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Citations per year

Number of citations per year for the bioinformatics software tool tQN
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This map represents all the scientific publications referring to tQN per scientific context
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Protocols

tQN specifications

Information


Unique identifier OMICS_02605
Name tQN
Software type Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for tQN

tQN citations

 (9)
library_books

Distinct epigenetic landscapes underlie the pathobiology of pancreatic cancer subtypes

2018
Nat Commun
PMCID: 5958058
PMID: 29773832
DOI: 10.1038/s41467-018-04383-6

[…] raw fluorescent signals and to obtain log R ratio (LRR) and B allele frequency (BAF) values. Asymmetry in BAF signals due to bias between the two dyes used in Illumina assays was corrected using the tQN normalization procedure. We used the circular binary segmentation algorithm to segment genomic profiles and assign corresponding smoothed values of LRR and BAF. The Genome Alteration Print method […]

library_books

Gene expression profiling of patient‐derived pancreatic cancer xenografts predicts sensitivity to the BET bromodomain inhibitor JQ1: implications for individualized medicine efforts

2017
PMCID: 5376755
PMID: 28275007
DOI: 10.15252/emmm.201606975

[…] raw fluorescent signals and to obtain log R ratio (LRR) and B allele frequency (BAF) values. Asymmetry in BAF signals due to bias between the two dyes used in Illumina assays was corrected using the tQN normalization procedure (Staaf et al, ). We used the circular binary segmentation algorithm (Venkatraman & Olshen, ) to segment genomic profiles and assign corresponding smoothed values of log R r […]

library_books

Integrated multi omics analysis of oligodendroglial tumours identifies three subgroups of 1p/19q co deleted gliomas

2016
Nat Commun
PMCID: 4838899
PMID: 27090007
DOI: 10.1038/ncomms11263

[…] raw fluorescent signals and to obtain log R ratio (LRR) and B allele frequency (BAF) values. Asymmetry in BAF signals due to bias between the two dyes used in Illumina assays was corrected using the tQN normalization procedure. We used the circular binary segmentation algorithm to segment genomic profiles and assign corresponding smoothed values of log R ratio and B allele frequency. The Genome A […]

call_split

Copy number variations alter methylation and parallel IGF2 overexpression in adrenal tumors

2015
Endocr Relat Cancer
PMCID: 4621769
PMID: 26400872
DOI: 10.1530/ERC-15-0086
call_split See protocol

[…] ina's Genome Studio Software (). This affected both the allelic proportions and the copy number estimates. Data were corrected for this bias using a quantile normalization approach implemented in the tQN method (). Bias in the estimated copy number related to GC binding artifacts was corrected for using the method by (). Allele specific copy number estimates corrected for ploidy and infiltration o […]

library_books

Loss of photoreceptorness and gain of genomic alterations in retinoblastoma reveal tumor progression

2015
PMCID: 4534696
PMID: 26288838
DOI: 10.1016/j.ebiom.2015.06.022

[…] DR) adjustments (). Obtained FDR-adjusted two-sided p-values < 0.05 were considered significant.Copy number estimates and allelic intensity ratios exported by Illumina Beadstudio were normalized with tQN-procedure (). Subsequently, log2-R-ratios (LRR) were calculated from normalized copy number estimates of the tumors and matched blood samples. For tumors with no matching blood sample, sex-matched […]

library_books

Identification of Allelic Imbalance with a Statistical Model for Subtle Genomic Mosaicism

2014
PLoS Comput Biol
PMCID: 4148184
PMID: 25166618
DOI: 10.1371/journal.pcbi.1003765

[…] otyping error by applying small deviations from the quantities above.) This assumption seems to work well for our purpose of identifying regions of aberration. In fact, in our results, after applying tQN we simply called genotypes (AA, BB or AB) via simple thresholds for BAFs (e.g. 0.8 and 0.2) from mixture sample itself. Critically, at heterozygous sites (  = 1) our model differentiates the two […]


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tQN institution(s)
Department of Oncology, Clinical Sciences, Lund University, Lund, Sweden

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