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GPHMM specifications


Unique identifier OMICS_02568
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


  • person_outline David Tuck

Publication for GPHMM

GPHMM citations


Combined clinical and genomic signatures for the prognosis of early stage non small cell lung cancer based on gene copy number alterations

BMC Genomics
PMCID: 4595201
PMID: 26444668
DOI: 10.1186/s12864-015-1935-0

[…] umber values were estimated using NSA []. Since copy number profiling can be affected by stromal contamination, copy number values for each sample were re-scaled according to their tumor purity using GPHMM [] (Core algorithm in Additional file ). This correction also reduces variation among samples both within the same dataset, and across datasets. Next, values were segmented using CBS [] to get r […]


Alterations of the spindle checkpoint pathway in clinicopathologically aggressive CpG island methylator phenotype clear cell renal cell carcinomas

Int J Cancer
PMCID: 4755138
PMID: 26061684
DOI: 10.1002/ijc.29630

[…] .It is well known that AURKA (Aurora‐A) and AURKB (Aurora‐B) are key kinases in the spindle checkpoint., All 14 CIMP‐positive RCCs (100%) showed overexpression of AURKA and AURKB (Table ). ASCAT and GPHMM analyses based on SNP microarray data revealed that overexpression of the AURKA and AURKB genes was associated with increased copy number (3 or more) in 10 (71%) out of 14 CIMP‐positive RCCs (Ta […]


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

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

[…] of aberration type and proportions of the components of the mixture (tumor and normal DNA). In terms of the aberration types that are explicitly captured, our model is most similar to that underlying GPHMM , in which the observed data (mBAF and LRR) are related to the hidden aberration states by normal density functions. To this framework, we add a HMM for the inherited haplotypes that can be fit […]


Multilayer omics analysis of renal cell carcinoma, including the whole exome, methylome and transcriptome

PMCID: 4235299
PMID: 24504440
DOI: 10.1002/ijc.28768

[…] mation Fig. ). Copy number data has been obtained using Allele-Specific Copy Number Analysis of Tumors (ASCAT; and Global Parameter Hidden Markov Model (GPHMM; software. […]


Genome Wide Identification of Somatic Aberrations from Paired Normal Tumor Samples

PLoS One
PMCID: 3907544
PMID: 24498045
DOI: 10.1371/journal.pone.0087212

[…] and distinguishes recurrent aberrations from random genomic changes.In this study, we present an efficient bioinformatic tool called GIANT, which is based on the statistical framework of our previous GPHMM method . By incorporating genotype information of matched normal sample, GIANT provides identification of various kinds of somatic/germline aberrations with superior performance, even for aneupl […]


Sensitive and specific detection of mosaic chromosomal abnormalities using the Parent of Origin based Detection (POD) method

BMC Genomics
PMCID: 3680018
PMID: 23724825
DOI: 10.1186/1471-2164-14-367

[…] ol which is capable of improved detection using parent–child trios, but is not designed to detect UPD or partial copy number states []. Other HMM-based approaches, including PSCN, genoCN, MixHMM, and GPHMM, can detect CNVs and UPD events in tumor/normal mixtures and are thus capable of detecting mosaic changes at a certain level of resolution [-]. A Bayesian-based algorithm, gBPCR, also reports su […]


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GPHMM institution(s)
Department of Electronic Science and Technology, University of Science and Technology of China, China

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