Performance assessment of copy number microarray platforms using a spike-in experiment

Eitan Halper-Stromberg; Laurence Frelin; Ingo Ruczinski; Robert Scharpf; Chunfa Jie; Benilton Carvalho; Haiping Hao; Kurt Hetrick; Anne Jedlicka; Amanda Dziedzic; Kim Doheny; Alan F. Scott; Steve Baylin; Jonathan Pevsner; Forrest Spencer; Rafael A. Irizarry

doi:10.1093/bioinformatics/btr106

Performance assessment of copy number microarray platforms using a spike-in experiment

Eitan Halper-Stromberg, Laurence Frelin, Ingo Ruczinski, Robert Scharpf, Chunfa Jie, Benilton Carvalho, Haiping Hao, Kurt Hetrick, Anne Jedlicka, Amanda Dziedzic, Kim Doheny, Alan F. Scott, Steve Baylin, Jonathan Pevsner, Forrest Spencer, Rafael A. Irizarry

Research output: Contribution to journal › Article › peer-review

20 Scopus citations

Abstract

Motivation: Changes in the copy number of chromosomal DNA segments [copy number variants (CNVs)] have been implicated in human variation, heritable diseases and cancers. Microarray-based platforms are the current established technology of choice for studies reporting these discoveries and constitute the benchmark against which emergent sequence-based approaches will be evaluated. Research that depends on CNV analysis is rapidly increasing, and systematic platform assessments that distinguish strengths and weaknesses are needed to guide informed choice. Results: We evaluated the sensitivity and specificity of six platforms, provided by four leading vendors, using a spike-in experiment. NimbleGen and Agilent platforms outperformed Illumina and Affymetrix in accuracy and precision of copy number dosage estimates. However, Illumina and Affymetrix algorithms that leverage single nucleotide polymorphism (SNP) information make up for this disadvantage and perform well at variant detection. Overall, the NimbleGen 2.1M platform outperformed others, but only with the use of an alternative data analysis pipeline to the one offered by the manufacturer.

Original language	English (US)
Article number	btr106
Pages (from-to)	1052-1060
Number of pages	9
Journal	Bioinformatics
Volume	27
Issue number	8
DOIs	https://doi.org/10.1093/bioinformatics/btr106
State	Published - Apr 2011

ASJC Scopus subject areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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10.1093/bioinformatics/btr106

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Halper-Stromberg, E., Frelin, L., Ruczinski, I., Scharpf, R., Jie, C., Carvalho, B., Hao, H., Hetrick, K., Jedlicka, A., Dziedzic, A., Doheny, K., Scott, A. F., Baylin, S., Pevsner, J., Spencer, F., & Irizarry, R. A. (2011). Performance assessment of copy number microarray platforms using a spike-in experiment. Bioinformatics, 27(8), 1052-1060. Article btr106. https://doi.org/10.1093/bioinformatics/btr106

Halper-Stromberg, E, Frelin, L, Ruczinski, I , Scharpf, R, Jie, C, Carvalho, B, Hao, H, Hetrick, K, Jedlicka, A, Dziedzic, A, Doheny, K , Scott, AF , Baylin, S, Pevsner, J, Spencer, F & Irizarry, RA 2011, 'Performance assessment of copy number microarray platforms using a spike-in experiment', Bioinformatics, vol. 27, no. 8, btr106, pp. 1052-1060. https://doi.org/10.1093/bioinformatics/btr106

