BTGenZIntegrated computational PCR analysis, from assay design to experimental data
A single PCR project rarely stops at one question. It can need new primers, a check of primers already on the shelf, a SNP-specific assay, a multiplex panel and a qPCR assay, and then analysis of sequencing reads, Ct values, gel images, Sanger traces and digital PCR partitions. BTGenZ has built a coordinated computational environment that covers eleven analytical workflows, keeps each one scientifically separate and brings the results together in one project record.
Figures come from the BTGenZ acceptance project and from the project team's development reporting. The test total is a project-level figure and is not an independent experimental validation. See Development & Validation.
The problem this infrastructure addresses
PCR analysis is spread across tools that were never designed to work together. Primer design lives in one program, thermodynamic checks in another, sequencing and qPCR data in vendor exports, and results end up in separate files that someone must reconcile by hand. Each hand-off is a place where a coordinate convention changes, a parameter is retyped or a QC decision is forgotten.
Integrating these steps is valuable only if the scientific reasoning of each step survives. That is the difficult part: a primer design engine, a multiplex optimiser, an amplicon aligner and a digital PCR classifier each rest on different models and different failure modes. The work behind this project was to coordinate them without flattening them. The research challenges page describes how.
Workflows supported
The analytical scope follows the BTGenZ Master Blueprint. Six workflows cover assay design and five cover the analysis of experimental data.
Assay design and evaluation
Blueprint Section 7
Conventional PCR Assay Design
5 ranked candidate pairs, mean Tm of the top candidates 59.97 °C.
Blueprint Section 8
Existing Primer Evaluation & Validation
2 submitted primers evaluated against the template.
Blueprint Section 9
SNP / Mutation-Specific PCR Design
10 allele-specific candidates designed and tested for discrimination.
Blueprint Section 10
Multiplex PCR Optimisation
3 targets, 15 candidate pairs, 30 oligonucleotides profiled, 125 combinations considered and 10 ranked sets reported.
Blueprint Section 11
qPCR / RT-qPCR Assay Design
dye-based chemistry, 5 candidate assays, with a 121 bp amplicon shown in the binding map.
Blueprint Section 12
Targeted Amplicon & Sequencing Design
3 target regions covered by 6 amplicons, 87.65% interval coverage.
Experimental-data analysis
Module 7.1
Amplicon Sequencing Analysis
240 reads processed, with coverage tables and a variant evidence table produced.
Module 7.2
qPCR Experimental-Data Analysis
24 wells analysed and 6 fold-change values computed for one target gene against GAPDH.
Module 7.3
Gel Electrophoresis Image Analysis
4 lanes and 12 bands detected, with a ladder calibration fit of R² = 0.9913.
Module 7.4
Sanger Sequencing Analysis
a forward read trimmed to 230 bases and aligned across its full length.
Module 7.5
Digital PCR Analysis
6 wells analysed in 4 replicate groups, with four partition clusters resolved.
How the modules work together
Every project begins with intake: files are identified by content, given a role and checked. A workflow assessment then decides which of the eleven workflows apply, which files each one needs, what depends on what and in what order to run them. Each module runs with its own scientific logic and reports its own scientific QC outcome. A consolidated project summary then brings everything into one report with a checksum manifest.
Individual modules stay usable on their own, so a laboratory can ask for a single analysis such as a Sanger review or a digital PCR quantification without running anything else. The architecture page shows the connections in a diagram.
Evidence you can examine
Validation, stated carefully
What testing covers, what an acceptance run shows, and why scientific QC is reported separately from software execution.
Read the validation page →The platform dashboard
The research workspace itself, with project records, module navigation and selected analytical outputs.
Open the technical showcase →Engineering decisions
Ten problems met during development, each with the approach and the evidence for the outcome.
Read the challenges →Who this work is for
- Academic research groups and molecular biology laboratories that need assay design or data analysis without building the tooling.
- Biotechnology and pharmaceutical teams, and startups, developing PCR, qPCR or amplicon sequencing assays.
- Contract research organisations that need computational PCR support alongside their wet-lab work.
- Institutions looking for outsourced computational PCR analysis and assay development support.
Next step
If you have a PCR design or data analysis requirement, the collaboration page explains what a first conversation covers and what to include.