Ensembl 2014

Flicek, Paul; Amode, M Ridwan; Barrell, Daniel; Beal, Kathryn; Billis, Konstantinos; Brent, Simon; Carvalho-Silva, Denise; Clapham, Peter; Coates, Guy; Fitzgerald, Stephen; Gil, Laurent; Girón, Carlos García; Gordon, Leo I.; Hourlier, Thibaut; Hunt, Sarah; Johnson, Nathan; Juettemann, Thomas; Kähäri, Andreas; Keenan, Stephen; Kulesha, Eugene; Martin, Fergal J.; Maurel, Thomas; McLaren, William; Murphy, Daniel N.; Nag, Rishi; Overduin, Bert; Pignatelli, Miguel; Pritchard, Bethan; Pritchard, Emily; Riat, Harpreet Singh; Ruffier, Magali; Sheppard, Dan; Taylor, Kieron; Thormann, Anja; Trevanion, Stephen J.; Vullo, Alessandro; Wilder, Steven P.; Wilson, Mark; Zadissa, Amonida; Aken, Bronwen; Birney, Ewan; Cunningham, Fiona; Harrow, Jennifer; Herrero, Javier; Hubbard, Tim; Kinsella, Rhoda; Muffato, Matthieu; Parker, Anne; Spudich, Giulietta; Yates, Andy; Zerbino, Daniel R.; Searle, Stephen M. J.

doi:10.1093/nar/gkt1196

Cited by 1,235 publications

(1,227 citation statements)

References 44 publications

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“…The results were then extrapolated to all genome based on the genome and chromosome 21 sizes taken from Ensembl browser. 11 Only 512 samples taken at random from each population were chosen for the WGS ancestry comparison as this was the minimum number of samples for one of our ancestry groups (Sweden). The same was applied for the WES ancestry comparison (minimum number of samples = 861).…”

Section: Introductionmentioning

confidence: 99%

The (in)famous GWAS P-value threshold revisited and updated for low-frequency variants

et al. 2016

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Genome-wide association studies (GWAS) have long relied on proposed statistical significance thresholds to be able to differentiate true positives from false positives. Although the genome-wide significance P-value threshold of 5 × 10 À8 has become a standard for common-variant GWAS, it has not been updated to cope with the lower allele frequency spectrum used in many recent array-based GWAS studies and sequencing studies. Using a whole-genome-and -exome-sequencing data set of 2875 individuals of European ancestry from the Genetics of Type 2 Diabetes (GoT2D) project and a whole-exome-sequencing data set of 13 000 individuals from five ancestries from the GoT2D and T2D-GENES (Type 2 Diabetes Genetic Exploration by Next-generation sequencing in multi-Ethnic Samples) projects, we describe guidelines for genome-and exome-wide association P-value thresholds needed to correct for multiple testing, explaining the impact of linkage disequilibrium thresholds for distinguishing independent variants, minor allele frequency and ancestry characteristics. We emphasize the advantage of studying recent genetic isolate populations when performing rare and low-frequency genetic association analyses, as the multiple testing burden is diminished due to higher genetic homogeneity.

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Section: Introductionmentioning

confidence: 99%

The (in)famous GWAS P-value threshold revisited and updated for low-frequency variants

et al. 2016

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“…2014), SNPs and indels were located in 9265 and 5305 genes respectively (Table S1). Furthermore, 2690 SNPs and 224 indels were mapped to exons.…”

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confidence: 99%

Genetic variation and genetic structure of five Chinese indigenous pig populations in Jiangsu Province revealed by sequencing data

et al. 2017

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SummaryIn this study, we investigated the genetic variants, including SNPs and indels (short insertions or deletions, less than 50 bp in length), in the genomes and genetic structures of five pig populations (in the northern Taihu Lake region, Jiangsu Province) using the genotyping by genome reducing and sequencing (GGRS) approach. A total of 581 million good reads with an average depth of 11× and an average coverage of 2.16% were used to call variants. In general, 202 106 SNPs and 34 415 indels were obtained, of which 2690 SNPs and 224 indels were capable of inducing protein‐coding changes. The genes containing these variants were extracted for functional annotation. The results of gene enrichment analysis revealed that the SNPs under investigation may be associated with reproduction, disease resistance, meat quality and adipose tissue traits, whereas the indels were associated mainly with adipose tissue and disease. Analysis of the genetic structure showed that each population displayed comparable, large differentiations from the others, indicating their uniqueness. In conclusion, the results of our study provide the first genomic overview of the genetic variants and population structures of five Chinese indigenous pig populations.

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“…The protein coding sequence (CDS) was predicted by TransDecoder implemented in Trinity with a minimum length of 100 amino acids. The assembled transcripts then were annotated using BLASTX against NCBI‐NR, UniProt protein databases, and Ensembl zebrafish protein sequences (Zv9; Flicek et al., 2014, UniProt Consortium, 2014), with a cutoff E ‐value less than 1 × 10 −10 . Gene Ontology (GO) and KEGG analyses were performed with the BLAST2GO program (Conesa et al., 2005).…”

Section: Methodsmentioning

confidence: 99%

Transcriptomic comparison of invasive bigheaded carps (Hypophthalmichthys nobilis and Hypophthalmichthys molitrix) and their hybrids

Wang

Lamer

Gaughan

et al. 2016

Ecology and Evolution

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Bighead carp (Hypophthalmichthys nobilis) and silver carp (Hypophthalmichthys molitrix), collectively called bigheaded carps, are invasive species in the Mississippi River Basin (MRB). Interspecific hybridization between bigheaded carps has been considered rare within their native rivers in China; however, it is prevalent in the MRB. We conducted de novo transcriptome analysis of pure and hybrid bigheaded carps and obtained 40,759 to 51,706 transcripts for pure, F1 hybrid, and backcross bigheaded carps. The search against protein databases resulted in 20,336–28,133 annotated transcripts (over 50% of the transcriptome) with over 13,000 transcripts mapped to 23 Gene Ontology biological processes and 127 KEGG metabolic pathways. More transcripts were detected in silver carp than in bighead carp; however, comparable numbers of transcripts were annotated. Transcriptomic variation detected between two F1 hybrids may indicate a potential loss of fitness in hybrids. The neighbor‐joining distance tree constructed using over 2,500 one‐to‐one orthologous sequences suggests transcriptomes could be used to infer the history of introgression and hybridization. Moreover, we detected 24,792 candidate SNPs that can be used to identify different species. The transcriptomes, orthologous sequences, and candidate SNPs obtained in this study should provide further knowledge of interspecific hybridization and introgression.

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Ensembl 2014

Cited by 1,235 publications

References 44 publications

The (in)famous GWAS P-value threshold revisited and updated for low-frequency variants

The (in)famous GWAS P-value threshold revisited and updated for low-frequency variants

Genetic variation and genetic structure of five Chinese indigenous pig populations in Jiangsu Province revealed by sequencing data

Transcriptomic comparison of invasive bigheaded carps (Hypophthalmichthys nobilis and Hypophthalmichthys molitrix) and their hybrids

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