scholarly journals Assessing Runs of Homozygosity: A comparison of SNP Array and Whole Genome Sequence low coverage data

2017 ◽  
Author(s):  
Francisco C. Ceballos ◽  
Scott Hazelhurst ◽  
Michèle Ramsay
Keyword(s):  
Genome Sequence ◽  
Complex Traits ◽  
Genetic Basis ◽  
Snp Array ◽  
Population History ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Runs Of Homozygosity ◽  
Technological Advances ◽  
Low Coverage

AbstractRuns of Homozygosity (ROH) are sequences that arise when identical haplotypes are inherited from each parent. Since their first detection due to technological advances in the late 1990s, ROHs have been shedding light on human population history and deciphering the genetic basis of monogenic and complex traits and diseases. ROH studies have predominantly exploited SNP array data, but are gradually moving to whole genome sequence (WGS) data as it becomes available. WGS data, covering more genetic variability, can add value to ROH studies, but require additional considerations during analysis. Using SNP array and low coverage WGS data from 1885 individuals from 20 world populations, our aims were to compare ROH from the two datasets and to establish software conditions to get comparable results, thus providing guidelines for combining disparate datasets in joint ROH analyses. Using the PLINK Homozygosity functions, we found that by allowing 3 heterozygous SNPs per window when dealing with WGS low coverage data, it is possible to establish meaningful comparisons between data using the two technologies.

scholarly journals Assessing runs of Homozygosity: a comparison of SNP Array and whole genome sequence low coverage data

BMC Genomics ◽  
2018 ◽  
Vol 19 (1) ◽  
Author(s):  
Francisco C. Ceballos ◽  
Scott Hazelhurst ◽  
Michèle Ramsay
Keyword(s):  
Genome Sequence ◽  
Snp Array ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Runs Of Homozygosity ◽  
Low Coverage

scholarly journals Inferring Demography from Runs of Homozygosity in Whole-Genome Sequence, with Correction for Sequence Errors

2013 ◽  
Vol 30 (9) ◽  
pp. 2209-2223 ◽  
Author(s):  
Iona M. MacLeod ◽  
Denis M. Larkin ◽  
Harris A. Lewin ◽  
Ben J. Hayes ◽  
Mike E. Goddard
Keyword(s):  
Genome Sequence ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Runs Of Homozygosity ◽  
Sequence Errors

scholarly journals Elucidating the genetic basis of an oligogenic birth defect using whole genome sequence data in a non-model organism, Bubalus bubalis

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Lynsey K. Whitacre ◽  
Jesse L. Hoff ◽  
Robert D. Schnabel ◽  
Sara Albarella ◽  
Francesca Ciotola ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Birth Defect ◽  
Genetic Basis ◽  
Sequence Data ◽  
Model Organism ◽  
Bubalus Bubalis ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequence Data

scholarly journals An accurate assignment test for extremely low‐coverage whole‐genome sequence data

2021 ◽  
Author(s):  
Giada Ferrari ◽  
Lane M. Atmore ◽  
Sissel Jentoft ◽  
Kjetill S. Jakobsen ◽  
Daniel Makowiecki ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Sequence Data ◽  
Assignment Test ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequence Data ◽  
Low Coverage

scholarly journals Complete Genome Sequence of Streptococcus agalactiae GD201008-001, Isolated in China from Tilapia with Meningoencephalitis

2012 ◽  
Vol 194 (23) ◽  
pp. 6653-6653 ◽  
Author(s):  
Guangjin Liu ◽  
Wei Zhang ◽  
Chengping Lu
Keyword(s):  
Genome Sequence ◽  
Streptococcus Agalactiae ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Genetic Basis ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Content Type ◽  
Host Tropism

ABSTRACTThis work describes a whole-genome sequence ofStreptococcus agalactiaestrain GD201008-001, a pathogen causing meningoencephalitis in cultural tilapia in China. The genome sequence provides opportunities to understand the piscine GBS pathogenicity and its genetic basis associated with host tropism.

scholarly journals Whole-Genome Sequence of Corynebacterium pseudotuberculosis PAT10 Strain Isolated from Sheep in Patagonia, Argentina

2011 ◽  
Vol 193 (22) ◽  
pp. 6420-6421 ◽  
Author(s):  
Louise Teixeira Cerdeira ◽  
Anne Cybelle Pinto ◽  
Maria Paula Cruz Schneider ◽  
Sintia Silva de Almeida ◽  
Anderson Rodrigues dos Santos ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Genetic Basis ◽  
Lung Abscess ◽  
Corynebacterium Pseudotuberculosis ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Content Type

