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In the drop collapsing test, a drop of surfactant producing culture was flattened on oil surface leading to positive reaction.
The BS producing ability of the isolate P4 was studied using standard parameters, described earlier such as foaming test (Ferhat et al. 2011), drop collapsing test (Tugrul and Cansunar 2005), emulsification index (Deepak and Jayapradha 2015), BATH assay (Rosenberg 1984), cetyl trimethyl ammonium bromide (CTAB) agar test (Satpute et al. 2010).
Collapsing test is then examined on G−1 and a two-sided p-value is obtained.
Two other existing tests, namely combined multivariate collapsing test (CMC) [15] and group-wise weighted sum statistic test (GWWS) [16], were also included in our analysis for comparison.
We extend the population-based collapsing test to families with either known or unknown population structures.
"1" indicates single marker test; "2" indicates family-based collapsing test; "3" indicates family-based VT test; "4" indicates family-based WSS test.
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The power of collapsing tests increased more sharply as the number of causal variants increased.
These tests show that in both single-marker and collapsing tests, failure to correct for population structure results in inflated type I error rates.
The locus-wide collapsing tests examining low-frequency and rare variants (MAF <0.05) in aggregate demonstrated lower power to detect association.
Simulation results also indicate that with or without weights, Type I error rates for all collapsing tests do not deviate from the nominal level (Table 2).
Our main goal is to investigate the performance of haplotype and variants based tests in general pedigrees, which will allow us to address the question of whether or not haplotype-based collapsing tests would outperform the variant-based collapsing tests for detecting rare variants in human pedigrees under difference cases of scenarios.
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