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Variant analysis of RNA sequences in severe equine asthma

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Variant analysis of RNA sequences in severe equine asthma https://t.co/KNzjp02OB7 Background. Severe equine asthma is a chronic inflammatory disease of the lung in horses similar to low-Th2 late-onset asthma in humans. This study aimed to determine the utility of RNA-S…
266 days ago
Variant analysis of RNA sequences in severe equine asthma https://t.co/OBlYMCGoG3
Variant analysis of RNA sequences in severe equine asthma https://t.co/0nHyNzH43F Background. Severe equine asthma is a chronic inflammatory disease of the lung in horses similar to low-Th2 late-onset asthma in humans. The disease in horses has complex inheritance incl…
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Supplemental Information

Variants detected in asthmatic and non-asthmatic horses with Genome Analysis Toolkit (GATK)

The Venn diagram was generated with SeqMule to identify variants present in all asthmatics before (red) and after challenge (green), and in non-asthmatics before (turquoise) and after challenge (purple).

DOI: 10.7287/peerj.preprints.3491v2/supp-1

Predicted effect of variants in all (left) and coding (right) regions for asthmatic horses before (upper) and after (lower) challenge

Analysis was done using Ensembl Variant Effect Predictor (VEP) tools.

DOI: 10.7287/peerj.preprints.3491v2/supp-2

Predicted effect of variants from all (left) and coding (right) regions for asthmatic horses before (upper) and after (lower) challenge

Analysis was done using Ensembl Variant Effect Predictor (VEP) tools.

DOI: 10.7287/peerj.preprints.3491v2/supp-3

Results of analysis of PACRG (A) and RTTN (B) mutations with PolyPhen2 software

Mutations were predicted as probably damaging in PACRG and RTTN proteins with confidence scores of 0.993 and 0.979, respectively.

DOI: 10.7287/peerj.preprints.3491v2/supp-4

Supplementary Figure Caption

DOI: 10.7287/peerj.preprints.3491v2/supp-5

Predicted effect of amino acid substitution at position 182 in PACRG

DOI: 10.7287/peerj.preprints.3491v2/supp-6

Predicted effect of amino acid substitution at position 1807 for RTTN

DOI: 10.7287/peerj.preprints.3491v2/supp-7

Allelic frequencies for PACRG and RTTN in asthmatic and non-asthmatic horses

DOI: 10.7287/peerj.preprints.3491v2/supp-8

Pearson’s residual for PACRG and RTTN allele frequency calculation in asthmatic and non-asthmatic horses

DOI: 10.7287/peerj.preprints.3491v2/supp-9

Genotype frequency for PACRG and RTTN in asthmatic and non-asthmatic horses

DOI: 10.7287/peerj.preprints.3491v2/supp-10

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Laurence Tessier conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, prepared figures and/or tables, authored or reviewed drafts of the paper, approved the final draft.

Olivier Côté conceived and designed the experiments, performed the experiments, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.

Dorothee Bienzle conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, authored or reviewed drafts of the paper, approved the final draft.

Animal Ethics

The following information was supplied relating to ethical approvals (i.e., approving body and any reference numbers):

All procedures were approved by the Institutional Animal Care Committee of the University of Guelph (protocol R10-031) and conducted in compliance with Canadian Council on Animal Care guidelines.

Data Deposition

The following information was supplied regarding data availability:

The raw sequences were previously submitted to NCBI sequence read archive (SRA) on May 2nd, 2017, and are publicly available under study PRJNA384774 (SRP106023).

Funding

This work was supported by Equine Guelph and the Ontario Ministry of Agriculture and Rural Affairs (no. 051644), and a doctoral scholarship to L. Tessier from the Ontario Veterinary College. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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