{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,29]],"date-time":"2025-10-29T13:11:22Z","timestamp":1761743482062},"reference-count":36,"publisher":"Oxford University Press (OUP)","issue":"8","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,4,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>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.<\/jats:p>\n               <jats:p>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.<\/jats:p>\n               <jats:p>Availability: The data is available from http:\/\/rafalab.jhsph.edu\/cnvcomp\/.<\/jats:p>\n               <jats:p>Contact: \u00a0pevsner@jhmi.edu; fspencer@jhmi.edu; rafa@jhu.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr106","type":"journal-article","created":{"date-parts":[[2011,4,8]],"date-time":"2011-04-08T12:04:15Z","timestamp":1302264255000},"page":"1052-1060","source":"Crossref","is-referenced-by-count":20,"title":["Performance assessment of copy number microarray platforms using a spike-in experiment"],"prefix":"10.1093","volume":"27","author":[{"given":"Eitan","family":"Halper-Stromberg","sequence":"first","affiliation":[{"name":"1 Department of Biostatistics, Bloomberg School of Public Health, 2Program in Human Genetics and Molecular Biology, Johns Hopkins University School of Medicine, 3Department of Neurology, Hugo W. Moser Research Institute at Kennedy Krieger, 4JHMI Microarray Core, High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA, 5Department of Oncology, University of Cambridge, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK, 6Center for Inherited Disease Research, Johns Hopkins University, 7Department of Molecular Microbiology and Immunology, Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, 8Department of Oncology, Johns Hopkins University School of Medicine, 9Department of Neuroscience, Johns Hopkins School of Medicine and 10McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA"},{"name":"1 Department of Biostatistics, Bloomberg School of Public Health, 2Program in Human Genetics and Molecular Biology, Johns Hopkins University School of Medicine, 3Department of Neurology, Hugo W. Moser Research Institute at Kennedy Krieger, 4JHMI Microarray Core, High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA, 5Department of Oncology, University of Cambridge, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK, 6Center for Inherited Disease Research, Johns Hopkins University, 7Department of Molecular Microbiology and Immunology, Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, 8Department of Oncology, Johns Hopkins University School of Medicine, 9Department of Neuroscience, Johns Hopkins School of Medicine and 10McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Laurence","family":"Frelin","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics, Bloomberg School of Public Health, 2Program in Human Genetics and Molecular Biology, Johns Hopkins University School of Medicine, 3Department of Neurology, Hugo W. Moser Research Institute at Kennedy Krieger, 4JHMI Microarray Core, High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA, 5Department of Oncology, University of Cambridge, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK, 6Center for Inherited Disease Research, Johns Hopkins University, 7Department of Molecular Microbiology and Immunology, Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, 8Department of Oncology, Johns Hopkins University School of Medicine, 9Department of Neuroscience, Johns Hopkins School of Medicine and 10McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ingo","family":"Ruczinski","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics, Bloomberg School of Public Health, 2Program in Human Genetics and Molecular Biology, Johns Hopkins University School of Medicine, 3Department of Neurology, Hugo W. 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Moser Research Institute at Kennedy Krieger, 4JHMI Microarray Core, High Throughput Biology Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA, 5Department of Oncology, University of Cambridge, CRUK Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK, 6Center for Inherited Disease Research, Johns Hopkins University, 7Department of Molecular Microbiology and Immunology, Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, 8Department of Oncology, Johns Hopkins University School of Medicine, 9Department of Neuroscience, Johns Hopkins School of Medicine and 10McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Chunfa","family":"Jie","sequence":"additional","affiliation":[{"name":"1 Department of Biostatistics, Bloomberg School of Public Health, 2Program in Human Genetics and Molecular Biology, Johns Hopkins University School of Medicine, 3Department of Neurology, Hugo W. 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