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Soft Windowing Application to Improve Analysis of High-throughput Phenotyping Data

Hamed Haselimashhadi, Mason C. Jeremy, Violeta Munoz-Fuentes, Federico López-Gómez, Kolawole Babalola, Elif F. Acar, Vivek Kumar, Jacqui White, Ann M. Flenniken, Ruairidh King, Ewan Straiton, John Richard Seavitt, Angelina Gaspero, Arturo Garza, Audrey E. Christianson, Chih-Wei Hsu, Corey L. Reynolds, Denise G. Lanza, Isabel Lorenzo, Jennie R. Green, Juan J. Gallegos, Ritu Bohat, Rodney C. Samaco, Surabi Veeraragavan, Jong Kyoung Kim, Gregor Miller, Helmut Fuchs, Lillian Garrett, Lore Becker, Yeon Kyung Kang, David Clary, Soo Young Cho, Masaru Tamura, Nobuhiko Tanaka, Kyung Dong Soo, Alexandr Bezginov, Ghina Bou About, Marie-France Champy, Laurent Vasseur, Sophie Leblanc, Hamid Meziane, Mohammed Selloum, Patrick T. Reilly, Nadine Spielmann, Holger Maier, Valerie Gailus-Durner, Tania Sorg, Masuya Hiroshi, Obata Yuichi, Jason D. Heaney, Mary E Dickinson, Wurst Wolfgang, Glauco P. Tocchini-Valentini, Kevin C. Kent Lloyd, Colin McKerlie, Je Kyung Seong, Herault Yann, Martin Hrabé de Angelis, Steve D.M. Brown, Damian Smedley, Paul Flicek, Ann-Marie Mallon, Helen Parkinson, Terrence F. Meehan
doi: https://doi.org/10.1101/656678
Hamed Haselimashhadi
1European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
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  • For correspondence: hamedhm@ebi.ac.uk
Mason C. Jeremy
1European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
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Violeta Munoz-Fuentes
1European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
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Federico López-Gómez
1European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
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Kolawole Babalola
1European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
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Elif F. Acar
2The Centre for Phenogenomics, Toronto, Canada; The Hospital for Sick Children, Toronto, Canada
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Vivek Kumar
3The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609
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Jacqui White
3The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609
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Ann M. Flenniken
4The Centre for Phenogenomics, Toronto, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
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Ruairidh King
5MRC Harwell Institute, Harwell, OX11 0RD, UK
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Ewan Straiton
5MRC Harwell Institute, Harwell, OX11 0RD, UK
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John Richard Seavitt
6Baylor College of Medicine, Houston, TX, USA
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Angelina Gaspero
6Baylor College of Medicine, Houston, TX, USA
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Arturo Garza
6Baylor College of Medicine, Houston, TX, USA
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Audrey E. Christianson
6Baylor College of Medicine, Houston, TX, USA
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Chih-Wei Hsu
6Baylor College of Medicine, Houston, TX, USA
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Corey L. Reynolds
6Baylor College of Medicine, Houston, TX, USA
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Denise G. Lanza
6Baylor College of Medicine, Houston, TX, USA
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Isabel Lorenzo
6Baylor College of Medicine, Houston, TX, USA
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Jennie R. Green
6Baylor College of Medicine, Houston, TX, USA
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Juan J. Gallegos
6Baylor College of Medicine, Houston, TX, USA
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Ritu Bohat
6Baylor College of Medicine, Houston, TX, USA
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Rodney C. Samaco
6Baylor College of Medicine, Houston, TX, USA
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Surabi Veeraragavan
6Baylor College of Medicine, Houston, TX, USA
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Jong Kyoung Kim
7Daegu Gyeongbuk Institute of Science & Technology(DGIST), Korea
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Gregor Miller
8HelmholtzCenter Munich, Neuherberg, Germany
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Helmut Fuchs
8HelmholtzCenter Munich, Neuherberg, Germany
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Lillian Garrett
8HelmholtzCenter Munich, Neuherberg, Germany
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Lore Becker
8HelmholtzCenter Munich, Neuherberg, Germany
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Yeon Kyung Kang
9Korea Mouse Phenotyping Center(KMPC), Korea
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David Clary
