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NEXTFLEX Amplicon Panels2018-08-31T20:52:52+00:00

NEXTFLEX® Amplicon Panel Kits

Complete Amplicon Panel Library Prep Kits that Deliver on Performance

As next-gen sequencing (NGS) becomes more and more commonplace due to its unrivaled multiplexing capabilities and potential for molecular discovery, the power of targeted sequencing must be highlighted for its applicability in almost any field of basic, clinical, or translational research. Amplicon panels are the technology of choice for small target panels, typically under 50kb of sequence. No doubt, they are also the least expensive and most versatile option for sequencing, as fewer reads are required and different strategies can be employed to tackle the resolution of difficult genomic regions, such as those that are highly AT-rich, GC-rich, or possess paralogues or pseudogenes that may be masking the actual gene of interest. Proper amplicon panel design and tactics are needed to ensure high coverage, uniformity, and specificity to assure complete coverage of the sequence without gaps in the intended target regions, as well as to minimize off-target reads, which can be a problem in other sequencing approaches.

  • 100% coverage of exons, flanking intron-exon boundaries, and other regions

  • High uniformity and on-target reads

  • Up to 384 unique barcodes allowing for high multiplexing capabilities

  • Low input requirements for gDNA from fresh or frozen tissues

  • Simple workflow and < 3 hours hands-on time

As amplicon sequencing is based on ultra-deep sequencing of PCR products for analyzing genetic variations, the technical design and performance of an amplicon-based assay must allow researchers to focus on the interrogation of key genomic regions of interest using a simple workflow and dependable chemistry. The NEXTFLEX® amplicon panels allow researchers to sequence large numbers of targeted gene regions for the analysis of mutational hot spots within a subset of genes, and gain insight into copy number variations (CNVs), well-defined gene fusions, SNPs or indels.

NEXTFLEX® amplicon panel technology boasts high levels of uniformity with no amplicon drop outs, essentially creating a gap guard for your target region which is verified by sequencing. Primers are designed to have high levels of specificity and minimize reads lost to non-alignment that may be caused by primer dimers, adapter dimers, or unaligned low quality and/or chimeric reads. High coverage is attained even with a low number of reads, thereby allowing high level multiplexing or the use of a smaller sequencing cartridge. The NEXTFLEX® amplicon panels are easily scalable, simple to use, fast, and cost-effective kits which can be applied to a broad range of genes.

The pre-designed NEXTFLEX® amplicon panels cater to the needs of researchers investigating cancer & cancer predisposition, newborn syndromes, and inherited disorders using low inputs of gDNA. All pre-designed panels have been performance-verified by Illumina® Miseq® sequencing, but are easily portable to Thermo Fisher® Scientific Ion Torrent sequencing. Please inquire for additional details.

Furthermore, the NEXTFLEX® amplicon panel technology can be optimized for researchers interested in custom panel design and collaboration. The contact form can be found below.

Kits are comprised of target-specific primer pools, library prep reagents, including beads, and barcodes for up to 384 samples for Illumina® sequencing. The kit contains enough material to prepare 8, 48, or 96 samples and has a shelf life of 12 months when stored properly.

RANGE OF NEXTFLEX® AMPLICON PANELS

NEXTFLEX Amplicon Panels for Cancer & Cancer Predisposition

Cancer & Cancer Predisposition Panels


Explore our oncology panel offerings and associated genes. Read more details about our popular panels for breast cancer and myeloid leukemia.

Breast cancer is the second most common cancer diagnosed in women in the US after skin cancer, and despite the decline in deaths, it remains the second leading cause of death among women overall according to the Centers for Disease Control and Prevention (CDC). Breast cancer gene 1 and 2 (BRCA1 and BRCA2) are tumor suppressor genes that play an important role in DNA repair and cell cycle control. Together, BRCA1 and BRCA2 mutations account for around 25% of hereditary breast cancers and 10-15% of all breast cancers. Its relevance in increasing the risk of breast cancer and ovarian cancer is also well known. Over 35% of women with breast cancer history meet genetic testing eligibility criteria, and advocacy groups are leading the charge in providing the support needed to increase awareness and provide research funding that ultimately helps empower individuals to better understand the disease.

