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An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabilities.

ABSTRACT: Copy number variants have emerged as a major cause of human disease such as autism and intellectual disabilities. Because copy number variants are common in normal individuals, determining the functional and clinical significance of rare copy number variants in patients remains challenging. The adoption of whole-genome chromosomal microarray analysis as a first-tier diagnostic test for individuals with unexplained developmental disabilities provides a unique opportunity to obtain large copy number variant datasets generated through routine patient care.A consortium of diagnostic laboratories was established (the International Standards for Cytogenomic Arrays consortium) to share copy number variant and phenotypic data in a central, public database. We present the largest copy number variant case-control study to date comprising 15,749 International Standards for Cytogenomic Arrays cases and 10,118 published controls, focusing our initial analysis on recurrent deletions and duplications involving 14 copy number variant regions.Compared with controls, 14 deletions and seven duplications were significantly overrepresented in cases, providing a clinical diagnosis as pathogenic.Given the rapid expansion of clinical chromosomal microarray analysis testing, very large datasets will be available to determine the functional significance of increasingly rare copy number variants. This data will provide an evidence-based guide to clinicians across many disciplines involved in the diagnosis, management, and care of these patients and their families.

SUBMITTER: Kaminsky EB

PROVIDER: S-EPMC3661946 | biostudies-literature | 2011 Sep

REPOSITORIES: biostudies-literature

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An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabilities.

Kaminsky Erin B EB Kaul Vineith V Paschall Justin J Church Deanna M DM Bunke Brian B Kunig Dawn D Moreno-De-Luca Daniel D Moreno-De-Luca Andres A Mulle Jennifer G JG Warren Stephen T ST Richard Gabriele G Compton John G JG Fuller Amy E AE Gliem Troy J TJ Huang Shuwen S Collinson Morag N MN Beal Sarah J SJ Ackley Todd T Pickering Diane L DL Golden Denae M DM Aston Emily E Whitby Heidi H Shetty Shashirekha S Rossi Michael R MR Rudd M Katharine MK South Sarah T ST Brothman Arthur R AR Sanger Warren G WG Iyer Ramaswamy K RK Crolla John A JA Thorland Erik C EC Aradhya Swaroop S Ledbetter David H DH Martin Christa L CL

Genetics in medicine : official journal of the American College of Medical Genetics 20110901 9

<h4>Purpose</h4>Copy number variants have emerged as a major cause of human disease such as autism and intellectual disabilities. Because copy number variants are common in normal individuals, determining the functional and clinical significance of rare copy number variants in patients remains challenging. The adoption of whole-genome chromosomal microarray analysis as a first-tier diagnostic test for individuals with unexplained developmental disabilities provides a unique opportunity to obtain ...[more]

PMID: 21844811

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Project description:ImportanceAt least 11 rare copy number variants (CNVs) have been shown to be major risk factors for schizophrenia (SZ). These CNVs also increase the risk for other neurodevelopmental disorders, such as intellectual disability. It is possible that additional intellectual disability-associated CNVs increase the risk for SZ but have not yet been implicated in SZ because of previous studies being underpowered.ObjectiveTo examine whether additional CNVs implicated in intellectual disability represent novel SZ risk loci.Design, setting, and participantsWe used single-nucleotide polymorphism (SNP) array data to evaluate a set of 51 CNVs implicated in intellectual disability (excluding the known SZ loci) in a large data set of patients with SZ and healthy persons serving as controls recruited in a variety of settings. We analyzed a new sample of 6934 individuals with SZ and 8751 controls and combined those data with previously published large data sets for a total of 20 403 cases of SZ and 26 628 controls.Main outcomes and measuresBurden analysis of CNVs implicated in intellectual disability (excluding known SZ CNVs) for association with SZ. Association of individual intellectual disability CNV loci with SZ.ResultsOf data on the 20 403 cases (6151 [30.15%] female) and 26 628 controls (14 252 [53.52%] female), 51 intellectual disability CNVs were analyzed. Collectively, intellectual disability CNVs were significantly enriched for SZ (P = 1.0 × 10-6; odds ratio [OR], 1.9 [95% CI, 1.46-2.49]). Of the 51 CNVs tested, 19 (37%) were more common in SZ cases; only 4 (8%) were more common in controls (no observations were made for the remaining 28 [55%] loci). One novel locus, deletion at 16p12.1, was significantly associated with SZ after correction for multiple testing (rate in SZ, 33 [0.16%]; rate in controls, 12 [0.05%]; corrected P = .017; OR, 3.3; 95% CI, 1.61-7.05), and 2 loci reached nominal levels of significance (deletions at 2q11.2: 6 [0.03%] vs 1 [0.004%]; OR, 9.3; 95% CI, 1.03-447.76; corrected P > .99; and duplications at 10q11.21q11.23: 5 [0.2%] vs 0 [0.03%]; OR, infinity; 95% CI, 1.26-infinity; corrected P = .71). Our new data set also provided independent support for the 11 SZ risk loci previously reported to be associated with the disorder and for the protective effect of 22q11.2 duplication.Conclusions and relevanceA large proportion of CNV loci implicated in intellectual disability are risk factors for SZ, but the available sample size precludes statistical confirmation for additional individual loci.

