Ion AmpliSeq Cancer

Hotspot Panel v2
Just one tube. Just 10 ng of DNA. Just one day.
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 96well platebased protocolsfurther simplifying the workflow and allowing large projects
to be rapidly completed without additional sample transfer steps.
Ion AmpliSeq Cancer Hotspot Panel v2
Targets

 otspot regions, including ~2,800 COSMIC mutations of 50 oncogenes and tuH

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 coverage

Ion 316 Chip: 8 samples, ~1,400x average coverage
Ion 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

*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

Recent publications
CHEST 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

Ideal for FFPE sequencingrequires only 10 ng of DNA

The Ion AmpliSeq Cancer Panel targets 50 genes

The Ion AmpliSeq technologys breakthrough requirement of only

10 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.

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

Fastest time to targeted libraries3.5 hours

CDKN2A

GNAS

MPL

SRC

The single-day workflow 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).

CSF1R

GNAQ

NOTCH1

STK11

CTNNB1

HNF1A

NPM1

TP53

EGFR

HRAS

NRAS

VHL

ERBB2

IDH1

PDGFRA

ERBB4

JAK2

PIK3CA

Construct
Library

Prepare
Template

3.5

Hours

Hours

Run
Sequence

1.5
Hours

Analyze
Data

Annotate
Results

0.5

0.5

TORRENT SERVER

ION REPORTER SOFTWARE

Hours

Hours

Ion Reporter

ION AMPLISEQ PANELS

ION ONETOUCH SYSTEM

ION PGM SEQUENCER

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

Confirm variants using TaqMan Assays

TaqMan 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 conrmation 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 conrm variants at
lifetechnologies.com/ordertaqman

Figure 1. Ion AmpliSeq Panel workow using an Ion 314 Chip

and a 90-minute, 1 x 100 base sequencing run.

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 amplication 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

Find out how to transform your oncology research at

lifetechnologies.com/ampliseq
FOR 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