Quality control method for RNA-seq using single nucleotide polymorphism allele frequency.
Bottom Line: 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 mRNAs 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.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.
Affiliation: RIKEN Center for Integrative Medical Science (IMS-RIKEN), 1-7-22 Suehiro-Cho, Tsurumi-Ku, Yokohama, Kanagawa, 230-0045, Japan.Show MeSH
Related in: MedlinePlus
Mentions: SNP distribution analysis can also be applied to detect aneuploidy. In examining allele frequencies for each chromosome, abnormal chromosomes are assumed to have skewed distributions when paired chromosomes do not have the equal number of duplicates. As shown in Fig.3A, chromosomal analysis showed abnormality of chromosome 8 in the STAP cells used in the original study. We can expect the peak allele frequency to occur at approximately 50% if a cell has two chromosomes from parents of different strains. The peak allele frequency of the STAP cells, however, was at approximately 33%, meaning that one of the two chromosomes appears to be duplicated leading to three copies of chromosome 8. The STAP cells used in the experiments were derived from 129 and B6 cells, and the duplicated chromosome is presumed to be from the 129 parent because it contained only non-B6 SNP alleles. It is notable that trisomy 8 is the most common chromosomal aberration in mouse ESCs, with 31 of 97 examined cell lines reported to carry this abnormality (Mayshar et al. 2010). ESCs having trisomy 8 have a growth advantage, but chimeras will not transmit the mutation to the germ-line (Ben-David et al. 2013), and trisomy 8 in mice results in prenatal death by day 12 or 13 (Kim et al. 2013).
Affiliation: RIKEN Center for Integrative Medical Science (IMS-RIKEN), 1-7-22 Suehiro-Cho, Tsurumi-Ku, Yokohama, Kanagawa, 230-0045, Japan.