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Protocols

HISAP specifications

Information


Unique identifier OMICS_09521
Name HISAP
Alternative name High-Througput Insertion Site Analysis Pipeline
Interface Web user interface
Restrictions to use None
Biological technology Roche
Computer skills Basic
Stability No
Maintained No

Maintainer


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Publication for High-Througput Insertion Site Analysis Pipeline

HISAP citations

 (3)
library_books

Genome wide Specificity of Highly Efficient TALENs and CRISPR/Cas9 for T Cell Receptor Modification

2017
PMCID: 5363317
PMID: 28345006
DOI: 10.1016/j.omtm.2017.01.005

[…] platform, barcode-containing adapters were added to LAM-PCR products by an additional PCR step, and the integration site data were analyzed using the high-throughput insertion site analysis pipeline (HISAP). Additional in silico off-target prediction for βC1 and βC3 was accomplished with the web-based COSMID tool. For all analyses, the UCSC Assembly hg19 (February 2009) was used as reference genom […]

library_books

GENE IS: Time Efficient and Accurate Analysis of Viral Integration Events in Large Scale Gene Therapy Data

2016
Mol Ther Nucleic Acids
PMCID: 5363413
PMID: 28325279
DOI: 10.1016/j.omtn.2016.12.001

[…] (). The advent of high-throughput sequencing technologies has revolutionized the possibilities of in-depth genome analyses. However, computational tools available for LAM IS analysis, like QuickMap, HISAP, and VISA, have issues with time efficiency and are not offering targeted sequencing IS analysis. Besides, these tools admit a limited set of reference genomes, do not expose multi-threading, an […]

call_split

Comparison of Lentiviral and Sleeping Beauty Mediated αβ T Cell Receptor Gene Transfer

2013
PLoS One
PMCID: 3695921
PMID: 23840834
DOI: 10.1371/journal.pone.0068201
call_split See protocol

[…] the second round primers. LM-PCR products were 454 pyrosequenced as previously described .Raw sequence reads obtained after sequencing were trimmed and aligned to the human genome (NCBI, hg19) using HISAP . Integration sites were considered to be valid if vector-genome junction sequence was present and the flanking genomic region had a unique sequence match of at least 95% after alignment to the […]

Citations

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HISAP institution(s)
Department of Translational Oncology, National Center for Tumor Diseases (NCT) and German Cancer Research Center (DKFZ), Heidelberg, Germany; University Paris-Descartes, Department of Pediatric Neurology, Hôpital Bicêtre-Paris Sud, Le Kremlin-Bicêtre, France

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