Paper Info
Title
Genome measures used for quality control are dependent on gene function and ancestry.
Abstract
Motivation: The transition/transversion (Ti/Tv) ratio and heterozygous/nonreference-homozygous (het/nonref-hom) ratio have been commonly computed in genetic studies as a quality control (QC) measurement. Additionally, these two ratios are helpful in our understanding of the patterns of DNA sequence evolution. Results: To thoroughly understand these two genomic measures, we performed a study using 1000 Genomes Project (1000G) released genotype data (N = 1092). An additional two datasets (N = 581 and N = 6) were used to validate our findings from the 1000G dataset. We compared the two ratios among continental ancestry, genome regions and gene functionality. We found that the Ti/Tv ratio can be used as a quality indicator for single nucleotide polymorphisms inferred from high-throughput sequencing data. The Ti/Tv ratio varies greatly by genome region and functionality, but not by ancestry. The het/nonref-hom ratio varies greatly by ancestry, but not by genome regions and functionality. Furthermore, extreme guanine + cytosine content (either high or low) is negatively associated with the Ti/Tv ratio magnitude. Thus, when performing QC assessment using these two measures, care must be taken to apply the correct thresholds based on ancestry and genome region. Failure to take these considerations into account at the QC stage will bias any following analysis.
Year
DOI
Venue
2015
10.1093/bioinformatics/btu668
BIOINFORMATICS
Field
DocType
Volume
Genome,Genotype,Transversion,Gene,Biology,Genome-wide association study,1000 Genomes Project,Single-nucleotide polymorphism,DNA sequencing,Bioinformatics,Genetics
Journal
31
Issue
ISSN
Citations 
3
1367-4803
1
PageRank 
References 
Authors
0.44
2
5
Name
Order
Citations
PageRank
Jing Wang110.44
Leon Raskin210.44
David C. Samuels3186.68
Yu Shyr417121.81
Yan Guo57712.73