Volume 145, Issue 5, Pages 1098-1109.e1 (November 2013) Genetic Alterations Associated With Progression From Pancreatic Intraepithelial Neoplasia to Invasive Pancreatic Tumor  Stephen J. Murphy, Steven N. Hart, Joema Felipe Lima, Benjamin R. Kipp, Mitchell Klebig, Jennifer L. Winters, Csilla Szabo, Lizhi Zhang, Bruce W. Eckloff, Gloria M. Petersen, Steven E. Scherer, Richard A. Gibbs, Robert R. McWilliams, George Vasmatzis, Fergus J. Couch  Gastroenterology  Volume 145, Issue 5, Pages 1098-1109.e1 (November 2013) DOI: 10.1053/j.gastro.2013.07.049 Copyright © 2013 AGA Institute Terms and Conditions

Figure 1 LCM of PanIN and tumor yields high-quality DNA after WGA. (A) Representative examples of PanIN and tumor pathology. (B) LCM of ductal epithelial cells from PDAC. (C) Reproducibility of in situ WGA. Five replicate amplifications from normal, PanINs, and tumor LCM samples yielded equivalent size and quantities of DNA, compared with non–LCM-positive controls (+ve). –ve, phosphate-buffered saline–negative control; L, size marker. (D) Multiplex polymerase chain reaction of 5 targets from 5 chromosomes. Five replicate WGA (i–v) from representative normal (left panel) and tumor (right panel) samples are shown. Gastroenterology 2013 145, 1098-1109.e1DOI: (10.1053/j.gastro.2013.07.049) Copyright © 2013 AGA Institute Terms and Conditions

Figure 2 Numbers of somatic mutations and relatedness of tumors and adjacent PanINs. (A) Numbers of somatic mutations (gray) and insertions and deletions (black) per sample (grouped by case). P2, PanIN2; P3, PanIN3. (B) Percentage of commonality of PanINs with associated tumors. (C) Venn diagrams of somatic variants in each case. (D) Hierarchical clustering of tumors and PanINs using Euclidean distance measures for each possible comparison. INDEL, insertion and deletion. Gastroenterology 2013 145, 1098-1109.e1DOI: (10.1053/j.gastro.2013.07.049) Copyright © 2013 AGA Institute Terms and Conditions

Supplementary Figure 1 Alternative allele frequency ratios show that there is little bias for variant detection due to whole genome amplification (WGA). Top Panel: For each non-reference allele, the fractional composition of that variant is displayed. One would expect that heterozygous variants would be 50% reference and 50% alternate allele. Bottom Panel: Using the mean value from each of the samples, we show that there is no bias due to tissue histology. Gastroenterology 2013 145, 1098-1109.e1DOI: (10.1053/j.gastro.2013.07.049) Copyright © 2013 AGA Institute Terms and Conditions