DNA Sequencing

Sequence through regions where other systems fail

Would you choose a robust technology over hoping to find what may have caused your sequence to fail?
Though you can investigate what may have caused a sequence to fail, often there may not be much you can do. Investigating issues can be confusing, frustrating, and time consuming. Your best solution is to start with a superior technology to improve your laboratory performance. It is the proactive way of controlling your future.

Sequence Through Regions Where Other Systems Fail
The GenomeLab™ GeXP Genetic Analysis System features unique DNA sequencing reagents—including linear polyacrylamide gel (LPA), coated capillaries, deoxyinosine triphosphate (dITP) chemistry, deoxyguanosine triphosphate (dGTP) chemistry, and cyanine-based (near) infrared dyes—coupled with online denaturation. This results in less correction, more meaningful raw data, and higher-quality final analyses. All of which enables the GenomeLab™ GeXP Genetic Analysis System to resolve complex sequences where other systems fail, filling in the gaps with high-quality sequences.

In this example, the GeXP Genetic Analyzer Series is compared with another automated sequencing system for the completion of a problematic human genome sequence region. A section of sequence the other system couldn't resolve was accomplished using the innovative chemistry of the GeXP system.

Genomic tandem repeats identified by dye terminator cycle sequencing (DTCS)

Dye Terminator Cycle Sequencing

The GenomeLab GeXP is a completely automated genetic analysis system that delivers the highest analytical performance of all commercially available sequencing platforms. The system typically sequences 200 nucleotides in less than 30 minutes, 600 nucleotides in less than 50 minutes and reads out beyond 800 quality bases with greater than 98% accuracy.

The GeXP utilizes dye terminator cycle sequencing methodology in this process. Cycle sequencing utilizes successive rounds of denaturation, annealing and extension in a thermal cycler to create a linear amplification of extension products. These sequencing protocols are robust, requiring much less template than single-temperature methods.

With dye terminator labeling, each of the four dideoxy terminators is tagged with a different fluorescent dye. The growing chain is simultaneously terminated and labeled with the dye that corresponds to that base. With this methodology you can use unlabeled primers, all reactions are carried out in the same tube, all four colors are assessed within the same capillary and false stops go undetected because no dye is attached.

Automated Base Calling
The GenomeLab sequence analysis software automatically calls each base and assigns a confidence value to the call to allow you to immediately assess the quality of the sequence data.

Sequence analysis includes signal processing, base calling and the determination of confidence values for each called base. No calibrations are required to compensate for spectral overlap or mobility variations between the dyes. A two pass base-caller first identifies significant peaks then employs a directed graph technique1 to refine the called base sequence. Finally, the error-probabilities of called bases are estimated and quality values are assigned.

Automated Heterozygote Detection
Identifying heterozygous base positions in genomic DNA can be of great utility in locating mutations or polymorphisms in diploid organisms. DNA sequencing is the ultimate confirmation of the presence of more than one base at a single nucleotide position.

The GenomeLab software allows the user to toggle the automatic detection of heterozygotes from the sequence analysis parameters editor.

Heterozygotes are automatically detected and identified using the standard IUB nomenclature. This provides a rapid mechanism to highlight polymorphisms or mutations within the sequence data.

Multiple heterozygotes are automatically identified using the GenomeLab control and analysis software

Automated Trimming
Note - The trimming function will trim based on matching user input sequence information (Sequence based trimming) or by quality values (Quality based trimming).

Multiple Analysis Capabilities

• Automatic base calling and report generation after each row of eight samples
• Editable parameter set for base calling algorithm
• Audio playback of selected DNA segments
• Call scores and quality values generated for each sequence for base call assurance with quality score based trimming
• Exporting capability for third-party data analysis (.scf, FASTA, PHRED, SEQ, Tab-Delimited)

For every researcher there is an ideal analytical technology—one that helps you achieve your goals. Let us demonstrate how we can help you, request sample analysis now.

Brochure

• DTCS Quick Start Kit for Dye Terminator Cycle Sequencing
• Sequencing Template Conversion

Posters

• Fast Sequencing Analysis for Investigation of Sterility Positives
• Recombinant DNA Sequencing

Technical Notes

• Accurate and Rapid DNA Barcoding Technique for Herbal and Botanical Products
• Automating Heterozygote Detection Using the Human p53 Gene
• Bacterial Artificial Chromosome End Sequencing Analysis
• Precise DNA Sizing on the CEQ Genetic Analysis System
• Improved Sequencing of Plasmids on the CEQ
• Method for Long Sequencing Read Lengths
• Sequencing of Difficult DNA Templates