10Mouse Biology Program, University of California Davis
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Soo Young Cho
11National Cancer Center(NCC) & Korea Mouse Phenotyping Center(KMPC), Korea
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Masaru Tamura
12RIKEN BioResource Research Center, Tsukuba, Japan
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Nobuhiko Tanaka
12RIKEN BioResource Research Center, Tsukuba, Japan
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Kyung Dong Soo
13Seoul National University & Korea Mouse Phenotyping Center(KMPC), Korea
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Alexandr Bezginov
2The Centre for Phenogenomics, Toronto, Canada; The Hospital for Sick Children, Toronto, Canada
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Ghina Bou About
14Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris, PHENOMIN-ICS 1 rue Laurent Fries, 67404 ILLKIRCH
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Marie-France Champy
14Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris, PHENOMIN-ICS 1 rue Laurent Fries, 67404 ILLKIRCH
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Laurent Vasseur
14Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris, PHENOMIN-ICS 1 rue Laurent Fries, 67404 ILLKIRCH
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Sophie Leblanc
14Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris, PHENOMIN-ICS 1 rue Laurent Fries, 67404 ILLKIRCH
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Hamid Meziane
14Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris, PHENOMIN-ICS 1 rue Laurent Fries, 67404 ILLKIRCH
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Mohammed Selloum
14Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris, PHENOMIN-ICS 1 rue Laurent Fries, 67404 ILLKIRCH
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Patrick T. Reilly
14Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris, PHENOMIN-ICS 1 rue Laurent Fries, 67404 ILLKIRCH
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Nadine Spielmann
8HelmholtzCenter Munich, Neuherberg, Germany
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Holger Maier
8HelmholtzCenter Munich, Neuherberg, Germany
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Valerie Gailus-Durner
8HelmholtzCenter Munich, Neuherberg, Germany
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Tania Sorg
14Université de Strasbourg, CNRS, INSERM, Institut Clinique de la Souris, PHENOMIN-ICS 1 rue Laurent Fries, 67404 ILLKIRCH
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Masuya Hiroshi
12RIKEN BioResource Research Center, Tsukuba, Japan
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Obata Yuichi
12RIKEN BioResource Research Center, Tsukuba, Japan
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Jason D. Heaney
6Baylor College of Medicine, Houston, TX, USA
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Mary E Dickinson
6Baylor College of Medicine, Houston, TX, USA
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Wurst Wolfgang
15Institute of Developmental Genetics, HelmholtzCentre Munich, Germany
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Glauco P. Tocchini-Valentini
16CNR EMMA Monterotondo, Italy
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Kevin C. Kent Lloyd
10Mouse Biology Program, University of California Davis
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Colin McKerlie
2The Centre for Phenogenomics, Toronto, Canada; The Hospital for Sick Children, Toronto, Canada
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Je Kyung Seong
13Seoul National University & Korea Mouse Phenotyping Center(KMPC), Korea
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Herault Yann
17Université de Strasbourg, CNRS, INSERM, Institut de Génétique, Biologie Moléculaire et Cellulaire, Institut Clinique de la Souris, IGBMC, PHENOMIN-ICS 1 rue Laurent Fries, 67404 ILLKIRCH
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Martin Hrabé de Angelis
8HelmholtzCenter Munich, Neuherberg, Germany
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Steve D.M. Brown
5MRC Harwell Institute, Harwell, OX11 0RD, UK
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Damian Smedley
18William Harvey Research Institute, Charterhouse Square Barts and the London School of Medicine and Dentistry Queen Mary University of London, London EC1M 6BQ
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Paul Flicek
1European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
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Ann-Marie Mallon
5MRC Harwell Institute, Harwell, OX11 0RD, UK
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Helen Parkinson
1European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
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Terrence F. Meehan
1European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
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Abstract

