scholarly journals Rawcopy: Improved copy number analysis with Affymetrix arrays

2015 ◽  
Author(s):  
Markus Mayrhofer ◽  
Bjorn Viklund ◽  
Anders Isaksson
Keyword(s):  
Copy Number ◽  
Signal To Noise Ratio ◽  
R Package ◽  
Copy Number Analysis ◽  
Genome Wide ◽  
Microarray Sample ◽  
Allele Specific ◽  
Log Ratio ◽  
Reference Samples ◽  
Total Copy Number

Rawcopy is an R package for processing of Affymetrix CytoScan HD, CytoScan 750k and SNP 6.0 microarray raw intensities (CEL files). It uses data from a large number of reference samples to produce log ratio for total copy number analysis and B-allele frequency for allele-specific copy number and heterozygosity analysis. Rawcopy achieves higher signal-to-noise ratio than commonly used free and proprietary alternatives, leading to improved identification of copy number alterations. In addition, Rawcopy visualises each microarray sample for assessment of technical quality, patient identity and genome-wide absolute copy number states.

Genome-Wide Analysis of Copy Number Alterations/LOH/Allelic Imbalances in Non-Hodgkin Lymphoma Using Ultrahigh-Density SNP-Genotyping Microarrays with the Robust CNAG Algorithms.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 420-420
Author(s):  
Kumi Nakazaki ◽  
Yasuhito Nannya ◽  
Masashi Sanada ◽  
Go Yamamoto ◽  
Chiaki Aoyama ◽  
...  
Keyword(s):  
Copy Number ◽  
B Cell Lymphoma ◽  
Genetic Alterations ◽  
Snp Genotyping ◽  
High Grade ◽  
Copy Number Alterations ◽  
Copy Number Analysis ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Allele Specific

Abstract Non-Hodgkin lymphomas (NHL) are hematopoietic malignancies originated from diversity of peripheral lymphoid organs. During the past two decades, there have been significant advances in the pathogenesis of NHL including identification of a number of genes associated with the disease-specific translocations and other genetic alterations. In view of cytogenetics, however, NHL frequently shows complex chromosomal abnormalities involving copy number alterations as well as other unbalanced translocations, many of which have not been unveiled at the molecular levels. Affymetrix® 100K/500K mapping arrays were originally developed for large-scale SNP typing required for genome-wide association studies, but the quantitative nature of the whole-genome amplification and hybridization used in these platforms also makes them powerful tools for genome-wide analysis of cancer genomes with use of uniformly distributed 116,204/520,000 SNP-specific probes. Moreover the use of SNP specific probes enables allele-specific copy number analysis that is totally impossible with other platforms. Here we developed the robust algorithms (Copy number analyzer for Affymetrix® GeneChip®; CNAG) for high-quality processing of 100K/500K data and analyzed a total of 72 NHL samples (61 primary samples including 34 diffuse large B-cell lymphoma, 18 follicular lymphoma and 11 cell lines including 3 adult T cell leukemia/ lymphoma) for genome-wide copy number alterations, LOH, and allelic imbalances at the resolutions of 23.6/5.4 kb. In 100K analysis, 34 homozygous deletions and 42 high-grade amplifications and other numerous copy number alternations and/or LOH, were identified together with possible gene targets as for some regions. 500K analysis disclosed even more subtle changes. Common overlapping alternations included deletions in 1p31.1 and 9p21.3, and 19p13.32 and high-grade amplifications in 3p14.2–p14.1,7q21.13–q21.3, and 20q11.21. Of particular importance is, however, the finding of otherwise undetected copy number neutral LOHs, which are revealed only by allele-specific copy-number analysis. In fact the copy number neutral LOHs represented a novel type of genetic abnormality in NHL because they were very frequent and found in more than 87% (20/23) of NHL cases examined with allele-specific copy number analysis, making a stark contrast to ALL, in which these abnormalities were rare. They typically involved chromosomal ends, indicating somatic recombinations are the potential mechanism of generating these abnormalities. Notably, there was a clear predisposition of the copy number neutral LOH to specific chromosomal loci including 1p, 1q, 6p, 9p, 17q, and 19p suggesting existence of relevant genes to NHL pathogenesis within these common regions. In conclusion, Affymetrix® SNP-genotyping microarrays and our CNAG algorithms provide a powerful platform of dissecting NHL genomes and could facilitate identification of the novel molecular mechanisms for lymphomagenesis.

scholarly journals Genome-Wide Detection of Allele Specific Copy Number Variation Associated with Insulin Resistance in African Americans from the HyperGEN Study

PLoS ONE ◽  
2011 ◽  
Vol 6 (8) ◽  
pp. e24052 ◽  
Author(s):  
Marguerite R. Irvin ◽  
Nathan E. Wineinger ◽  
Treva K. Rice ◽  
Nicholas M. Pajewski ◽  
Edmond K. Kabagambe ◽  
...  
Keyword(s):  
Insulin Resistance ◽  
African Americans ◽  
Copy Number Variation ◽  
Copy Number ◽  
Genome Wide ◽  
Number Variation ◽  
Allele Specific

scholarly journals Estimating Genome-Wide Copy Number Using Allele Specific Mixture Models

2007 ◽  
pp. 137-150 ◽  
Author(s):  
Wenyi Wang ◽  
Benilton Carvalho ◽  
Nate Miller ◽  
Jonathan Pevsner ◽  
Aravinda Chakravarti ◽  
...  
Keyword(s):  
Mixture Models ◽  
Copy Number ◽  
Genome Wide ◽  
Allele Specific

Abstract 1447: Investigating susceptibility to sporadic osteosarcoma by genome-wide copy number analysis

2012 ◽  
Author(s):  
Rinnat M. Porat ◽  
Ivan Pasic ◽  
Adan Shlien ◽  
Nalan Gokgoz ◽  
Irene Andrulis ◽  
...  
Keyword(s):  
Copy Number ◽  
Copy Number Analysis ◽  
Genome Wide

scholarly journals Involvement of cyclin D3 in liver metastasis of colorectal cancer, revealed by genome-wide copy-number analysis

2005 ◽  
Vol 85 (9) ◽  
pp. 1118-1129 ◽  
Author(s):  
Hideaki Tanami ◽  
Hitoshi Tsuda ◽  
Satoshi Okabe ◽  
Takehisa Iwai ◽  
Kenichi Sugihara ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Liver Metastasis ◽  
Copy Number ◽  
Cyclin D3 ◽  
Copy Number Analysis ◽  
Genome Wide
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