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POLYSOLVER specifications

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Unique identifier OMICS_19815
Name POLYSOLVER
Alternative name POLYmorphic loci reSOLVER
Software type Application/Script
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
License MIT License
Computer skills Advanced
Stability Stable
Maintained No

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Publication for POLYmorphic loci reSOLVER

POLYSOLVER citations

 (24)
library_books

Population level distribution and putative immunogenicity of cancer neoepitopes

2018
BMC Cancer
PMCID: 5899330
PMID: 29653567
DOI: 10.1186/s12885-018-4325-6

[…] To do this, we generated a list of HLA alleles to use for subsequent analysis based on allele frequencies originating from the Allele Frequency Net Database [] and summarized for use in the software POLYSOLVER (v1.0) []. The average frequencies across races (Asian, Black, and Caucasian) of alleles for each HLA gene (HLA-A, HLA-B, and HLA-C) were calculated and normalized to sum to 100%. We then s […]

library_books

Immunopharmacogenomics towards personalized cancer immunotherapy targeting neoantigens

2018
Cancer Sci
PMCID: 5834780
PMID: 29288513
DOI: 10.1111/cas.13498

[…] an bind to HLA molecules. Several tools have been developed to obtain HLA allele information from genome‐wide sequencing data (whole‐exome, whole‐genome, and RNA sequencing data), including OptiType, Polysolver, PHLAT, HLAreporter, HLAforest, HLAminer, and seq2HLA. We have tested 961 whole‐exome data from the 1000 Genomes Project to evaluate the accuracy of these programs. Among these algorithms, […]

library_books

Contraction of T cell richness in lung cancer brain metastases

2018
Sci Rep
PMCID: 5794798
PMID: 29391594
DOI: 10.1038/s41598-018-20622-8

[…] were used to generate peptide sequences of different lengths (8–12 mers) using a custom script and HLA type of the individual was determined using the matching normal sample whenever available using Polysolver version v1.0. In cases where there was no matching normal tissue, the matching primary tumor was used. The HLA type and peptide sequences from respective individuals were used to predict th […]

library_books

Mutational patterns in chemotherapy resistant muscle invasive bladder cancer

2017
Nat Commun
PMCID: 5736752
PMID: 29259186
DOI: 10.1038/s41467-017-02320-7

[…] HLA-type was inferred using POLYSOLVER, which uses a normal tissue bam file as input and employs a Bayesian classifier to determine genotype for each patient. Neoantigens were predicted for each patient by defining all novel ami […]

library_books

Allele Specific HLA Loss and Immune Escape in Lung Cancer Evolution

2017
Cell
PMCID: 5720478
PMID: 29107330
DOI: 10.1016/j.cell.2017.10.001

[…] As input, LOHHLA requires: a tumor and germline BAM; patient-specific HLA calls, either predicted by an HLA inference tool (e.g., POLYSOLVER [] or Optitype []) or through HLA serotyping; the HLA fasta file location; purity and ploidy estimates. (For implementation of LOHHLA in this manuscript, ASCAT was used to estimate tumor pu […]

library_books

Neoantigens Generated by Individual Mutations and Their Role in Cancer Immunity and Immunotherapy

2017
Front Immunol
PMCID: 5712389
PMID: 29234329
DOI: 10.3389/fimmu.2017.01679

[…] re for variant annotation to predict the affected proteins (). Patient-specific NGS data from WES, WGS, or RNA sequencing (RNA-seq) can be also used to predict HLA types with computational tools like Polysolver () and Optiptype (), which are able to extract the reads covering the HLA locus and predict the major alleles at 4-digit resolution or more. Finally, machine learning algorithms such as Net […]

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POLYSOLVER institution(s)
Cancer Vaccine Center, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Massachusetts General Hospital Cancer Center and Department of Pathology, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA; Department of Statistics, Iowa State University, Ames, IA, USA; Harvard/MIT Division of Health Sciences and Technology, Cambridge, MA, USA; Department of Pathology, Brigham and Women’s Hospital, Boston, MA, USA; Harvard Medical School, Boston, MA, USA
POLYSOLVER funding source(s)
Supported by the Blavatnik Family Foundation, AACR (SU2C Innovative Research Grant), NHLBI (1RO1HL103532-01), and NCI (1R01CA155010-01A1).

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