CNstream: A method for the identification and genotyping of copy number polymorphisms using Illumina microarrays

Background: Understanding the genetic basis of disease risk in depth requires an exhaustive knowledge of the types of genetic variation. Very recently, Copy Number Variants (CNVs) have received much attention because of their potential implication in common disease susceptibility. Copy Number Polymorphisms (CNPs) are of interest as they segregate at an appreciable frequency in the general population (i.e. > 1%) and are potentially implicated in the genetic basis of common diseases. Results: This paper concerns CNstream, a method for whole-genome CNV discovery and genotyping, using Illumina Beadchip arrays. Compared with other methods, a high level of accuracy was achieved by analyzing the measures of each intensity channel separately and combining information from multiple samples. The CNstream method uses heuristics and parametrical statistics to assign a confidence score to each sample at each probe; the sensitivity of the analysis is increased by jointly calling the copy number ...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Arnald Alonso, Antonio Julià, Raül Tortosa, Cristina Canaleta, Juan D. Cañete, Javier Ballina, Alejandro Balsa, Jesús Tornero, Sara Marsal
• Keywords: BMCBI 2010, Common Diseases, Copy Number, Genetic Basis