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Evaluating the quality of the 1000 genomes project data
Saurabh Belsare1, Michal Levy-Sakin2, Yulia Mostovoy2
1Institute for Human Genetics, University of California, San Francisco, CA, 94143, USA. saurabh.belsare@ucsf.edu.
BMC Genomics
|August 17, 2019
Summary
The 1000 Genomes project data shows unreliable phasing and imputation for rare variants, impacting human genomic analysis. Accuracy assessments are crucial for reliable predictions using this reference dataset.
Area of Science:
- Genomics
- Bioinformatics
Background:
- The 1000 Genomes project is a widely used reference for human genomic analysis.
- Assessing its accuracy is vital for reliable genomic predictions.
Purpose of the Study:
- To evaluate the genotyping, phasing, and imputation accuracy of the 1000 Genomes project data.
- To compare 1000 Genomes phased haplotypes with experimentally phased haplotypes.
Main Methods:
- Comparison of phased haplotype calls from 1000 Genomes data with experimentally phased haplotypes.
- Analysis of 28 individuals sequenced using 10X Genomics platform.
Main Results:
- Phasing and imputation for rare variants are unreliable due to limited sample size.
- Population-specific reference panels do not improve imputation accuracy over the full 1000 Genomes dataset.
- Error rates are dependent on the definition of error used.
Conclusions:
- The quality of 1000 Genomes data must be considered in downstream studies.
- This analysis provides a framework for assessing the data's reliability.
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