HEAT-Seq Ultra Choice Designs

Overview

HEAT-Seq Ultra Choice enables custom designs of between 32 and 6,000 probes with low-frequency allele detection in mind. As with HEAT-Seq Choice, probes are selected from our database of empirically tested and balanced probes, and are designed to enable the detection of low-frequency variants. The HEAT-Seq Ultra database contains probes for the coding region of 60 common oncogenes.

Benefits

 A focus on cancer content: The HEAT-Seq Ultra Choice database contains probes targeting both strands of nearly all of the coding regions 60 oncogenes, enabling creation of cancer panels tailored to your specific targets of interest.

  • Simple and easy custom design creation: Custom designs are made using our online design software, NimbleDesign. Simply input your genes or coordinates and NimbleDesign will guide you in making a panel that best meets your needs.
  • No need for reoptimization: Thanks to the empirical information on relative probe performance in the database, custom designs are automatically configured with probes in the right concentrations to ensure high performance and uniformity. 
  • Flexible design size options: HEAT-Seq Choice allows researchers to build custom designs of various sizes, with pricing and configuration options available based on the design size.
  • Engineered for sensitivity: HEAT-Seq Ultra Choice Designs are made to help you detect low-frequency variants. 

 

Why use a database?
The design and refinement of custom amplicon designs can be quite challenging. This is particular true for the approaches based on Molecular Inversion Probes (MIPs), where the advantages of an easy workflow and high precision can be outweighed by the challenges of designing probes that work reliably and provide uniform performance.

Using our expertise and proprietary technology, we have built databases that make the customization process easier. Drawing probes from our databases enable you to spend more time on your research and less time worrying about poor uniformity, dead or poison probes, or creating the probe pools from many individual oligos.

Custom HEAT-Seq Ultra Choice designs made using NimbleDesign offer >90% accuracy and low-frequency variant detection.

The power of empirical probe balancing

The performance of HEAT-Seq designs is dramatically improved thanks to proprietary empirical probe performance information.

HSC Data 07-Jul-2016

Figure 1: Sequencing coverage and uniformity improvement from probe balancing

Sequencing coverage is plotted above for equivalent designs made with probes at equimolar ratios (blue) and using the HEAT-Seq Choice product (green). Designs with probes in equimolar concentration can lead to low uniformity and reduced overall coverage. The proprietary HEAT-Seq Choice probe balancing method helps enable a higher level of uniformity and coverage. In this example, uniformity for the entire design was 78.1% and mean coverage was 31.0 X. The equivalent design made using HEAT-Seq Choice systems, whose probe concentrations were adjusted by the proprietary automated process to account for their properties, provides greatly informed uniformity (88.2%) and mean coverage (66.1x). The specific region shown above is of a portion of the MEF2C gene, associated with developmental disorders. The entire custom HEAT-Seq design was made targeting the coding region of 500 genes associated with human genetic or inherited disease.

HSQ Choice Figure 2

Figure 2: Sequencing coverage 

With equal amounts of sequencing (5M reads in this experiment), the optimized design provides significantly better coverage depth over targets than the design with the probes in equimolar concentrations. This means sequencing resources are used more efficiently and can generate more variant calls. 

Consistent Uniformity

HEAT-Seq custom designs offer high uniformity even with large designs. 

HSQ Choice Uniformity v2

Figure 3: The uniformity of various designs made using the HEAT-Seq Choice database.

Leveraging the empirical data about the performance of probes enables the rapid configuration of designs with reliable uniformity. In the figure above, the uniformity of designs of a variety of sizes is plotted. High uniformity is achieved regardless of design size, which can be exceedingly difficult for other methods. Uniformity is defined is the percentage of probes giving coverage that is greater than or equal to 20% of the mean. 

ABL1

EZH2

KDR

PDGFRA

AKT1

FBXW7

KIT

PIK3CA

ALK

FGFR1

KRAS

PTEN

APC

FGFR2

MAP2K1

PTPN11

ATM

FGFR3

MAP2k4

RB1

BRAF

FLT3

MET

RET

BRCA1

GNA11

MLH1

RUNX1

BRCA2

GNAQ

MPL

SMAD4

CDH1

GNAS

MSH2

SMARCB1

CDKN2A

HNF1A

MSH6

SMO

CSF1R

HRAS

NF1

SRC

CTNNB1

IDH1

NF2

STK11

EGFR

IDH2

NOTCH1

TERT

ERBB2

JAK2

NPM1

TP53

ERBB4

JAK3

NRAS

VHL

Table 1. Genes that it is possible to target using HEAT-Seq Ultra Choice Target Enrichment Systems. 

HEAT-Seq Ultra Choice System Performance 

Custom Design Performance

HEAT-Seq Choice systems provide consistent high performance in the metrics that define high quality data. Create a custom design using your genes or coordinates of interest and proceed to sequencing with confidence. 

HSQ Ultra Choice XXL
HSQ Ultra Choice S

Figures 4a and 4b: HEAT-Seq Ultra Choice Design Performance

In a custom design made using the HEAT-Seq Choice system, the quality of the sequencing data enables highly accurate and complete detection of variants. High uniformity and a high level of probe activity combine to deliver excellent overall coverage, enabling such complete and accurate variant detection. Data is shown for a 2056-probe HEAT-Seq Ultra Choice XXL design (1.3-2.6 million reads per sample) and a 96-probe HEAT-Seq Ultra Choice S design, both targeting pediatric cancer variants. Uniformity is defined is the percentage of probes giving coverage that is greater than or equal to 20% of the mean. 

Product Overview

Product Design Size Sizes Available Catalog Number

HEAT-Seq Ultra Choice S

32-200 Probes 96 Rxn 7757077001
32-200 Probes 384 Rxn 7768672001
32-200 Probes 1536 Rxn 7768699001

HEAT-Seq Ultra Choice M

201-500 Probes 96 Rxn 7768702001
201-500 Probes
384 Rxn 7768729001
201-500 Probes
1536 Rxn 7768737001

HEAT-Seq Ultra Choice L

501-1000 Probes 384 Rxn 7768753001
501-1000 Probes 1536 Rxn 7768761001

HEAT-Seq Ultra Choice XL

1001-2000 Probes 1536 Rxn 7768770001

HEAT-Seq Ultra Choice XXL

2001-6000 Probes 1536 Rxn 7768788001

Please Contact Us for ordering and questions

For life science research only. Not for use in diagnostic procedures. Unless otherwise stated in references, all data on file.

Related Products

Description Pack Size Catalog Number
HEAT-Seq Ultra Oncology HotSpot Panel

24 Reactions

07757069001

HEAT-Seq Ultra Oncology HotSpot Panel

96 reactions

07768613001

HEAT-Seq Oncology Panel

24 Reactions

07757042001

HEAT-Seq Oncology Panel  

96 reactions

07768605001

HEAT-Seq Reagents

24 Reactions

07338350001

HEAT-Seq Reagents

96 reactions

07338368001

HEAT-Seq Reagents

384 Reactions

07338376001