Comparative analysis of copy number detection by whole-genome BAC and oligonucleotide array CGH

Signature Genomic Laboratories, Spokane, WA, USA. .
Molecular Cytogenetics (Impact Factor: 2.14). 06/2010; 3(1):11. DOI: 10.1186/1755-8166-3-11
Source: PubMed


Microarray-based comparative genomic hybridization (aCGH) is a powerful diagnostic tool for the detection of DNA copy number gains and losses associated with chromosome abnormalities, many of which are below the resolution of conventional chromosome analysis. It has been presumed that whole-genome oligonucleotide (oligo) arrays identify more clinically significant copy-number abnormalities than whole-genome bacterial artificial chromosome (BAC) arrays, yet this has not been systematically studied in a clinical diagnostic setting.
To determine the difference in detection rate between similarly designed BAC and oligo arrays, we developed whole-genome BAC and oligonucleotide microarrays and validated them in a side-by-side comparison of 466 consecutive clinical specimens submitted to our laboratory for aCGH. Of the 466 cases studied, 67 (14.3%) had a copy-number imbalance of potential clinical significance detectable by the whole-genome BAC array, and 73 (15.6%) had a copy-number imbalance of potential clinical significance detectable by the whole-genome oligo array. However, because both platforms identified copy number variants of unclear clinical significance, we designed a systematic method for the interpretation of copy number alterations and tested an additional 3,443 cases by BAC array and 3,096 cases by oligo array. Of those cases tested on the BAC array, 17.6% were found to have a copy-number abnormality of potential clinical significance, whereas the detection rate increased to 22.5% for the cases tested by oligo array. In addition, we validated the oligo array for detection of mosaicism and found that it could routinely detect mosaicism at levels of 30% and greater.
Although BAC arrays have faster turnaround times, the increased detection rate of oligo arrays makes them attractive for clinical cytogenetic testing.

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Available from: Nicholas J Neill, Aug 22, 2014
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    • "Please cite this article as: Chakrabarty, S., et al., Comprehensive DNA copy number profile and BAC library construction of an Indian individual , Gene (2012), doi:10.1016/j.gene.2012.03.054 limitations while addressing small structural variations and complex chromosomal rearrangements (Neill et al., 2010; Ylstra et al., 2006). "
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    ABSTRACT: Bacterial artificial chromosomes (BACs) are used in genomic variation studies due to their capacity to carry a large insert, their high clonal stability, low rate of chimerism and ease of manipulation. In the present study, an attempt was made to create the first genomic BAC library of an anonymous Indian male (IMBL4) consisting of 100,224 clones covering the human genome more than three times. Restriction mapping of 255 BAC clones by pulse field gel electrophoresis confirmed an average insert size of 120 kb. The library was screened by PCR using SHANK3 (SH3 and multiple ankyrin repeat domains 3) and OLFM3 (olfactomedin 3) specific primers. A selection of clones was analyzed by fluorescent in situ hybridization (FISH) and sequencing. Fine mapping of copy number variable regions by array based comparative genomic hybridization identified 467 CNVRs in the IMBL4 genome. The IMBL4 BAC library represents the first cataloged Indian genome resource for applications in basic and clinical research.
    Full-text · Article · Mar 2012 · Gene
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    • "BAC probes vary from 150 to 200 Kb and require high amounts of DNA for hybridization, having been superseded by oligonucleotide-based arrays (oligo arrays), which are considered to have large advantages over the BAC arrays. These platforms are characterized by singlestranded oligonucleotides (25 to 85 bp in length) attached to the array slide, allowing the detection and analysis of copy-number variation with a much higher resolution (Neill et al., 2010). The development of the aCGH platforms has led to an important increase in the detection of copy number variations. "

    Full-text · Chapter · Feb 2012
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    • "Therefore, microarray designs generally avoid or provide low probe coverage in intervals that have genomic architectures such as SDs that confound the interpretation of copy number differences [43,44]. In relating the breakage intervals to the duplicon architecture and genes, we noted probes in the Agilent SurePrint 244K microarray [13] (Figure 1B) that were present in duplicons with paralogous sequences on other chromosomes and within segmentally duplicated sequences in the BP1, BP2, and BP3 regions (Table 1). "
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    ABSTRACT: Segmental duplicons (SDs) predispose to an increased frequency of chromosomal rearrangements. These rearrangements can cause a diverse range of phenotypes due to haploinsufficiency, in cis positional effects or gene interruption. Genomic microarray analysis has revealed gene dosage changes adjacent to duplicons, but the high degree of similarity between duplicon sequences has confounded unequivocal assignment of chromosome breakpoints within these intervals. In this study, we localize rearrangements within duplicon-enriched regions of Angelman/Prader-Willi (AS/PWS) syndrome chromosomal deletions with fluorescence in situ hybridization (FISH). Breakage intervals in AS deletions were localized recursively with short, coordinate-defined, single copy (SC) and low copy (LC) genomic FISH probes. These probes were initially coincident with duplicons and regions of previously reported breakage in AS/PWS. Subsequently, probes developed from adjacent genomic intervals more precisely delineated deletion breakage intervals involving genes, pseudogenes and duplicons in 15q11.2q13. The observed variability in the deletion boundaries within previously described Class I and Class II deletion AS samples is related to the local genomic architecture in this chromosomal region. Chromosome 15 abnormalities associated with SDs were precisely delineated at a resolution equivalent to genomic Southern analysis. This context-dependent approach can define the boundaries of chromosome rearrangements for other genomic disorders associated with SDs.
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