The accumulation of somatic mutations in BRCA1 and BRCA2 genes has been observed to occur during tumor development. To support clinical research efforts surrounding BRCA and other associated genes, NEXTFLEX® offers a variety of solutions. The NEXTFLEX® BRCA 1/2 core panel helps interrogate all coding exons of the BRCA1 and BRCA2 genes with 100% uniformity at 0.2x coverage for both germline and somatic mutations. Expanding on this core panel, the NEXTFLEX® BRCA1/2 plus-1 panel adds all PALB2 and CHECK2 exons with 98% uniformity at 0.2x coverage and 100% uniformity at greater than 0.1x coverage. The NEXTFLEX® BRCA 1/2 for FFPE panel allows robust sequencing of DNA obtained by extraction from formalin-fixed, paraffin-embedded (FFPE) blocks of clinical tumor samples for research purposes. This DNA is partially degraded at the time of extraction. The panel facilitates 97% uniformity at greater than 0.2x coverage, and 100% uniformity at 0.1x coverage from low sample inputs.

NEXTFLEX® Amplicon PanelsGenes Covered
BRCA1/2 XPBRCA1, BRCA2
BRCA1/2 Plus-1BRCA1, BRCA2, PALB2, CHEK2
BRCA FFPEBRCA1, BRCA2

Acute myeloid leukemia (AML), a heterogeneous group of hematological malignancies, is the most common type of acute leukemia in adults, with an incidence of over 350,000 cases per year worldwide. A report of the de novo sequencing of the AML genomes by the Cancer Genome Atlas (TCGA) demonstrated that in ≥99% of known cases, a single nucleotide substitution or indel existed in the coding regions of select genes. Moreover, around 40%-50% of all AML cases have normal karyotype, which suggests the importance of somatic mutations for the progressive development of AML. TCGA demonstrated that on average there 13 different mutations per patient sample, and the most common mutations are in NPM1 (45-60%), FLT3 (28-34%), DNMT3A (30-37%), IDH1 and IDH2 (25-30%), ASXL1 (5-12%), TET2 (9-23%) and RUNX1 (8-16%). Transcription factor CCAAT/enhancer binding protein-alpha (CEBPA) is also essential in mediating granulocytic differentiation and cellular growth arrest. Somatic CEBPA mutations occur in 10-15% of sporadic acute myeloid leukemias displaying a normal karyotype, and those with double mutations have been shown to be associated with favorable outcomes in clinical research.

The need for high sensitivity in the detection of somatic mutations in heterogeneous and unpurified samples necessitates the use of advanced technologies, such as the NEXTFLEX® myeloid amplicon panel. The panel covers critical coding exons in 21 genes, including the entire GC-rich CEBPA exon, with a 25 bp buffer at exon-intron boundaries, and exhibits greater than 96% uniformity at >0.2x mean coverage and 99% uniformity at >0.1x mean coverage.

NEXTFLEX Amplicon Panels for Inherited diseases and newborn syndromes

Newborn Syndromes & Inherited Conditions Panels


Check out our offering of panels that interrogates genes associated with numerous newborn and inherited disorders. Learn more about our highlight panels for cystic fibrosis and cardiovascular disease.

Cystic fibrosis (CF) is the most common fatal hereditary lung disease, affecting ~70,000 individuals worldwide. As a result of a deletion of the amino acid phenylalanine (F508) in the interior of the cystic fibrosis transmembrane conductance regulator (CFTR), chloride flow becomes hindered and a thick layer of mucus develops across the exterior of the lungs and pancreas, in most cases leading to decreased life expectancy and male sterility. In addition to the F508 deletion, over 1900 separate mutations spanning the intronic and promoter regions bordering the CFTR gene have known or suspected molecular consequences ranging from defective channel synthesis, altered ion gating and conductance, to reduced protein expression1,2,5.

The NEXTFLEX® cystic fibrosis amplicon panel facilitates variant interrogation of 28 coding exons, 1 promoter region, and 3 deep intron regions of the CFTR genes, and exhibits greater than 98% uniformity at >0.2x mean coverage and 100% uniformity at >0.1x mean coverage.

