. P. M., & Jorge, P. (2021) · BMC Genomics · doi:10.1186/s12864-021-08227-4 · Cited by 105 · see citing works
“DNA copy-number variants (CNVs) containing few to hundreds of genes, have increasingly been identified as ID causes [26].”
BackgroundFrom microscopes to microarrays: dissecting recurrent chromosomal rearrangements
Emanuel, B. S., & Saitta, S. C. (2007) · Nature Reviews Genetics · doi:10.1038/nrg2136 · Cited by 101 · see citing works
Hehir‐Kwa, J. Y., Egmont-Petersen, M., Janssen, I. M., Smeets, D., van Kessel, A. G., & Veltman, J. A. (2007) · DNA Research · doi:10.1093/dnares/dsm002 · Cited by 98 · see citing works
Self-citationDNA microarray analysis identifies candidate regions and genes in unexplained mental retardation
Engels, H., Brockschmidt, A., Hoischen, A., Landwehr, C., Bosse, K., Walldorf, C., Toedt, G., Radlwimmer, B., Propping, P., Lichter, P., et al. (2007) · Neurology · doi:10.1212/01.wnl.0000256367.70365.e0 · Cited by 94 · see citing works
Historical prospective of human cytogenetics: from microscope to microarray
Smeets, D. (2004) · Clinical Biochemistry · doi:10.1016/j.clinbiochem.2004.03.006 · Cited by 91 · see citing works
“Subsequent analysis of the parents of the patients, however, revealed that only two aberrations were de novo and therefore probably directly related to the clinical symptoms, whereas the three others appeared to be present in one of the parents and apparently constitute polymorphisms [39].”
BackgroundSelf-citationPrice, T. S. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki643 · Cited by 93 · see citing works
“Furthermore, a whole genome study, using probes spaced every 1 Mb across the genome, reported a 10% false positive rate and 10–15% polymorphisms (1).”
BackgroundGenetic Evaluation of Intellectual Disabilities
Moeschler, J. B. (2008) · Seminars in Pediatric Neurology · doi:10.1016/j.spen.2008.01.002 · Cited by 87 · see citing works
Lichtenbelt, K. D., Hochstenbach, R., van Dam, W. M., Eleveld, M. J., Poot, M., & Beemer, F. A. (2004) · American Journal of Medical Genetics Part A · doi:10.1002/ajmg.a.30408 · Cited by 91 · see citing works
“The array has been created by spotting in triplicate DOP-PCR products of 3,343 BAC DNA probes, which have been chromosomally-localized using FISH, and cover the entire human genome with a spacing of approximately 1 Mb [Vissers et al., 2003].”
Cukier, H. N., Lee, J. M., Ma, D., Young, J. I., Mayo, V., Butler, B. L., Ramsook, S. S., Rantus, J. A., Abrams, A. J., Whitehead, P. L., et al. (2012) · Autism Research · doi:10.1002/aur.1251 · Cited by 89 · see citing works
“…the identification of microdeletions on chromosome 2q22–2q23 [Chung et al., 2011; de Vries et al., 2005; Jaillard et al., 2008; Koolen et al., 2004; Noh & Graham Jr. 2012; Talkowski et al., 2011; van Bon et al., 2009; Vissers et al., 2003; Wagenstaller et al., 2007; Williams et al., 2009].”
BackgroundInfluentialJaillard, S., Dubourg, C., Gérard‐Blanluet, M., Delahaye‐Duriez, A., Pasquier, L., Dupont, C., Henry, C., Tabet, A.-C., Lucas, J., Aboura, A., et al. (2008) · Journal of Medical Genetics · doi:10.1136/jmg.2008.058156 · Cited by 89 · see citing works
“This 2q23.1 deletion is encompassed by three microdeletions previously reported in this chromosomal region: a 2 Mb genomic interval on 2q22.3q23.3,”
BackgroundHeidenblad, M., Schoenmakers, E., Jonson, T., Gorunova, L., Veltman, J. A., van Kessel, A. G., & Höglund, M. (2004) · Cancer Research · doi:10.1158/0008-5472.can-03-3159 · Cited by 89 · see citing works
Self-citationFiorentino, F., Napoletano, S., Caiazzo, F., Sessa, M., Bono, S., Spizzichino, L., Gordon, A. T., Nuccitelli, A., Rizzo, G., & Baldi, M. (2012) · European Journal of Human Genetics · doi:10.1038/ejhg.2012.253 · Cited by 88 · see citing works
Disorders caused by chromosome abnormalities
Shaffer, L. G., & Theisen (2010) · The Application of Clinical Genetics · doi:10.2147/tacg.s8884 · Cited by 91 · see citing works
- Authors
- Vissers, L. E. L. M., de Vries, B. B. A., Osoegawa, K., Janssen, I. M., Feuth, T., Choy, C. O., Straatman, H., van der Vliet, W., Huys, E. H. L. P. G., van Rijk, A., Smeets, D., van Ravenswaaij-Arts, C. M. A., Knoers, N. V., van der Burgt, I., de Jong, P. J., Brunner, H. G., van Kessel, A. G., Schoenmakers, E. F. P. M., & Veltman, J. A.
- Corresponding author
- Veltman, Joris A.
- ORCID
- Venue
- The American Journal of Human Genetics
- Publisher
- Elsevier BV
- Published
- 2003-12
- Volume
- 73
- Issue
- 6
- Pages
- 1261-1270
- ISSN
- 0002-9297 (ISSN-L)
- PMC
- PMC1180392
- OpenAlex
- W2063739474
- Cited by
- 469
- References
- 40
- Citations by year
- 2026: 2 · 2025: 1 · 2024: 5 · 2023: 10 · 2022: 6 · 2021: 7 · 2020: 4 · 2019: 8 · 2018: 9 · 2017: 10 · 2016: 19 · 2015: 16 · 2014: 8 · 2013: 16 · 2012: 29
- FWCI
- 22.55
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- The American Journal of Human Genetics (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Radboud Repository (Radboud University) (submittedVersion)
- University of Groningen research database (University of Groningen / Centre for Information Technology) (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Keywords
- array comparative genomic hybridization, microdeletion syndromes, microduplication, submicroscopic chromosomal abnormalities, intellectual disability, dysmorphology, sensitivity and specificity, genomic clones
- MeSH terms
- Chromosome Aberrations, Humans, Intellectual Disability, Polymorphism, Genetic, Sensitivity and Specificity, Genome, Human, In Situ Hybridization, Fluorescence
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