Genetic events detected in the peripheral blood of ISKS probands.

*<p>Database version R16 November, 2012; del: deleterious; neut: neutral; FS: frame shift; LOH: loss of heterozygosity; NA: not applicable. The assignment of pathogenicity was performed as outlined in supplementary Figure 3.</p

Characteristics of the ISKS cohort.

*<p>some probands have >1 sarcoma; SD, standard deviation; LPS, liposarcoma.</p

Expression of SseK3 in host cells.

<p>A. Graphs showing GFP fluorescence intensity of intracellular wild-type or <i>ssrB Salmonella</i> containing an <i>sseK3</i> promoter GFP fusion plasmid. Cells were infected for 0.5 h and 8 h before being processed for flow cytometry. B. Western blots of infected HeLa cell lysates made at the indicated times post-infection (hours PI), with the indicated strains transformed with plasmids encoding the indicated effector fused to tandem HA epitopes. The western blots were probed for the HA epitope and DnaK as a loading control.</p

Strain distribution of phage encoded effectors of <i>Salmonella</i>.

<p>Strain distribution of phage encoded effectors of <i>Salmonella</i>.</p

Secretion of SseK3.

<p>Western blots of concentrated culture supernatant proteins and whole <i>Salmonella</i> cell lysates (pellet) from strains genotypes indicated at the top of the figure were probed with the antibodies indicated to the left of the figure. The arrow to the right of the α-HA panel indicates the bands corresponding to SseK3-HA.</p

The role SseK effector in virulence.

<p>Competitive indices were determined 3 days following oral inoculation of 129/svImJ mice infected with an equal mixture of the indicated 2 strains. Values from spleen and liver for individual mice are shown as diamonds and circles respectively, and the mean is shown as a horizontal bar.</p

Translocation of SseK3 into infected HeLa cells.

<p>Western blots from fractionated, infected HeLa cells probed with the antibodies indicated to the left of the figure. SseK3-HA and SifA-HA indicated at the top of the figure refer to the HA-tagged protein expressed in the respective strain, and under this, wt and <i>ssaR</i> refer to the genotype of the respective strain. P, C and M refer to the fractions collected from the infected cells as described in the text. The arrow to the right of the α-HA panel indicates the bands corresponding to SseK3-HA and SifA-HA (which are approximately the same MW).</p

Primary analysis pipelines.

<p>Red colour highlights the difference between our Somatic Pipeline and Familial (Germline) Pipeline.</p

The TREVA workflow: execution of primary and secondary pipelines for variant calling on individual and related groups of samples.

<p>The TREVA workflow: execution of primary and secondary pipelines for variant calling on individual and related groups of samples.</p