A portable and scalable workflow for detecting structural variants in whole-genome sequencing data

2018 ◽  
Author(s):  
Arnold Kuzniar ◽  
Jason Maassen ◽  
Stefan Verhoeven ◽  
Luca Santuari ◽  
Carl Shneider ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Structural Variants ◽  
Sequencing Data

scholarly journals Cyrius: accurate CYP2D6 genotyping using whole genome sequencing data

2020 ◽  
Author(s):  
Xiao Chen ◽  
Fei Shen ◽  
Nina Gonzaludo ◽  
Alka Malhotra ◽  
Cande Rogert ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Sequence Similarity ◽  
Ethnically Diverse ◽  
Haplotype Frequency ◽  
Superior Performance ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Structural Variants ◽  
Sequencing Data

AbstractResponsible for the metabolism of 25% of clinically used drugs, CYP2D6 is a critical component of personalized medicine initiatives. Genotyping CYP2D6 is challenging due to sequence similarity with its pseudogene paralog CYP2D7 and a high number and variety of common structural variants (SVs). Here we describe a novel bioinformatics method, Cyrius, that accurately genotypes CYP2D6 using whole-genome sequencing (WGS) data. We show that Cyrius has superior performance (96.5% concordance with truth genotypes) compared to existing methods (84-86.8%). After implementing the improvements identified from the comparison against the truth data, Cyrius’s accuracy has since been improved to 99.3%. Using Cyrius, we built a haplotype frequency database from 2504 ethnically diverse samples and estimate that SV-containing star alleles are more frequent than previously reported. Cyrius will be an important tool to incorporate pharmacogenomics in WGS-based precision medicine initiatives.

scholarly journals Development and evaluation of an outbreak surveillance system integrating whole genome sequencing data for non-typhoidal Salmonella in London and South East of England, 2016-17

2021 ◽  
pp. 1-26
Author(s):  
Karthik Paranthaman ◽  
Piers Mook ◽  
Daniele Curtis ◽  
Edward-Wynne Evans ◽  
Emma Crawley-Boevey ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Surveillance System ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data

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.

scholarly journals Norgal: extraction and de novo assembly of mitochondrial DNA from whole-genome sequencing data

2017 ◽  
Vol 18 (1) ◽  
Author(s):  
Kosai Al-Nakeeb ◽  
Thomas Nordahl Petersen ◽  
Thomas Sicheritz-Pontén
Keyword(s):  
Mitochondrial Dna ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
De Novo Assembly ◽  
De Novo ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data

scholarly journals Fast and low-cost decentralized surveillance of transmission of tuberculosis based on strain-specific PCRs tailored from whole genome sequencing data: a pilot study

2015 ◽  
Vol 21 (3) ◽  
pp. 249.e1-249.e9 ◽  
Author(s):  
L. Pérez-Lago ◽  
M. Martínez Lirola ◽  
M. Herranz ◽  
I. Comas ◽  
E. Bouza ◽  
...  
Keyword(s):  
Pilot Study ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Low Cost ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Sequencing Data

scholarly journals Identification of individuals by trait prediction using whole-genome sequencing data

2017 ◽  
Vol 114 (38) ◽  
pp. 10166-10171 ◽  
Author(s):  
Christoph Lippert ◽  
Riccardo Sabatini ◽  
M. Cyrus Maher ◽  
Eun Yong Kang ◽  
Seunghak Lee ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Predictive Accuracy ◽  
Large Fraction ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
Demographic Information ◽  
Personal Privacy ◽  
Sequencing Data ◽  
Legal Implications

Prediction of human physical traits and demographic information from genomic data challenges privacy and data deidentification in personalized medicine. To explore the current capabilities of phenotype-based genomic identification, we applied whole-genome sequencing, detailed phenotyping, and statistical modeling to predict biometric traits in a cohort of 1,061 participants of diverse ancestry. Individually, for a large fraction of the traits, their predictive accuracy beyond ancestry and demographic information is limited. However, we have developed a maximum entropy algorithm that integrates multiple predictions to determine which genomic samples and phenotype measurements originate from the same person. Using this algorithm, we have reidentified an average of >8 of 10 held-out individuals in an ethnically mixed cohort and an average of 5 of either 10 African Americans or 10 Europeans. This work challenges current conceptions of personal privacy and may have far-reaching ethical and legal implications.

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