CleanPlex™ BRCA1 & BRCA2 Panel

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CleanPlex™ BRCA1 & BRCA2 Panel

$726.00$24,687.00

The CleanPlex™ BRCA1 & BRCA2 Panel contains 218 pairs of PCR primers targeting the full exon of the BRCA1 and BRCA2 genes. The panel kit contains primers, multiplex PCR reagent, digestion reagent and other reagent components necessary for constructing amplicon libraries for Next-Generation Sequencing on Illumina Sequencers.

 

Product Description

The CleanPlex™ BRCA1 & BRCA2 Panel contains 218 pairs of PCR primers targeting the full exon of the BRCA1 and BRCA2 genes. The panel kit contains primers, multiplex PCR reagent, digestion reagent and other reagent components necessary for constructing amplicon libraries for Next-Generation Sequencing on Illumina Sequencers.

Product Features

  • 100% coverage of BRCA1 and BRCA2 with superior uniformity

The panel covers 100% of the coding regions and 10 bases beyond the exon–intron boundaries of the BRCA1 and BRCA2 genes. The observed uniformity of this panel (at ≥ 0.2x mean coverage) is over 99%.

  • Simplify your workflow

The entire library preparation workflow can be finished in 2.5 hours with only 30-minute hands-on time from sample DNA to sequencing-ready libraries. No need of ligation, end repair, DNA fragmentation, overnight hybridization, or microfluidic devices!

  • Take on difficult samples with limited DNA input

With an average amplicon size of 158 bp, this panel is compatible with degraded samples such as formalin-fixed, paraffin-embedded (FFPE) tissue DNA and circulating cell-free DNA (cfDNA). You can obtain high quality sequencing data for germline genotype calling even with just 200 pg of input DNA.

About BRCA1 and BRCA2

BRCA1 and BRCA2 are human genes that produce tumor suppressor proteins that help repair damaged DNA and ensure the stability of the cell’s genetic material. When either of these genes is mutated, DNA damage might not be properly repaired. As a result, cells are more likely to develop additional genetic alterations that can lead to cancer.

Specific inherited mutations in BRCA1 and BRCA2 increase the risk of female breast and ovarian cancers, and they have been associated with increased risks of several additional types of cancer. Together, BRCA1 and BRCA2 mutations account for about 20 to 25 percent of hereditary breast cancers and about 5 to 10 percent of all breast cancers. In addition, mutations in BRCA1 and BRCA2 account for around 15 percent of ovarian cancers overall. Breast and ovarian cancers associated with BRCA1 and BRCA2 mutations tend to develop at younger ages than their nonhereditary counterparts.

 

Sequencing Platform Illumina Sequencers (MiniSeq, MiSeq, NextSeq, Hiseq)
Enrichment Method Multiplex PCR
# of Primer Pools 2
# of Primer Pairs 218
# of Target Genes 2
Target Region Size (bp) 19268
Amplicon Size Average 158 bp (from 125-180 bp)
Species Human
Recommended DNA Input (Amount) For germline genotype calling: minimum 200 pg;
For somatic mutation calling with an LOD of 1%: minimum 20 ng
Sample Type Genomic DNA, FFPE DNA, cfDNA, and DNA from Blood, Tissue, Cell Culture, and Fine Needle Aspirate (FNA)
Sample Multiplexing
(at ~2000x mean coverage)
Miseq 2×150 Read Length: ~55 samples
NextSeq Series Mid Output 2×150 Read Length: ~425
NextSeq Series High Output @ 2×150 Read Length: ~1300
Coverage Uniformity (at ≥ 0.2x mean coverage) >95%
On-target Reads % (% reads aligned to target regions out of total aligned reads) >95%

Additional Information

Weight 1.5 kg
Dimensions 12 x 10 x 9 cm
Pack Size (Reactions)

8, 96, 384

What is the CleanPlex™ amplicon sequencing workflow for a multi-pool panel?

For a panel with two or more primer pools, follow the procedure shown below.

What should I do when the library yield is lower or higher than expected?

Increase or decrease the number of cycles for the 2nd PCR by 2 to 3.

There is very little or no library peak when assayed with Agilent™ 2100 Bioanalyzer.

The possible causes are:

(1) 30% ethanol instead of 70% ethanol is used in DNA purification with magnetic beads; or

(2) forgetting to add magnetic beads after digestion. The workflow does not require users to change tubes, nor to remove magnetic beads from previous steps. One can easily tell if magnetic beads in each purification steps are added or not by checking the volume; or

(3) forgetting to add Stop Buffer after digestion, especially when handling a large number of samples.

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