{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,4,5]],"date-time":"2024-04-05T23:40:18Z","timestamp":1712360418730},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"11","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: With the expansion of whole-genome studies, there is rapid evolution of genotyping platforms. This leads to practical issues such as upgrading of genotyping equipment which often results in research groups having data from different platforms for the same samples. While having more data can potentially yield more accurate copy-number estimates, combining such data is not straightforward as different platforms show different degrees of attenuation of the true copy-number or different noise characteristics and marker panels. Currently, there is still a relative lack of procedures for combining information from different platforms.<\/jats:p><jats:p>Results: We develop a method, called MPSS, based on a correlated random-effect model for the unobserved patterns and extend the robust smooth segmentation approach to the multiple-platform scenario. We also propose an objective criterion for discrete segmentation required for downstream analyses. For each identified segment, the software reports a P-value to indicate the likelihood of the segment being a true CNV. From the analyses of real and simulated data, we show that MPSS has better operating characteristics when compared to single-platform methods, and have substantially higher sensitivity compared to an existing multiplatform method.<\/jats:p><jats:p>Availability: The methods are implemented in an R package MPSS, and the source is available from http:\/\/www.meb.ki.se\/~yudpaw.<\/jats:p><jats:p>Contact: \u00a0agus_salim@nuhs.edu.sg<\/jats:p><jats:p>Supplementary Information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr162","type":"journal-article","created":{"date-parts":[[2011,4,7]],"date-time":"2011-04-07T00:42:01Z","timestamp":1302136921000},"page":"1555-1561","source":"Crossref","is-referenced-by-count":7,"title":["Multi-platform segmentation for joint detection of copy number variants"],"prefix":"10.1093","volume":"27","author":[{"given":"Shu Mei","family":"Teo","sequence":"first","affiliation":[{"name":"1 Centre for Molecular Epidemiology, Department of Epidemiology and Public Health, National University of Singapore, Singapore, 2Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden 3NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore and 4Human Genetics, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore"},{"name":"1 Centre for Molecular Epidemiology, Department of Epidemiology and Public Health, National University of Singapore, Singapore, 2Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden 3NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore and 4Human Genetics, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore"},{"name":"1 Centre for Molecular Epidemiology, Department of Epidemiology and Public Health, National University of Singapore, Singapore, 2Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden 3NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore and 4Human Genetics, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yudi","family":"Pawitan","sequence":"additional","affiliation":[{"name":"1 Centre for Molecular Epidemiology, Department of Epidemiology and Public Health, National University of Singapore, Singapore, 2Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden 3NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore and 4Human Genetics, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vikrant","family":"Kumar","sequence":"additional","affiliation":[{"name":"1 Centre for Molecular Epidemiology, Department of Epidemiology and Public Health, National University of Singapore, Singapore, 2Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden 3NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore and 4Human Genetics, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Anbupalam","family":"Thalamuthu","sequence":"additional","affiliation":[{"name":"1 Centre for Molecular Epidemiology, Department of Epidemiology and Public Health, National University of Singapore, Singapore, 2Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden 3NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore and 4Human Genetics, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mark","family":"Seielstad","sequence":"additional","affiliation":[{"name":"1 Centre for Molecular Epidemiology, Department of Epidemiology and Public Health, National University of Singapore, Singapore, 2Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden 3NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore and 4Human Genetics, Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kee Seng","family":"Chia","sequence":"additional","affiliation":[{"name":"1 Centre for Molecular Epidemiology, Department of Epidemiology and Public Health, National University of Singapore, Singapore, 2Department 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