RetroSnake: A modular pipeline to detect human endogenous retroviruses in genome sequencing data

Renata Kabiljo; Harry Bowles; Chad Swanson; Richard Dobson; Ahmad Al Khleifat; Heather Marriott; Ashley Jones; Clement Bouton; John Quinn; Ammar Al-Chalabi; Alfredo Iacoangeli

doi:10.1016/j.isci.2022.105289

RetroSnake: A modular pipeline to detect human endogenous retroviruses in genome sequencing data

Renata Kabiljo, Harry Bowles, Chad Swanson, Richard Dobson, Ahmad Al Khleifat, Heather Marriott, Ashley Jones, Clement Bouton, John Quinn, Ammar Al-Chalabi, Alfredo Iacoangeli^*

^*Corresponding author for this work

University of Liverpool

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

1 Citation (Scopus)

Abstract

Human endogenous retroviruses (HERVs) integrated into the human genome as a result of ancient exogenous infections and currently comprise ∼8% of our genome. The members of the most recently acquired HERV family, HERV-Ks, still retain the potential to produce viral molecules and have been linked to a wide range of diseases including cancer and neurodegeneration. Although a range of tools for HERV detection in NGS data exist, most of them lack wet lab validation and they do not cover all steps of the analysis. Here, we describe RetroSnake, an end-to-end, modular, computationally efficient, and customizable pipeline for the discovery of HERVs in short-read NGS data. RetroSnake is based on an extensively wet-lab validated protocol, it covers all steps of the analysis from raw data to the generation of annotated results presented as an interactive html file, and it is easy to use by life scientists without substantial computational training.

Availability and implementation: The Pipeline and an extensive documentation are available on GitHub.

Original language	English
Article number	105289
Journal	iScience
Volume	25
Issue number	11
Early online date	29 Oct 2022
DOIs	https://doi.org/10.1016/j.isci.2022.105289
Publication status	Published - 18 Nov 2022

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10.1016/j.isci.2022.105289Licence: CC BY

Cite this

@article{7d201deec33b4acba68346e35a90aa8e,

title = "RetroSnake: A modular pipeline to detect human endogenous retroviruses in genome sequencing data",

abstract = "Human endogenous retroviruses (HERVs) integrated into the human genome as a result of ancient exogenous infections and currently comprise ∼8% of our genome. The members of the most recently acquired HERV family, HERV-Ks, still retain the potential to produce viral molecules and have been linked to a wide range of diseases including cancer and neurodegeneration. Although a range of tools for HERV detection in NGS data exist, most of them lack wet lab validation and they do not cover all steps of the analysis. Here, we describe RetroSnake, an end-to-end, modular, computationally efficient, and customizable pipeline for the discovery of HERVs in short-read NGS data. RetroSnake is based on an extensively wet-lab validated protocol, it covers all steps of the analysis from raw data to the generation of annotated results presented as an interactive html file, and it is easy to use by life scientists without substantial computational training.Availability and implementation: The Pipeline and an extensive documentation are available on GitHub.",

author = "Renata Kabiljo and Harry Bowles and Chad Swanson and Richard Dobson and {Al Khleifat}, Ahmad and Heather Marriott and Ashley Jones and Clement Bouton and John Quinn and Ammar Al-Chalabi and Alfredo Iacoangeli",