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abstract = "Motivation: Changes in the copy number of chromosomal DNA segments [copy number variants (CNVs)] have been implicated in human variation, heritable diseases and cancers. Microarray-based platforms are the current established technology of choice for studies reporting these discoveries and constitute the benchmark against which emergent sequence-based approaches will be evaluated. Research that depends on CNV analysis is rapidly increasing, and systematic platform assessments that distinguish strengths and weaknesses are needed to guide informed choice. Results: We evaluated the sensitivity and specificity of six platforms, provided by four leading vendors, using a spike-in experiment. NimbleGen and Agilent platforms outperformed Illumina and Affymetrix in accuracy and precision of copy number dosage estimates. However, Illumina and Affymetrix algorithms that leverage single nucleotide polymorphism (SNP) information make up for this disadvantage and perform well at variant detection. Overall, the NimbleGen 2.1M platform outperformed others, but only with the use of an alternative data analysis pipeline to the one offered by the manufacturer.",

author = "Eitan Halper-Stromberg and Laurence Frelin and Ingo Ruczinski and Robert Scharpf and Chunfa Jie and Benilton Carvalho and Haiping Hao and Kurt Hetrick and Anne Jedlicka and Amanda Dziedzic and Kim Doheny and Scott, {Alan F.} and Steve Baylin and Jonathan Pevsner and Forrest Spencer and Irizarry, {Rafael A.}",

note = "Funding Information: Funding: F.S. was supported by R01GM077456, R.I. by R01GM083084 and R01RR021967, E.H.-S. by T32GM974906, J.P. by HD24061 and I.R. by UL1 RR 025005. All grants were received from the National Institutes of Health.",

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doi = "10.1093/bioinformatics/btr106",

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AU - Halper-Stromberg, Eitan

AU - Frelin, Laurence

AU - Ruczinski, Ingo

AU - Scharpf, Robert

AU - Jie, Chunfa

AU - Carvalho, Benilton

AU - Hao, Haiping

AU - Hetrick, Kurt

AU - Jedlicka, Anne

AU - Dziedzic, Amanda

AU - Doheny, Kim

AU - Scott, Alan F.

AU - Baylin, Steve

AU - Pevsner, Jonathan

AU - Spencer, Forrest

AU - Irizarry, Rafael A.

N1 - Funding Information: Funding: F.S. was supported by R01GM077456, R.I. by R01GM083084 and R01RR021967, E.H.-S. by T32GM974906, J.P. by HD24061 and I.R. by UL1 RR 025005. All grants were received from the National Institutes of Health.

PY - 2011/4

Y1 - 2011/4

N2 - Motivation: Changes in the copy number of chromosomal DNA segments [copy number variants (CNVs)] have been implicated in human variation, heritable diseases and cancers. Microarray-based platforms are the current established technology of choice for studies reporting these discoveries and constitute the benchmark against which emergent sequence-based approaches will be evaluated. Research that depends on CNV analysis is rapidly increasing, and systematic platform assessments that distinguish strengths and weaknesses are needed to guide informed choice. Results: We evaluated the sensitivity and specificity of six platforms, provided by four leading vendors, using a spike-in experiment. NimbleGen and Agilent platforms outperformed Illumina and Affymetrix in accuracy and precision of copy number dosage estimates. However, Illumina and Affymetrix algorithms that leverage single nucleotide polymorphism (SNP) information make up for this disadvantage and perform well at variant detection. Overall, the NimbleGen 2.1M platform outperformed others, but only with the use of an alternative data analysis pipeline to the one offered by the manufacturer.

AB - Motivation: Changes in the copy number of chromosomal DNA segments [copy number variants (CNVs)] have been implicated in human variation, heritable diseases and cancers. Microarray-based platforms are the current established technology of choice for studies reporting these discoveries and constitute the benchmark against which emergent sequence-based approaches will be evaluated. Research that depends on CNV analysis is rapidly increasing, and systematic platform assessments that distinguish strengths and weaknesses are needed to guide informed choice. Results: We evaluated the sensitivity and specificity of six platforms, provided by four leading vendors, using a spike-in experiment. NimbleGen and Agilent platforms outperformed Illumina and Affymetrix in accuracy and precision of copy number dosage estimates. However, Illumina and Affymetrix algorithms that leverage single nucleotide polymorphism (SNP) information make up for this disadvantage and perform well at variant detection. Overall, the NimbleGen 2.1M platform outperformed others, but only with the use of an alternative data analysis pipeline to the one offered by the manufacturer.

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Performance assessment of copy number microarray platforms using a spike-in experiment

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