Quality characteristics for samples by timepoint.

Quality characteristics for samples by timepoint.</p

Overall gene alterations from swab acquired tumor samples (patients 2–30) is similar to landscape of TCGA cervical squamous cell carcinoma dataset.

(A) Ninety-four percent (1339/1430) of altered genes in baseline samples (defined as substitutions, insertions or deletions in gene) were also identified in the TCGA dataset, suggesting accurate identification of mutated genes related to cervical cancer. (B) The distribution of the top 30 most altered genes in study samples 2–30 and in TCGA(C) was also similar. (TIF)</p

Sample and sequencing quality control metrics and tumor purity estimates for each tumor sample.

(XLSX)</p

Fig 3 -

Quality Characteristics and DNA alterations for all Samples by Time (A) Total DNA yield did not differ by acquisition timepoint. Total reads (B), mean target coverage (C) and mapping rate (D) did not differ by timepoint. Number of DNA alterations at baseline decreased at week 5 of CRT in all patients (E, p = 0.008) as well as when 33 patients with samples at all 4 time points were examined (F, p = 0.03).</p

Overall study design and CONSORT diagram.

(A) Patients with cervical cancer underwent five weeks of external beam radiation therapy (EBRT) followed by two brachytherapy treatments (B1 and B2), with swab samples collected at baseline, week 1, week 3, and week 5 of radiation therapy as well as week 12 (after completion of radiation therapy). (B) Of the 73 patients accrued on protocol, 70 patients with 217 total samples had DNA of adequate quantity and quality for sequencing. One tumor sample failed sequencing due to low quantity and high degradation and was not included in the analysis.</p

CONSORT 2010 checklist of information to include when reporting a pilot or feasibility trial*.

(PDF)</p

Top 50 gene alterations over time for 70 patients with paired normals.

Heat map displaying the top 50 genes ranked by occurrence for 70 patients (216 samples) grouped by timepoint collection during chemoradiation.</p

Computational pipeline for whole exome sequencing data.

Workflow depicting preprocessing, variant calling and data analysis tools and parameters implemented to analyze WES data acquired from tumor DNA collected by cervical swab.</p

Lollipop plots showing mutation site, type, and frequency of canonical genes associated with cervical cancer pathogenesis for all samples.

(TIF)</p

Top 50 gene alterations over time for 33 patients with all four-time points.

Heat map displaying the top 50 genes ranked by occurrence for 33 patients (132 samples) grouped by timepoint collection during chemoradiation.</p