GeneRead DNAseq Custom Panel V2

For targeted enrichment of a customized set of genes or genomic regions specific for your NGS needs

Features

  • Outstanding sequencing performance
  • As little as 10 ng DNA needed
  • Compatible with many samples types, including FFPE samples
  • Can be used on any sequencing platform
  • Customizable for any region in the genome
GeneRead Custom DNAseq Gene Panels

Cat. No. / ID: 181902

Primer sets for targeted enrichment of genomic regions of interest
GeneRead DNAseq Custom Panel V2 are intended for molecular biology applications. These products are not intended for the diagnosis, prevention, or treatment of a disease.

Product Details

GeneRead DNAseq Custom Panels V2 are the simplest tools for analyzing the genetic variants of a customized panel of genes or genomic regions via next-generation sequencing. Each panel consists of multiplex PCR primer sets, sufficient for 480 samples, to amplify genomic regions of interest tailored to your specific NGS needs. Our primer design and targeted enrichment chemistry provide high design coverage, specificity, and uniformity, which are essential for detecting low-frequency variants in your precious samples.

Performance

The performance of GeneRead DNAseq Custom Panels V2 is assessed by three criteria: design coverage, specificity, and coverage uniformity. Greater than 90% of exonic regions are covered by the panel primer design, enhancing potential variant discovery. The high specificity of the system maximizes efficient use of sequencing capacity, as more than 90% of sequencing reads align to target regions. Finally, the high coverage uniformity of the system, with more than 90% of targeted bases covered at >20% median sequencing depth, ensures high-quality variant calls.

Principle

The GeneRead DNAseq Custom Panels V2 employ overlapping primer sets across the exonic portions of a gene or group of genes to maximize target coverage (see figure  Multiplex PCR-enabled target enrichment of genomic regions of interest). Overlapping primer sets are divided into 4 pools, thereby increasing the specificity of coverage without primer dimers and nonspecific amplifications. Following amplification and purification, enriched regions from each sample are pooled together, yielding one library preparation for each sample.

Virtual panels are custom panels created from gene lists compiled by bioinformatics experts for specific diseases not covered by the GeneRead DNAseq Targeted Panels V2 catalog. For a complete list, scroll down to Applications.
See figures

Procedure

GeneRead DNAseq Custom Panels V2 are part of a total workflow for targeted next-generation sequencing (see  GeneRead DNAseq Targeted Panels V2 workflow). Simply extract DNA from your samples (the QIAamp DNA Mini Kit, QIAamp DNA FFPE Tissue Kit, or the GeneRead DNA FFPE Kit are recommended), quantify and qualify your DNA sample with the GeneRead DNA QuantiMIZE System, and then use the GeneRead DNAseq Custom Panels V2 in combination with GeneRead DNAseq Panel PCR Kit V2 to perform targeted enrichment using multiplex PCR. Once targets have been enriched, construct the NGS library with the GeneRead Library Prep Kits and use the GeneRead DNAseq Library Quant Array to quantify and perform quality control. Perform NGS and analyze your data using the QIAGEN NGS Data Analysis Web Portal.

Note: The GeneRead DNAseq Custom Panel Builder is under construction. To build your custom panel, please email your design request to BRC.Custom@qiagen.com, and one of our scientists will follow up with you. 

See figures

Applications

GeneRead DNAseq Custom Panels V2 are highly suited for enriching a panel of any genomic regions of interest in the human genome to determine genetic variants through NGS analysis. Virtual panels are highly suited for enriching a panel of recommended genomic regions of interest for particular diseases and pathways. 

