Chromosomal microarray analysis of consecutive individuals with autism spectrum disorders or learning disability presenting for genetic services
Chromosomal microarray analysis is now commonly used in clinical practice to identify copy number variants (CNVs) in the human genome. We report our experience with the use of the 105K and 180K oligonucleotide microarrays in 215 consecutive patients referred with either autism or autism spectrum dis...
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| Published in | Gene Vol. 535; no. 1; pp. 70 - 78 |
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| Main Authors | , , , , |
| Format | Journal Article |
| Language | English |
| Published |
Netherlands
Elsevier B.V
01.02.2014
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| Online Access | Get full text |
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| Abstract | Chromosomal microarray analysis is now commonly used in clinical practice to identify copy number variants (CNVs) in the human genome. We report our experience with the use of the 105K and 180K oligonucleotide microarrays in 215 consecutive patients referred with either autism or autism spectrum disorders (ASD) or developmental delay/learning disability for genetic services at the University of Kansas Medical Center during the past 4years (2009–2012). Of the 215 patients [140 males and 75 females (male/female ratio=1.87); 65 with ASD and 150 with learning disability], abnormal microarray results were seen in 45 individuals (21%) with a total of 49 CNVs. Of these findings, 32 represented a known diagnostic CNV contributing to the clinical presentation and 17 represented non-diagnostic CNVs (variants of unknown significance). Thirteen patients with ASD had a total of 14 CNVs, 6 CNVs recognized as diagnostic and 8 as non-diagnostic. The most common chromosome involved in the ASD group was chromosome 15. For those with a learning disability, 32 patients had a total of 35 CNVs. Twenty-six of the 35 CNVs were classified as a known diagnostic CNV, usually a deletion (n=20). Nine CNVs were classified as an unknown non-diagnostic CNV, usually a duplication (n=8). For the learning disability subgroup, chromosomes 2 and 22 were most involved. Thirteen out of 65 patients (20%) with ASD had a CNV compared with 32 out of 150 patients (21%) with a learning disability. The frequency of chromosomal microarray abnormalities compared by subject group or gender was not statistically different. A higher percentage of individuals with a learning disability had clinical findings of seizures, dysmorphic features and microcephaly, but not statistically significant. While both groups contained more males than females, a significantly higher percentage of males were present in the ASD group.
•Chromosome microarray analysis was performed for autism and learning disability.•Abnormal results were seen in 1 in 5 subjects with autism or learning disability.•Selected genes and chromosome regions of interest are discussed.•Most common microarray abnormality in autism involved chromosome 15q11-q13 region. |
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| AbstractList | Chromosomal microarray analysis is now commonly used in clinical practice to identify copy number variants (CNVs) in the human genome. We report our experience with the use of the 105 K and 180K oligonucleotide microarrays in 215 consecutive patients referred with either autism or autism spectrum disorders (ASD) or developmental delay/learning disability for genetic services at the University of Kansas Medical Center during the past 4 years (2009-2012). Of the 215 patients [140 males and 75 females (male/female ratio=1.87); 65 with ASD and 150 with learning disability], abnormal microarray results were seen in 45 individuals (21%) with a total of 49 CNVs. Of these findings, 32 represented a known diagnostic CNV contributing to the clinical presentation and 17 represented non-diagnostic CNVs (variants of unknown significance). Thirteen patients with ASD had a total of 14 CNVs, 6 CNVs recognized as diagnostic and 8 as non-diagnostic. The most common chromosome involved in the ASD group was chromosome 15. For those with a learning disability, 32 patients had a total of 35 CNVs. Twenty-six of the 35 CNVs were classified as a known diagnostic CNV, usually a deletion (n=20). Nine CNVs were classified as an unknown non-diagnostic CNV, usually a duplication (n=8). For the learning disability subgroup, chromosomes 2 and 22 were most involved. Thirteen out of 65 patients (20%) with ASD had a CNV compared with 32 out of 150 patients (21%) with a learning disability. The frequency of chromosomal microarray abnormalities compared by subject group or gender was not statistically different. A higher percentage of individuals with a learning disability had clinical findings of seizures, dysmorphic features and microcephaly, but not statistically significant. While both groups contained more males than females, a significantly higher percentage of males were present in the ASD group. Chromosomal microarray analysis is now commonly used in clinical practice to identify copy number variants (CNVs) in the human genome. We report our experience with the use of the 105K