The Ion AmpliSeq Cancer Hotspot Panel v2 is now expanded to allow translational and disease researchers to fast-track oncology research by surveying hotspot regions of 50 oncogenes and tumor suppressor genes, with wide coverage of the KRAS, BRAF, and EGFR genes.

This panel, with improved primer design, contains 207 primer pairs in a single tube and requires only 10 ng of DNA, enabling researchers to sequence challenging samples like FFPE tissue. The convenient predesigned panel allows researchers to focus on data generation and analysis, not on the labor-intensive primer design and target selection steps. While hybridization-based target selection methods require 7 to 72 hours to complete both target selection and library preparation, Ion AmpliSeq technology makes it possible to complete the entire process in just 3.5 hours using simple PCR reactions. Additionally, Ion AmpliSeq library construction steps are automated using standard 96-well platebased protocolsfurther simplifying the workflow and allowing large projects to be rapidly completed without additional sample transfer steps.

Ion AmpliSeq Cancer Hotspot Panel v2Just one tube. Just 10 ng of DNA. Just one day.

Recent publicationsCHEST Journal Samuel A. Yousem, January 2013, doi:10.1378/chest.12-1917

The Journal of Molecular Diagnostics Carol Beadling, December 2012, doi:10.1016/j.jmoldx.2012.09.003

Virchows Archiv Willemina R. Geurts-Giele, December 2012, doi:10.1007/s00428-012-1346-4

Journal of Neurosurgery: Pediatrics Michael M. H. Yang, May 2012, doi:10.3171/2012.1.PEDS11326

Dataset for this panel is available at lifetechnologies.com/ioncommunity

*Coverage uniformity = percentage of bases covered at 20% of the mean coverage On-target reads = percentage of reads that mapped to target regions out of total mapped reads per run

Ion AmpliSeq Cancer Hotspot Panel v2

Targets Hotspot regions, including ~2,800 COSMIC mutations of 50 oncogenes and tu-mor suppressor genes, with wide coverage of the KRAS, BRAF, and EGFR genes

Amplicon length 111187 bp, average 154 bp

Primer pool size 207 primer pairs in 1 tube

Input DNA required Only 10 ng per DNA sample

Time-to-results 10 hours (DNA to annotated variants)

Sample multiplexing(observed performance)

Ion 314 Chip: 2 samples, ~1,400x average coverageIon 316 Chip: 8 samples, ~1,400x average coverageIon 318 Chip: 16 samples, ~1,400x average coverage

Specification Observed performance (Ion 314 Chip)

Coverage uniformity* 95% 98%

On-target reads 90% 96%

Average depth of coverage NA >2,000x

SNP detection sensitivity NA 98% detection rate for 5% variant frequency at positions with average sequencing coverage from 1,000x to 4,000x

Ordering information

Product Cat. No.

Ion AmpliSeq Cancer Hotspot Panel v2 (primer pool) 4475346

Ion AmpliSeq Library Kit 2.0(8, 96, 384 reactions for both PCR ampli cation and library construction)

4475345, 4480441, 4480442

Ion Xpress Barcode Adapters Kits 4474517, 4471250, 4474009, 4474518, 4474519, 4474520, 4474521

Additional Ion AmpliSeq Products

Ion AmpliSeq Cancer Panel Primer Pool (v1 covering 46 oncogenes) 4471262

Ion AmpliSeq Comprehensive Cancer Panel (primer pool) 4477685

Ion AmpliSeq Inherited Disease Panel (primer pool) 4477686

Ion AmpliSeq Sample ID Panel (primer pool) 4479790

Ion AmpliSeq Custom Panels can be ordered via Ion AmpliSeq Designer.Learn more at lifetechnologies.com/ampliseqcustom

Ideal for FFPE sequencingrequires only 10 ng of DNAThe Ion AmpliSeq technologys breakthrough requirement of only10 ng of input DNA for the entire Ion AmpliSeq Cancer Panel is designed to deliver accurate sample representation even from FFPE samples, which are typically available only in small amounts and often exhibit variable quality. In addition, the primers in this panel are designed to produce, on average, 154 bp amplicons, so that even degraded samples can be used to generate reliable data. Targeted selection is completed using standard PCR equipment, so no additional capital investment is required.

Fastest time to targeted libraries3.5 hours The single-day workfl ow from DNA to annotated variants allows you to address time-sensitive assays. No other target selection method produces targeted libraries in just 3.5 hours using simple PCR reactions . Transfer the libraries to the Ion OneTouch 2 System for template preparation, and sequence them on the Ion PGM Sequencer. Automated analysis is then performed with Torrent Suite Software on the PGM Torrent Server. The nal step, using Ion Reporter Software, is optional and can be used to automate bioinformatics analysis including variant annotations. This software is ideal for use with routine DNA assays (Figure 1).

The Ion AmpliSeq Cancer Panel targets 50 genes

TaqMan Mutation Detection Assays are available for the genes listed above.

Confi rm variants using TaqMan AssaysTaqMan Mutation Detection Assays detect somatic mutations in 45 genes associated with cancer. Our assays, powered by castPCR technology, can detect mutations down to 0.1% in a background of wild type DNA, as demonstrated in spiking experiments. Optionally, variant con rmation can be completed using Custom TaqMan SNP Genotyping Assays with digital PCR. Integrated with the search portal for TaqMan Assays, Torrent Suite Software enables direct submission of detected variants for further analysis with TaqMan Assays.

Find out how to con rm variants at lifetechnologies.com/ordertaqman

Find out how to transform your oncology research atlifetechnologies.com/ampliseqFOR RESEARCH USE ONLY. NOT FOR USE IN DIAGNOSTIC PROCEDURES. 2013 Life Technologies Corporation. All rights reserved. The trademarks mentioned herein are the property of Life Technologies Corporation or their respective owners. TaqMan is a registered trademark of Roche Molecular Systems, Inc., used under permission and license. CO04647 0113

Figure 1. Ion AmpliSeq Panel work ow using an Ion 314 Chip and a 90-minute, 1 x 100 base sequencing run.

ConstructLibrary

ION AMPLISEQ PANELS ION ONETOUCH SYSTEM ION PGM SEQUENCER TORRENT SERVER

PrepareTemplate

Run Sequence

AnalyzeData

1.5Hours Hours

0.50.5Hours

4Hours

3.5Hours

ION REPORTER SOFTWARE

AnnotateResults

Ion Reporter

ABL1 EZH2 JAK3 PTEN

AKT1 FBXW7 IDH2 PTPN11

ALK FGFR1 KDR RB1

APC FGFR2 KIT RET

ATM FGFR3 KRAS SMAD4

BRAF FLT3 MET SMARCB1

CDH1 GNA11 MLH1 SMO

CDKN2A GNAS MPL SRC

CSF1R GNAQ NOTCH1 STK11

CTNNB1 HNF1A NPM1 TP53

EGFR HRAS NRAS VHL

ERBB2 IDH1 PDGFRA

ERBB4 JAK2 PIK3CA