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. 2017 Jun 29;13(6):e1005567.
doi: 10.1371/journal.pcbi.1005567. eCollection 2017 Jun.

Landscape and Variation of Novel Retroduplications in 26 Human Populations

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Free PMC article

Landscape and Variation of Novel Retroduplications in 26 Human Populations

Yan Zhang et al. PLoS Comput Biol. .
Free PMC article

Abstract

Retroduplications come from reverse transcription of mRNAs and their insertion back into the genome. Here, we performed comprehensive discovery and analysis of retroduplications in a large cohort of 2,535 individuals from 26 human populations, as part of 1000 Genomes Phase 3. We developed an integrated approach to discover novel retroduplications combining high-coverage exome and low-coverage whole-genome sequencing data, utilizing information from both exon-exon junctions and discordant paired-end reads. We found 503 parent genes having novel retroduplications absent from the reference genome. Based solely on retroduplication variation, we built phylogenetic trees of human populations; these represent superpopulation structure well and indicate that variable retroduplications are effective population markers. We further identified 43 retroduplication parent genes differentiating superpopulations. This group contains several interesting insertion events, including a SLMO2 retroduplication and insertion into CAV3, which has a potential disease association. We also found retroduplications to be associated with a variety of genomic features: (1) Insertion sites were correlated with regular nucleosome positioning. (2) They, predictably, tend to avoid conserved functional regions, such as exons, but, somewhat surprisingly, also avoid introns. (3) Retroduplications tend to be co-inserted with young L1 elements, indicating recent retrotranspositional activity, and (4) they have a weak tendency to originate from highly expressed parent genes. Our investigation provides insight into the functional impact and association with genomic elements of retroduplications. We anticipate our approach and analytical methodology to have application in a more clinical context, where exome sequencing data is abundant and the discovery of retroduplications can potentially improve the accuracy of SNP calling.

Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Overview of the retroduplication calling pipeline.
A—A simplified flow chart of our calling pipeline. B—A schematic diagram of our strategies. We first align unmapped reads to exon junction libraries and use decoy libraries to control the false discovery rate (FDR). Then, we collect discordant paired-end reads, and cluster the reads that are mapped distal to the parent genes. Clustered distal reads indicate retroduplication insertion site.
Fig 2
Fig 2. Common retroduplication frequency spectrum and phylogenetic tree.
A—Frequency spectrum of 29 retroduplication events that are detected in more than 10 populations. Hierarchical clustering. B—PCA biplot of the populations based on frequencies of these 29 retroduplication events. Different colors indicate five superpopulations, i.e. AFR (African), AMR (Ad Mixed American), EAS (East Asian), EUR (European), and SAS (South Asian). Arrows represent loadings of parent genes. Ad Mixed Americans are marked with ‘*’. C—Consensus phylogenetic tree built based on novel retroduplications from all 26 populations enrolled in the 1000 Genome Project Phase 3. Bootstrap probability (BP) value is computed from ordinary bootstrap resampling. It is the frequency of the cluster appearing in bootstrap replicates. Approximately unbiased (AU) probability value is calculated from multiscale bootstrap resampling [33,34]. AU is less biased than BP. Bootstrap resampling was performed 1,000 times for generating the trees that are summarized in the consensus tree. Manhattan distance and average linkage was used in hierarchical clustering.
Fig 3
Fig 3. Overlap between retroduplication insertion sites and genomic features/functional elements.
A—Aggregation plot around insertion sites with strongly positioned nucleosomes. B—Association between discordant read clusters that only have support on one side and L1 element subfamilies. Fold change and empirical p-values were obtained from permutations tests. *** indicates adjusted p-value < 0.001. C—Overlap between genomic elements and retroduplication insertion sites. The enrichment of overlap is expressed as log2 fold change of the observed overlap statistic versus the mean of its null distribution. Positive (negative) log2 fold change indicates enriched (depleted) genomic element-insertion overlap, compared to random background. * indicates empirical p-value ≤ 0.002.

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