and 180K oligonucleotide microarrays in 215 consecutive patients referred with either autism or autism spectrum disorders (ASD) or developmental delay/learning disability for genetic services at the University of Kansas Medical Center during the past 4years (2009–2012). Of the 215 patients [140 males and 75 females (male/female ratio=1.87); 65 with ASD and 150 with learning disability], abnormal microarray results were seen in 45 individuals (21%) with a total of 49 CNVs. Of these findings, 32 represented a known diagnostic CNV contributing to the clinical presentation and 17 represented non-diagnostic CNVs (variants of unknown significance). Thirteen patients with ASD had a total of 14 CNVs, 6 CNVs recognized as diagnostic and 8 as non-diagnostic. The most common chromosome involved in the ASD group was chromosome 15. For those with a learning disability, 32 patients had a total of 35 CNVs. Twenty-six of the 35 CNVs were classified as a known diagnostic CNV, usually a deletion (n=20). Nine CNVs were classified as an unknown non-diagnostic CNV, usually a duplication (n=8). For the learning disability subgroup, chromosomes 2 and 22 were most involved. Thirteen out of 65 patients (20%) with ASD had a CNV compared with 32 out of 150 patients (21%) with a learning disability. The frequency of chromosomal microarray abnormalities compared by subject group or gender was not statistically different. A higher percentage of individuals with a learning disability had clinical findings of seizures, dysmorphic features and microcephaly, but not statistically significant. While both groups contained more males than females, a significantly higher percentage of males were present in the ASD group. Chromosomal microarray analysis is now commonly used in clinical practice to identify copy number variants (CNVs) in the human genome. We report our experience with the use of the 105K and 180K oligonucleotide microarrays in 215 consecutive patients referred with either autism or autism spectrum disorders (ASD) or developmental delay/learning disability for genetic services at the University of Kansas Medical Center during the past 4 years (2009–2012). Of the 215 patients [140 males and 75 females (male/female ratio = 1.87); 65 with ASD and 150 with learning disability], abnormal microarray results were seen in 45 individuals (21%) with a total of 49 CNVs. Of these findings, 32 represented a known diagnostic CNV contributing to the clinical presentation and 17 represented non-diagnostic CNVs (variants of unknown significance). Thirteen patients with ASD had a total of 14 CNVs, 6 CNVs recognized as diagnostic and 8 as non-diagnostic. The most common chromosome involved in the ASD group was chromosome 15. For those with a learning disability, 32 patients had a total of 35 CNVs. Twenty-six of the 35 CNVs were classified as a known diagnostic CNV, usually a deletion (n = 20). Nine CNVs were classified as an unknown non-diagnostic CNV, usually a duplication (n = 8). For the learning disability subgroup, chromosomes 2 and 22 were most involved. Thirteen out of 65 patients (20%) with ASD had a CNV compared with 32 out of 150 patients (21%) with a learning disability. The frequency of chromosomal microarray abnormalities compared by subject group or gender was not statistically different. A higher percentage of individuals with a learning disability had clinical findings of seizures, dysmorphic features and microcephaly, but not statistically significant. While both groups contained more males than females, a significantly higher percentage of males were present in the ASD group. Chromosomal microarray analysis is now commonly used in clinical practice to identify copy number variants (CNVs) in the human genome. We report our experience with the use of the 105K and 180K oligonucleotide microarrays in 215 consecutive patients referred with either autism or autism spectrum disorders (ASD) or developmental delay/learning disability for genetic services at the University of Kansas Medical Center during the past 4years (2009–2012). Of the 215 patients [140 males and 75 females (male/female ratio=1.87); 65 with ASD and 150 with learning disability], abnormal microarray results were seen in 45 individuals (21%) with a total of 49 CNVs. Of these findings, 32 represented a known diagnostic CNV contributing to the clinical presentation and 17 represented non-diagnostic CNVs (variants of unknown significance). Thirteen patients with ASD had a total of 14 CNVs, 6 CNVs recognized as diagnostic and 8 as non-diagnostic. The most common chromosome involved in the ASD group was chromosome 15. For those with a learning disability, 32 patients had a total of 35 CNVs. Twenty-six of the 35 CNVs were classified as a known diagnostic CNV, usually a deletion (n=20). Nine CNVs were classified as an unknown non-diagnostic CNV, usually a duplication (n=8). For the learning disability subgroup, chromosomes 2 and 22 were most involved. Thirteen out of 65 patients (20%) with ASD had a CNV compared with 32 out of 150 patients (21%) with a learning disability. The frequency of chromosomal microarray abnormalities compared by subject group or gender was not statistically different. A higher percentage of individuals with a learning disability had clinical findings of seizures, dysmorphic features and microcephaly, but not statistically significant. While both groups contained more males than females, a significantly higher percentage of males were present in the ASD group. •Chromosome microarray analysis was performed for autism and learning disability.