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This study describes a new tool for accurate and reliable high-throughput detection of copy number variation in the human genome. We have constructed a large-insert clone DNA microarray covering the entire human genome in tiling path resolution that we have used to identify copy number variation in human populations. Crucial to this study has been the development of a robust array platform and analytic process for the automated identification of copy number variants (CNVs). The array consists of 26,574 clones covering 93.7% of euchromatic regions. Clones were selected primarily from the published "Golden Path," and mapping was confirmed by fingerprinting and BAC-end sequencing. Array performance was extensively tested by a series of validation assays. These included determining the hybridization characteristics of each individual clone on the array by chromosome-specific add-in experiments. Estimation of data reproducibility and false-positive/negative rates was carried out using self-self hybridizations, replicate experiments, and independent validations of CNVs. Based on these studies, we developed a variance-based automatic copy number detection analysis process (CNVfinder) and have demonstrated its robustness by comparison with the SW-ARRAY method.

Original publication

DOI

10.1101/gr.5630906

Type

Journal article

Journal

Genome Res

Publication Date

12/2006

Volume

16

Pages

1566 - 1574

Keywords

Algorithms, Chromosome Mapping, DNA, DNA Fingerprinting, Euchromatin, False Negative Reactions, False Positive Reactions, Gene Dosage, Gene Expression Profiling, Genetic Variation, Genome, Human, Humans, Nucleic Acid Hybridization, Oligonucleotide Array Sequence Analysis, Reproducibility of Results