publication . Article . 2016

Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary.

Ola Brynildsrud; Bohlin J; Scheffer L; Eldholm V;
Open Access
  • Published: 01 Nov 2016 Journal: Genome Biology, volume 17 (eissn: 1474-760X, Copyright policy)
  • Publisher: Springer Science and Business Media LLC
  • Country: Norway
Abstract
Genome-wide association studies (GWAS) have become indispensable in human medicine and genomics, but very few have been carried out on bacteria. Here we introduce Scoary, an ultra-fast, easy-to-use, and widely applicable software tool that scores the components of the pan-genome for associations to observed phenotypic traits while accounting for population stratification, with minimal assumptions about evolutionary processes. We call our approach pan-GWAS to distinguish it from traditional, single nucleotide polymorphism (SNP)-based GWAS. Scoary is implemented in Python and is available under an open source GPLv3 license at https://github.com/AdmiralenOla/Scoary...
Subjects
free text keywords: Software, Pan-genome, Accessory genome, Annotation, Prokaryote, Genomics, Whole-genome sequencing (WGS), Next-generation sequencing (NGS), Python, Bacteria, Genome-wide association studies (GWAS), Association
35 references, page 1 of 3

Chewapreecha, C, Harris, SR, Croucher, NJ, Turner, C, Marttinen, P, Cheng, L. Dense genomic sampling identifies highways of pneumococcal recombination. Nat Genet. 2014; 46 (3): 305-309 [OpenAIRE] [PubMed] [DOI]

Laabei, M, Recker, M, Rudkin, JK, Aldeljawi, M, Gulay, Z, Sloan, TJ. Predicting the virulence of MRSA from its genome sequence. Genome Res. 2014; 24 (5): 839-849 [OpenAIRE] [PubMed] [DOI]

Sheppard, SK, Didelot, X, Meric, G, Torralbo, A, Jolley, KA, Kelly, DJ. Genome-wide association study identifies vitamin B5 biosynthesis as a host specificity factor in Campylobacter. Proc Natl Acad Sci. 2013; 110 (29): 11923-11927 [OpenAIRE] [PubMed] [DOI]

Desjardins, CA, Cohen, KA, Munsamy, V, Abeel, T, Maharaj, K, Walker, BJ. Genomic and functional analyses of Mycobacterium tuberculosis strains implicate ald in D-cycloserine resistance. Nat Genet. 2016; 48 (5): 544-551 [OpenAIRE] [PubMed] [DOI]

Farhat, MR, Shapiro, BJ, Kieser, KJ, Sultana, R, Jacobson, KR, Victor, TC. Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis. Nat Genet. 2013; 45 (10): 1183-1189 [OpenAIRE] [PubMed] [DOI]

Earle, SG, Wu, C-H, Charlesworth, J, Stoesser, N, Gordon, NC, Walker, TM. Identifying lineage effects when controlling for population structure improves power in bacterial association studies. Nat Microbiol. 2016; 1: 16041 [OpenAIRE] [PubMed] [DOI]

Hall, BG. SNP-associations and phenotype predictions from hundreds of microbial genomes without genome alignments. PLoS One. 2014; 9 (2): e90490 [OpenAIRE] [PubMed] [DOI]

Holt, KE, Wertheim, H, Zadoks, RN, Baker, S, Whitehouse, CA, Dance, D. Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health. Proc Natl Acad Sci. 2015; 112 (27): E3574-E3581 [OpenAIRE] [PubMed] [DOI]

Lees, JA, Vehkala, M, Valimaki, N, Harris, SR, Chewapreecha, C, Croucher, NJ, Marttinen, P, Davies, MR, Steer, AC, Tong, SY. Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes. Nat Commun. 2016; 7: 12797 [OpenAIRE] [PubMed] [DOI]

Chen, PE, Shapiro, BJ. The advent of genome-wide association studies for bacteria. Curr Opin Microbiol. 2015; 25: 17-24 [OpenAIRE] [PubMed] [DOI]

Medini, D, Donati, C, Tettelin, H, Masignani, V, Rappuoli, R. The microbial pan-genome. Curr Opin Genet Dev. 2005; 15 (6): 589-594 [OpenAIRE] [PubMed] [DOI]

Tettelin, H, Masignani, V, Cieslewicz, MJ, Donati, C, Medini, D, Ward, NL. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial “pan-genome”. Proc Natl Acad Sci U S A. 2005; 102 (39): 13950-13955 [OpenAIRE] [PubMed] [DOI]

Page, AJ, Cummins, CA, Hunt, M, Wong, VK, Reuter, S, Holden, MT. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics. 2015; 31 (22): 3691-3693 [OpenAIRE] [PubMed] [DOI]

Purcell, S, Neale, B, Todd-Brown, K, Thomas, L, Ferreira, MA, Bender, D. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. 2007; 81 (3): 559-575 [OpenAIRE] [PubMed] [DOI]

15.Jones E, Oliphant E, Peterson P, et al. SciPy: Open Source Scientific Tools for Python. 2001. http://www.scipy.org/. Accessed 21 Nov 2016.

