Towards mouse genetic-specific RNA-sequencing read mapping Article Swipe
Nastassia Gobet
,
Maxime Jan
,
Paul Franken
,
Ioannis Xénarios
·
YOU?
·
· 2022
· Open Access
·
· DOI: https://doi.org/10.1371/journal.pcbi.1010552
YOU?
·
· 2022
· Open Access
·
· DOI: https://doi.org/10.1371/journal.pcbi.1010552
Genetic variations affect behavior and cause disease but understanding how these variants drive complex traits is still an open question. A common approach is to link the genetic variants to intermediate molecular phenotypes such as the transcriptome using RNA-sequencing (RNA-seq). Paradoxically, these variants between the samples are usually ignored at the beginning of RNA-seq analyses of many model organisms. This can skew the transcriptome estimates that are used later for downstream analyses, such as expression quantitative trait locus (eQTL) detection. Here, we assessed the impact of reference-based analysis on the transcriptome and eQTLs in a widely-used mouse genetic population: the BXD panel of recombinant inbred lines. We highlight existing reference bias in the transcriptome data analysis and propose practical solutions which combine available genetic variants, genotypes, and genome reference sequence. The use of custom BXD line references improved downstream analysis compared to classical genome reference. These insights would likely benefit genetic studies with a transcriptomic component and demonstrate that genome references need to be reassessed and improved.
Related Topics
Concepts
Biology
Transcriptome
Genetics
Expression quantitative trait loci
Computational biology
Reference genome
Genome
Quantitative trait locus
RNA-Seq
Locus (genetics)
Population
Genetic analysis
Genomics
Gene
Genotype
Single-nucleotide polymorphism
Gene expression
Demography
Sociology
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1371/journal.pcbi.1010552
- https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010552&type=printable
- OA Status
- gold
- Cited By
- 2
- References
- 32
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4297248764
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4297248764Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.1371/journal.pcbi.1010552Digital Object Identifier
- Title
-
Towards mouse genetic-specific RNA-sequencing read mappingWork title
- Type
-
articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2022Year of publication
- Publication date
-
2022-09-26Full publication date if available
- Authors
-
Nastassia Gobet, Maxime Jan, Paul Franken, Ioannis XénariosList of authors in order
- Landing page
-
https://doi.org/10.1371/journal.pcbi.1010552Publisher landing page
- PDF URL
-
https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010552&type=printableDirect link to full text PDF
- Open access
-
YesWhether a free full text is available
- OA status
-
goldOpen access status per OpenAlex
- OA URL
-
https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1010552&type=printableDirect OA link when available
- Concepts
-
Biology, Transcriptome, Genetics, Expression quantitative trait loci, Computational biology, Reference genome, Genome, Quantitative trait locus, RNA-Seq, Locus (genetics), Population, Genetic analysis, Genomics, Gene, Genotype, Single-nucleotide polymorphism, Gene expression, Demography, SociologyTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
2Total citation count in OpenAlex
- Citations by year (recent)
-
2025: 2Per-year citation counts (last 5 years)
- References (count)
-
32Number of works referenced by this work
- Related works (count)
-
10Other works algorithmically related by OpenAlex
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