PBAT: A comprehensive software package for genome-wide association analysis of complex family-based studies.
Open accessAbstract
The PBAT software package (v2.5) provides a unique set of tools for complex family-based association analysis at a genome-wide level. PBAT can handle nuclear families with missing parental genotypes, extended pedigrees with missing genotypic information, analysis of single nucleotide polymorphisms (SNPs), haplotype analysis, quantitative traits, multivariate/longitudinal data and time to onset phenotypes. The data analysis can be adjusted for covariates and gene/environment interactions. Haplotype-based features include sliding windows and the reconstruction of the haplotypes of the probands. PBAT's screening tools allow the user successfully to handle the multiple comparisons problem at a genome-wide level, even for 100,000 SNPs and more. Moreover, PBAT is computationally fast. A genome scan of 300,000 SNPs in 2,000 trios takes 4 central processing unit (CPU)-days. PBAT is available for Linux, Sun Solaris and Windows XP.
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Haplotype-based features include sliding windows and the reconstruction of the haplotypes of the probands.
“Haplotype-based features include sliding windows and the reconstruction of the haplotypes of the probands.”
From The oxytocin receptor (OXTR) contributes to prosocial fund allocations in the dictator game and the social value orientations task (2009) · cites this paper as [65]
PBAT can handle nuclear families with missing parental genotypes, extended pedigrees with missing genotypic information, analysis of single nucleotide polymorphisms (SNPs), haplotype analysis, quantitative traits, multivariate/longitudinal data and time to onset phenotypes.
“PBAT can handle nuclear families with missing parental genotypes, extended pedigrees with missing genotypic information, analysis of single nucleotide polymorphisms (SNPs), haplotype analysis, quantitative traits, multivariate/longitudinal data and time to onset phenotypes.”
From The oxytocin receptor (OXTR) contributes to prosocial fund allocations in the dictator game and the social value orientations task (2009) · cites this paper as [65]
The data analysis can be adjusted for covariates and gene/environment interactions.
“The data analysis can be adjusted for covariates and gene/environment interactions.”
From The oxytocin receptor (OXTR) contributes to prosocial fund allocations in the dictator game and the social value orientations task (2009) · cites this paper as [65]
The PBAT software package provides a unique set of tools for complex family-based association analysis at a genome-wide level.
“The PBAT software package provides a unique set of tools for complex family-based association analysis at a genome-wide level [65], [66].”
From The oxytocin receptor (OXTR) contributes to prosocial fund allocations in the dictator game and the social value orientations task (2009) · cites this paper as [65]
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References 25 · Cited by 73
- Authors
- Van Steen, K., & Lange, C.
- Affiliations
- Harvard University (US)
- Corresponding author
- Lange, Christoph
- ORCID
- Lange, Christoph
- Venue
- Human Genomics
- Published
- 2005
- Volume
- 2
- Issue
- 1
- Pages
- 67
- ISSN
- 1473-9542 (ISSN-L)
- 1479-7364
- PMC
- PMC3525120
- OpenAlex
- W2117802822
- Cited by
- 73
- References
- 25
- Citations by year
- 2023: 1 · 2020: 2 · 2019: 1 · 2018: 1 · 2017: 4 · 2016: 3 · 2014: 6 · 2013: 2 · 2012: 2
- FWCI
- 5.75
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Human Genomics (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Lirias (acceptedVersion, other-oa)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- ORBi (University of Liège) (submittedVersion, other-oa)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Keywords
- genome-wide association study, family-based association, nuclear family, extended pedigrees, single nucleotide polymorphisms, haplotype analysis, haplotype reconstruction, quantitative traits, longitudinal data, gene-environment interaction, multiple testing correction, genome scan, trios
- MeSH terms
- Family, Humans, Models, Genetic, Software, Genome, Human, Polymorphism, Single Nucleotide, Genomics
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