PAIR: paired allelic log-intensity-ratio-based normalization method for SNP-CGH arrays
نویسندگان
چکیده
منابع مشابه
PAIR: paired allelic log-intensity-ratio-based normalization method for SNP-CGH arrays
MOTIVATION Normalization is critical in DNA copy number analysis. We propose a new method to correctly identify two-copy probes from the genome to obtain representative references for normalization in single nucleotide polymorphism arrays. The method is based on a two-state Hidden Markov Model. Unlike most currently available methods in the literature, the proposed method does not need to assum...
متن کاملHigh-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping.
Array-CGH is a powerful tool for the detection of chromosomal aberrations. The introduction of high-density SNP genotyping technology to genomic profiling, termed SNP-CGH, represents a further advance, since simultaneous measurement of both signal intensity variations and changes in allelic composition makes it possible to detect both copy number changes and copy-neutral loss-of-heterozygosity ...
متن کاملA probe-density-based analysis method for array CGH data: simulation, normalization and centralization
MOTIVATION Genomic instability is one of the fundamental factors in tumorigenesis and tumor progression. Many studies have shown that copy-number abnormalities at the DNA level are important in the pathogenesis of cancer. Array comparative genomic hybridization (aCGH), developed based on expression microarray technology, can reveal the chromosomal aberrations in segmental copies at a high resol...
متن کاملA Linear-Time Algorithm for Analyzing Array CGH Data Using Log Ratio Triangulation
DNA copy number is the number of replicates of a contiguous segment of DNA on the genome. Copy number alteration (CNA) is a genetic abnormality in which the number of these segments differs from the normal copy number, which is two for human chromosomal DNA. The association of CNA with cancer has led to a proliferation of research into algorithmic methods for detecting these regions of genetic ...
متن کاملITALICS: an algorithm for normalization and DNA copy number calling for Affymetrix SNP arrays
MOTIVATION Affymetrix SNP arrays can be used to determine the DNA copy number measurement of 11 000-500 000 SNPs along the genome. Their high density facilitates the precise localization of genomic alterations and makes them a powerful tool for studies of cancers and copy number polymorphism. Like other microarray technologies it is influenced by non-relevant sources of variation, requiring cor...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Bioinformatics
سال: 2012
ISSN: 1460-2059,1367-4803
DOI: 10.1093/bioinformatics/bts683