In this work, we report the complete genome sequence of aCorynebacterium pseudotuberculosisPAT10 isolate, collected from a lung abscess in an Argentine sheep in Patagonia, whose pathogen also required an investigation of its pathogenesis. Thus, the analysis of the genome sequence offers a means to better understanding of the molecular and genetic basis of virulence of this bacterium.

scholarly journals An accurate assignment test for extremely low-coverage whole-genome sequence data

2021 ◽  
Author(s):  
Giada Ferrari ◽  
Lane M Atmore ◽  
Sissel Jentoft ◽  
Kjetill S Jakobsen ◽  
Daniel Makowiecki ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Atlantic Cod ◽  
Sequence Data ◽  
Biological Characteristics ◽  
Assignment Test ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequence Data ◽  
Assignment Tests ◽  
Low Coverage

Genomic assignment tests can provide important diagnostic biological characteristics, such as population of origin or ecotype. In ancient DNA research, such characters can provide further information on population continuity, evolution, climate change, species migration, or trade, depending on archaeological context. Yet, assignment tests often rely on moderate- to high-coverage sequence data, which can be difficult to obtain for many ancient specimens and in ecological studies, which often use sequencing techniques such as ddRAD to bypass the need for costly whole-genome sequencing. We have developed a novel approach that efficiently assigns biologically relevant information (such as population identity or structural variants) in extremely low-coverage sequence data. First, we generate databases from existing reference data using a subset of diagnostic Single Nucleotide Polymorphisms (SNPs) associated with a biological characteristic. Low coverage alignment files from ancient specimens are subsequently compared to these databases to ascertain allelic state yielding a joint probability for each association. To assess the efficacy of this approach, we assigned inversion haplotypes and population identity in several species including Heliconius butterflies, Atlantic herring, and Atlantic cod. We used both modern and ancient specimens, including the first whole-genome sequence data recovered from ancient herring bones. The method accurately assigns biological characteristics, including population membership, using extremely low-coverage (e.g. 0.0001x fold) based on genome-wide SNPs. This approach will therefore increase the number of ancient samples in ecological and bioarchaeological research for which relevant biological information can be obtained.

Predicting causal variants affecting expression using whole genome sequence and RNA-seq from multiple human tissues

2016 ◽  
Author(s):  
Andrew Anand Brown ◽  
Ana Viñuela ◽  
Olivier Delaneau ◽  
Tim Spector ◽  
Kerrin Small ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complex Traits ◽  
Causal Variant ◽  
Whole Genome Sequence ◽  
Open Chromatin ◽  
Whole Genome ◽  
Rna Seq ◽  
Derived Properties ◽  
Causal Variants ◽  
Genomic Regions

Genetic association mapping produces statistical links between phenotypes and genomic regions, but identifying the causal variants themselves remains difficult. Complete knowledge of all genetic variants, as provided by whole genome sequence (WGS), will help, but is currently financially prohibitive for well powered GWAS studies. To explore the advantages of WGS in a well powered setting, we performed eQTL mapping using WGS and RNA-seq, and showed that the lead eQTL variants called using WGS are more likely to be causal. We derived properties of the causal variant from simulation studies, and used these to propose a method for implicating likely causal SNPs. This method predicts that 25% - 70% of the causal variants lie in open chromatin regions, depending on tissue and experiment. Finally, we identify a set of high confidence causal variants and show that they are more enriched in GWAS associations than other eQTL. Of these, we find 65 associations with GWAS traits and show examples where the gene implicated by expression has been functionally validated as relevant for complex traits.

scholarly journals Whole-Genome Sequence of Starmerella bacillaris PAS13, a Nonconventional Enological Yeast with Antifungal Activity

2017 ◽  
Vol 5 (32) ◽  
Author(s):  
Wilson José Fernandes Lemos Junior ◽  
Laura Treu ◽  
Vinícius da Silva Duarte ◽  
Milena Carlot ◽  
Chiara Nadai ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Genetic Basis ◽  
Gene Sequence ◽  
Potential Role ◽  
Biocontrol Agent ◽  
Draft Genome ◽  
Gray Mold ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Fermentative Yeast

ABSTRACT Starmerella bacillaris is a fermentative yeast commonly found in vineyards. Here, we present the draft genome sequence of S. bacillaris PAS13, a nonconventional enological yeast with a potential role as a biocontrol agent. This gene sequence will provide insights into the genetic basis of yeast activity against gray mold disease (Botrytis cinerea).

scholarly journals Comparison among three variant callers and assessment of the accuracy of imputation from SNP array data to whole-genome sequence level in chicken

BMC Genomics ◽  
2015 ◽  
Vol 16 (1) ◽  
Author(s):  
Guiyan Ni ◽  
Tim M. Strom ◽  
Hubert Pausch ◽  
Christian Reimer ◽  
Rudolf Preisinger ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Snp Array ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Array Data
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