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Genome measures used for quality control are dependent on gene function and ancestry
Jing Wang1, Leon Raskin1, David C Samuels1
1Center for Quantitative Sciences and Department of Medicine and Center for Human Genetics Research, Vanderbilt University, Nashville, TN 37212, USA.
Bioinformatics (Oxford, England)
|October 10, 2014
Summary
The transition/transversion (Ti/Tv) ratio and heterozygous/nonreference-homozygous (het/nonref-hom) ratio are crucial for genetic quality control. Their interpretation requires careful consideration of ancestry and genomic regions to avoid analysis bias.
Area of Science:
- Genomics
- Population Genetics
- Bioinformatics
Background:
- The transition/transversion (Ti/Tv) ratio and heterozygous/nonreference-homozygous (het/nonref-hom) ratio are standard quality control metrics in genetic studies.
- These genomic measures also offer insights into DNA sequence evolution patterns.
Purpose of the Study:
- To comprehensively analyze the transition/transversion (Ti/Tv) ratio and heterozygous/nonreference-homozygous (het/nonref-hom) ratio.
- To evaluate the influence of ancestry, genomic regions, and gene functionality on these ratios.
- To determine the utility of these ratios as quality indicators for high-throughput sequencing data.
Main Methods:
- Utilized genotype data from the 1000 Genomes Project (N=1092) for primary analysis.
- Validated findings using two additional datasets (N=581 and N=6).
- Compared Ti/Tv and het/nonref-hom ratios across continental ancestries, genome regions, and gene functionalities.
Main Results:
- The Ti/Tv ratio serves as a reliable quality indicator for single nucleotide polymorphisms from sequencing data.
- Ti/Tv ratio varies significantly with genomic region and functionality, but not ancestry.
- het/nonref-hom ratio is highly dependent on ancestry, with no significant variation across genomic regions or functionalities.
- Extreme guanine-cytosine content negatively correlates with Ti/Tv ratio magnitude.
Conclusions:
- Correct interpretation of Ti/Tv and het/nonref-hom ratios necessitates accounting for ancestry and genomic region.
- Failure to implement ancestry and region-specific thresholds during quality control can introduce bias into downstream analyses.
- These findings underscore the importance of context-aware quality control in genetic studies.
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