•Abnormal results were seen in 1 in 5 subjects with autism or learning disability.•Selected genes and chromosome regions of interest are discussed.•Most common microarray abnormality in autism involved chromosome 15q11-q13 region. Chromosomal microarray analysis is now commonly used in clinical practice to identify copy number variants (CNVs) in the human genome. We report our experience with the use of the 105 K and 180K oligonucleotide microarrays in 215 consecutive patients referred with either autism or autism spectrum disorders (ASD) or developmental delay/learning disability for genetic services at the University of Kansas Medical Center during the past 4 years (2009-2012). Of the 215 patients [140 males and 75 females (male/female ratio=1.87); 65 with ASD and 150 with learning disability], abnormal microarray results were seen in 45 individuals (21%) with a total of 49 CNVs. Of these findings, 32 represented a known diagnostic CNV contributing to the clinical presentation and 17 represented non-diagnostic CNVs (variants of unknown significance). Thirteen patients with ASD had a total of 14 CNVs, 6 CNVs recognized as diagnostic and 8 as non-diagnostic. The most common chromosome involved in the ASD group was chromosome 15. For those with a learning disability, 32 patients had a total of 35 CNVs. Twenty-six of the 35 CNVs were classified as a known diagnostic CNV, usually a deletion (n=20). Nine CNVs were classified as an unknown non-diagnostic CNV, usually a duplication (n=8). For the learning disability subgroup, chromosomes 2 and 22 were most involved. Thirteen out of 65 patients (20%) with ASD had a CNV compared with 32 out of 150 patients (21%) with a learning disability. The frequency of chromosomal microarray abnormalities compared by subject group or gender was not statistically different. A higher percentage of individuals with a learning disability had clinical findings of seizures, dysmorphic features and microcephaly, but not statistically significant. While both groups contained more males than females, a significantly higher percentage of males were present in the ASD group.Chromosomal microarray analysis is now commonly used in clinical practice to identify copy number variants (CNVs) in the human genome. We report our experience with the use of the 105 K and 180K oligonucleotide microarrays in 215 consecutive patients referred with either autism or autism spectrum disorders (ASD) or developmental delay/learning disability for genetic services at the University of Kansas Medical Center during the past 4 years (2009-2012). Of the 215 patients [140 males and 75 females (male/female ratio=1.87); 65 with ASD and 150 with learning disability], abnormal microarray results were seen in 45 individuals (21%) with a total of 49 CNVs. Of these findings, 32 represented a known diagnostic CNV contributing to the clinical presentation and 17 represented non-diagnostic CNVs (variants of unknown significance). Thirteen patients with ASD had a total of 14 CNVs, 6 CNVs recognized as diagnostic and 8 as non-diagnostic. The most common chromosome involved in the ASD group was chromosome 15. For those with a learning disability, 32 patients had a total of 35 CNVs. Twenty-six of the 35 CNVs were classified as a known diagnostic CNV, usually a deletion (n=20). Nine CNVs were classified as an unknown non-diagnostic CNV, usually a duplication (n=8). For the learning disability subgroup, chromosomes 2 and 22 were most involved. Thirteen out of 65 patients (20%) with ASD had a CNV compared with 32 out of 150 patients (21%) with a learning disability. The frequency of chromosomal microarray abnormalities compared by subject group or gender was not statistically different. A higher percentage of individuals with a learning disability had clinical findings of seizures, dysmorphic features and microcephaly, but not statistically significant. While both groups contained more males than females, a significantly higher percentage of males were present in the ASD group. |
| Author | Butler, Merlin G. Dasouki, Majed Manzardo, Ann M. Hovanes, Karine Roberts, Jennifer L. |
| AuthorAffiliation | a Departments of Psychiatry, Behavioral Sciences and Pediatrics, The University of Kansas Medical Center, Kansas City, Kansas d King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia c Department of Neurology, The University of Kansas Medical Center, Kansas City, Kansas b CombiMatrix Diagnostics, Irvine, California |
| AuthorAffiliation_xml | – name: d King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia – name: c Department of Neurology, The University of Kansas Medical Center, Kansas City, Kansas – name: b CombiMatrix Diagnostics, Irvine, California – name: a Departments of Psychiatry, Behavioral Sciences and Pediatrics, The University of Kansas Medical Center, Kansas City, Kansas |
