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Diversity in non-repetitive human sequences not found in the reference genome
Birte Kehr1,2, Anna Helgadottir1, Pall Melsted1,3
1deCODE Genetics/Amgen, Inc., Reykjavik, Iceland.
Nature Genetics
|March 3, 2017
Summary
This study identified 3,791 non-repetitive, non-reference (NRNR) sequence variants in Icelanders. Many NRNR sequences are ancestral and linked to potential disease associations, including myocardial infarction.
Area of Science:
- Genomics
- Population Genetics
- Human Evolution
Background:
- Genomes contain non-repetitive, non-reference (NRNR) sequences absent from reference genomes and present in population subsets.
- These NRNR sequences are largely unexplored for their characterization and downstream applications.
Purpose of the Study:
- To characterize NRNR sequence variants in a large human population.
- To investigate the evolutionary origins and potential disease relevance of NRNR sequences.
Main Methods:
- Whole-genome sequencing data from 15,219 Icelanders.
- Variant calling using the PopIns algorithm to identify breakpoint-resolved NRNR sequences.
- Analysis of NRNR sequence conservation in chimpanzees and linkage disequilibrium with GWAS catalog markers.
Main Results:
- Identified 3,791 breakpoint-resolved NRNR sequence variants.
- Over 95% of NRNR sequences (≥200 bp) are conserved in chimpanzees, suggesting an ancestral origin.
- 149 NRNR variant loci showed linkage disequilibrium with GWAS markers, indicating potential disease relevance.
- A specific 766-bp NRNR sequence variant was associated with myocardial infarction (P = 3.8 × 10-8).
Conclusions:
- NRNR sequences represent a significant and often overlooked component of human genomic variation.
- The ancestral nature and disease associations of NRNR sequences highlight their importance in genetic studies.
- Comprehensive analysis of all variation types, including NRNR sequences, is crucial for understanding disease etiology.
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