Models for primary and met tumors.

<p><b>a.</b> Primary and met are genetically identical, and metastasis occurs via epigenetic or regulatory changes, such as those contributing to EMT/MET phenotypes. <b>b</b>. Primary and met are genetically distinct, suggesting the cells diverged rapidly after the split, or that they are independent events. <b>c.</b> Primary and met tumors share many mutations, but each has some that are unique. <b>d.</b> Illustrations of possible tumor composition.</p

Clinical Characteristics of the 18 Colorectal Cancer Patients.

<p>Note: Asc. = Ascending, Desc. = Descending.</p><p>Clinical Characteristics of the 18 Colorectal Cancer Patients.</p

Co-Evolution of Somatic Variation in Primary and Metastatic Colorectal Cancer May Expand Biopsy Indications in the Molecular Era

<div><p>Introduction</p><p>Metastasis is thought to be a clonal event whereby a single cell initiates the development of a new tumor at a distant site. However the degree to which primary and metastatic tumors differ on a molecular level remains unclear. To further evaluate these concepts, we used next generation sequencing (NGS) to assess the molecular composition of paired primary and metastatic colorectal cancer tissue specimens.</p><p>Methods</p><p>468 colorectal tumor samples from a large personalized medicine initiative were assessed by targeted gene sequencing of 1,321 individual genes. Eighteen patients produced genomic profiles for 17 paired primary:metastatic (and 2 metastatic:metastatic) specimens.</p><p>Results</p><p>An average of 33.3 mutations/tumor were concordant (shared) between matched samples, including common well-known genes (APC, KRAS, TP53). An average of 2.3 mutations/tumor were discordant (unshared) among paired sites. KRAS mutational status was always concordant. The overall concordance rate for mutations was 93.5%; however, nearly all (18/19 (94.7%)) paired tumors showed at least one mutational discordance. Mutations were seen in: <i>TTN</i>, the largest gene (5 discordant pairs), <i>ADAMTS20</i>, <i>APC</i>, <i>MACF1</i>, <i>RASA1</i>, <i>TP53</i>, and <i>WNT2</i> (2 discordant pairs), <i>SMAD2</i>, <i>SMAD3</i>, <i>SMAD4</i>, <i>FBXW7</i>, and 66 others (1 discordant pair).</p><p>Conclusions</p><p>Whereas primary and metastatic tumors displayed little variance overall, co-evolution produced incremental mutations in both. These results suggest that while biopsy of the primary tumor alone is likely sufficient in the chemotherapy-naïve patient, additional biopsies of primary or metastatic disease may be necessary to precisely tailor therapy following chemotherapy resistance or insensitivity in order to adequately account for tumor evolution.</p></div

Discrepant Non-silent Mutations among paired samples from 18 Patients.

<p>* Genes in bold are recurrent mutations, with the number in parentheses being the other samples having a mutation in the same position. Genes underlined represent instances in which no alternate reads were identified in the paired tissue lacking the mutation.</p><p>Discrepant Non-silent Mutations among paired samples from 18 Patients.</p

Shared and unique mutations among the paired primary and metastatic samples.

<p>The vast majority of mutations are shared. Pairs A through F represent regional lymph node metastases and pairs G through R represent distant metastases.</p

Numbers of Haplotypes of the 48 CNVs.

<p>Numbers of Haplotypes of the 48 CNVs.</p

Correlation between genotypes of the donors and their sperm samples for CNV Rs879886.

<p>Meanings of the graphics are the same as those in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005236#pone-0005236-g002" target="_blank">Figure 2</a>.</p

dbSNP access numbers of 65 markers and classification by Fredman <i>et al.</i>[28].

<p>dbSNP access numbers of 65 markers and classification by Fredman <i>et al.</i><a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005236#pone.0005236-Fredman1" target="_blank">[28]</a>.</p

Schematic illustration of genotypes, haplotypes, and paralogous variants.

<p>Cells with three different genotypes comprised of two haplotypes are shown. The top and bottom cells are homozygous for either the longer or shorter haplotype, while the cell in the middle has both. Each haplotype has two paralogous variants that are distinguished by grey and white colors, and discriminated by analyzing a single-base substitution experimentally. Each variant may have zero to multiple copies.</p

Comparison between data from microarray and gel electrophoresis.

<p>Meanings of the x- and y-axes in all scatter plots are the same as those in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0005236#pone-0005236-g002" target="_blank">Figure 2</a>.</p