Cargando…

Adjustment of genomic waves in signal intensities from whole-genome SNP genotyping platforms

Whole-genome microarrays with large-insert clones designed to determine DNA copy number often show variation in hybridization intensity that is related to the genomic position of the clones. We found these ‘genomic waves’ to be present in Illumina and Affymetrix SNP genotyping arrays, confirming tha...

Descripción completa

Detalles Bibliográficos
Autores principales:	Diskin, Sharon J., Li, Mingyao, Hou, Cuiping, Yang, Shuzhang, Glessner, Joseph, Hakonarson, Hakon, Bucan, Maja, Maris, John M., Wang, Kai
Formato:	Texto
Lenguaje:	English
Publicado:	Oxford University Press 2008
Materias:	Methods Online
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2577347/ https://www.ncbi.nlm.nih.gov/pubmed/18784189 http://dx.doi.org/10.1093/nar/gkn556

Ejemplares similares

Modeling genetic inheritance of copy number variations
por: Wang, Kai, et al.
Publicado: (2008)

ParseCNV integrative copy number variation association software with quality tracking
por: Glessner, Joseph T., et al.
Publicado: (2013)

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data
por: Wang, Kai, et al.
Publicado: (2010)

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

Ranking causal variants and associated regions in genome-wide association studies by the support vector machine and random forest
por: Roshan, Usman, et al.
Publicado: (2011)

SNP-specific extraction of haplotype-resolved targeted genomic regions
por: Dapprich, Johannes, et al.
Publicado: (2008)

Efficacy assessment of SNP sets for genome-wide disease association studies
por: Wollstein, Andreas, et al.
Publicado: (2007)

SNP identification in unamplified human genomic DNA with gold nanoparticle probes
por: Bao, Y. Paul, et al.
Publicado: (2005)

Genomic Landscape of a Three-Generation Pedigree Segregating Affective Disorder
por: Yang, Shuzhang, et al.
Publicado: (2009)

Highly cost-efficient genome-wide association studies using DNA pools and dense SNP arrays
por: Macgregor, Stuart, et al.
Publicado: (2008)

SNP genotyping using alkali cleavage of RNA/DNA chimeras and MALDI time-of-flight mass spectrometry
por: Mauger, Florence, et al.
Publicado: (2006)

Accurate SNP and mutation detection by targeted custom microarray-based genomic enrichment of short-fragment sequencing libraries
por: Mokry, Michal, et al.
Publicado: (2010)

Genome contact map explorer: a platform for the comparison, interactive visualization and analysis of genome contact maps
por: Kumar, Rajendra, et al.
Publicado: (2017)

Genotyping pooled DNA using 100K SNP microarrays: a step towards genomewide association scans
por: Meaburn, Emma, et al.
Publicado: (2006)

FadE: whole genome methylation analysis for multiple sequencing platforms
por: Souaiaia, Tade, et al.
Publicado: (2013)

SNVer: a statistical tool for variant calling in analysis of pooled or individual next-generation sequencing data
por: Wei, Zhi, et al.
Publicado: (2011)

Dual priming oligonucleotide system for the multiplex detection of respiratory viruses and SNP genotyping of CYP2C19 gene
por: Chun, Jong-Yoon, et al.
Publicado: (2007)

Identification of candidate regulatory SNPs by combination of transcription-factor-binding site prediction, SNP genotyping and haploChIP
por: Ameur, Adam, et al.
Publicado: (2009)

EnsembleCNV: an ensemble machine learning algorithm to identify and genotype copy number variation using SNP array data
por: Zhang, Zhongyang, et al.
Publicado: (2019)

Multiplexed direct genomic selection (MDiGS): a pooled BAC capture approach for highly accurate CNV and SNP/INDEL detection
por: Alvarado, David M., et al.
Publicado: (2014)

SNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence
por: Lopez-Maestre, Hélène, et al.
Publicado: (2016)

Analyzing whole genome bisulfite sequencing data from highly divergent genotypes
por: Wulfridge, Phillip, et al.
Publicado: (2019)

Accurate single-cell genotyping utilizing information from the local genome territory
por: Tu, Kailing, et al.
Publicado: (2021)

PBrowse: a web-based platform for real-time collaborative exploration of genomic data
por: Szot, Peter S., et al.
Publicado: (2017)

An integrated framework for discovery and genotyping of genomic variants from high-throughput sequencing experiments
por: Duitama, Jorge, et al.
Publicado: (2014)

Capturing genomic signatures of DNA sequence variation using a standard anonymous microarray platform
por: Cannon, C. H., et al.
Publicado: (2006)

CODEX: a normalization and copy number variation detection method for whole exome sequencing
por: Jiang, Yuchao, et al.
Publicado: (2015)

A novel procedure for genotyping of single nucleotide polymorphisms in trisomy with genomic DNA and the invader assay
por: Duffy, Kelly J., et al.
Publicado: (2008)

Single-cell genome-wide concurrent haplotyping and copy-number profiling through genotyping-by-sequencing
por: Masset, Heleen, et al.
Publicado: (2022)

Global transcript structure resolution of high gene density genomes through multi-platform data integration
por: O'Grady, Tina, et al.
Publicado: (2016)

A low-cost open-source SNP genotyping platform for association mapping applications
por: Macdonald, Stuart J, et al.
Publicado: (2005)

SNP discovery by mismatch-targeting of Mu transposition
por: Orsini, Luisa, et al.
Publicado: (2007)

TypeTE: a tool to genotype mobile element insertions from whole genome resequencing data
por: Goubert, Clément, et al.
Publicado: (2020)

From genotype to phenotype in Arabidopsis thaliana: in-silico genome interpretation predicts 288 phenotypes from sequencing data
por: Raimondi, Daniele, et al.
Publicado: (2021)

Microplate-based chromatin immunoprecipitation method, Matrix ChIP: a platform to study signaling of complex genomic events
por: Flanagin, Steve, et al.
Publicado: (2008)

Performance comparison of SNP detection tools with illumina exome sequencing data—an assessment using both family pedigree information and sample-matched SNP array data
por: Yi, Ming, et al.
Publicado: (2014)

A bioinformatic filter for improved base-call accuracy and polymorphism detection using the Affymetrix GeneChip® whole-genome resequencing platform
por: Pandya, Gagan A., et al.
Publicado: (2007)

Facile SNP detection using bifunctional, cross-linking oligonucleotide probes
por: Peng, Xiaohua, et al.
Publicado: (2008)

Multiplex SNP typing by bioluminometric assay coupled with terminator incorporation (BATI)
por: Zhou, Guo-Hua, et al.
Publicado: (2005)

PyroHMMsnp: an SNP caller for Ion Torrent and 454 sequencing data
por: Zeng, Feng, et al.
Publicado: (2013)

Cannot write session to /tmp/vufind_sessions/sess_7td07kb7i9t1g44d54kpq48s9h