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Journal article
Evaluating the quality of the 1000 genomes project data
BMC genomics, v 20(1), pp 620-620
16 Aug 2019
PMID: 31416423
Featured in Collection : UN Sustainable Development Goals @ Drexel
Abstract
Background Data from the 1000 Genomes project is quite often used as a reference for human genomic analysis. However, its accuracy needs to be assessed to understand the quality of predictions made using this reference. We present here an assessment of the genotyping, phasing, and imputation accuracy data in the 1000 Genomes project. We compare the phased haplotype calls from the 1000 Genomes project to experimentally phased haplotypes for 28 of the same individuals sequenced using the 10X Genomics platform. Results We observe that phasing and imputation for rare variants are unreliable, which likely reflects the limited sample size of the 1000 Genomes project data. Further, it appears that using a population specific reference panel does not improve the accuracy of imputation over using the entire 1000 Genomes data set as a reference panel. We also note that the error rates and trends depend on the choice of definition of error, and hence any error reporting needs to take these definitions into account. Conclusions The quality of the 1000 Genomes data needs to be considered while using this database for further studies. This work presents an analysis that can be used for these assessments.
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Details
- Title
- Evaluating the quality of the 1000 genomes project data
- Creators
- Saurabh Belsare - University of California, San FranciscoMichal Levy-Sakin - University of California, San FranciscoYulia Mostovoy - University of California, San FranciscoSteffen Durinck - GenentechSubhra Chaudhuri - GenentechMing Xiao - Drexel UniversityAndrew S. Peterson - GenentechPui-Yan Kwok - University of California, San FranciscoSomasekar Seshagiri - GenentechJeffrey D. Wall - University of California, San Francisco
- Publication Details
- BMC genomics, v 20(1), pp 620-620
- Publisher
- Springer Nature
- Number of pages
- 14
- Grant note
- CA0095684 / Genentech research grant R01GM115433 / NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Institute of General Medical Sciences (NIGMS) R01 GM115433 / NIH; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- School of Biomedical Engineering, Science, and Health Systems
- Web of Science ID
- WOS:000481741100001
- Scopus ID
- 2-s2.0-85071046433
- Other Identifier
- 991019168102904721
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- Collaboration types
- Industry collaboration
- Domestic collaboration
- Web of Science research areas
- Biotechnology & Applied Microbiology
- Genetics & Heredity