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Phenopath specifications

Information


Unique identifier OMICS_19668
Name Phenopath
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++, R
License Apache License version 2.0
Computer skills Advanced
Version 0.99.4
Stability Stable
Maintained Yes

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  • person_outline kieranc <>

Publication for Phenopath

Phenopath in publications

 (11)
PMCID: 5927542
PMID: 29721379
DOI: 10.1080/2162402X.2017.1423173

[…] one representative tumor-resection block, chosen by the site pathologist according to standardized tissue-block selection guidelines, for each consented and enrolled subject. blocks were shipped to phenopath laboratories (seattle, wa), where sections were cut from the paraffin blocks to perform hematoxylin and eosin (h&e) and ihc staining. in order to minimize site-to-site variations […]

PMCID: 4938529
PMID: 27391784
DOI: 10.1371/journal.pone.0158888

[…] deparaffinized and processed for ihc following a general process according to a polymer-based method (envision, dako). ihc for smarcb1 and cd57 ihc, as well as ss18-ssx fish was performed at phenopath from tumor samples prepared as described above. the scoring indicates the percentage of positive tumor cells and the modal intensity of staining in the positive cells on an intensity scale […]

PMCID: 4646049
DOI: 10.1186/2051-1426-3-S2-P84

[…] infiltrating lymphocyte and the gene signature of infiltrating cells (pi: kunle odunsi). here we describe preliminary comparative analyses of nanostring's ncounter gene expression technology, ihc (phenopath) and flow cytometry (citn immune monitoring laboratory) using ffpe slides and pbmcs from treated subjects., tumor biopsies, whole blood and ficoll-gradient purified pbmcs were collected […]

PMCID: 4684153
PMID: 26504153
DOI: 10.1093/annonc/mdv487

[…] the review boards at all participating institutions approved the study, and all patients gave written informed consent., a central pathology review was planned and conducted for this analysis at phenopath labs (seattle, wa, usa). expression of er (thermo fisher #rm-9101-s; clone sp1), progesterone receptor (pr; dako # m3569, clone pgr636) and ar (dako, #m3562, clone ar441) were assessed […]

PMCID: 4065310
PMID: 24919462
DOI: 10.1186/1756-8722-7-44

[…] monocytes (cd14+), and nk cells (cd16+ cd56+) were measured by flow cytometry at roswell park cancer institute (buffalo, ny)., a retrospective central pathologic review was conducted by a core lab (phenopath laboratories, seattle, wa). cases with discordant pathology were adjudicated by r. gascoyne, md, university of british columbia, vancouver, canada. immunohistochemistry was performed […]


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Phenopath institution(s)
Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, UK; Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK; Centre for Computational Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
Phenopath funding source(s)
Supported by a UK Medical Research Council funded doctoral studentship, a UK Medical Research Council New Investigator Research Grant (Ref. No. MR/L001411/1) and Methodology Research Grant (MR/P02646X/1) and the Wellcome Trust Core Award Grant 474 Number 090532/Z/09/Z.

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