Enhanced detection of clinically relevant genomic imbalances using a target plus whole genome oligonucleotide microarray

Department of Human Genetics, Emory University, Atlanta, Georgia 30322, USA.
Genetics in medicine: official journal of the American College of Medical Genetics (Impact Factor: 7.33). 07/2008; 10(6):415-29. DOI: 10.1097/GIM.0b013e318177015c
Source: PubMed


Array comparative genomic hybridization is rapidly becoming an integral part of cytogenetic diagnostics. We report the design, validation, and clinical utility of an oligonucleotide array which combines genome-wide coverage with targeted enhancement at known clinically relevant regions.
Probes were placed every 75 kb across the entire euchromatic genome to establish a chromosomal "backbone" with a resolution of approximately 500 kb, which is increased to approximately 50 kb in targeted regions.
For validation, 30 samples showed 100% concordance with previous G-banding and/or fluorescence in situ hybridization results. Prospective array analysis of 211 clinical samples identified 33 (15.6%) cases with clinically significant abnormalities. Of these, 23 (10.9%) were detected by the "targeted" coverage and 10 (4.7%) by the genome-wide coverage (average size of 3.7 Mb). All abnormalities were verified by fluorescence in situ hybridization, using commercially available or homebrew probes using the 32K bacterial artificial chromosome set. Four (1.9%) cases had previously reported imbalances of uncertain clinical significance. Five (2.4%) cases required parental studies for interpretation and all were benign familial variants.
Our results highlight the enhanced diagnostic utility of a genome-wide plus targeted array design, as the use of only a targeted array would have failed to detect 4.7% of the clinically relevant imbalances.

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Available from: Brian Bunke, Oct 06, 2015
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    • "The horizontal stripes of data points are due to the integer nature of the read counts. Experience based on classical cytogenetics and array CGH suggests that many features of this profile reflect characteristics of the sequencing and analysis process rather than true copy number variation (Baldwin et al. 2008). "
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    ABSTRACT: Detection of DNA copy number aberrations by shallow whole-genome sequencing (WGS) faces many challenges including lack of completion and errors in the human reference genome, repetitive sequences, polymorphisms, variable sample quality, and biases in the sequencing procedures. Formalin-fixed paraffin-embedded (FFPE) archival material, the analysis of which is important for studies of cancer, presents particular analytical difficulties due to degradation of the DNA and frequent lack of matched reference samples. We present a robust, cost-effective WGS method for DNA copy number analysis that addresses these challenges more successfully than currently available procedures. In practice, very useful profiles can be obtained with ~0.1x genome coverage. We improve on previous methods by; first, implementing a combined correction for sequence mappability and GC content, and second, applying this procedure to sequence data from the 1000 Genomes Project in order to develop a blacklist of problematic genome regions. A small subset of these blacklisted regions were previously identified by ENCODE, but the vast majority are novel unappreciated problematic regions. Our procedures are implemented in a pipeline called QDNAseq. We have analyzed over 1,000 samples, most of which were obtained from the fixed tissue archives of over 25 institutions. We demonstrate that for most samples our sequencing and analysis procedures yield genome profiles with noise levels near the statistical limit imposed by read counting. The described procedures also provide better correction of artifacts introduced by low DNA quality than prior approaches, and better copy number data than high-resolution microarrays at substantially lower cost.
    Genome Research 09/2014; 24(12). DOI:10.1101/gr.175141.114 · 14.63 Impact Factor
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    • "These advances included the addition of large genomic clones (e.g., bacterial artificial chromosomes, or BACs) to allow for the detection of single-copy losses or gains [6] followed by the replacement of genomic clones with synthetic oligonucleotides [7] for genome-wide interrogation and more precise identification of breakpoints. By the late 2000s, oligonucleotide CMA designs were implemented for clinical testing that included both targeted (representing known clinically relevant regions) and genome-wide backbone coverage [8]. This design schema enabled CMA to identify all imbalances detectable by karyotype plus submicroscopic CNVs, thus surpassing the diagnostic yield of a G-banded karyotype [9••]. "
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    ABSTRACT: One of the most fundamental goals of the study of human genetics was to determine the relationship between genomic variation and human disease. The effects of large-scale structural variation, such as aneuploidy and other cytogenetically visible imbalances, as well as sequence-level variation, have been studied for several decades. However, compared to these, the impact of submicroscopic copy number variants (CNV) has only recently been appreciated. Despite this, lessons learned from the study of CNVs have already proven significant and broadly applicable. From expanding the concept of normal human variation to providing concrete examples of the utility of genomics in clinical care and challenging notions of the genetic architecture of complex disease, CNVs have provided valuable insights into the genomics of human health and development.
    09/2014; 2(3). DOI:10.1007/s40142-014-0048-4
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    • "Microduplications of Xp22.31 have been described by several authors, mostly as single case reports and retrospective microarray analyses. Some have reported it as a benign variant [Shaw-Smith et al., 2004; Baldwin et al., 2008], others as a cause or risk factor for developmental delay [Li et al., 2010; Liu et al., 2011; Faletra et al., 2012], and still others describe it as a variant of unknown significance [Shaffer et al., 2007; Mencarelli et al., 2008]. The classification as a benign variant is supported by the observation that the duplication can be inherited from a phenotypically normal parent. "
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    ABSTRACT: Comparative genomic hybridization (CGH) arrays have significantly changed the approach to identifying genetic alterations causing intellectual disability and congenital anomalies. Several studies have described the microduplication of Xp22.31, involving the STS gene. In such reports characteristic features and pathogenicity of Xp22.31 duplications remains a subject of debate. Here we present a series of nine previously unreported individuals with Xp22.31 duplications, found through microarray analysis in the course of genetic workup for developmental delay, associated with a combination of talipes anomalies, seizures and/or feeding difficulties. The size of the Xp22.31 duplications ranged from 294 kb to 1.6 Mb. We show a comparison of the breakpoints, inheritance and clinical phenotype, and a review of the literature. This clinically detailed series of Xp22.31 duplication patients provides evidence that the Xp22.31 duplication contributes to a common phenotype. © 2014 Wiley Periodicals, Inc.
    American Journal of Medical Genetics Part A 08/2014; 164A(8). DOI:10.1002/ajmg.a.36598 · 2.16 Impact Factor
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