Browsing by Subject "Segmental duplication"

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Open Access
Paralog-specific gene copy number discovery within segmental duplications
(2019-09) Doğru, Emre
With the advancing technology in genome sequencing and analysis, it has become evident that the structural variations are the main source of alteration in human genome. Despite their signi cance in understanding disease susceptibility, there is no algorithm yet to nd all types and sizes of structural variations at once. Structural variation discovery remained problematic since they often overlap with the segmental duplications, nearly identical segments of DNA that appear more than once in the genome. Researchers often excluded these regions that made up 5% of the genome because of the complexity it brings to their studies. Only few of them are working in these regions, however, they require a special sequence alignment le where reads are mapped to multiple locations. Here, we present ParaCoND to discover paralog speci c gene copy number within segmental duplications using a sequence alignment le with unique mapping. We utilize the singly unique nucleotides (SUN) that distinguish paralogs from each other in the sequence alignment of the duplicated regions. Our method is based on read depth and is limited to detect only duplications and deletions. We computed the absolute copy numbers of genes using only read depth of SUN. Furthermore, we also computed the paralog speci c absolute copy numbers for genes residing in the same segmental duplication.
Open Access
Reconstructing complex regions of genomes using long-read sequencing technology
(Cold Spring Harbor Laboratory Press, 2014) Huddleston, J.; Ranade, S.; Malig, M.; Antonacci, F.; Chaisson, M.; Hon, L.; Sudmant, P. H.; Alkan C.; Eichler, E. E.; Graves, T. A.; Dennis, M. Y.; Wilson, R. K.; Turner, S. W.; Korlach, J.
Obtaining high-quality sequence continuity of complex regions of recent segmental duplication remains one of the major challenges of finishing genome assemblies. In the human and mouse genomes, this was achieved by targeting large-insert clones using costly and laborious capillary-based sequencing approaches. Sanger shotgun sequencing of clone inserts, however, has now been largely abandoned, leaving most of these regions unresolved in newer genome assemblies generated primarily by next-generation sequencing hybrid approaches. Here we show that it is possible to resolve regions that are complex in a genome-wide context but simple in isolation for a fraction of the time and cost of traditional methods using long-read single molecule, real-time (SMRT) sequencing and assembly technology from Pacific Biosciences (PacBio). We sequenced and assembled BAC clones corresponding to a 1.3-Mbp complex region of chromosome 17q21.31, demonstrating 99.994% identity to Sanger assemblies of the same clones. We targeted 44 differences using Illumina sequencing and find that PacBio and Sanger assemblies share a comparable number of validated variants, albeit with different sequence context biases. Finally, we targeted a poorly assembled 766-kbp duplicated region of the chimpanzee genome and resolved the structure and organization for a fraction of the cost and time of traditional finishing approaches. Our data suggest a straightforward path for upgrading genomes to a higher quality finished state.