Variants detected on pseudomyxoma peritonei by exome sequencing and validated by ultra-deep amplicon sequencing.

<p>Variants detected on pseudomyxoma peritonei by exome sequencing and validated by ultra-deep amplicon sequencing.</p

Gene mutations related to PKA and TGF-β pathways in pseudomyxoma peritonei.

<p>(A) Variants of PKA pathway. (B) Variants of TGF-β pathway. Pathways have been modified from KEGG [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0174898#pone.0174898.ref040" target="_blank">40</a>]. PKA: protein kinase A; TGF-β: transforming growth factor beta.</p

Gene mutations identified in pseudomyxoma peritonei (PMP).

<p>Nine appendix-derived PMP samples were analyzed for grade and cellularity, using HE slides and NGS, respectively. Somatic mutations were identified using exome sequencing and validated by ultra-deep amplicon sequencing. HG: high-grade; LG: low-grade. * [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0174898#pone.0174898.ref009" target="_blank">9</a>].</p

Workflow used for exome sequencing of nine pseudomyxoma peritonei specimens and their matching control samples.

<p>Workflow used for exome sequencing of nine pseudomyxoma peritonei specimens and their matching control samples.</p

Comparison of <i>KRAS</i> and <i>GNAS</i> mutations detected with targeted sequencing, exome sequencing and validation sequencing.

<p>Comparison of <i>KRAS</i> and <i>GNAS</i> mutations detected with targeted sequencing, exome sequencing and validation sequencing.</p

Exome-wide statistics of filtered somatic SNV and indel calls.

<p>(A) Number of SNVs and indels. (B) Total number of somatic nucleotide base changes. (C) Ts to Tv ratio of each tumor. SNV: single nucleotide variation; indel: insertion/deletion; Ts: transition; Tv: transversion.</p

Tumor cell content of pseudomyxoma peritonei FFPE samples estimated from HE stainings, and variant allele frequencies (VAF) of <i>KRAS</i> and <i>GNAS</i> from targeted sequencing.

<p>Tumor cell content of pseudomyxoma peritonei FFPE samples estimated from HE stainings, and variant allele frequencies (VAF) of <i>KRAS</i> and <i>GNAS</i> from targeted sequencing.</p

Clinical characteristics of the 96 cases with familial colorectal cancer.

<p>NOTE: some of the numbers do not match due to missing data.</p><p>Abbreviations: MSI, microsatellite instability; MSS, microsatellite stable.</p>*<p>Distal, from splenic flexure to rectum; proximal, from cecum to transverse colon.</p

Schematic representation of the overall study design.

<p>We performed exome sequencing analysis of germline DNA from 96 independent familial CRC cases. Initially, quality, frequency and control filtering were applied to the exome data. Next, genes with putative truncating loss-of-function variants in at least 2/96 cases were validated by Sanger sequencing. Confirmed truncating variants were then screened in Finnish population matched controls. Loss of heterozygosity was analyzed in the respective tumor tissues. Variants in genes showing loss of the wild-type allele in tumor tissue were genotyped in a set of validation phase samples. Overall, 11 novel candidate CRC predisposing genes were identified. CRC, colorectal cancer; MAF, minor allele frequency; LOH, loss of heterozygosity.</p

Pedigrees of families found to carry <i>UACA</i> and <i>TWSG1</i> truncating variants.

<p>Carrier status is depicted for all the cases for whom readily extracted DNA was available. The individuals that underwent exome sequencing are marked with an arrow. Numbers represent the age at diagnosis of the affected individuals. The following abbreviations are used: CRC, colorectal cancer; BCC, basal cell carcinoma, MG, meningioma; HD, Hodgkin lymphoma; PC, prostate cancer; MM, melanoma and LC, lung cancer.</p