Family-Based Benchmarking of Copy Number Variation Detection Software

scientific article published on 21 July 2015

Family-Based Benchmarking of Copy Number Variation Detection Software is …
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P819ADS bibcode2015PLoSO..1033465N
P356DOI10.1371/JOURNAL.PONE.0133465
P932PMC publication ID4510559
P698PubMed publication ID26197066
P5875ResearchGate publication ID281820676

P50authorStefan SchreiberQ2337595
Annegret FischerQ114721517
Michael KrawczakQ60985300
Almut NebelQ87034473
Michael NothnagelQ30500455
P2093author name stringSylvia Hofmann
Marcel Elie Nutsua
P2860cites workThe diploid genome sequence of an individual humanQ21090194
Towards a comprehensive structural variation map of an individual human genomeQ21184038
Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectivesQ21284304
The diploid genome sequence of an Asian individualQ21972851
An integrated map of genetic variation from 1,092 human genomesQ22122153
Finding the missing heritability of complex diseasesQ22122198
Mapping and sequencing of structural variation from eight human genomesQ22122215
Five years of GWAS discoveryQ24610574
Mapping copy number variation by population-scale genome sequencingQ24615307
Large, rare chromosomal deletions associated with severe early-onset obesityQ24623878
Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controlsQ24628710
Strong association of de novo copy number mutations with autismQ24633543
Accurate whole human genome sequencing using reversible terminator chemistryQ24641887
Genome-wide association of early-onset myocardial infarction with single nucleotide polymorphisms and copy number variantsQ24645076
Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encodingQ24647100
Single nucleotide polymorphism arrays: a decade of biological, computational and technological advancesQ37273694
Deletion polymorphism upstream of IRGM associated with altered IRGM expression and Crohn's diseaseQ37318174
A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays including GenomeWideSNP 5 & 6.Q37324776
Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVsQ37373867
Comparing CNV detection methods for SNP arraysQ37593774
A robust algorithm for copy number detection using high-density oligonucleotide single nucleotide polymorphism genotyping arraysQ40396914
An integrated view of copy number and allelic alterations in the cancer genome using single nucleotide polymorphism arraysQ40559185
Estimation and assessment of raw copy numbers at the single locus levelQ42642744
A genome-wide scalable SNP genotyping assay using microarray technologyQ46111789
VEGA: variational segmentation for copy number detectionQ48177255
The first Korean genome sequence and analysis: full genome sequencing for a socio-ethnic groupQ24647197
A second generation human haplotype map of over 3.1 million SNPsQ24651939
Paired-end mapping reveals extensive structural variation in the human genomeQ24653260
Large recurrent microdeletions associated with schizophreniaQ24654741
Global variation in copy number in the human genomeQ24658083
A haplotype map of the human genomeQ24679827
The International HapMap ProjectQ27860695
Origins and functional impact of copy number variation in the human genomeQ28730507
Comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variantsQ28732264
Integrating common and rare genetic variation in diverse human populationsQ29547220
Personal genomes: The case of the missing heritabilityQ29614582
Integrated detection and population-genetic analysis of SNPs and copy number variationQ29614584
PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping dataQ29614933
Linkage disequilibrium and heritability of copy-number polymorphisms within duplicated regions of the human genomeQ30477871
Whole genome distribution and ethnic differentiation of copy number variation in Caucasian and Asian populationsQ30945351
Analysis of array CGH data: from signal ratio to gain and loss of DNA regionsQ30961366
QuantiSNP: an Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping dataQ31104515
Assessment of algorithms for high throughput detection of genomic copy number variation in oligonucleotide microarray dataQ31131810
Population-genetic nature of copy number variations in the human genomeQ33630664
R-Gada: a fast and flexible pipeline for copy number analysis in association studiesQ33634615
Accuracy of CNV Detection from GWAS DataQ33797878
A highly annotated whole-genome sequence of a Korean individualQ33815862
Software comparison for evaluating genomic copy number variation for Affymetrix 6.0 SNP array platform.Q33917558
The genetic variability and commonality of neurodevelopmental diseaseQ33965270
Copy number variation across European populationsQ33988707
The International HapMap Project Web siteQ34206586
Reference-unbiased copy number variant analysis using CGH microarraysQ34298242
An exome sequencing pipeline for identifying and genotyping common CNVs associated with disease with application to psoriasisQ34409659
A multilevel model to address batch effects in copy number estimation using SNP arrays.Q34425384
Deletion of the late cornified envelope LCE3B and LCE3C genes as a susceptibility factor for psoriasisQ34603580
High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotypingQ35012994
Deep whole-genome sequencing of 100 southeast Asian MalaysQ36524738
Methods and strategies for analyzing copy number variation using DNA microarraysQ36863499
P275copyright licenseCreative Commons Attribution 4.0 InternationalQ20007257
P6216copyright statuscopyrightedQ50423863
P433issue7
P407language of work or nameEnglishQ1860
P304page(s)e0133465
P577publication date2015-07-21
P1433published inPLOS OneQ564954
P1476titleFamily-Based Benchmarking of Copy Number Variation Detection Software
P478volume10

Reverse relations

cites work (P2860)
Q88989553Comparing complex variants in family trios
Q37379591Rawcopy: Improved copy number analysis with Affymetrix arrays
Q57461461geck: trio-based comparative benchmarking of variant calls

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