note = "Funding Information: UK Research and Innovation; Medical Research Council; South London and Maudsley NHS Foundation Trust; MND Scotland; Motor Neurone Disease Association; National Institute for Health Research; Spastic Paraplegia Foundation; Rosetrees Trust; Darby Rimmer MND Foundation. Funding for open access charge: UKRI. R.K. is funded by the MND Scotland. H.M. is supported by a GSK studentship and the KCL funded Centre for Doctoral Training (CDT) in Data-Driven Health. A.I. is funded by the Motor Neurone Disease Association and South London and Maudsley NHS Foundation Trust. This is an EU Joint Programme-Neurodegenerative Disease Research (JPND) project. The project is supported through the following funding organizations under the aegis of JPND-http://www.neurodegenerationresearch.eu/(United Kingdom, Medical Research Council MR/L501529/1 to A.A.-C. principal investigator [PI] and MR/R024804/1 to A.A.-C. PI]; Economic and Social Research Council ES/L008238/1 to A.A.-C. [co-PI]) and through the Motor Neurone Disease Association. This study represents independent research partly funded by the National Institute for Health Research (NIHR) Biomedical Research Center at South London and Maudsley NHS Foundation Trust and King's College London. The work leading up to this publication was funded by the European Community's Horizon 2020 Programme (H2020-PHC-2014-two-stage; grant 633413). A.A.K. is funded by ALS Association Milton Safenowitz Research Fellowship (grant number22-PDF-609.DOI:10.52546/pc.gr.150909.{"} title = {"}doi:DOI:10.52546/pc.gr.150909.{"}>DOI:10.52546/pc.gr.150909.), The Motor Neurone Disease Association (MNDA) Fellowship (Al Khleifat/Oct21/975-799), The Darby Rimmer Foundation, and The NIHR Maudsley Biomedical Research Centre. H.B. his is funded by the National Institute for Health and Care Research (NIHR) Biomedical Research Center based at Guy's and St Thomas{\textquoteright} NHS Foundation Trust and King's College London. C.R.B. is funded by MRC (MR/S000844/1). We acknowledge use of the research computing facility at King's College London, Rosalind (https://rosalind.kcl.ac.uk), which is delivered in partnership with the National Institute for Health Research (NIHR) Biomedical Research Centers at South London & Maudsley and Guy's & St. Thomas{\textquoteright} NHS Foundation Trusts and part-funded by capital equipment grants from the Maudsley Charity (award 980) and Guy's and St Thomas' Charity (TR130505). The views expressed are those of the author(s) and not necessarily those of the NHS, the NIHR, King's College London, or the Department of Health and Social Care. R.K. H.B. and A.I. contributed to concept and design the study. R.K. implemented the software, run the analyses, and drafted the manuscript. H.M. and H.B. have tested the pipeline. H.B. C.R.B. and C.M.S. have designed and preformed the wet lab validation. A.I. supervised the study. A.A.-C. and A.I. raised the study funding. All authors contributed to the write-up. The authors declare no competing interests. Funding Information: UK Research and Innovation ; Medical Research Council ; South London and Maudsley NHS Foundation Trust ; MND Scotland ; Motor Neurone Disease Association ; National Institute for Health Research ; Spastic Paraplegia Foundation ; Rosetrees Trust ; Darby Rimmer MND Foundation . Funding for open access charge: UKRI. R.K. is funded by the MND Scotland. H.M. is supported by a GSK studentship and the KCL funded Centre for Doctoral Training (CDT) in Data-Driven Health. A.I. is funded by the Motor Neurone Disease Association and South London and Maudsley NHS Foundation Trust . This is an EU Joint Programme-Neurodegenerative Disease Research (JPND) project. The project is supported through the following funding organizations under the aegis of JPND - http://www.neurodegenerationresearch.eu/ (United Kingdom, Medical Research Council MR/L501529/1 to A.A.-C., principal investigator [PI] and MR/R024804/1 to A.A.-C., PI]; Economic and Social Research Council ES/L008238/1 to A.A.-C. [co-PI]) and through the Motor Neurone Disease Association . This study represents independent research partly funded by the National Institute for Health Research (NIHR) Biomedical Research Center at South London and Maudsley NHS Foundation Trust and King{\textquoteright}s College London . The work leading up to this publication was funded by the European Community{\textquoteright}s Horizon 2020 Programme (H2020-PHC-2014-two-stage; grant 633413 ). A.A.K. is funded by ALS Association Milton Safenowitz Research Fellowship (grant number 22-PDF-609 .DOI:10.52546/pc.gr.150909.{"} title = {"}doi:DOI:10.52546/pc.gr.150909.{"}>DOI:10.52546/pc.gr.150909.), The Motor Neurone Disease Association (MNDA) Fellowship (Al Khleifat/Oct21/975-799), The Darby Rimmer Foundation , and The NIHR Maudsley Biomedical Research Centre . H.B. his is funded by the National Institute for Health and Care Research (NIHR) Biomedical Research Center based at Guy{\textquoteright}s and St Thomas{\textquoteright} NHS Foundation Trust and King{\textquoteright}s College London . C.R.B. is funded by MRC ( MR/S000844/1 ). We acknowledge use of the research computing facility at King{\textquoteright}s College London, Rosalind ( https://rosalind.kcl.ac.uk ), which is delivered in partnership with the National Institute for Health Research (NIHR) Biomedical Research Centers at South London & Maudsley and Guy{\textquoteright}s & St. Thomas{\textquoteright} NHS Foundation Trusts and part-funded by capital equipment grants from the Maudsley Charity (award 980) and Guy's and St Thomas' Charity ( TR130505 ). The views expressed are those of the author(s) and not necessarily those of the NHS, the NIHR, King{\textquoteright}s College London, or the Department of Health and Social Care. Publisher Copyright: {\textcopyright} 2022",

year = "2022",

month = nov,

day = "18",

doi = "10.1016/j.isci.2022.105289",

language = "English",

volume = "25",

journal = "iScience",

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publisher = "Elsevier publishing company",

