AmpliSeq for Illumina Comprehensive Panel v3

Targeted DNA and RNA research panel investigating variants across 161 genes associated with a range of cancer types.

5-6 hr (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 Comprehensive Panel v3 offers coverage of key cancer genes, including kinase domains and genes involved in DNA repair.

Key features

  • Relevant gene content - Target 161 unique cancer-associated 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) input samples

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

The panel content spans hotspot regions, full-length genes*, copy number genes, and inter- and intragenic gene fusions. This ready-to-use panel saves you the time and effort of identifying targets, designing primers, and optimizing panels.

The Comprehensive Panel v3 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.

*For this panel, Illumina defines full-length gene content as covering the majority of the gene’s coding regions, generally having > 90% in silico coverage and with most genes having > 99% coverage. Please refer to the provided product manifest file for further detail.


Specifications

Applications

Example workflow


Project recommendations

Instrument Recommended number of samples Read length
MiniSeq System

3 samples per run (high output; assumes minimum coverage of 500×)

2 × 150 bp

MiSeq System

3 samples per run with v3 reagents (assumes minimum coverage of 500×)

2 × 150 bp

NextSeq 550 System

Samples per run: mid output: 16, high output: 48 (assumes minimum coverage of 500×)

2 × 150 bp


Related applications and methods

Compare

AmpliSeq for Illumina Comprehensive Panel v3 TruSight Tumor 170 TruSight Tumor 15 AmpliSeq for Illumina Focus Panel AmpliSeq for Illumina Cancer Hotspot Panel v2
Assay time 5-6 hr (library prep only; doesn't include library quantification, normalization, or pooling time) ~2 days 7 hr 5-6 hr (library prep only; doesn't include library quantification, normalization, or pooling time) 5 hours (library prep only; doesn't include library quantification, normalization, or pooling time)
Cancer type Solid Tumor Solid Tumor Pan-Cancer, Solid Tumor Solid Tumor Pan-Cancer, Solid Tumor
Content specifications DNA and RNA targets for 161 oncogenes Probes enrich for full coding sequences of 170 genes. Calls single nucleotide variants, small insertions, and deletions in 151 genes, amplifications in 59 genes, and fusions plus splice variants in 55 genes. Amplifies 250 amplicons from 15 genes associated with solid tumors DNA and RNA targets for 52 oncogenes Hotspot regions of 50 genes with known associations to cancer
Description Somatic analysis research on hotspot and full-length targets of genes* associated with solid tumor cancers. Perform comprehensive somatic variant detection research in solid tumors using variant calling information from both DNA and RNA.

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

Somatic analysis research on 52 genes associated with solid tumor cancers. Somatic analysis research into hotspot regions of 50 cancer-related genes.
Hands-on time <1.5 hr ~10.5 hr 3.5 hr < 1.5 hr < 1.5 hr
Input quantity 1–100 ng (10 ng recommended per pool) 40 ng DNA and/or RNA

