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xGen™ Pan-Cancer Hybridization Panel

Research the genes implicated in several cancers

The xGen Pan-Cancer Hyb Panel consists of 7,816 xGen Hyb Probes for research, spanning 800 kb of the human genome, for enrichment of 127 mutated genes implicated across 12 tumor tissue types for deeper sequencing coverage in research studies.

xGen NGS—made for cancer research.

Ordering

  • Obtain high coverage uniformity across all targets
  • Identify variations reliably with increased depth of coverage
  • Enjoy fast turnaround (TAT) via easy online ordering and next-day shipping

For the xGen Hybridization and Wash Kit, xGen Universal Blockers, xGen Library Amplification Primer Mix, and/or xGen Human Cot DNA, please visit the xGen Hybridization Capture Core Reagents page.

Product details

Every year, approximately 450 people in every 100,000 are diagnosed with cancer with a 5-year relative survival rate at 67.7%. Although survival rates have increased from less than 50% in 1975, there is a need for more basic research into the types of mutations and whether they are driver mutations or passenger mutations [1]. 

Research studies to produce a short list of mutated genes that are relevant to a multitude of cancer types, and that can be expanded to include additional cancer type–specific genes, would be invaluable in research. The Cancer Genome Atlas (TCGA) network performed a systematic analysis research study of more than 3,000 tumors from 12 cancer types to investigate underlying mechanisms of cancer initiation and progression and have identified 127 significantly mutated genes (SMGs) across these tumor types [2].

The xGen Pan-Cancer Hyb Panel is a hybridization capture panel based on the research findings of the TCGA network. The panel comprises xGen Hyb Probes, individually synthesized and quality controlled 120mer oligonucleotides bearing a 5′ biotin modification and manufactured using proprietary Ultramer™ synthesis technology.

Panel composition (target genes)

Table 1. List of genes that are associated with 12 different cancer types organized by gene pathway.

Cellular process Gene
Transcription factor/regulator

VHL
GATA3
TSHZ3
EP300
CTCF
TAF1
TSHZ2
RUNX1
MECOM
TBX3
SIN3A
WT1
EIF4A2
FOXA1
PHF6
CBFB
SOX9
ELF3
VEZF1
CEBPA
FOXA2

Histone modifier

MLL3
MLL3
ARID1A
PBRM1
SETD2
NSSD1
SETBP1
KDM5C
KDM6A
MLL4
ARID5B
ASXL1
EZH2

Genome integrity

TP53
ATM
ATRX
BRCA2
ATR
STAG2
BAP1
BRCA1
SMC1A
SMC3
CHEK2
RAD21
ERCC2

RTK signaling

EGFR
FLT3
EPHA3
ERBB4
PDGFRA
EPHB6
FGFR2
KIT
FGFR3

Cell cycle

CDKNA2
RB1
CDK12
CDKN1B
CCND1
CDKN1A
CDKN2C

MAPK signaling

KRAS
NF1
MAP3K1
BRAF
NRAS
MAP2K4
MAPK8IP1

PI(3)K signaling

PIK3CA
PTEN
PIK3R1
TLR4
PIK3CG
AKT1

TGF-β signaling

SMAD4
TGFBR2
ACVR1B
SMAD2
ACVR2A

Wnt/β-catenin signaling

APC
CTNNB1
AXIN2
TBL1XR1
SOX17

Histone

HIST1H1C
H3F3C
HIST1H2BD

Proteolysis

FBXW7
KEAP1
SPOP

Splicing

SF3B1
U2AF1
PCBP1

HIPPO signaling

CDH1
AJUBA

DNA methylation

DNMT3A
TET2

Metabolism

IDH1
IDH2

NFE2L

NEF2L2
NEF2L3

Protein phosphatase

PPP2R1A
PTPN11

Ribosome

RPL22
RPL5

TOR signaling

MTOR
STK11

Other

NAV3
NOTCH1
LRRK2
MALAT1
ARHGAP35
POLQ
NCOR1
USP9X
NPM1
HGF
EPPK1
AR
LIFR
PRX
CRPAK
EGR3
B4GAL53
MIR142

Product data

30X coverage depth for 99% of the targets

Figure 1. An example of, deep coverage of targeted regions using xGen Pan-Cancer Hyb Panel. Genomic DNA libraries (n=8) were enriched using the xGen Pan-Cancer Hyb Panel and sequenced on a NextSeq® 550 system using 2 x 150 paired-end reads. Total reads for each sample were sub-sampled to 4M total reads. In all samples, there was >1X coverage for 99.9% of targets and >30X coverage for 99.7% of targets.

Coverage uniformity for the xGen Pan-Cancer Hyb Panel

Figure 2. An example of high coverage uniformity obtained with xGen Pan-Cancer Hyb Panel. Greater than 0.2X mean coverage is observed for >99.3% of targets. Genomic DNA Illumina TruSeq® HT libraries (n=8) were enriched using the xGen Pan-Cancer Hyb Panel and sequenced on a NextSeq® 550 system using 2 x 150 paired-end reads. Each sample was sub-sampled to 4M total reads. 

Consistent data from one lot to the next

Figure 3. An example of lot to lot consistency obtained with xGen Pan-Cancer Hyb Panel. Genomic DNA libraries were enriched with two lots of the xGen Pan-Cancer Hyb Panel (n=8 for each lot). The enriched samples were sequenced on the NextSeq 550 sequencing platform using 2 x150 paired-end reads. All samples were sub-sampled to a level of 4M total reads. The probe-by-probe target coverage was averaged for eight replicate samples for each lot of the xGen Pan-Cancer Hyb Panel. A comparison of probe-by-probe target coverage between two lots showed excellent consistency, with an R2 value of 0.8378.

References

  1. SEER Cancer Stat Facts: Cancer of Any Site. https://seer.cancer.gov/statfacts/html/all.html. Accessed Sept. 2, 2021.
  2. Cancer Genome Atlas Research N, Ley TJ, Miller C, et al. Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. N Engl J Med. 2013;368(22):2059-2074.

 

 

*RUO—For research use only. Not for use in diagnostic procedures. Unless otherwise agreed to in writing, IDT does not intend for these products to be used in clinical applications and does not warrant their fitness or suitability for any clinical diagnostic use. Purchaser is solely responsible for all decisions regarding the use of these products and any associated regulatory or legal obligations.

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