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Candidate Explorer: a tool for discovery, evaluation, and display of mutations causing significant immune phenotypes

Darui Xu, Stephen Lyon, Chun Hui Bu, Sara Hildebrand, Jin Huk Choi, Xue Zhong, Aijie Liu, Emre E. Turer, Zhao Zhang, Evan Nair-Gill, Hexin Shi, Ying Wang, Duanwu Zhang, Tao Yue, Jeff SoRelle, Takuma Misawa, Lei Sun, Jianhui Wang, Roxana Farokhnia, Andrew Sakla, Sara Schneider, Nathan Stewart, Hannah Coco, Gabrielle Coolbaugh, Braden Hayse, Sara Mazal, Dawson Medler, Brandon Nguyen, Edward Rodriguez, Andrew Wadley, Miao Tang, Xiaohong Li, Priscilla Anderton, Katie Keller, Lindsay Scott, Jiexia Quan, Sydney Cooper, Baifang Qin, Jennifer Cardin, Rochelle Simpson, Meron Tadesse, Qihua Sun, John Santoyo, Amy Bronikowski, Alexyss Johnson, View ORCID ProfileEva Marie Y. Moresco, View ORCID ProfileBruce Beutler
doi: https://doi.org/10.1101/2020.11.07.371914
Darui Xu
1Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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Stephen Lyon
1Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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Chun Hui Bu
1Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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Sara Hildebrand
1Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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Jin Huk Choi
1Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390
2Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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Xue Zhong
1Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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Aijie Liu
1Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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Emre E. Turer
1Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390
3Department of Internal Medicine, Division of Gastroenterology, University of Texas Southwestern Medical Center, Dallas, TX 75390
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Zhao Zhang
1Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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Evan Nair-Gill
1Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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Hexin Shi
1Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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Ying Wang
1Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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Duanwu Zhang
1Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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Tao Yue
1Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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Jeff SoRelle
1Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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Takuma Misawa
1Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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Lei Sun
1Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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Jianhui Wang
1Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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Roxana Farokhnia
1Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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Andrew Sakla
1Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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Sara Schneider
1Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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Nathan Stewart
1Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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Hannah Coco
1Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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Gabrielle Coolbaugh
1Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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Braden Hayse
1Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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Sara Mazal
1Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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Dawson Medler
1Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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Brandon Nguyen
1Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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Edward Rodriguez
1Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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Andrew Wadley
1Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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Miao Tang
1Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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Xiaohong Li
1Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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Priscilla Anderton
1Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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Katie Keller
1Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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Lindsay Scott
1Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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Jiexia Quan
1Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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Sydney Cooper
1Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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Baifang Qin
1Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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Jennifer Cardin
1Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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Rochelle Simpson
1Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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Meron Tadesse
1Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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Qihua Sun
1Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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John Santoyo
1Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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Amy Bronikowski
1Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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Alexyss Johnson
1Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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Eva Marie Y. Moresco
1Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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  • ORCID record for Eva Marie Y. Moresco
Bruce Beutler
1Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas 75390
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  • ORCID record for Bruce Beutler
  • For correspondence: Bruce.Beutler@UTSouthwestern.edu
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Abstract

When applied to immunity, forward genetic studies use meiotic mapping to provide strong statistical evidence that a particular mutation is causative of a particular immune phenotype. Notwithstanding this, co-segregation of multiple mutations, occasional unawareness of mutations, and paucity of homozygotes may lead to erroneous declarations of cause and effect. We sought to improve the selection of authentic causative mutations using a machine learning software tool, Candidate Explorer (CE), which integrates 65 data features into a single numeric score, mathematically convertible to the likelihood of verification of any putative mutation-phenotype association. CE has identified most genes within which mutations can be causative of flow cytometric phenovariation in Mus musculus. The majority of these genes were not previously known to support immune function or homeostasis. Mouse geneticists will find CE data informative in identifying causative mutations within quantitative trait loci, while clinical geneticists may use CE to help connect causative variants with rare heritable diseases of immunity, even in the absence of linkage information. CE displays integrated mutation, phenotype, and linkage data, and is freely available for query online.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Candidate Explorer: a tool for discovery, evaluation, and display of mutations causing significant immune phenotypes
Darui Xu, Stephen Lyon, Chun Hui Bu, Sara Hildebrand, Jin Huk Choi, Xue Zhong, Aijie Liu, Emre E. Turer, Zhao Zhang, Evan Nair-Gill, Hexin Shi, Ying Wang, Duanwu Zhang, Tao Yue, Jeff SoRelle, Takuma Misawa, Lei Sun, Jianhui Wang, Roxana Farokhnia, Andrew Sakla, Sara Schneider, Nathan Stewart, Hannah Coco, Gabrielle Coolbaugh, Braden Hayse, Sara Mazal, Dawson Medler, Brandon Nguyen, Edward Rodriguez, Andrew Wadley, Miao Tang, Xiaohong Li, Priscilla Anderton, Katie Keller, Lindsay Scott, Jiexia Quan, Sydney Cooper, Baifang Qin, Jennifer Cardin, Rochelle Simpson, Meron Tadesse, Qihua Sun, John Santoyo, Amy Bronikowski, Alexyss Johnson, Eva Marie Y. Moresco, Bruce Beutler
bioRxiv 2020.11.07.371914; doi: https://doi.org/10.1101/2020.11.07.371914
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Candidate Explorer: a tool for discovery, evaluation, and display of mutations causing significant immune phenotypes
Darui Xu, Stephen Lyon, Chun Hui Bu, Sara Hildebrand, Jin Huk Choi, Xue Zhong, Aijie Liu, Emre E. Turer, Zhao Zhang, Evan Nair-Gill, Hexin Shi, Ying Wang, Duanwu Zhang, Tao Yue, Jeff SoRelle, Takuma Misawa, Lei Sun, Jianhui Wang, Roxana Farokhnia, Andrew Sakla, Sara Schneider, Nathan Stewart, Hannah Coco, Gabrielle Coolbaugh, Braden Hayse, Sara Mazal, Dawson Medler, Brandon Nguyen, Edward Rodriguez, Andrew Wadley, Miao Tang, Xiaohong Li, Priscilla Anderton, Katie Keller, Lindsay Scott, Jiexia Quan, Sydney Cooper, Baifang Qin, Jennifer Cardin, Rochelle Simpson, Meron Tadesse, Qihua Sun, John Santoyo, Amy Bronikowski, Alexyss Johnson, Eva Marie Y. Moresco, Bruce Beutler
bioRxiv 2020.11.07.371914; doi: https://doi.org/10.1101/2020.11.07.371914

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