HPVDetector protocols

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HPVDetector specifications

Information


Unique identifier OMICS_21870
Name HPVDetector
Interface Command line interface, Graphical user interface
Restrictions to use Academic or non-commercial use
Input data A paired-end whole-exome, whole-genome or whole-transcriptome data set.
Output data A result file which enlists one or more HPV type(s) and number of HPV reads or a result file containing HPV integration loci on the human genome, annotation of HPV genes, human genes and human genome cytobands.
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Amit Dutt <>

Publication for HPVDetector

HPVDetector in pipeline

2018
PMCID: 5880257
PMID: 29610388
DOI: 10.1101/mcs.a002279

[…] of cancer-specific genes, as previously defined ()., presence of hpv was determined by alignment of tumor sample reads using bwa (). hpv was confirmed and the hpv-35 subtype further classified by hpvdetector ()., to explore whether we would have obtained similar or identical results from wes to those obtained by wgs, we applied an in silico filter using the agilent sureselect exome panel. […]


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HPVDetector in publications

 (4)
PMCID: 5880257
PMID: 29610388
DOI: 10.1101/mcs.a002279

[…] of cancer-specific genes, as previously defined ()., presence of hpv was determined by alignment of tumor sample reads using bwa (). hpv was confirmed and the hpv-35 subtype further classified by hpvdetector ()., to explore whether we would have obtained similar or identical results from wes to those obtained by wgs, we applied an in silico filter using the agilent sureselect exome panel. […]

PMCID: 5628952
PMID: 28939077
DOI: 10.1016/j.oraloncology.2017.08.003

[…] nuclei was used for data analysis. clinical, histological and etiological features were collected along with follow-up data for recurrence (). none of the samples showed the presence of hpv using hpvdetector and pcr-based validation using the my09/11 method as described previously , ., exome capture and sequencing were performed as described previously . briefly, truseq exome enrichment kit […]

PMCID: 5226594
PMID: 27391340
DOI: 10.18632/oncotarget.10419

[…] of hpv using my09/11 pcr and e6 transcript pcr primers. 40 of 71 samples analyzed, all were found to be hpv negative. where exome sequence was available, the absence of hpv was re-confirmed using hpvdetector, as previously described []. tscc samples of indian origin to be hpv negative is consistent with other studies [-]., to characterize somatic alterations across 48 genes of notch signaling […]

PMCID: 4776363
PMID: 26941832
DOI: 10.1186/s13027-016-0057-x

[…] common salmonella serotypes (s. typhi ty2, s. typhi ct18, s. typhimurium lt2, s. choleraesuis scb67, s. paratyphi tcc, and s. paratyphi spb7) using a computational subtraction pipeline based on the hpvdetector, we recently described. based on our evaluation of 26 whole exome gallbladder primary tumours and matched normal samples: association of typhoidal salmonella species were found in 11 […]


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HPVDetector institution(s)
Advanced Centre for Treatment, Research and Education in Cancer, Tata Memorial Centre, Kharghar, Navi Mumbai, India
HPVDetector funding source(s)
Supported by an Intermediate Fellowship from the Wellcome Trust/DBT India Alliance (IA/I/11/2500278); by a grant from DBT (BT/PR2372/ AGR/36/696/2011); intramural grants (IRB project 92 and 55); a senior research fellowship from ACTREC and a senior research fellowship from CSIR.

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