Comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants.
Nat Biotechnol
; 29(6): 512-20, 2011 May 08.
Article
em En
| MEDLINE
| ID: mdl-21552272
ABSTRACT
We have systematically compared copy number variant (CNV) detection on eleven microarrays to evaluate data quality and CNV calling, reproducibility, concordance across array platforms and laboratory sites, breakpoint accuracy and analysis tool variability. Different analytic tools applied to the same raw data typically yield CNV calls with <50% concordance. Moreover, reproducibility in replicate experiments is <70% for most platforms. Nevertheless, these findings should not preclude detection of large CNVs for clinical diagnostic purposes because large CNVs with poor reproducibility are found primarily in complex genomic regions and would typically be removed by standard clinical data curation. The striking differences between CNV calls from different platforms and analytic tools highlight the importance of careful assessment of experimental design in discovery and association studies and of strict data curation and filtering in diagnostics. The CNV resource presented here allows independent data evaluation and provides a means to benchmark new algorithms.
Texto completo:
1
Base de dados:
MEDLINE
Assunto principal:
Análise de Sequência com Séries de Oligonucleotídeos
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Polimorfismo de Nucleotídeo Único
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Hibridização Genômica Comparativa
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Variações do Número de Cópias de DNA
Tipo de estudo:
Diagnostic_studies
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Evaluation_studies
/
Prognostic_studies
Idioma:
En
Revista:
Nat Biotechnol
Assunto da revista:
BIOTECNOLOGIA
Ano de publicação:
2011
Tipo de documento:
Article
País de afiliação:
Canadá