AmpliSeq for Illumina Focus Panel

Targeted DNA and RNA research panel investigating 52 genes with known relevance to solid tumors.

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

The AmpliSeq for Illumina Focus Panel is the recommended replacement for TruSight Tumor 26, which has been discontinued.

Overview

The AmpliSeq for Illumina Focus Panel is a targeted resequencing assay for biomarker analysis of 52 genes with known relevance to solid tumors. Using the Focus Panel, researchers can analyze both DNA and RNA concurrently.

Key features

  • Relevant gene content - Target biomarkers across 52 genes relevant to solid tumors

  • 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 Focus 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 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 Focus Panel panel includes both DNA and RNA workflows.  Each workflow requires its own Library PLUS reaction and index adapter. RNA workflow also requires cDNA Synthesis.

/ Results

Applications

Example workflow


Project recommendations

Instrument Recommended number of samples Read length
iSeq 100 System

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

2 × 150 bp

MiniSeq System

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

2 × 150 bp

MiSeq System

Samples per run (by reagent kit version): v2 micro: 8, v2: 30, v3: 48 (assumes minimum coverage of 500×)

2 × 150 bp


Related applications and methods

Compare

AmpliSeq for Illumina Focus Panel AmpliSeq for Illumina Comprehensive Panel v3 AmpliSeq for Illumina Cancer Hotspot Panel v2 TruSight Tumor 15
Assay 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) 5 hours (library prep only; doesn't include library quantification, normalization, or pooling time) 7 hr
Cancer type Solid tumor Solid tumor Pan-cancer, Solid tumor Pan-cancer, Solid tumor
Content specifications DNA and RNA targets for 52 oncogenes DNA and RNA targets for 161 oncogenes Hotspot regions of 50 genes with known associations to cancer Amplifies 250 amplicons from 15 genes associated with solid tumors
Description 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. Somatic analysis research into hotspot regions of 50 cancer-related genes. 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 NextSeq 550 System, NextSeq 2000 System, NextSeq 1000 System, NextSeq 550Dx in Research Mode MiSeq System, iSeq 100 System, MiSeqDx in Research Mode, MiniSeq System MiSeq 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, Amplicon sequencing, Targeted RNA sequencing Targeted DNA sequencing, Amplicon 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, RNA DNA, RNA DNA DNA
Number of amplicons 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.) 207 total. 1 pool.
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), 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) Single nucleotide polymorphisms (SNPs), Somatic variants, Insertions-deletions (indels) Somatic variants, Insertions-deletions (indels)

Figures

High coverage uniformity and on-target alignment

DNA extracted from FFPE tissues of varying quality and HD samples was evaluated using the AmpliSeq for Illumina Focus Panel and sequenced on the MiniSeq and MiSeq Systems. Cq is an indicator of the quality of DNA islolated from FFPE tissues.

High concordance between expected and detected variant frequency

DNA from formalin-fixed HD samples was evaluated using the AmpliSeq for Illumina Focus Panel and sequenced on the MiniSeq and MiSeq Systems. Results showed 100% concordance between the expected detected variant frequency.

Panel (2)

AmpliSeq™ Focus Panel for Illumina®

20019164

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

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Ampliseq™ for Illumina® Focus Panel MiSeq Kit

20024183

The Ampliseq™ Focus Panel MiSeq Kit contains library prep and MiSeq sequencing reagents for 48 samples. This includes two AmpliSeq for Illumina® Focus Panels, one Ampliseq™ for Illumina® Library PLUS (96 Reactions), one Ampliseq™ for Illumina® CD Indexes Set A, and two MiSeq Reagent Kits v2 300 cycle.

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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 (4)

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).

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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.

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