Your browser doesn't support javascript.
loading
CNV-ROC: A cost effective, computer-aided analytical performance evaluator of chromosomal microarrays.
Goodman, Corey W; Major, Heather J; Walls, William D; Sheffield, Val C; Casavant, Thomas L; Darbro, Benjamin W.
Afiliación
  • Goodman CW; Department of Electrical and Computer Engineering, The University of Iowa, United States; Center for Bioinformatics and Computational Biology, The University of Iowa, United States. Electronic address: corey-goodman@uiowa.edu.
  • Major HJ; Department of Pediatrics, The University of Iowa, United States. Electronic address: heather-major@uiowa.edu.
  • Walls WD; Department of Electrical and Computer Engineering, The University of Iowa, United States; Center for Bioinformatics and Computational Biology, The University of Iowa, United States. Electronic address: daniel-walls@uiowa.edu.
  • Sheffield VC; Ph.D. Program in Genetics, The University of Iowa, United States; Department of Pediatrics, The University of Iowa, United States. Electronic address: val-sheffield@uiowa.edu.
  • Casavant TL; Department of Electrical and Computer Engineering, The University of Iowa, United States; Department of Biomedical Engineering, The University of Iowa, United States; Center for Bioinformatics and Computational Biology, The University of Iowa, United States; Ph.D. Program in Genetics, The University
  • Darbro BW; Department of Pediatrics, The University of Iowa, United States. Electronic address: benjamin-darbro@uiowa.edu.
J Biomed Inform ; 54: 106-13, 2015 Apr.
Article en En | MEDLINE | ID: mdl-25595567
Chromosomal microarrays (CMAs) are routinely used in both research and clinical laboratories; yet, little attention has been given to the estimation of genome-wide true and false negatives during the assessment of these assays and how such information could be used to calibrate various algorithmic metrics to improve performance. Low-throughput, locus-specific methods such as fluorescence in situ hybridization (FISH), quantitative PCR (qPCR), or multiplex ligation-dependent probe amplification (MLPA) preclude rigorous calibration of various metrics used by copy number variant (CNV) detection algorithms. To aid this task, we have established a comparative methodology, CNV-ROC, which is capable of performing a high throughput, low cost, analysis of CMAs that takes into consideration genome-wide true and false negatives. CNV-ROC uses a higher resolution microarray to confirm calls from a lower resolution microarray and provides for a true measure of genome-wide performance metrics at the resolution offered by microarray testing. CNV-ROC also provides for a very precise comparison of CNV calls between two microarray platforms without the need to establish an arbitrary degree of overlap. Comparison of CNVs across microarrays is done on a per-probe basis and receiver operator characteristic (ROC) analysis is used to calibrate algorithmic metrics, such as log2 ratio threshold, to enhance CNV calling performance. CNV-ROC addresses a critical and consistently overlooked aspect of analytical assessments of genome-wide techniques like CMAs which is the measurement and use of genome-wide true and false negative data for the calculation of performance metrics and comparison of CNV profiles between different microarray experiments.
Asunto(s)
Palabras clave
Texto completo
Añadir a Mi BVS
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: ADN / Análisis de Secuencia por Matrices de Oligonucleótidos / Variaciones en el Número de Copia de ADN Tipo de estudio: Diagnostic_studies / Health_economic_evaluation / Prognostic_studies Límite: Female / Humans / Male Idioma: En Revista: J Biomed Inform Asunto de la revista: INFORMATICA MEDICA Año: 2015 Tipo del documento: Article Pais de publicación: Estados Unidos
Texto completo
Añadir a Mi BVS
Imprimir
XML
PubMed Links
Buscar en Google

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: ADN / Análisis de Secuencia por Matrices de Oligonucleótidos / Variaciones en el Número de Copia de ADN Tipo de estudio: Diagnostic_studies / Health_economic_evaluation / Prognostic_studies Límite: Female / Humans / Male Idioma: En Revista: J Biomed Inform Asunto de la revista: INFORMATICA MEDICA Año: 2015 Tipo del documento: Article Pais de publicación: Estados Unidos