Motivation High-throughput phenomic projects generate complex data from small treatment and large control groups that increase the power of the analyses but introduce variation over time. A method is needed to utlize a set of temporally local controls that maximises analytic power while minimising noise from unspecified environmental factors.

Results Here we introduce “soft windowing”, a methodological approach that selects a window of time that includes the most appropriate controls for analysis. Using phenotype data from the International Mouse Phenotyping Consortium (IMPC), adaptive windows were applied such that control data collected proximally to mutants were assigned the maximal weight, while data collected earlier or later had less weight. We applied this method to IMPC data and compared the results with those obtained from a standard non-windowed approach. Validation was performed using a resampling approach in which we demonstrate a 10% reduction of false positives from 2.5 million analyses. We applied the method to our production analysis pipeline that establishes genotype-phenotype associations by comparing mutant versus control data. We report an increase of 30% in significant p-values, as well as linkage to 106 versus 99 disease models via phenotype overlap with the soft windowed and non-windowed approaches, respectively, from a set of 2,082 mutant mouse lines. Our method is generalisable and can benefit large-scale human phenomic projects such as the UK Biobank and the All of Us resources.

Availability and Implementation The method is freely available in the R package SmoothWin, available on CRAN http://CRAN.R-project.org/package=SmoothWin.

Footnotes

  • https://wwwdev.ebi.ac.uk/mi/impc/dev/phenotype-archive/media/images/windowing/

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Soft Windowing Application to Improve Analysis of High-throughput Phenotyping Data
Hamed Haselimashhadi, Mason C. Jeremy, Violeta Munoz-Fuentes, Federico López-Gómez, Kolawole Babalola, Elif F. Acar, Vivek Kumar, Jacqui White, Ann M. Flenniken, Ruairidh King, Ewan Straiton, John Richard Seavitt, Angelina Gaspero, Arturo Garza, Audrey E. Christianson, Chih-Wei Hsu, Corey L. Reynolds, Denise G. Lanza, Isabel Lorenzo, Jennie R. Green, Juan J. Gallegos, Ritu Bohat, Rodney C. Samaco, Surabi Veeraragavan, Jong Kyoung Kim, Gregor Miller, Helmut Fuchs, Lillian Garrett, Lore Becker, Yeon Kyung Kang, David Clary, Soo Young Cho, Masaru Tamura, Nobuhiko Tanaka, Kyung Dong Soo, Alexandr Bezginov, Ghina Bou About, Marie-France Champy, Laurent Vasseur, Sophie Leblanc, Hamid Meziane, Mohammed Selloum, Patrick T. Reilly, Nadine Spielmann, Holger Maier, Valerie Gailus-Durner, Tania Sorg, Masuya Hiroshi, Obata Yuichi, Jason D. Heaney, Mary E Dickinson, Wurst Wolfgang, Glauco P. Tocchini-Valentini, Kevin C. Kent Lloyd, Colin McKerlie, Je Kyung Seong, Herault Yann, Martin Hrabé de Angelis, Steve D.M. Brown, Damian Smedley, Paul Flicek, Ann-Marie Mallon, Helen Parkinson, Terrence F. Meehan
bioRxiv 656678; doi: https://doi.org/10.1101/656678
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Soft Windowing Application to Improve Analysis of High-throughput Phenotyping Data
Hamed Haselimashhadi, Mason C. Jeremy, Violeta Munoz-Fuentes, Federico López-Gómez, Kolawole Babalola, Elif F. Acar, Vivek Kumar, Jacqui White, Ann M. Flenniken, Ruairidh King, Ewan Straiton, John Richard Seavitt, Angelina Gaspero, Arturo Garza, Audrey E. Christianson, Chih-Wei Hsu, Corey L. Reynolds, Denise G. Lanza, Isabel Lorenzo, Jennie R. Green, Juan J. Gallegos, Ritu Bohat, Rodney C. Samaco, Surabi Veeraragavan, Jong Kyoung Kim, Gregor Miller, Helmut Fuchs, Lillian Garrett, Lore Becker, Yeon Kyung Kang, David Clary, Soo Young Cho, Masaru Tamura, Nobuhiko Tanaka, Kyung Dong Soo, Alexandr Bezginov, Ghina Bou About, Marie-France Champy, Laurent Vasseur, Sophie Leblanc, Hamid Meziane, Mohammed Selloum, Patrick T. Reilly, Nadine Spielmann, Holger Maier, Valerie Gailus-Durner, Tania Sorg, Masuya Hiroshi, Obata Yuichi, Jason D. Heaney, Mary E Dickinson, Wurst Wolfgang, Glauco P. Tocchini-Valentini, Kevin C. Kent Lloyd, Colin McKerlie, Je Kyung Seong, Herault Yann, Martin Hrabé de Angelis, Steve D.M. Brown, Damian Smedley, Paul Flicek, Ann-Marie Mallon, Helen Parkinson, Terrence F. Meehan
bioRxiv 656678; doi: https://doi.org/10.1101/656678

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