Virtual panels
Panel name Gene list # amplicons   Catalog number
 Autism iADSL, AFF2, AP1S2, ARX, ATRX, BCKDK, BRAF, CACNA1C, CASK, CDKL5, CHD7, CNTNAP2, CREBBP, DHCR7, DMD, EHMT1, FGD1, FMR1, FOLR1, FOXG1, FOXP1, FOXP2, GABRB3, HPRT1, KDM5C, L1CAM, MBD5, MECP2, MED12, MEF2C, MET, MID1, NHS, NIPBL, NLGN3, NLGN4X, NR1I3, NRXN1, NSD1, OPHN1, PAFAH1B1, PCDH19, PHF6, PNKP, PQBP1, PTCHD1, PTEN, PTPN11, RAB39B, RAI1, RELN, SCN1A, SLC2A1, SLC9A6, SMARCB1, SMC1A, TCF4, UBE2A, UBE3A, VPS13B, ZEB2  5580 CNGHS-00425Z-2806, CNGHS-00426Z-2774
 BRCA1 &  BRCA2 BRCA1, BRCA2  276 MNGHS-00363Z-276 (24 samples) & CNGHS-00432Z-276 (500 samples)
 EGFR Pathway EGFR, AKT1, BRAF, KRAS, HRAS, NRAS, MAP2K1, PIK3CA, PTEN  499 CNGHS-00430Z-499
 Epilepsy ABAT, ABCB1, ADSL, ALDH7A1, ARFGEF2, ARHGEF9, ARX, ASPM, ATP1A2, ATP6AP2, ATR, CACNA1A, CACNA1H, CACNB4, CASK, CASR, CCL2, CDK5RAP2, CDKL5, CDON, CENPJ, CEP152, CHRNA2, CHRNA4, CHRNB2, CLCN2, CLN3, CLN5, CLN6, CLN8, CNTNAP2, CSTB, CTSD, DCX, EFHC1, EFHC2, EMX2, EPM2A, FLNA, FLVCR2, FOLR1, FOXG1, FOXH1, GABRA1, GABRB3, GABRD, GABRG2, GAMT, GATM, GLI2, GPR56, GRIN1, GRIN2A, HCN1, HCN4, KCNA1, KCNJ10, KCNJ11, KCNMA1, KCNQ2, KCNQ3, KCNV2, LGI1, MAGI2, MBD5, MCPH1, MECP2, MEF2C, MFSD8, MTHFR, NDE1, NDUFA1, NHLRC1, NODAL, NRXN1, OPHN1, OPRM1, PAFAH1B1, PCDH19, PCNT, PHF6, PLCB1, PNKP, PNPO, POLG, PPT1, PRICKLE1, PRICKLE2, PRRT2, PTCH1, RELN, SCN1A, SCN1B, SCN2B, SCN3A, SCN3B, SCN4A, SCN4B, SCN5A, SCN8A, SCN9A, SHH, SIX3, SLC25A19, SLC25A22, SLC2A1, SLC9A6, SPTAN1, SRPX2, STIL, STXBP1, SYN1, TCF4, TGIF1, TPP1, TSEN2, TSEN34, TSEN54, UBE3A, VANGL1, WDR62, ZEB2, ZIC2  8960 CNGHS-00422Z-2950 & CNGHS-00423Z-3114 & CNGHS-00424Z-2896
 Mitochondria ATP6, ATP8, COX1, COX2, COX3, CYTB, ND1, ND2, ND3, ND4, ND4L, ND5, ND6, MT  346 CNGHS-00442Z-346
 Myelodysplastic
 Syndromes
ASXL1, CBL, DNMT3A, EZH2, IDH1, IDH2, NRAS, RUNX1, TET2, TP53, SF3B1, SRSF2  960 CNGHS-00431Z-960
 RTK Signaling ABL1, AKT1, ALK, BRAF, CBL, CRLF2, CSF1R, CTNNB1, EGFR, ERBB2, FBXW7, FGFR2, FGFR3, FLT3, GNAQ, GNAS, HRAS, JAK2, KIT, KRAS, MAP2K1, MET, NOTCH1, NOTCH2  1816 CNGHS-00429Z-1816
Panel source references:
Autism:
1. Autism and Developmental Disabilities Monitoring Network Surveillance Year 2006
2. Principal Investigators and the CDC (2009) MMWR Surveill. Summ. 58, 1.
3. Bolton, et al. (2011) Br. J. Psychiatry. 198, 289.

Supporting data and figures

Resources

Kit Handbooks (1)
All-bead protocol for targeted enrichment prior to next-generation sequencing
Brochures & Guides (2)
GeneRead Panels and NGS product configurator guide
Analysis Software (3)
For identifying disease-causing variants from human whole genome, exome, and gene panel next-generation sequencing studies
For basic analysis of NGS data using the GeneRead DNAseq panels V2; acceptable file formats include FASTQ or BAM
For analyzing, comparing, and visualizing next-generation sequencing data

FAQ

Are there important considerations for plasma generation and urine handling?

It is strongly advised to follow the recommendations for preparing sample material provided in the corresponding Protocol Sheet to ensure reliable results.

Plasma: It is recommended to perform plasma separation immediately after blood collection when using EDTA or citrate as anticoagulant to prevent the release of genomic DNA into the plasma fraction.

Urine: Because circulating cell-free DNA in non-stabilized urine samples is rapidly degraded after sample collection due to high nuclease activity, eluates may contain no DNA or exhibit low DNA concentration. Therefore, it is recommended to stabilize urine samples. Even when using stabilized urine, it is recommended to perform a centrifugation step immediately after stabilization to prevent the release of genomic DNA from cells. Alternatively, non-stabilized urine samples can be processed immediately after collection and centrifugation using ATL-pretreatment and automated DNA extraction as described in the corresponding Protocol Sheet.

FAQ ID - 3699