| Author_xml | – sequence: 1 givenname: Jennifer L. surname: Roberts fullname: Roberts, Jennifer L. organization: Departments of Psychiatry, Behavioral Sciences and Pediatrics, The University of Kansas, Medical Center, Kansas City, KS, USA – sequence: 2 givenname: Karine surname: Hovanes fullname: Hovanes, Karine organization: CombiMatrix Diagnostics, Irvine, CA, USA – sequence: 3 givenname: Majed surname: Dasouki fullname: Dasouki, Majed organization: Department of Neurology, The University of Kansas Medical Center, Kansas City, KS, USA – sequence: 4 givenname: Ann M. surname: Manzardo fullname: Manzardo, Ann M. organization: Departments of Psychiatry, Behavioral Sciences and Pediatrics, The University of Kansas, Medical Center, Kansas City, KS, USA – sequence: 5 givenname: Merlin G. surname: Butler fullname: Butler, Merlin G. email: mbutler4@kumc.edu organization: Departments of Psychiatry, Behavioral Sciences and Pediatrics, The University of Kansas, Medical Center, Kansas City, KS, USA |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/24188901$$D View this record in MEDLINE/PubMed |
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| Keywords | YWHAE PTEN Developmental delay PARK2 EEF1B2 ACOXL ACADL Learning disability ZNF407 SACS POLG LINS USP6 EEG ADIPOQ COBL PTH2R SUMF1 HAX1 MYL1 IL1RAPL1 NDUFS1 SHANK3 HDAC NLGN2 ANKRD11 CHRNA7 NRXN1 RPE MRPL19 ITPR1 Chromosomal microarray analysis XIAP Autism spectrum disorders (ASD) CNV FBXO45 CACNA1C PRPF8 aCGH FAM117B KNG1 SD ASD BCL2L11 FXR2 ANOVA MAP2 GALR1 LMNA NPHP1 SHOX A2BP1 MBP PAK2 SH2B1 TRAPPC2 Copy number variant (CNV) BAC FZD5 IDH1 GATAD2B SMARCA4 ALS2CR8 CT KLF7 DLG1 STAG2 DLG4 DNA FAT1 FISH PMP22 UCSC GZF1 ataxin 2-binding protein 1 gene inositol 1,4,5-triphosphate receptor, type 1 gene lamin A gene neurexin 1 gene frizzled 5 gene histone deacetylase gene parathyroid hormone receptor 2 gene calcium channel, voltage dependent, L-type, alpha 1C subunit gene acyl-coA dehydrogenase, long chain gene GATA zinc finger domain-containing protein 2B gene GDNF-inducible zinc finger protein 1 gene SH3 and multiple ankyrin repeat domains 3 gene tracking protein particle complex, subunit 2 gene polymerase gamma gene kininogen 1 gene interleukin 1 receptor accessory protein-like 1 gene fluorescence in situ hybridization array comparative genomic hybridization microtubule-associated protein 2 gene X-linked inhibitor of apoptosis gene F-box only 45 gene ribulose 5-phosphate 3-epimerase gene discs, large homolog 1 gene copy number variant stromal antigen 2 gene family with sequence similarity 117, member B gene phosphatase and tensin homolog gene SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily A, member gene ubiquitin-specific protease 6 gene bacterial artificial chromosome zinc finger protein 407 gene discs, large homolog 4 gene NADH-ubiquinone oxidoreductase Fe-S protein 1 gene sacsin gene cordon-bleu gene ankyrin repeat domain-containing protein 11 gene FAT tumor suppressor 1 gene sulfatase-modifying factor 1 gene parkin gene precursor mRNA-processing factor 8 gene protein-activated kinase 2 gene eukaryotic translation elongation factor 1, beta-2 gene nephrocystin 1 gene cholinergic receptor, neuronal nicotinic, alpha polypeptide 7 gene isocitrate dehydrogenase 1 gene galanin receptor 1 gene BCL2-like 11 gene autism spectrum disorder lines homolog gene kruppel-like factor 7 gene electroencephalogram short stature homeobox gene myelin basic protein gene acyl-coA oxidase-like gene neuroligin 2 gene standard deviation ALS2 chromosome region gene 8 myosin, light peptide 1 gene analysis of variance deoxyribonucleic acid HCLS1-associated protein X1 gene mitochondrial ribosomal protein L19 gene computed tomography University of California, Santa Cruz fragile X mental retardation, autosomal homolog 2 gene peripheral myelin protein 22 gene adipocyte-, C1q-, and collagen domain containing gene SH2B adaptor protein 1 gene tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon isoform gene |
| Language | English |
| License | 2013 Elsevier B.V. All rights reserved. |
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| Snippet | Chromosomal microarray analysis is now commonly used in clinical practice to identify copy number variants (CNVs) in the human genome. We report our experience... |
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| SubjectTerms | Adolescent Adult autism Autism spectrum disorders (ASD) Child Child Development Disorders, Pervasive - genetics Child, Preschool Chromosomal microarray analysis Chromosome Aberrations chromosomes Copy number variant (CNV) Developmental delay Female females Genetic Services genome Humans Infant learning Learning Disabilities - genetics Learning disability Male males Microarray Analysis microarray technology Middle Aged oligonucleotides patients seizures Young Adult |
| Title | Chromosomal microarray analysis of consecutive individuals with autism spectrum disorders or learning disability presenting for genetic services |
| URI | https://dx.doi.org/10.1016/j.gene.2013.10.020 https://www.ncbi.nlm.nih.gov/pubmed/24188901 https://www.proquest.com/docview/1477565284 https://www.proquest.com/docview/2000162979 https://pubmed.ncbi.nlm.nih.gov/PMC4423794 |
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