Because no truncating mutations passed our filters, further functional studies are required to assess whether any of the confirmed variants is ultimately a causal mutation, specifically those variants considered of interest because of their functional implications (missense and 3'UTR) and gene function.
The effect sizes of the confirmed variants were similar to or smaller than those of the initially identified ones.
None of the 15 confirmed variant sites were located in genes that have been associated with antimicrobial resistance.
As designed, this cutoff was able to distinguish the confirmed from the non-confirmed variants quite well, so we went back and filtered the novel non-synonymous variants using this criterion.
Fifty-six of the confirmed somatic variants were predicted and only 1 of the tested, but not confirmed variants, was predicted.
Three field isolates (CH1, CH8, CHGD-01) formed a unique cluster with the sequence-confirmed variant strain CH-FJND-3, which had been isolated from China in 2011 (7 ).
The mean DS for confirmed variants was 115 (74–185), whereas the mean DS for ruled out variants was 56.5 (56 57), which means that our DS score is a suitable variable for the filtering process.
Assuming a pattern of allele frequencies and ORs "similar" to what has been observed for confirmed variants, they also estimated the number of susceptibility variants for type 2 diabetes.
All confirmed variants were submitted to locus-specific databases within the LOVD 3.0 shared installation: www.LOVD.nl/DYNC2H1 (individual ID 00016506); www.LOVD.nl/RYR1 (individual ID 00011457); www.LOVD.nl/GLE1 (individual ID 00016592).
Subsequently, all confirmed variants in a given sample were sequenced in available samples from relatives (Supp. Fig. S3).
The final column provides the accession number of our sequences for the confirmed alternate splice variant.
