Identifying viral integration sites using SeqMap 2.0

Troy B. Hawkins; Jessica Dantzer; Brandon Peters; Mary Dinauer; Keithanne Mockaitis; Sean Mooney; Kenneth Cornetta

doi:10.1093/bioinformatics/btq722

Identifying viral integration sites using SeqMap 2.0

Troy B. Hawkins, Jessica Dantzer, Brandon Peters, Mary Dinauer, Keithanne Mockaitis, Sean Mooney, Kenneth Cornetta

Research output: Contribution to journal › Article › peer-review

32 Scopus citations

Abstract

Summary: Retroviral integration has been implicated in several biomedical applications, including identification of cancerassociated genes and malignant transformation in gene therapy clinical trials. We introduce an efficient and scalable method for fast identification of viral vector integration sites from long read high-throughput sequencing. Individual sequence reads are masked to remove non-genomic sequence, aligned to the host genome and assembled into contiguous fragments used to pinpoint the position of integration.

Original language	English
Article number	btq722
Pages (from-to)	720-722
Number of pages	3
Journal	Bioinformatics
Volume	27
Issue number	5
DOIs	https://doi.org/10.1093/bioinformatics/btq722
State	Published - Mar 2011

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10.1093/bioinformatics/btq722

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title = "Identifying viral integration sites using SeqMap 2.0",

abstract = "Summary: Retroviral integration has been implicated in several biomedical applications, including identification of cancerassociated genes and malignant transformation in gene therapy clinical trials. We introduce an efficient and scalable method for fast identification of viral vector integration sites from long read high-throughput sequencing. Individual sequence reads are masked to remove non-genomic sequence, aligned to the host genome and assembled into contiguous fragments used to pinpoint the position of integration.",

author = "Hawkins, {Troy B.} and Jessica Dantzer and Brandon Peters and Mary Dinauer and Keithanne Mockaitis and Sean Mooney and Kenneth Cornetta",

note = "Funding Information: Funding: This work was supported by the National Institutes of Health (P40 RR024928, R01LM009722, T32 HL007910, P01 HL53586); Indiana Clinical and Translational Sciences Institute Bioinformatics and Advanced Information Technology Cores (U54 RR025761).",

year = "2011",

month = mar,

doi = "10.1093/bioinformatics/btq722",

language = "English",

volume = "27",

pages = "720--722",

journal = "Bioinformatics",

issn = "1367-4803",

number = "5",

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TY - JOUR

T1 - Identifying viral integration sites using SeqMap 2.0

AU - Hawkins, Troy B.

AU - Dantzer, Jessica

AU - Peters, Brandon

AU - Dinauer, Mary

AU - Mockaitis, Keithanne

AU - Mooney, Sean

AU - Cornetta, Kenneth

N1 - Funding Information: Funding: This work was supported by the National Institutes of Health (P40 RR024928, R01LM009722, T32 HL007910, P01 HL53586); Indiana Clinical and Translational Sciences Institute Bioinformatics and Advanced Information Technology Cores (U54 RR025761).

PY - 2011/3

Y1 - 2011/3

N2 - Summary: Retroviral integration has been implicated in several biomedical applications, including identification of cancerassociated genes and malignant transformation in gene therapy clinical trials. We introduce an efficient and scalable method for fast identification of viral vector integration sites from long read high-throughput sequencing. Individual sequence reads are masked to remove non-genomic sequence, aligned to the host genome and assembled into contiguous fragments used to pinpoint the position of integration.

AB - Summary: Retroviral integration has been implicated in several biomedical applications, including identification of cancerassociated genes and malignant transformation in gene therapy clinical trials. We introduce an efficient and scalable method for fast identification of viral vector integration sites from long read high-throughput sequencing. Individual sequence reads are masked to remove non-genomic sequence, aligned to the host genome and assembled into contiguous fragments used to pinpoint the position of integration.

UR - http://www.scopus.com/inward/record.url?scp=79951972332&partnerID=8YFLogxK

U2 - 10.1093/bioinformatics/btq722

DO - 10.1093/bioinformatics/btq722

M3 - Article

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AN - SCOPUS:79951972332

SN - 1367-4803

VL - 27

SP - 720

EP - 722

JO - Bioinformatics

JF - Bioinformatics

IS - 5

M1 - btq722

ER -

Identifying viral integration sites using SeqMap 2.0

Abstract

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