PIK3CA and TP53 Gene Mutations in Human Breast Cancer Tumors Frequently Detected by Ion Torrent DNA Sequencing

Abstract

Breast cancer is the most common malignancy and the leading cause of cancer deaths in women worldwide. While specific genetic mutations have been linked to 5–10% of breast cancer cases, other environmental and epigenetic factors influence the development and progression of the cancer. Since unique mutations patterns have been observed in individual cancer samples, identification and characterization of the distinctive breast cancer molecular profile is needed to develop more effective target therapies. Until recently, identifying genetic cancer mutations via personalized DNA sequencing was impractical and expensive. The recent technological advancements in next-generation DNA sequencing, such as the semiconductor-based Ion Torrent sequencing platform, has made DNA sequencing cost and time effective with more reliable results. Using the Ion Torrent Ampliseq Cancer Panel, we sequenced 737 loci from 45 cancer-related genes to identify genetic mutations in 105 human breast cancer samples. The sequencing analysis revealed missense mutations in PIK3CA, and TP53 genes in the breast cancer samples of various histologic types. Thus, this study demonstrates the necessity of sequencing individual human cancers in order to develop personalized drugs or combination therapies to effectively target individual, breast cancer-specific mutations.

Comparison of plasma to tissue DNA mutations in surgical patients with non–small cell lung cancer

“…4,5 Few data are available to indicate whether ctDNA analyses is applicable for patients with stage I-IIIA nonsmall cell lung cancer (NSCLC), largely because the low level of micrometastatic disease makes detection of ctDNA challenging. 6 Next-generation sequencing using the Ion Personal Genome Machine has been shown previously to have high sensitivity and can screen for mutations in multiple genes simultaneously, 7 which may be useful for identifying plasma ctDNA from patients with lung cancer. Thus, our prospective study evaluated the feasibility of identifying ctDNA in plasma of surgical patients with NSCLC with matched tumor tissue using targeted sequencing and investigated potential clinical applications.…”

Detection of genes mutations in cerebrospinal fluid circulating tumor DNA from neoplastic meningitis patients using next generation sequencing

“…Preparation of the ctDNA library and the next generation DNA sequencing The ctDNA samples were subjected to preparation of the Ion Proton library and DNA sequencing, according to the methodologies from previous studies [10][11][12]. Briefly, for each sample, an adapterligated library was generated using the Ion AmpliSeq Library Kit 2.0 (Invitrogen).…”

“…The raw DNA sequencing data were processed and analyzed using the Ion Proton platform-specific pipeline (Torrent Suite v5.0) with a specific plug-in (Variant Caller v5.0), which included the readouts of the raw DNA sequences, the trimming of the adapter sequences, and the filtering and removal of poor signal sequences according to previous studies [10][11][12]. These three filtering steps were applied to eliminate the erroneous base calling, and the final variant calling was generated.…”

Evaluating the Cerebrospinal Fluid ctDNA detection by Next-Generation Sequencing in the diagnosis of Meningeal Carcinomatosis

“…Preparation of the Ion Proton library and DNA sequencing were performed as described in our previous publications [20][21][22]. For each sample type, an adapter-ligated library was generated with the Ion AmpliSeq Library Kit 2.0 (Life Technologies) according to the manufacturer's protocol.…”

“…Initial data from the sequencing runs were processed with the Ion Proton platform-specific pipeline software Torrent Suite v5.0 including generating sequencing reads, trim adapter sequences, filtering and removing poor signal-profile reads as described in our previous publications [20][21][22]. Initial variant calling from the sequencing data was generated with the TorrentSuite Software with a plug-in 'variant caller v5.0'.…”