Clinical next‐generation sequencing successfully applied to fine‐needle aspirations of pulmonary and pancreatic neoplasms. Issue 12 (24th July 2013)

• Record Type: Journal Article
• Authors: Young, Geneva; Wang, Kai; He, Jie; Otto, Geoff; Hawryluk, Matthew; Zwirco, Zac; Brennan, Tina; Nahas, Michelle; Donahue, Amy; Yelensky, Roman; Lipson, Doron; Sheehan, Christine E.; Boguniewicz, Ann B.; Stephens, Philip J.; Miller, Vincent A.; Ross, Jeffrey S.
• Is Part Of: Cancer cytopathology. Volume 121:Issue 12(2013:Dec.)
• Page Start: 688
• Page End: 694
• Publication Date: 2013-07-24
• Subjects: Cancer -- Cytopathology -- Periodicals; Pathology, Cellular -- Periodicals; Cytology -- Technique -- Periodicals; 611.01815
• DOI: 10.1002/cncy.21338
• Languages: English
• ISSNs: 1934-662X

Abstract

<abstract abstract-type="main"> <title> <x xml:space="preserve">Abstract</x> </title> <sec id="cncy21338-sec-0001" sec-type="section"> <title>BACKGROUND</title> <p>Next‐generation sequencing was performed on pulmonary and pancreatic fine‐needle aspirations (FNAs) and on paired FNAs and resected primary tumors from the same patient.</p> </sec> <sec id="cncy21338-sec-0002" sec-type="section"> <title>METHODS</title> <p>DNA was isolated in formalin‐fixed, paraffin‐embedded cell blocks from 16 pulmonary FNAs, 23 pancreatic FNAs, and 5 resected pancreatic primary tumors. Next‐generation sequencing was performed for 4561 exons of 287 cancer‐related genes and for 47 introns of 19 genes on indexed, adaptor‐ligated, hybridization‐captured libraries using a proprietary sequencing system (the Illumina HiSeq 2000).</p> </sec> <sec id="cncy21338-sec-0003" sec-type="section"> <title>RESULTS</title> <p>Genomic profiles were generated successfully from 16 of 16 (100%) pulmonary FNAs, which included 14 nonsmall cell lung cancers (NSCLCs) and 2 small cell lung cancers (SCLCs). The NSCLC group included 6 adenocarcinomas, 5 squamous cell carcinomas, and 3 NSCLCs not otherwise specified. Genomic profiles were successfully obtained from 23 of 23 (100%) pancreatic FNAs and from 5 of 5 (100%) matched pancreatic primary tumors, which included 17 ductal adenocarcinomas, 3 mucinous adenocarcinomas, 2 adenocarcinomas NOS, and 1 neuroendocrine tumor. Eighty‐one genomic alterations were identified in the 16 pulmonary FNAs (average, 5.1 genomic alterations per patient); and the most common genomic alterations were TP53, RB1, SOX2, PIK3CA, and KRAS. Eighty‐seven genomic alterations were identified in the 23 pancreatic tumor FNAs (average, 3.8 genomic alterations per patient); and the most common genomic alterations were KRAS, TP53, CDKN2A/B, SMAD4, and PTEN. Among the pancreatic tumors, there was 100% concordance of 20 genomic alterations that were identified in 5 patient‐matched FNA and surgical primary tumor pairs.</p> </sec> <sec id="cncy21338-sec-0004" sec-type="section"> <title>CONCLUSIONS</title> <p>The authors were able to perform next‐generation sequencing reliably on FNAs of pulmonary and pancreatic tumors, and the genomic alterations discovered correlated well with those identified in matched resected pancreatic tumors. <bold><italic>Cancer (Cancer Cytopathol)</italic> 2013;121:688–694</bold>. © <italic>2013 American Cancer Society</italic>.</p> </sec> </abstract>