ArticlePloS one2013
Development of strategies for SNP detection in RNA-seq data: application to lymphoblastoid cell lines and evaluation using 1000 Genomes data.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 77 papers.
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Who cites it
77 citing papers in PubMed, 139 citations in OpenAlex.
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- Application of RNA-seq for single nucleotide variation identification in a cohort of patients with hypertrophic cardiomyopathy.Scientific reports · 2025Article
- LILRB3 genetic variation is associated with kidney transplant failure in African American recipients.Nature medicine · 2025Article
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- Molecular targets and strategies in the development of nucleic acid cancer vaccines: from shared to personalized antigens.Journal of biomedical science · 2024Review
- Genetic variants in androgenetic alopecia: insights from scalp RNA sequencing data.Archives of dermatological research · 2024Article
- BBmix: a Bayesian beta-binomial mixture model for accurate genotyping from RNA-sequencing.Bioinformatics (Oxford, England) · 2023Article
- RNA-Seq-Pop: Exploiting the sequence in RNA sequencing-A Snakemake workflow reveals patterns of insecticide resistance in the malaria vector Anopheles gambiae.Molecular ecology resources · 2023Article
- Integrated omic techniques and their genomic features for invasive weeds.Functional & integrative genomics · 2023Review
- Whole genome re-sequencing reveals the genetic diversity and evolutionary patterns of Eucommia ulmoides.Molecular genetics and genomics : MGG · 2022Article
- Integrating pathway knowledge with deep neural networks to reduce the dimensionality in single-cell RNA-seq data.BioData mining · 2022Article
- RNA-SSNV: A Reliable Somatic Single Nucleotide Variant Identification Framework for Bulk RNA-Seq Data.Frontiers in genetics · 2022Article
- Screening of Variants in the Transcript Profile of Eutopic Endometrium from Infertile Women with Endometriosis during the Implantation Window.Revista brasileira de ginecologia e obstetricia : revista da Federacao Brasileira das Sociedades de Ginecologia e Obstetricia · 2021Article
- Whole-Transcriptome Analysis by RNA Sequencing for Genetic Diagnosis of Mendelian Skin Disorders in the Context of Consanguinity.Clinical chemistry · 2021Article
- RNA-Seq Data for Reliable SNP Detection and Genotype Calling: Interest for Coding Variant Characterization andFrontiers in genetics · 2021Article
- Genome-wide Identification and Analysis of Splicing QTLs in Multiple Sclerosis by RNA-Seq Data.Frontiers in genetics · 2021Article
- Epigenetic Regulation of the Vascular Endothelium by Angiogenic LncRNAs.Frontiers in genetics · 2021Review
- Finding a suitable library size to call variants in RNA-Seq.BMC bioinformatics · 2020Article
- Article
17 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors at 1 institution in 1 country.
Funding
Abstract
Next-generation RNA sequencing (RNA-seq) maps and analyzes transcriptomes and generates data on sequence variation in expressed genes. There are few reported studies on analysis strategies to maximize the yield of quality RNA-seq SNP data. We evaluated the performance of different SNP-calling methods following alignment to both genome and transcriptome by applying them to RNA-seq data from a HapMap lymphoblastoid cell line sample and comparing results with sequence variation data from 1000 Genomes. We determined that the best method to achieve high specificity and sensitivity, and greatest number of SNP calls, is to remove duplicate sequence reads after alignment to the genome and to call SNPs using SAMtools. The accuracy of SNP calls is dependent on sequence coverage available. In terms of specificity, 89% of RNA-seq SNPs calls were true variants where coverage is >10X. In terms of sensitivity, at >10X coverage 92% of all expected SNPs in expressed exons could be detected. Overall, the results indicate that RNA-seq SNP data are a very useful by-product of sequence-based transcriptome analysis. If RNA-seq is applied to disease tissue samples and assuming that genes carrying mutations relevant to disease biology are being expressed, a very high proportion of these mutations can be detected.
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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.