20 ng FFPE DNA 

1–100 ng (10 ng recommended per pool) 1–100 ng (10 ng recommended per pool)
Instruments NextSeq 550 System, NextSeq 2000 System, NextSeq 1000 System, NextSeq 550Dx in Research Mode NextSeq 550 System, NextSeq 500 System, HiSeq 2500 System MiSeq System, MiSeqDx in Research Mode, MiniSeq System MiSeq System, iSeq 100 System, MiSeqDx in Research Mode, MiniSeq System MiSeq System, iSeq 100 System, MiSeqDx in Research Mode, MiniSeq System
Mechanism of action Multiplex PCR Multiplex PCR Multiplex PCR
Method Targeted DNA sequencing, Amplicon sequencing, Targeted RNA sequencing Targeted DNA sequencing, Targeted RNA sequencing, Target enrichment Targeted DNA sequencing, Amplicon sequencing Targeted DNA sequencing, Amplicon sequencing, Targeted RNA sequencing Targeted DNA sequencing, Amplicon sequencing
Multiplexing 96 dual index combinations Up to 32-plex for DNA using both index sets, up to 16-plex for RNA 1-24-plex 96 dual index combinations 96 dual index combinations
Nucleic acid type DNA, RNA DNA, RNA DNA DNA, RNA DNA
Number of 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.) 553 total. 2 pools. (DNA Pool: 269 amplicons. RNA Pool: 284 amplicons.) 207 total. 1 pool.
Specialized sample types FFPE Tissue Low-Input Samples, FFPE Tissue FFPE Tissue FFPE Tissue FFPE Tissue
Species category Human Human Human Human Human
Technology Sequencing Sequencing Sequencing Sequencing Sequencing
Variant class Single nucleotide polymorphisms (SNPs), Gene fusions, Somatic variants, Insertions-deletions (indels), Copy number variants (CNVs) Gene fusions, Somatic variants, Structural variants, Single nucleotide variants (SNVs), Insertions-deletions (indels), Copy number variants (CNVs) Somatic variants, Insertions-deletions (indels) Single nucleotide polymorphisms (SNPs), Gene fusions, Somatic variants, Insertions-deletions (indels), Copy number variants (CNVs) Single nucleotide polymorphisms (SNPs), Somatic variants, Insertions-deletions (indels)

Panel (1)

AmpliSeq™ Comprehensive Panel v3 for Illumina®

20019109

DNA and RNA targeted panel that targets SNVs, Indels, CNVs and gene fusions. Kit contains 24 reactions. Library PLUS and index adapters sold separately.

Sign in to add to cart or see pricing.

List Price:

Discounts:

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.

Sign in to add to cart or see pricing.

List Price:

Discounts:

AmpliSeq™ Library PLUS (96 Reactions) for Illumina®

20019102

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

Sign in to add to cart or see pricing.

List Price:

Discounts:

AmpliSeq™ Library PLUS (384 Reactions) for Illumina®

20019103

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

Sign in to add to cart or see pricing.

List Price:

Discounts:

Index adapters (7)

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.

Sign in to add to cart or see pricing.

List Price:

Discounts:

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.

Sign in to add to cart or see pricing.

List Price:

Discounts:

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.

Sign in to add to cart or see pricing.

List Price:

Discounts:

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.

Sign in to add to cart or see pricing.

List Price:

Discounts:

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.

Sign in to add to cart or see pricing.

List Price:

Discounts:

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.

Sign in to add to cart or see pricing.

List Price:

Discounts:

Ampliseq™ CD Indexes Large Volume for Illumina® (96 Indexes, 96 Samples)

20019108

AmpliSeq for Illumina CD Indexes Large Volume offers higher fill volumes for added convenience when performing AmpliSeq for Illumina Exome or automated AmpliSeq for Illumina library prep workflows involving panels with 4 or more pools.

Sign in to add to cart or see pricing.

List Price:

Discounts:

Accessory products (3)

Ampliseq™ cDNA Synthesis for Illumina®

20022654

Includes reaction mix and enzyme blend to convert total RNA to cDNA when working with AmpliSeq for Illumina RNA Panels (eg, AmpliSeq for Illumina Immune Response, Immune Repertoire Plus, TCR beta Panel, Myeloid, Transcriptome Human Gene Expression, Focus, and Comprehensive Panel v3 as well as Custom or Community RNA Panels). Number of reactions vary by panel (eg, 100 reactions per kit for AmpliSeq for Illumina Immune Response, Focus, Comprehensive Panel v3, and Custom panels and 200 reactions per kit for AmpliSeq for Illumina Transcriptome Human Gene Expression, Myeloid, Immune Repertoire Plus, and TCR beta Panels).

Sign in to add to cart or see pricing.

List Price:

Discounts:

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.

Sign in to add to cart or see pricing.

List Price:

Discounts:

AmpliSeq™ Library Equalizer for Illumina®

20019171

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

Sign in to add to cart or see pricing.

List Price:

Discounts:

Showing of

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.

Speak with a specialist

Reach out for information about our products and services, or get answers to questions about our technology.