Project description:BACKGROUND:Chromosomal microarray analysis has been shown to be a valuable and cost effective assay for elucidating copy number variants (CNVs) in children with intellectual disability and developmental delay (ID/DD). METHODS:In our study, we performed array-based comparative genomic hybridization (array-CGH) analysis using oligonucleotide-based platforms in 542 Czech patients with ID/DD, autism spectrum disorders and multiple congenital abnormalities. Prior to the array-CGH analysis, all the patients were first examined karyotypically using G-banding. The presence of CNVs and their putative derivation was confirmed using fluorescence in situ hybridization (FISH), multiplex ligation-dependent probe amplification (MLPA) and predominantly relative quantitative polymerase chain reaction (qPCR). RESULTS:In total, 5.9% (32/542) patients were positive for karyotypic abnormalities. Pathogenic/likely pathogenic CNVs were identified in 17.7% of them (96/542), variants of uncertain significance (VOUS) were detected in 4.8% (26/542) and likely benign CNVs in 9.2% of cases (50/542). We identified 6.6% (36/542) patients with known recurrent microdeletion (24 cases) and microduplication (12 cases) syndromes, as well as 4.8% (26/542) patients with non-recurrent rare microdeletions (21 cases) and microduplications (5 cases). In the group of patients with submicroscopic pathogenic/likely pathogenic CNVs (13.3%; 68/510) we identified 91.2% (62/68) patients with one CNV, 5.9% (4/68) patients with two likely independent CNVs and 2.9% (2/68) patients with two CNVs resulting from cryptic unbalanced translocations. Of all detected CNVs, 21% (31/147) had a de novo origin, 51% (75/147) were inherited and 28% (41/147) of unknown origin. In our cohort pathogenic/likely pathogenic microdeletions were more frequent than microduplications (69%; 51/74 vs. 31%; 23/74) ranging in size from 0.395?Mb to 10.676?Mb (microdeletions) and 0.544?Mb to 8.156?Mb (microduplications), but their sizes were not significantly different (P?=?0.83). The pathogenic/likely pathogenic CNVs (median 2.663?Mb) were significantly larger than benign CNVs (median 0.394?Mb) (P?<?0.00001) and likewise the pathogenic/likely pathogenic CNVs (median 2.663?Mb) were significantly larger in size than VOUS (median 0.469?Mb) (P?<?0.00001). CONCLUSIONS:Our results confirm the benefit of array-CGH in the current clinical genetic diagnostics leading to identification of the genetic cause of ID/DD in affected children.

Project description:IntroductionPostpartum health care among women with intellectual and developmental disabilities has not been well studied. This study uses administrative claims to compare postpartum outpatient visits among women with and without intellectual and developmental disabilities.MethodsMassachusetts All Payers Claims Database 2012-2015 was used to identify women with intellectual and developmental disabilities and a live birth during 2012-2014, matched by infant birth year to 3 women without intellectual and developmental disabilities. Women were followed up for 1 year after delivery. Analyses were conducted in 2019. Poisson regression compared guideline-concordant postpartum and other outpatient visits during the early (21-56 days after delivery) and late (57-365 days after delivery) periods. Types of nonpostpartum care visits were examined.ResultsOverall, 962 and 2,886 women with and without intellectual and developmental disabilities, respectively, comprised the sample. Among women with intellectual and developmental disabilities, 23.9% had a postpartum visit in the early and 33.3% in the late postpartum periods, compared with 25.2% and 32.1% of women without intellectual and developmental disabilities who had visits in the early and late postpartum periods, respectively (p=0.49, 0.59). Women with intellectual and developmental disabilities were more likely to have other outpatient visits than those without intellectual and developmental disabilities, both in the early (63.1% vs 40.3%, adjusted RR=1.42, 95% CI=1.28, 1.58, p<0.001) and late (94.2% vs 82.3%, RR=1.11, 95% CI=1.08, 1.14, p=0.008) postpartum periods. Ancillary services, home health services, and alcohol/drug-related visits were much more common among women with intellectual and developmental disabilities.ConclusionsWomen with intellectual and developmental disabilities are equally likely to receive guideline-concordant postpartum visits and more likely to have other outpatient visits than other women. Further research is needed to evaluate visit quality and identify best practices to support mothers with intellectual and developmental disabilities during the postpartum period.

Dataset Information

An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabilities.

Publications

An evidence-based approach to establish the functional and clinical significance of copy number variants in intellectual and developmental disabilities.

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