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Quality control method for RNA ‐seq using single nucleotide polymorphism allele frequency
Author(s) -
Endo Takaho A.
Publication year - 2014
Publication title -
genes to cells
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.912
H-Index - 115
eISSN - 1365-2443
pISSN - 1356-9597
DOI - 10.1111/gtc.12178
Subject(s) - biology , single nucleotide polymorphism , genetics , transcriptome , rna seq , rna , allele frequency , gene , allele , snp , population , computational biology , gene expression , genotype , demography , sociology
RNA sequencing (RNA‐seq) provides information not only about the level of expression of individual genes but also about genomic sequences of host cells. When we use transcriptome data with whole‐genome single nucleotide polymorphism (SNP) variant information, the allele frequency can show the genetic composition of the cell population and/or chromosomal aberrations. Here, I show how SNPs in mRNA s can be used to evaluate RNA‐seq experiments by focusing on RNA‐seq data based on a recently retracted paper on stimulus‐triggered acquisition of pluripotency (STAP) cells. The analysis indicated that different types of cells and chromosomal abnormalities might have been erroneously included in the dataset. This re‐evaluation showed that observing allele frequencies could help in assessing the quality of samples during a study and with retrospective evaluation of experimental quality.