AmpliSeq for Illumina Cancer Hotspot Panel v2

Targeted research panel investigating hotspot regions of 50 genes with known associations to cancer.

5 hours (library prep only; doesn't include library quantification, normalization, or pooling time)

Assay time

< 1.5 hr

Hands-on time

1–100 ng (10 ng recommended per pool)

Input quantity

See full details in the specifications table

Overview

The AmpliSeq for Illumina Cancer Hotspot Panel v2 is a targeted resequencing assay for researching somatic mutations across the hotspot regions of 50 genes with known associations to cancer, as identified in the Catalogue of Somatic Mutations in Cancer (COSMIC)1 database. 

Key features

  • Relevant Gene Content - Target ~2800 COSMIC mutations from 50 oncogenes and tumor suppressor genes

  • Fast, Streamlined Workflow - Prepare sequencing-ready libraries in a single day from as little as 1 ng of high quality or 10 ng of formalin-fixed, paraffin-embedded (FFPE) samples

  • Accurate Data - Detect somatic mutations down to 5% variant allele frequency using local or cloud-based analysis

The Cancer HotSpot Panel is part of an integrated workflow that includes AmpliSeq for Illumina polymerase chain reaction (PCR)-based library preparation, Illumina sequencing by synthesis (SBS) next-generation sequencing (NGS) technology, and automated analysis.

This panel enables highly sensitive variant detection within multiple cancer types, including lung, colon, breast, ovarian, melanoma, and prostate. The ready-to-use panel saves you the time and effort of identifying targets, designing primers, and optimizing panels.


Specifications


Required products

The AmpliSeq for Illumina Cancer Hotspot Panel workflow requires the Cancer Hotspot Panel, Library PLUS kit, and index adapter.

/ Results

Applications

Example workflow


Project recommendations

Instrument Recommended number of samples Read length
iSeq 100 System

16 samples per run (assumes minimum coverage of 500×)

2 × 150 bp

MiniSeq System

Samples per run: mid output: 32, high output: 96 (assumes minimum coverage of 500×)

2 × 150 bp

MiSeq System

Samples per run (by reagent kit version): v2 nano: 4, v2 micro: 16, v2: 60, v3: 96 (assumes minimum coverage of 500×)

2 × 150 bp


Related applications and methods

Compare

AmpliSeq for Illumina Cancer Hotspot Panel v2 AmpliSeq for Illumina Focus Panel AmpliSeq for Illumina Comprehensive Panel v3 TruSight Tumor 15
Assay time 5 hours (library prep only; doesn't include library quantification, normalization, or pooling time) 5-6 hr (library prep only; doesn't include library quantification, normalization, or pooling time) 5-6 hr (library prep only; doesn't include library quantification, normalization, or pooling time) 7 hr
Cancer type Pan-Cancer, Solid Tumor Solid Tumor Solid Tumor Pan-Cancer, Solid Tumor
Content specifications Hotspot regions of 50 genes with known associations to cancer DNA and RNA targets for 52 oncogenes DNA and RNA targets for 161 oncogenes Amplifies 250 amplicons from 15 genes associated with solid tumors
Description Somatic analysis research into hotspot regions of 50 cancer-related genes. Somatic analysis research on 52 genes associated with solid tumor cancers. Somatic analysis research on hotspot and full-length targets of genes* associated with solid tumor cancers.

NGS assay for 15 commonly mutated genes in solid tumors using 20 ng DNA. 

Hands-on time < 1.5 hr < 1.5 hr <1.5 hr 3.5 hr
Input quantity 1–100 ng (10 ng recommended per pool) 1–100 ng (10 ng recommended per pool) 1–100 ng (10 ng recommended per pool)

20 ng FFPE DNA 

Instruments MiSeq System, iSeq 100 System, MiSeqDx in Research Mode, MiniSeq System MiSeq System, iSeq 100 System, MiSeqDx in Research Mode, MiniSeq System NextSeq 550 System, NextSeq 2000 System, NextSeq 1000 System, NextSeq 550Dx in Research Mode MiSeq System, MiSeqDx in Research Mode, MiniSeq System
Mechanism of action Multiplex PCR Multiplex PCR Multiplex PCR
Method Targeted DNA sequencing, Amplicon sequencing Targeted DNA sequencing, Amplicon sequencing, Targeted RNA sequencing Targeted DNA sequencing, Amplicon sequencing, Targeted RNA sequencing Targeted DNA sequencing, Amplicon sequencing
Multiplexing 96 dual index combinations 96 dual index combinations 96 dual index combinations 1-24-plex
Nucleic acid type DNA DNA, RNA DNA, RNA DNA
Number of amplicons 207 total. 1 pool. 553 total. 2 pools. (DNA Pool: 269 amplicons. RNA Pool: 284 amplicons.) 4,648 total 4 pools (DNA pool 1: 1,891 amplicons. DNA pool 2: 1,890 amplicons. RNA pool 1: 447 amplicons. RNA pool 2: 420 amplicons.)
Specialized sample types FFPE Tissue FFPE Tissue FFPE Tissue FFPE Tissue
Species category Human Human Human Human
Technology Sequencing Sequencing Sequencing Sequencing
Variant class Single nucleotide polymorphisms (SNPs), Somatic variants, Insertions-deletions (indels) Single nucleotide polymorphisms (SNPs), Gene fusions, Somatic variants, Insertions-deletions (indels), Copy number variants (CNVs) Single nucleotide polymorphisms (SNPs), Gene fusions, Somatic variants, Insertions-deletions (indels), Copy number variants (CNVs) Somatic variants, Insertions-deletions (indels)