35 references, page 1 of 3
Abstract
Genome-wide association studies (GWAS) have become indispensable in human medicine and genomics, but very few have been carried out on bacteria. Here we introduce Scoary, an ultra-fast, easy-to-use, and widely applicable software tool that scores the components of the pan-genome for associations to observed phenotypic traits while accounting for population stratification, with minimal assumptions about evolutionary processes. We call our approach pan-GWAS to distinguish it from traditional, single nucleotide polymorphism (SNP)-based GWAS. Scoary is implemented in Python and is available under an open source GPLv3 license at https://github.com/AdmiralenOla/Scoary...
Subjects
free text keywords: Software, Pan-genome, Accessory genome, Annotation, Prokaryote, Genomics, Whole-genome sequencing (WGS), Next-generation sequencing (NGS), Python, Bacteria, Genome-wide association studies (GWAS), Association
35 references, page 1 of 3

Chewapreecha, C, Harris, SR, Croucher, NJ, Turner, C, Marttinen, P, Cheng, L. Dense genomic sampling identifies highways of pneumococcal recombination. Nat Genet. 2014; 46 (3): 305-309 [OpenAIRE] [PubMed] [DOI]

Laabei, M, Recker, M, Rudkin, JK, Aldeljawi, M, Gulay, Z, Sloan, TJ. Predicting the virulence of MRSA from its genome sequence. Genome Res. 2014; 24 (5): 839-849 [OpenAIRE] [PubMed] [DOI]

Sheppard, SK, Didelot, X, Meric, G, Torralbo, A, Jolley, KA, Kelly, DJ. Genome-wide association study identifies vitamin B5 biosynthesis as a host specificity factor in Campylobacter. Proc Natl Acad Sci. 2013; 110 (29): 11923-11927 [OpenAIRE] [PubMed] [DOI]

Desjardins, CA, Cohen, KA, Munsamy, V, Abeel, T, Maharaj, K, Walker, BJ. Genomic and functional analyses of Mycobacterium tuberculosis strains implicate ald in D-cycloserine resistance. Nat Genet. 2016; 48 (5): 544-551 [OpenAIRE] [PubMed] [DOI]

Farhat, MR, Shapiro, BJ, Kieser, KJ, Sultana, R, Jacobson, KR, Victor, TC. Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis. Nat Genet. 2013; 45 (10): 1183-1189 [OpenAIRE] [PubMed] [DOI]

Earle, SG, Wu, C-H, Charlesworth, J, Stoesser, N, Gordon, NC, Walker, TM. Identifying lineage effects when controlling for population structure improves power in bacterial association studies. Nat Microbiol. 2016; 1: 16041 [OpenAIRE] [PubMed] [DOI]

Hall, BG. SNP-associations and phenotype predictions from hundreds of microbial genomes without genome alignments. PLoS One. 2014; 9 (2): e90490 [OpenAIRE] [PubMed] [DOI]

Holt, KE, Wertheim, H, Zadoks, RN, Baker, S, Whitehouse, CA, Dance, D. Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health. Proc Natl Acad Sci. 2015; 112 (27): E3574-E3581 [OpenAIRE] [PubMed] [DOI]

Lees, JA, Vehkala, M, Valimaki, N, Harris, SR, Chewapreecha, C, Croucher, NJ, Marttinen, P, Davies, MR, Steer, AC, Tong, SY. Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes. Nat Commun. 2016; 7: 12797 [OpenAIRE] [PubMed] [DOI]

Chen, PE, Shapiro, BJ. The advent of genome-wide association studies for bacteria. Curr Opin Microbiol. 2015; 25: 17-24 [OpenAIRE] [PubMed] [DOI]

Medini, D, Donati, C, Tettelin, H, Masignani, V, Rappuoli, R. The microbial pan-genome. Curr Opin Genet Dev. 2005; 15 (6): 589-594 [OpenAIRE] [PubMed] [DOI]

Tettelin, H, Masignani, V, Cieslewicz, MJ, Donati, C, Medini, D, Ward, NL. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial “pan-genome”. Proc Natl Acad Sci U S A. 2005; 102 (39): 13950-13955 [OpenAIRE] [PubMed] [DOI]

Page, AJ, Cummins, CA, Hunt, M, Wong, VK, Reuter, S, Holden, MT. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics. 2015; 31 (22): 3691-3693 [OpenAIRE] [PubMed] [DOI]

Purcell, S, Neale, B, Todd-Brown, K, Thomas, L, Ferreira, MA, Bender, D. PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. 2007; 81 (3): 559-575 [OpenAIRE] [PubMed] [DOI]

15.Jones E, Oliphant E, Peterson P, et al. SciPy: Open Source Scientific Tools for Python. 2001. http://www.scipy.org/. Accessed 21 Nov 2016.

35 references, page 1 of 3
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