FBAT protocols

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FBAT specifications

Information


Unique identifier OMICS_07500
Name FBAT
Alternative name Family Based Association Test
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Stability No
Maintained No

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Publications for Family Based Association Test

FBAT in pipelines

 (13)
2016
PMCID: 5133523
PMID: 27980637
DOI: 10.1186/s12919-016-0031-z

[…] of hardy-weinberg equilibrium within the 91 founders were removed. this resulted in 850 sites in map4, 493 in tnn, and 899 in lepr., the transmission-based rare variant analyses were conducted using fbat-rv, fbat-lc, and fbat-min p. fbat-rv extends the basic family-based association test (fbat) statistic, a covariance between the offspring genotype and trait, by collapsing rare variants […]

2015
PMCID: 4382929
PMID: 25887117
DOI: 10.1186/s12863-015-0184-1

[…] snps with >1% mendelian errors (1334). after quality controls we retained 1,309,937 snps and 388 samples., association analysis for all cnv regions was performed using two different methods: a) fbat [] (version 2.0.4), a version of the transmission distortion test adapted for larger families and b) emmax [] (version from february 2012), a statistical test for association analysis using […]

2014
PMCID: 3916225
PMID: 24516392
DOI: 10.1371/journal.pgen.1003991

[…] and the case-control allelic and genotypic association tests using a bonferroni correction for multiple comparisons . as most of the old english sheepdogs genotyped belonged to a large pedigree, a family-based association test was also performed using the family based association test (fbat) toolkit (v2.0.3) (http://www.hsph.harvard.edu/~fbat/fbat.htm) . the fbat toolkit improves upon […]

2014
PMCID: 3953017
PMID: 24625924
DOI: 10.1371/journal.pgen.1004229

[…] of variants identified in the wgs, we then characterized each haplotype in terms of sequence variants present. as a final step, we examined association signals (from gwas data generated using fbat and emmax, see above) and carried-out family-based burden association analysis (using the rarefbat test) on genes under the linkage peaks., we performed linkage analysis of the 1991 […]

2013
PMCID: 3664012
PMID: 23291585
DOI: 10.1038/ng.2518

[…] an inverse variance fixed effects meta-analysis., in addition, for the brazilian family study we verified our results using two complementary alternative methods implemented in the software packages fbat and roadtrips. results were comparable across the different methods (data not shown)., the hla drb1 and dqb1 typing of 100 selected indian discovery individuals was performed using […]

FBAT in publications

 (260)
PMCID: 5902855
PMID: 29661184
DOI: 10.1186/s12944-018-0737-1

[…] 15 snps of slc12a3 gene was genotyped within a 424 mongolians pedigree cohort. the associations between slc12a3 polymorphisms and four lipid profiles were analyzed by family-based association test (fbat) and confirmed with haplotype analysis., from both single site and haplotype analyses, the results demonstrated a close relationship between slc12a3 polymorphisms and ldl-c level. two snps, […]

PMCID: 5847615
PMID: 29531279
DOI: 10.1038/s41598-018-21603-7

[…] = 4.66 × 10–9) reached a genome-wide significant level of association and a subsequent validation in nunavik inuit cohort further confirmed the significance of the fhit variant association (rs780365, fbat-o, p = 0.002839). additionally, among the other promising loci (p < 5 × 10−6), the one at 3q13.2 (rs78125721, p = 4.77 × 10−7), which encompasses ccdc80, also showed an increased mutation burd […]

PMCID: 5587310
PMID: 28877219
DOI: 10.1371/journal.pone.0183772

[…] of these [, , ] were based on the same gwas dataset as in the current study, enabling a comparison of findings across different methods. patel et al. (2013) used ‘family-based association tests’ (fbat) [, ] and wise and co-workers used their own methods, pix-lrt [] and pix-hap []. fonseca et al. [] used x-tdt [] to analyze 23,344 snps in 27 argentinian mother-child dyads of orofacial clefts., […]

PMCID: 5550983
PMID: 28808521
DOI: 10.1186/s13229-017-0161-9

[…] freedom, χ 2 χ 2 statistics, p p value , 1 rs3 (complex), 2 rs7294536, 3 rs1 (gata), 4 rs10877969, n number of informative nuclear families, df degree of freedom, χ 2 χ 2 statistics, p p value, the fbat analysis showed significant association between the snps (rs7294536 and rs10877969) and multiple quantitative traits related to sociality and social communication, including total scores of scq […]

PMCID: 5527118
PMID: 28744025
DOI: 10.1038/s41598-017-06795-8

[…] to schizophrenia was analysed using two approaches (table ). first, the association between the 14 candidate snps and affliction with schizophrenia was examined using an additive model of the fbat within the 185 multiplex families. the results showed that only 1 snp (rs571002) had a weak association signal (p = 0.049). second, by incorporating 925 age- and gender-matched community […]

FBAT institution(s)
Department of Biostatistics, Harvard University, Boston, MA, USA; Department of Biostatistics, Columbia University, New York, NY, USA
FBAT funding source(s)
Supported by FBAT (Family Based Association Tests) grant.

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