PMID- 25595567
OWN - NLM
STAT- MEDLINE
DCOM- 20160125
LR  - 20181113
IS  - 1532-0480 (Electronic)
IS  - 1532-0464 (Print)
IS  - 1532-0464 (Linking)
VI  - 54
DP  - 2015 Apr
TI  - CNV-ROC: A cost effective, computer-aided analytical performance evaluator of 
      chromosomal microarrays.
PG  - 106-13
LID - S1532-0464(15)00003-9 [pii]
LID - 10.1016/j.jbi.2015.01.001 [doi]
AB  - 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.
CI  - Copyright (c) 2015 Elsevier Inc. All rights reserved.
FAU - Goodman, Corey W
AU  - Goodman CW
AD  - 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.
FAU - Major, Heather J
AU  - Major HJ
AD  - Department of Pediatrics, The University of Iowa, United States. Electronic 
      address: heather-major@uiowa.edu.
FAU - Walls, William D
AU  - Walls WD
AD  - 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.
FAU - Sheffield, Val C
AU  - Sheffield VC
AD  - 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.
FAU - Casavant, Thomas L
AU  - Casavant TL
AD  - 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 of Iowa, United 
      States. Electronic address: tomc@eng.uiowa.edu.
FAU - Darbro, Benjamin W
AU  - Darbro BW
AD  - Department of Pediatrics, The University of Iowa, United States. Electronic 
      address: benjamin-darbro@uiowa.edu.
LA  - eng
GR  - R01 EY011298/EY/NEI NIH HHS/United States
GR  - R01 EY017168/EY/NEI NIH HHS/United States
PT  - Journal Article
DEP - 20150113
PL  - United States
TA  - J Biomed Inform
JT  - Journal of biomedical informatics
JID - 100970413
RN  - 9007-49-2 (DNA)
SB  - IM
MH  - Algorithms
MH  - DNA/*analysis/genetics
MH  - DNA Copy Number Variations/*genetics
MH  - Female
MH  - Humans
MH  - Male
MH  - Oligonucleotide Array Sequence Analysis/*methods
MH  - Polymorphism, Single Nucleotide
MH  - ROC Curve
MH  - Reproducibility of Results
MH  - Sensitivity and Specificity
PMC - PMC4936396
MID - NIHMS689821
OTO - NOTNLM
OT  - Microarray
OT  - Precision
OT  - ROC
OT  - Sensitivity
OT  - Specificity
EDAT- 2015/01/18 06:00
MHDA- 2016/01/26 06:00
PMCR- 2016/07/07
CRDT- 2015/01/18 06:00
PHST- 2013/12/30 00:00 [received]
PHST- 2014/11/22 00:00 [revised]
PHST- 2015/01/05 00:00 [accepted]
PHST- 2015/01/18 06:00 [entrez]
PHST- 2015/01/18 06:00 [pubmed]
PHST- 2016/01/26 06:00 [medline]
PHST- 2016/07/07 00:00 [pmc-release]
AID - S1532-0464(15)00003-9 [pii]
AID - 10.1016/j.jbi.2015.01.001 [doi]
PST - ppublish
SO  - J Biomed Inform. 2015 Apr;54:106-13. doi: 10.1016/j.jbi.2015.01.001. Epub 2015 
      Jan 13.