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Using the second criterion, genealogical non-discordance, the clade was well supported in at least one single-locus genealogy, as judged by both MP bootstrap proportions above 70% and Bayesian posterior probabilities above 95% and was not contradicted in any other single-locus genealogy at the same level of support [19], [20].
Throughout the main text, we use the first criterion; results using the second criterion are reported in supplementary Results (Supplementary Material online).
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Using the first criterion, genealogical concordance, the clade was present in the majority of the single-locus genealogies.
It seems to be clear that most sterile lines found by using the first criterion are false-positives.
Screening of the titles and abstracts using the first criterion excluded a further 3288 studies (see Additional file 3 for flowchart).
A total of 51 067 SNPs were detected from 20 609 contigs using the first criterion, resulting in the identification of an SNP site every 96 bp.
Using the first criterion, phenotype information of 31 experiments was removed (e.g. all strains grow or do not grow on a given sugar) leaving growth information on 19 different substrates.
When we used the second criterion, the quetiapine group also showed a significantly lower relapse rate (27%, 15%to3939%) than did the placebo group (63%, 46%to7979%) (χ=11.81, df=1; P=0.001 by log-rank).
When we used the first criterion, the quetiapine group showed a significantly lower relapse rate (30%, 95% confidence interval 18%to4242%) than did the placebo group (68%, 56%to8080%) (χ=14.67, df=1; P<0.001 by log-rank).
The NPV could be improved further by using the second branch criterion to separate the 1049 patients into likely non-responders and not predictable.
For using the second IHC criteria, no significant association was found between IHC and mutation or FISH.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com