Panel (1)

AmpliSeq™ Cancer HotSpot Panel v2 for Illumina®

20019161

Targeted panel for assessing somatic mutations across hotspot regions of 50 cancer-related genes. Kit contains 24 reactions. Library PLUS and index adapters sold separately.

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Library prep (3)

AmpliSeq™ Library PLUS (24 Reactions) for Illumina®

20019101

Includes reagents for preparing 24 libraries. Purchase AmpliSeq for Illumina panel and index adapters separately.

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AmpliSeq™ Library PLUS (96 Reactions) for Illumina®

20019102

Includes reagents for preparing 96 libraries. Purchase AmpliSeq for Illumina panel and index adapters separately.

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AmpliSeq™ Library PLUS (384 Reactions) for Illumina®

20019103

Includes reagents for preparing 384 libraries. Purchase AmpliSeq for Illumina panel and index adapters separately.

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Index adapters (6)

AmpliSeq™ UD Indexes for Illumina® (24 Indexes, 24 Samples)

20019104

Includes 24 indexes sufficient for labeling 24 samples. Purchase library prep and enrichment reagents and probe panels separately.

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AmpliSeq™ CD Indexes Set A for Illumina®

20019105

Includes 96 indexes sufficient for labeling 96 samples. Purchase library prep and enrichment reagents and probe panels separately.

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AmpliSeq™ CD Indexes Set B for Illumina®

20019106

Includes 96 indexes sufficient for labeling 96 samples. Purchase library prep and enrichment reagents and probe panels separately.

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AmpliSeq™ CD Indexes Set C for Illumina®

20019107

Includes 96 indexes sufficient for labeling 96 samples. Purchase library prep and enrichment reagents and probe panels separately.

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AmpliSeq™ CD Indexes Set D for Illumina®

20019167

Includes 96, 8 bp indexes sufficient for labeling 96 samples. Purchase library prep reagents and probe panels separately.

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AmpliSeq™ CD Indexes Set A-D for Illumina® (384 Indexes, 384 Samples)

20031676

Includes four sets of AmpliSeq CD Indexes for Illumina, Set A, Set B, Set C and Set D. Each set contains 96, 8 bp indexes sufficient for labeling 96 samples. Purchase library prep and probe panels separately.

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Accessory products (3)

AmpliSeq™ for Illumina® Sample ID Panel

20019162

Includes eight single nucleotide polymorphism (SNP)-targeting primer pairs and one gender discriminating primer pair sufficient for 96 reactions when paired with AmpliSeq Library PLUS for Illumina. Enables quick and accurate sample identification. Purchase library prep, probe panels, and index adapters separately.

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AmpliSeq™ for Illumina® Direct FFPE DNA

20023378

Includes 24 reactions to prepare DNA from unstained, slide-mounted FFPE tissues for library construction using AmpliSeq for Illumina protocol, without the need for deparaffinization or DNA purification.

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AmpliSeq™ Library Equalizer for Illumina®

20019171

Includes beads and reagents for library normalization when preparing AmpliSeq for Illumina libraries for sequencing.

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Selection summary

Product

Qty

Unit Price

Order the NovaSeq X Series

Advanced chemistry, optics, and informatics combine to deliver exceptional speed and data quality, outstanding throughput and scalability.

MiSeq Reagent Kit v3

Optimized reagent kit that provides increased cluster density and read length, improving sequencing quality scores compared to earlier versions.

TruSight Oncology 500

Enable CGP with a large pan-cancer panel covering all major variant classes plus gene signatures (TMB, MSI, and HRD) from FFPE tissue.

Illumina DNA Prep

A fast, integrated workflow for preparing libraries for use in a wide range of sequencing applications.

References

  1. Kingsmore S. Catalogue of Somatic Mutations in Cancer – Home Page. http://cancer.sanger.ac.uk/cosmic. Accessed October 25, 2017.

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