Limits...
Quality control method for RNA-seq using single nucleotide polymorphism allele frequency.

Endo TA - Genes Cells (2014)

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.

View Article: PubMed Central - PubMed

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

Examination of incorporated mRNAs in FI-SCs. (A) Expression of TSC marker genes in ESCs, TSCs, and FI-SCs. The solid line indicates the average TSC gene expression and dashed line indicates 10% of the average. (B) Heterozygous SNPs detected in Des, Grb2, Setd7, Fbxo21, and Chd4 where B6 and 129 share the same SNPs but TSCs did not. (C) Gene-wise analysis of distribution of heterozygous/homozygous SNPs having TSC-specific alleles.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4231238&req=5

fig04: Examination of incorporated mRNAs in FI-SCs. (A) Expression of TSC marker genes in ESCs, TSCs, and FI-SCs. The solid line indicates the average TSC gene expression and dashed line indicates 10% of the average. (B) Heterozygous SNPs detected in Des, Grb2, Setd7, Fbxo21, and Chd4 where B6 and 129 share the same SNPs but TSCs did not. (C) Gene-wise analysis of distribution of heterozygous/homozygous SNPs having TSC-specific alleles.

Mentions: The most likely cell type to be contaminating the FI-SCs in the original study, TSCs, had many more heterozygous (B6/non-B6) alleles than non-B6 homozygous alleles. SNPs of FI-SCs were counted in alleles where B6 and 129 have different nucleotides and duplicated experiments resulted in 6859 and 7243 heterozygous SNPs and 24 and 14 non-B6 homozygous alleles, respectively. The percentage of contaminating cells can be assumed with genotype observation because the peak allele frequencies were at approximately 95–96%, whereas the population peak is expected to be at approximately 10%. This result was concordant with the expression of TSC marker genes. All of the examined TSC marker genes examined were expressed in approximately 10% of TSCs (Fig.4A).


Quality control method for RNA-seq using single nucleotide polymorphism allele frequency.

Endo TA - Genes Cells (2014)

Examination of incorporated mRNAs in FI-SCs. (A) Expression of TSC marker genes in ESCs, TSCs, and FI-SCs. The solid line indicates the average TSC gene expression and dashed line indicates 10% of the average. (B) Heterozygous SNPs detected in Des, Grb2, Setd7, Fbxo21, and Chd4 where B6 and 129 share the same SNPs but TSCs did not. (C) Gene-wise analysis of distribution of heterozygous/homozygous SNPs having TSC-specific alleles.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4231238&req=5

fig04: Examination of incorporated mRNAs in FI-SCs. (A) Expression of TSC marker genes in ESCs, TSCs, and FI-SCs. The solid line indicates the average TSC gene expression and dashed line indicates 10% of the average. (B) Heterozygous SNPs detected in Des, Grb2, Setd7, Fbxo21, and Chd4 where B6 and 129 share the same SNPs but TSCs did not. (C) Gene-wise analysis of distribution of heterozygous/homozygous SNPs having TSC-specific alleles.
Mentions: The most likely cell type to be contaminating the FI-SCs in the original study, TSCs, had many more heterozygous (B6/non-B6) alleles than non-B6 homozygous alleles. SNPs of FI-SCs were counted in alleles where B6 and 129 have different nucleotides and duplicated experiments resulted in 6859 and 7243 heterozygous SNPs and 24 and 14 non-B6 homozygous alleles, respectively. The percentage of contaminating cells can be assumed with genotype observation because the peak allele frequencies were at approximately 95–96%, whereas the population peak is expected to be at approximately 10%. This result was concordant with the expression of TSC marker genes. All of the examined TSC marker genes examined were expressed in approximately 10% of TSCs (Fig.4A).

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.

View Article: PubMed Central - PubMed

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