ArticleGenetics2014
RNA-Seq alignment to individualized genomes improves transcript abundance estimates in multiparent populations.
Article in Genetics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 67 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
67 citing papers in PubMed, 1 synthesis or guideline pooled it.
- GenomeMUSter mouse genetic variation service enables multitrait, multipopulation data integration and analysis.Genome research · 2024Pooled it
- CellMAGE: cell-type deconvolution for multi-parent population analysis of gene expression.bioRxiv : the preprint server for biology · 2026Article
- The promise of long-read RNA-seq: reducing bias in analyses of allele imbalance.NAR genomics and bioinformatics · 2026Article
- Benchmarking genome choice in functional genomics analyses.Nature communications · 2026Article
- Distinct genetic architecture of gene and isoform level QTL in the Diversity Outbred (DO) mouse population.bioRxiv : the preprint server for biology · 2026Article
- Simplifying Systems Genetics with QTLretrievR: An R Package for Molecular QTL Identification.bioRxiv : the preprint server for biology · 2026Article
- High-quality mouse reference genomes reveal the structural complexity of the murine protein-coding landscape.Cell genomics · 2026Article
- Article
- Fifteen years of the Diversity Outbred mouse model: a review.Mammalian genome : official journal of the International Mammalian Genome Society · 2026Review
- Transcripts with high distal heritability mediate genetic effects on complex metabolic traits.Nature communications · 2025Article
- TheBiomolecules · 2025Review
- A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats.Cell genomics · 2024Article
- Introgressions lead to reference bias in wheat RNA-seq analysis.BMC biology · 2024Article
- A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats.bioRxiv : the preprint server for biology · 2023Article
- Genome-wide screen identifies host loci that modulate Mycobacterium tuberculosis fitness in immunodivergent mice.G3 (Bethesda, Md.) · 2023Article
- SEESAW: detecting isoform-level allelic imbalance accounting for inferential uncertainty.Genome biology · 2023Article
- Genetic variation in chromatin state across multiple tissues in Drosophila melanogaster.PLoS genetics · 2023Article
- Adding gene transcripts into genomic prediction improves accuracy and reveals sampling time dependence.G3 (Bethesda, Md.) · 2022Article
- Towards mouse genetic-specific RNA-sequencing read mapping.PLoS computational biology · 2022Article
- The value of genotype-specific reference for transcriptome analyses in barley.Life science alliance · 2022Article
7 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
13 authors.
Funding
Abstract
Massively parallel RNA sequencing (RNA-seq) has yielded a wealth of new insights into transcriptional regulation. A first step in the analysis of RNA-seq data is the alignment of short sequence reads to a common reference genome or transcriptome. Genetic variants that distinguish individual genomes from the reference sequence can cause reads to be misaligned, resulting in biased estimates of transcript abundance. Fine-tuning of read alignment algorithms does not correct this problem. We have developed Seqnature software to construct individualized diploid genomes and transcriptomes for multiparent populations and have implemented a complete analysis pipeline that incorporates other existing software tools. We demonstrate in simulated and real data sets that alignment to individualized transcriptomes increases read mapping accuracy, improves estimation of transcript abundance, and enables the direct estimation of allele-specific expression. Moreover, when applied to expression QTL mapping we find that our individualized alignment strategy corrects false-positive linkage signals and unmasks hidden associations. We recommend the use of individualized diploid genomes over reference sequence alignment for all applications of high-throughput sequencing technology in genetically diverse populations.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.