Cargando…

A Hidden Markov Model to estimate population mixture and allelic copy-numbers in cancers using Affymetrix SNP arrays

BACKGROUND: Affymetrix SNP arrays can interrogate thousands of SNPs at the same time. This allows us to look at the genomic content of cancer cells and to investigate the underlying events leading to cancer. Genomic copy-numbers are today routinely derived from SNP array data, but the proposed algor...

Descripción completa

Detalles Bibliográficos
Autores principales:	Lamy, Philippe, Andersen, Claus L, Dyrskjot, Lars, Torring, Niels, Wiuf, Carsten
Formato:	Texto
Lenguaje:	English
Publicado:	BioMed Central 2007
Materias:	Methodology Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2206057/ https://www.ncbi.nlm.nih.gov/pubmed/17996079 http://dx.doi.org/10.1186/1471-2105-8-434

Ejemplares similares

Genotyping and annotation of Affymetrix SNP arrays
por: Lamy, Philippe, et al.
Publicado: (2006)

Genome-wide analysis of allelic imbalance in prostate cancer using the Affymetrix 50K SNP mapping array
por: Tørring, N, et al.
Publicado: (2007)

Pooled DNA genotyping on Affymetrix SNP genotyping arrays
por: Kirov, George, et al.
Publicado: (2006)

Spatial normalization improves the quality of genotype calling for Affymetrix SNP 6.0 arrays
por: Chai, High Seng, et al.
Publicado: (2010)

hsegHMM: hidden Markov model-based allele-specific copy number alteration analysis accounting for hypersegmentation
por: Choo-Wosoba, Hyoyoung, et al.
Publicado: (2018)

Are microRNAs located in genomic regions associated with cancer?
por: Lamy, P, et al.
Publicado: (2006)

Fast MCMC sampling for hidden markov models to determine copy number variations
por: Mahmud, Md Pavel, et al.
Publicado: (2011)

A hidden Markov approach for ascertaining cSNP genotypes from RNA sequence data in the presence of allelic imbalance by exploiting linkage disequilibrium
por: Steibel, Juan P, et al.
Publicado: (2015)

A Mixture Model and a Hidden Markov Model to Simultaneously Detect Recombination Breakpoints and Reconstruct Phylogenies
por: Boussau, Bastien, et al.
Publicado: (2009)

Hybridization and amplification rate correction for affymetrix SNP arrays
por: Wang, Quan, et al.
Publicado: (2012)

Software comparison for evaluating genomic copy number variation for Affymetrix 6.0 SNP array platform
por: Eckel-Passow, Jeanette E, et al.
Publicado: (2011)

Rawcopy: Improved copy number analysis with Affymetrix arrays
por: Mayrhofer, Markus, et al.
Publicado: (2016)

Genome-wide analysis of antisense transcription with Affymetrix exon array
por: Ge, Xijin, et al.
Publicado: (2008)

A reaction network scheme for hidden Markov model parameter learning
por: Wiuf, Carsten, et al.
Publicado: (2023)

A hidden Markov model approach for determining expression from genomic tiling micro arrays
por: Munch, Kasper, et al.
Publicado: (2006)

Gene Expression and Isoform Variation Analysis using Affymetrix Exon Arrays
por: Bemmo, Amandine, et al.
Publicado: (2008)

Flexible hidden Markov models for behaviour-dependent habitat selection
por: Klappstein, N. J., et al.
Publicado: (2023)

Error statistics of hidden Markov model and hidden Boltzmann model results
por: Newberg, Lee A
Publicado: (2009)

Comparison of Affymetrix Gene Array with the Exon Array shows potential application for detection of transcript isoform variation
por: Ha, Kevin CH, et al.
Publicado: (2009)

A Single-Array-Based Method for Detecting Copy Number Variants Using Affymetrix High Density SNP Arrays and its Application to Breast Cancer
por: Li, Ming, et al.
Publicado: (2015)

GPHMM: an integrated hidden Markov model for identification of copy number alteration and loss of heterozygosity in complex tumor samples using whole genome SNP arrays
por: Li, Ao, et al.
Publicado: (2011)

QuantiSNP: an Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping data
por: Colella, Stefano, et al.
Publicado: (2007)

Riboswitch Detection Using Profile Hidden Markov Models
por: Singh, Payal, et al.
Publicado: (2009)

The chemiluminescence based Ziplex(® )automated workstation focus array reproduces ovarian cancer Affymetrix GeneChip(® )expression profiles
por: Quinn, Michael CJ, et al.
Publicado: (2009)

Fisher's combined p-value for detecting differentially expressed genes using Affymetrix expression arrays
por: Hess, Ann, et al.
Publicado: (2007)

Fast detection of de novo copy number variants from SNP arrays for case-parent trios
por: Scharpf, Robert B, et al.
Publicado: (2012)

Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios
por: Staaf, Johan, et al.
Publicado: (2008)

Combining Affymetrix microarray results
por: Stevens, John R, et al.
Publicado: (2005)

Estimation of tumor heterogeneity using CGH array data
por: Wang, Kai, et al.
Publicado: (2009)

Evaluating the performance of Affymetrix SNP Array 6.0 platform with 400 Japanese individuals
por: Nishida, Nao, et al.
Publicado: (2008)

A Beta-mixture model for dimensionality reduction, sample classification and analysis
por: Laurila, Kirsti, et al.
Publicado: (2011)

Implementing EM and Viterbi algorithms for Hidden Markov Model in linear memory
por: Churbanov, Alexander, et al.
Publicado: (2008)

Predicting nucleosome positioning using a duration Hidden Markov Model
por: Xi, Liqun, et al.
Publicado: (2010)

Quantitative prediction of the effect of genetic variation using hidden Markov models
por: Liu, Mingming, et al.
Publicado: (2014)

Predicting enhancers in mammalian genomes using supervised hidden Markov models
por: Zehnder, Tobias, et al.
Publicado: (2019)

Quality assessment and data handling methods for Affymetrix Gene 1.0 ST arrays with variable RNA integrity
por: Viljoen, Katie S, et al.
Publicado: (2013)

High throughput genotyping of structural variations in a complex plant genome using an original Affymetrix® axiom® array
por: Mabire, Clément, et al.
Publicado: (2019)

A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays including GenomeWideSNP 5 & 6
por: Bengtsson, Henrik, et al.
Publicado: (2009)

Equalizer reduces SNP bias in Affymetrix microarrays
por: Quigley, David
Publicado: (2015)

A fast and accurate method to detect allelic genomic imbalances underlying mosaic rearrangements using SNP array data
por: González, Juan R, et al.
Publicado: (2011)

Cannot write session to /tmp/vufind_sessions/sess_jo8kcq4054la505i1ggmrin1ab