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TY - JOUR

T1 - RetroSnake: A modular pipeline to detect human endogenous retroviruses in genome sequencing data

AU - Kabiljo, Renata

AU - Bowles, Harry

AU - Swanson, Chad

AU - Dobson, Richard

AU - Al Khleifat, Ahmad

AU - Marriott, Heather

AU - Jones, Ashley

AU - Bouton, Clement

AU - Quinn, John

AU - Al-Chalabi, Ammar

AU - Iacoangeli, Alfredo

N1 - Funding Information: UK Research and Innovation; Medical Research Council; South London and Maudsley NHS Foundation Trust; MND Scotland; Motor Neurone Disease Association; National Institute for Health Research; Spastic Paraplegia Foundation; Rosetrees Trust; Darby Rimmer MND Foundation. Funding for open access charge: UKRI. R.K. is funded by the MND Scotland. H.M. is supported by a GSK studentship and the KCL funded Centre for Doctoral Training (CDT) in Data-Driven Health. A.I. is funded by the Motor Neurone Disease Association and South London and Maudsley NHS Foundation Trust. This is an EU Joint Programme-Neurodegenerative Disease Research (JPND) project. The project is supported through the following funding organizations under the aegis of JPND-http://www.neurodegenerationresearch.eu/(United Kingdom, Medical Research Council MR/L501529/1 to A.A.-C. principal investigator [PI] and MR/R024804/1 to A.A.-C. PI]; Economic and Social Research Council ES/L008238/1 to A.A.-C. [co-PI]) and through the Motor Neurone Disease Association. This study represents independent research partly funded by the National Institute for Health Research (NIHR) Biomedical Research Center at South London and Maudsley NHS Foundation Trust and King's College London. The work leading up to this publication was funded by the European Community's Horizon 2020 Programme (H2020-PHC-2014-two-stage; grant 633413). A.A.K. is funded by ALS Association Milton Safenowitz Research Fellowship (grant number22-PDF-609.DOI:10.52546/pc.gr.150909." title = "doi:DOI:10.52546/pc.gr.150909.">DOI:10.52546/pc.gr.150909.), The Motor Neurone Disease Association (MNDA) Fellowship (Al Khleifat/Oct21/975-799), The Darby Rimmer Foundation, and The NIHR Maudsley Biomedical Research Centre. H.B. his is funded by the National Institute for Health and Care Research (NIHR) Biomedical Research Center based at Guy's and St Thomas’ NHS Foundation Trust and King's College London. C.R.B. is funded by MRC (MR/S000844/1). We acknowledge use of the research computing facility at King's College London, Rosalind (https://rosalind.kcl.ac.uk), which is delivered in partnership with the National Institute for Health Research (NIHR) Biomedical Research Centers at South London & Maudsley and Guy's & St. Thomas’ NHS Foundation Trusts and part-funded by capital equipment grants from the Maudsley Charity (award 980) and Guy's and St Thomas' Charity (TR130505). The views expressed are those of the author(s) and not necessarily those of the NHS, the NIHR, King's College London, or the Department of Health and Social Care. R.K. H.B. and A.I. contributed to concept and design the study. R.K. implemented the software, run the analyses, and drafted the manuscript. H.M. and H.B. have tested the pipeline. H.B. C.R.B. and C.M.S. have designed and preformed the wet lab validation. A.I. supervised the study. A.A.-C. and A.I. raised the study funding. All authors contributed to the write-up. The authors declare no competing interests. Funding Information: UK Research and Innovation ; Medical Research Council ; South London and Maudsley NHS Foundation Trust ; MND Scotland ; Motor Neurone Disease Association ; National Institute for Health Research ; Spastic Paraplegia Foundation ; Rosetrees Trust ; Darby Rimmer MND Foundation . Funding for open access charge: UKRI. R.K. is funded by the MND Scotland. H.M. is supported by a GSK studentship and the KCL funded Centre for Doctoral Training (CDT) in Data-Driven Health. A.I. is funded by the Motor Neurone Disease Association and South London and Maudsley NHS Foundation Trust . This is an EU Joint Programme-Neurodegenerative Disease Research (JPND) project. The project is supported through the following funding organizations under the aegis of JPND - http://www.neurodegenerationresearch.eu/ (United Kingdom, Medical Research Council MR/L501529/1 to A.A.-C., principal investigator [PI] and MR/R024804/1 to A.A.-C., PI]; Economic and Social Research Council ES/L008238/1 to A.A.-C. [co-PI]) and through the Motor Neurone Disease Association . This study represents independent research partly funded by the National Institute for Health Research (NIHR) Biomedical Research Center at South London and Maudsley NHS Foundation Trust and King’s College London . The work leading up to this publication was funded by the European Community’s Horizon 2020 Programme (H2020-PHC-2014-two-stage; grant 633413 ). A.A.K. is funded by ALS Association Milton Safenowitz Research Fellowship (grant number 22-PDF-609 .DOI:10.52546/pc.gr.150909." title = "doi:DOI:10.52546/pc.gr.150909.">DOI:10.52546/pc.gr.150909.), The Motor Neurone Disease Association (MNDA) Fellowship (Al Khleifat/Oct21/975-799), The Darby Rimmer Foundation , and The NIHR Maudsley Biomedical Research Centre . H.B. his is funded by the National Institute for Health and Care Research (NIHR) Biomedical Research Center based at Guy’s and St Thomas’ NHS Foundation Trust and King’s College London . C.R.B. is funded by MRC ( MR/S000844/1 ). We acknowledge use of the research computing facility at King’s College London, Rosalind ( https://rosalind.kcl.ac.uk ), which is delivered in partnership with the National Institute for Health Research (NIHR) Biomedical Research Centers at South London & Maudsley and Guy’s & St. Thomas’ NHS Foundation Trusts and part-funded by capital equipment grants from the Maudsley Charity (award 980) and Guy's and St Thomas' Charity ( TR130505 ). The views expressed are those of the author(s) and not necessarily those of the NHS, the NIHR, King’s College London, or the Department of Health and Social Care. Publisher Copyright: © 2022

