Comparative analyses of seven algorithms for copy number variant identification from single nucleotide polymorphism arrays.

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2010-05

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Abstract

Determination of copy number variants (CNVs) inferred in genome wide single nucleotide polymorphism arrays has shown increasing utility in genetic variant disease associations. Several CNV detection methods are available, but differences in CNV call thresholds and characteristics exist. We evaluated the relative performance of seven methods: circular binary segmentation, CNVFinder, cnvPartition, gain and loss of DNA, Nexus algorithms, PennCNV and QuantiSNP. Tested data included real and simulated Illumina HumHap 550 data from the Singapore cohort study of the risk factors for Myopia (SCORM) and simulated data from Affymetrix 6.0 and platform-independent distributions. The normalized singleton ratio (NSR) is proposed as a metric for parameter optimization before enacting full analysis. We used 10 SCORM samples for optimizing parameter settings for each method and then evaluated method performance at optimal parameters using 100 SCORM samples. The statistical power, false positive rates, and receiver operating characteristic (ROC) curve residuals were evaluated by simulation studies. Optimal parameters, as determined by NSR and ROC curve residuals, were consistent across datasets. QuantiSNP outperformed other methods based on ROC curve residuals over most datasets. Nexus Rank and SNPRank have low specificity and high power. Nexus Rank calls oversized CNVs. PennCNV detects one of the fewest numbers of CNVs.

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10.1093/nar/gkq040

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Dellinger, AE, SM Saw, LK Goh, M Seielstad, TL Young and YJ Li (2010). Comparative analyses of seven algorithms for copy number variant identification from single nucleotide polymorphism arrays. Nucleic Acids Res, 38(9). p. e105. 10.1093/nar/gkq040 Retrieved from https://hdl.handle.net/10161/10630.

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Scholars@Duke

Young

Terri Lois Young

Adjunct Professor in Ophthalmology

Terri L. Young, M.D., M.B.A. is a board-certified clinician-scientist ophthalmologist.  She is a Professor of Ophthalmology, Pediatrics, and Medicine at Duke University School of Medicine.  She is a Professor of Neuroscience at the Duke- National University of Singapore Graduate Medical School, with adjunct appointments at the Singapore Eye Research Institute and the Saw Swee Hock School of Public Health, National University of Singapore.  She is the founding Director of the Duke Eye Center Ophthalmic Genetics Program.  She is also the Associate Director of the Duke School of Medicine Clinical and Translational Sciences Award Predoctoral Research TL1 Training Award.

Dr. Young's clinical interests include ophthalmic genetics, pediatric eye disease including pediatric cataracts and retinal disorder, and the surgical correction of strabismus/ eye misalignment in children and adults.  Her laboratory research focuses on the genetic studies of refractive errors, eye development and growth, primary congenital glaucoma, retinal and corneal dystrophies, and other heritable disorders.  Her research program includes the development of animal models in zebrafish and mice for ocular diseases based on our understanding of genetic influences in humans.   

Dr. Young is an editorial board member of Experimental Eye Research, World Journal of Ophthalmology, Journal of Ophthalmology, and past editorial board member of the Journal of the Association of Pediatric Ophthalmology and Strabismus.   She has published over 180 scientific refereed articles, and multiple book chapters, reviews and abstracts.  Dr. Young has served as a strategic consultant to the National Eye Institute (NEI) and the National Human Genome Research Institute.  She has served as a National Institutes of Health (NIH) study section member for 14 years, and is currently a permanent member of the Diseases and Pathophysiology of the Visual System study section.  She also presently serves as a board member of the NIH NEI Scientific Board of Counselors.  She is the American Association of Ophthalmology Pediatric Ophthalmology Program Committee Chair, and the Association for Research in Vision and Ophthalmology Program Committee Vice Chair of the Biochemistry and Molecular Biology Section.  She is the Treasurer of Women in Ophthalmology, Inc. 

Dr. Young has garnered several prestigious awards as a Fellow of the Philadelphia College of Physicians, the American Ophthalmological Society, and the Association of Research in Vision and Ophthalmology.  She has garnered an Honor Award from the American Association of Pediatric Ophthalmology and Strabismus, and a Senior Honor Award from the American Association of Ophthalmology.  She is an international speaker, with multiple named lectureships.  She has been honored with citations of "Best Doctors in North Carolina", "America's Top Ophthalmologists", and in Becker's Review of "135 Leading Ophthalmolgists in America" for several years.  She has also been featured in the NIH National Library of Medicine "Changing the Face of Medicine" exhibit. (2004)

Li

Yi-Ju Li

Professor of Biostatistics & Bioinformatics

My research interest is in statistical genetics, including statistical method development and its application for understanding the genetic predisposition of human complex diseases. Here is the list of research topics:

  • Statistical genetics: development of family-based association methods for quantitative traits with or without censoring and for detecting X-linked genes for disease risk.  With the availability of next generation sequencing data, we have ongoing projects to develop the association methods for testing rare variants for different phenotypic measures.  
  • Genetics of Alzheimer's disease (AD) and Fuchs endothelial corneal dystrophy (FECD).
  • Genetic basis of age-at-onset of Alzheimer disease. 
  • Peri-operative genomic studies. Investigate the genetic risk factors for postoperative outcomes of patients underwent non-emergent coronary artery bypass grafting with cardiopulmonary bypass.

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