Cardiovascular disease encompasses various heart conditions that can be rooted in diseased vessels, obstructions to vascular structures, and other causes like abnormal blood pressure, blood clots, or plaque buildup. About 1 in every 4 deaths is attributed to heart disease, which makes it the leading cause of death for both men and women. A heart attack, which affects almost 735,000 people in the US yearly, is a real consequence of ignoring the signs of a cardiovascular issue such as chest and upper body discomfort or pain, as well as not being proactively mindful of key risk factors, including high cholesterol, high blood pressure, or leading a sedentary lifestyle with a poor diet.

Though early action and risk mitigation, especially for lifestyle choices, is important in both prevention and disease management, some risks and certain aspects of these conditions are heritable. Therefore, much work is being done in the clinical research space using sequencing to understand the genes and variants that are implicated in this heritability. The NEXTFLEX® cardiovascular disease panel covers 24 hotspots at 100% uniformity at 0.2x coverage for numerous genes such as APOB, MTHFR, and APOE that are implicated in coronary artery disease (CAD) and assessing low-density liproprotein cholesterol (LDL-C)4.

The purchase price of this Product includes a limited, non-transferable license under U.S. and foreign patents owned by BIO-RAD® Laboratories, Inc., to use this Product. No other license under these patents is conveyed expressly or by implication to the purchaser by the purchase of this Product. Phusion DNA Polymerase is manufactured by Thermo Fisher® Scientific. Phusion is trademark or registered trademark of Thermo Fisher® Scientific, Inc. or its subsidiaries.

Custom Amplicon Panels

Are you interested in developing your own custom panels? Please fill out the form below and we’ll be more than happy to discuss your project with you!

What types of samples will be used with this panel? (required)
DNA or RNA isolated from fresh or frozen tissueFFPECell free DNAUncertain

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Amplicon Panels & Genes

Below you will find our entire list of amplicon panel kits as well as the genes that they cover.

Amplicon Panels for use with Genomic DNAGenes Covered
 Autism Spectrum DisordersPDE8B, EN2, NLGN4X, CDKL5, NLGN3, MECP2, RPL10
BRCA1/2 XPBRCA1, BRCA2
BRCA1/2 Plus-1BRCA1, BRCA2, PALB2, CHEK2
CEBPACEBPA
Colorectal Cancer -1MLH1, MSH2
Colorectal Cancer-2MSH6, PMS2
Congenital Adrenal HyperplasiaCYP21A2
Congenital HyperinsulismABCC8, GLUD1, KCNJ11, GCK, HADH, HNF4A, INS, INSR, PDX1, SLC16A1 & UCP2
CVD22 hot spots for cardiovascular disease: MTHFR, F5, AGT, APOB, AGTR1, FGB, F13A1, LTA, SERPINE1, NOS3, JAK2, F2, ITGB3, APOE, PROCR, CBS
Cystic FibrosisCFTR
Duchenne Muscular DystrophyDMD
Epilepsy-2SCN2A, SCN9A
Female InfertilityFSHB, FSHR, LHB, LHCGR
HBOC-1RAD51D, RAD51C, BRIP1
HBOC-2PALB2, BARD1, TP53
Lysosomal Storage DiseasesSUMF1, GLB1, IDUA, ARSB, GUSB, SMPD1, GALC, GALNS, GAA, GLA, IDS
Male InfertilityAR, CATSPER1, CFTR, FSHR, LHCGR
Marfan SyndromeFBN1
Mediterranean FeverMEFV
MODY-1HNF1A, GCK
MODY-2HNF1B, HNF4A
MODY-3PDX1, NEUROD1, KLF11, CEL
MODY-4PAX4, INS, BLK
MODY-5GCK, HNF1A, HNF1B, HNF4A
MyeloidSelected CDS from 21 genes 
Nephrotic Syndrome-1NPSH1, NPSH2, WT1
Nephrotic Syndrome-2ARHGDIA, DGKE, LAMB2, PLCE1
NeurofibromatosisNF1, NF2
Neuronal Ceroid LipofuscinosesCLN3, CLN5, CLN6, CLN8, CTSD, MFSD8, PPT1, TPP1
Obesity-1LEP, LEPR, POMC, MC4R
Obesity-2KSR2, SH2B1, SIM1
Periodic Fever-1TNFRSF1A, NLRP3, MVK
Periodic Fever-2ELANE, LPIN2, PSTPIP1
PhenylketonuriaPAH
TP53TP53
Contact us to discuss your amplicon panel needs

For research use only. Not for use in diagnostic procedures.