PY - 2022/11/18

Y1 - 2022/11/18

N2 - Human endogenous retroviruses (HERVs) integrated into the human genome as a result of ancient exogenous infections and currently comprise ∼8% of our genome. The members of the most recently acquired HERV family, HERV-Ks, still retain the potential to produce viral molecules and have been linked to a wide range of diseases including cancer and neurodegeneration. Although a range of tools for HERV detection in NGS data exist, most of them lack wet lab validation and they do not cover all steps of the analysis. Here, we describe RetroSnake, an end-to-end, modular, computationally efficient, and customizable pipeline for the discovery of HERVs in short-read NGS data. RetroSnake is based on an extensively wet-lab validated protocol, it covers all steps of the analysis from raw data to the generation of annotated results presented as an interactive html file, and it is easy to use by life scientists without substantial computational training.Availability and implementation: The Pipeline and an extensive documentation are available on GitHub.

AB - Human endogenous retroviruses (HERVs) integrated into the human genome as a result of ancient exogenous infections and currently comprise ∼8% of our genome. The members of the most recently acquired HERV family, HERV-Ks, still retain the potential to produce viral molecules and have been linked to a wide range of diseases including cancer and neurodegeneration. Although a range of tools for HERV detection in NGS data exist, most of them lack wet lab validation and they do not cover all steps of the analysis. Here, we describe RetroSnake, an end-to-end, modular, computationally efficient, and customizable pipeline for the discovery of HERVs in short-read NGS data. RetroSnake is based on an extensively wet-lab validated protocol, it covers all steps of the analysis from raw data to the generation of annotated results presented as an interactive html file, and it is easy to use by life scientists without substantial computational training.Availability and implementation: The Pipeline and an extensive documentation are available on GitHub.

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U2 - 10.1016/j.isci.2022.105289

DO - 10.1016/j.isci.2022.105289

M3 - Article

SN - 2589-0042

VL - 25

JO - iScience

JF - iScience

IS - 11

M1 - 105289

ER -

RetroSnake: A modular pipeline to detect human endogenous retroviruses in genome sequencing data

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