Parent-specific copy number in paired tumor–normal studies using circular binary segmentation
AB Olshen, H Bengtsson, P Neuvial… - …, 2011 - academic.oup.com
Motivation: High-throughput techniques facilitate the simultaneous measurement of DNA
copy number at hundreds of thousands of sites on a genome. Older techniques allow …
copy number at hundreds of thousands of sites on a genome. Older techniques allow …
Major copy proportion analysis of tumor samples using SNP arrays
Abstract Background Single nucleotide polymorphisms (SNPs) are the most common
genetic variations in the human genome and are useful as genomic markers …
genetic variations in the human genome and are useful as genomic markers …
Copynumber: Efficient algorithms for single- and multi-track copy number segmentation
G Nilsen, K Liestøl, P Van Loo, HK Moen Vollan… - BMC genomics, 2012 - Springer
Background Cancer progression is associated with genomic instability and an accumulation
of gains and losses of DNA. The growing variety of tools for measuring genomic copy …
of gains and losses of DNA. The growing variety of tools for measuring genomic copy …
Circular binary segmentation for the analysis of array‐based DNA copy number data
AB Olshen, ES Venkatraman, R Lucito, M Wigler - Biostatistics, 2004 - academic.oup.com
DNA sequence copy number is the number of copies of DNA at a region of a genome.
Cancer progression often involves alterations in DNA copy number. Newly developed …
Cancer progression often involves alterations in DNA copy number. Newly developed …
Estimation of parent specific DNA copy number in tumors using high-density genotyping arrays
Chromosomal gains and losses comprise an important type of genetic change in tumors,
and can now be assayed using microarray hybridization-based experiments. Most current …
and can now be assayed using microarray hybridization-based experiments. Most current …
A faster circular binary segmentation algorithm for the analysis of array CGH data
ES Venkatraman, AB Olshen - Bioinformatics, 2007 - academic.oup.com
Motivation: Array CGH technologies enable the simultaneous measurement of DNA copy
number for thousands of sites on a genome. We developed the circular binary segmentation …
number for thousands of sites on a genome. We developed the circular binary segmentation …
Allele-specific amplification in cancer revealed by SNP array analysis
T LaFramboise, BA Weir, X Zhao… - PLoS Computational …, 2005 - journals.plos.org
Amplification, deletion, and loss of heterozygosity of genomic DNA are hallmarks of cancer.
In recent years a variety of studies have emerged measuring total chromosomal copy …
In recent years a variety of studies have emerged measuring total chromosomal copy …
CONDEL: detecting copy number variation and genotyping deletion zygosity from single tumor samples using sequence data
X Yuan, J Bai, J Zhang, L Yang, J Duan… - … /ACM transactions on …, 2018 - ieeexplore.ieee.org
Characterizing copy number variations (CNVs) from sequenced genomes is a both feasible
and cost-effective way to search for driver genes in cancer diagnosis. A number of existing …
and cost-effective way to search for driver genes in cancer diagnosis. A number of existing …
A single-sample method for normalizing and combining full-resolution copy numbers from multiple platforms, labs and analysis methods
Motivation: The rapid expansion of whole-genome copy number (CN) studies brings a
demand for increased precision and resolution of CN estimates. Recent studies have …
demand for increased precision and resolution of CN estimates. Recent studies have …
Performance evaluation of DNA copy number segmentation methods
A number of bioinformatic or biostatistical methods are available for analyzing DNA copy
number profiles measured from microarray or sequencing technologies. In the absence of …
number profiles measured from microarray or sequencing technologies. In the absence of …