scholarly journals Evaluation of Single-Molecule Sequencing Technologies for Structural Variant Detection in Two Swedish Human Genomes

Genes ◽  
2020 ◽  
Vol 11 (12) ◽  
pp. 1444
Author(s):  
Nazeefa Fatima ◽  
Anna Petri ◽  
Ulf Gyllensten ◽  
Lars Feuk ◽  
Adam Ameur
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Single Molecule ◽  
Large Scale ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data ◽  
Structural Variations ◽  
Single Molecule Sequencing ◽  
Human Samples

Long-read single molecule sequencing is increasingly used in human genomics research, as it allows to accurately detect large-scale DNA rearrangements such as structural variations (SVs) at high resolution. However, few studies have evaluated the performance of different single molecule sequencing platforms for SV detection in human samples. Here we performed Oxford Nanopore Technologies (ONT) whole-genome sequencing of two Swedish human samples (average 32× coverage) and compared the results to previously generated Pacific Biosciences (PacBio) data for the same individuals (average 66× coverage). Our analysis inferred an average of 17k and 23k SVs from the ONT and PacBio data, respectively, with a majority of them overlapping with an available multi-platform SV dataset. When comparing the SV calls in the two Swedish individuals, we find a higher concordance between ONT and PacBio SVs detected in the same individual as compared to SVs detected by the same technology in different individuals. Downsampling of PacBio reads, performed to obtain similar coverage levels for all datasets, resulted in 17k SVs per individual and improved overlap with the ONT SVs. Our results suggest that ONT and PacBio have a similar performance for SV detection in human whole genome sequencing data, and that both technologies are feasible for population-scale studies.

scholarly journals The MOBSTER R package for tumour subclonal deconvolution from bulk DNA whole-genome sequencing data

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Giulio Caravagna ◽  
Guido Sanguinetti ◽  
Trevor A. Graham ◽  
Andrea Sottoriva
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Large Scale ◽  
R Package ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data ◽  
Evolutionary Forces ◽  
Evolutionary Trajectories ◽  
Cancer Tissues

Abstract Background The large-scale availability of whole-genome sequencing profiles from bulk DNA sequencing of cancer tissues is fueling the application of evolutionary theory to cancer. From a bulk biopsy, subclonal deconvolution methods are used to determine the composition of cancer subpopulations in the biopsy sample, a fundamental step to determine clonal expansions and their evolutionary trajectories. Results In a recent work we have developed a new model-based approach to carry out subclonal deconvolution from the site frequency spectrum of somatic mutations. This new method integrates, for the first time, an explicit model for neutral evolutionary forces that participate in clonal expansions; in that work we have also shown that our method improves largely over competing data-driven methods. In this Software paper we present mobster, an open source R package built around our new deconvolution approach, which provides several functions to plot data and fit models, assess their confidence and compute further evolutionary analyses that relate to subclonal deconvolution. Conclusions We present the mobster package for tumour subclonal deconvolution from bulk sequencing, the first approach to integrate Machine Learning and Population Genetics which can explicitly model co-existing neutral and positive selection in cancer. We showcase the analysis of two datasets, one simulated and one from a breast cancer patient, and overview all package functionalities.

scholarly journals Rainbow: a tool for large-scale whole-genome sequencing data analysis using cloud computing

BMC Genomics ◽  
2013 ◽  
Vol 14 (1) ◽  
pp. 425 ◽  
Author(s):  
Shanrong Zhao ◽  
Kurt Prenger ◽  
Lance Smith ◽  
Thomas Messina ◽  
Hongtao Fan ◽  
...  
Keyword(s):  
Cloud Computing ◽  
Data Analysis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Large Scale ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data ◽  
Sequencing Data Analysis

Investigation of Hanwoo-specific structural variations using whole-genome sequencing data

2018 ◽  
Vol 41 (2) ◽  
pp. 233-240 ◽  
Author(s):  
Jangho Park ◽  
Wonseok Shin ◽  
Seyoung Mun ◽  
Man Hwan Oh ◽  
Dajeong Lim ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data ◽  
Structural Variations

scholarly journals Whole genome sequencing reveals high differentiation, low levels of genetic diversity and short runs of homozygosity among Swedish wels catfish

Heredity ◽  
2021 ◽  
Author(s):  
Axel Jensen ◽  
Mette Lillie ◽  
Kristofer Bergström ◽  
Per Larsson ◽  
Jacob Höglund
Keyword(s):  
Genetic Diversity ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome Sequencing Data ◽  
Peripheral Populations ◽  
Whole Genome ◽  
Runs Of Homozygosity ◽  
Sequencing Data ◽  
Isolated Populations ◽  
Native Populations

AbstractThe use of genetic markers in the context of conservation is largely being outcompeted by whole-genome data. Comparative studies between the two are sparse, and the knowledge about potential effects of this methodology shift is limited. Here, we used whole-genome sequencing data to assess the genetic status of peripheral populations of the wels catfish (Silurus glanis), and discuss the results in light of a recent microsatellite study of the same populations. The Swedish populations of the wels catfish have suffered from severe declines during the last centuries and persists in only a few isolated water systems. Fragmented populations generally are at greater risk of extinction, for example due to loss of genetic diversity, and may thus require conservation actions. We sequenced individuals from the three remaining native populations (Båven, Emån, and Möckeln) and one reintroduced population of admixed origin (Helge å), and found that genetic diversity was highest in Emån but low overall, with strong differentiation among the populations. No signature of recent inbreeding was found, but a considerable number of short runs of homozygosity were present in all populations, likely linked to historically small population sizes and bottleneck events. Genetic substructure within any of the native populations was at best weak. Individuals from the admixed population Helge å shared most genetic ancestry with the Båven population (72%). Our results are largely in agreement with the microsatellite study, and stresses the need to protect these isolated populations at the northern edge of the distribution of the species.

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