Fragment analysis remains a core technique across molecular biology, genetics, and clinical diagnostics, even as sequencing technologies evolve. In 2025, laboratories continue to rely on capillary electrophoresis (CE) for assays ranging from MLPA and MSI to chimerism and Fragile X. Rising workflow demands, however, call for more efficient, integrated analysis tools.
In this webinar, Dr. Teresa Snyder-Leiby, a veteran molecular researcher with over 30 years of experience, provides an in-depth walkthrough of current fragment analysis trends, practical workflow solutions, and how two leading tools, GeneMarker® and ChimeRMarker®, streamline CE-based post-genotyping interpretation.
While CE-based fragment analysis is robust and widely used, laboratories often encounter recurring workflow obstacles, including:
Large batches of CE data can slow down review and reporting, especially when relying on manual or legacy software.
Assays such as MLPA, MSI, LOH, Trisomy, Cystic Fibrosis, and Fragile X require precise size calling, quality assessment, and consistent interpretation across runs.
Chimeric and MCC analyses demand sensitive detection of minor peaks and accurate quantification across multiple markers.
Standardizing analysis across researchers, instruments, or sites remains a challenge without unified software workflows.
This webinar has demonstrated how GeneMarker® and ChimerMarker® simplify and accelerate CE fragment analysis through an integrated, user-friendly interface.
Both tools accept standard CE output formats. They automatically detect size standards, assign alleles, and flag quality issues. This automation reduces hands-on review time and speeds up the analysis.
Interactive electropherograms, automated peak labeling, and customizable quality checks help eliminate noise and improve confidence. This makes complex assays easier to interpret with higher accuracy.
The software supports a wide range of CE-based applications including:
MLPA
Microsatellite Instability (MSI) analysis
Loss of Heterozygosity (LOH) detection
Trisomy assays
Cystic Fibrosis panels
Fragile X repeat & methylation analysis
Maternal-cell contamination (MCC) analysis
Chimerism testing
GeneMarker and ChimeRMarker generate clear, consistent reports suitable for research teams or clinical diagnostic environments. This enhances reproducibility and eases data sharing across labs.
The webinar highlighted real-world contexts where modern fragment analysis tools make a measurable impact:
Molecular biology: Accurate fragment sizing, allele calling, and repeat analysis for standard CE assays.
Plant and animal genetics: Reliable genotyping and marker evaluation for breeding programs, trait studies, and biodiversity research.
Clinical diagnostics: Simplified workflows for MLPA, MSI, LOH, Fragile X, Trisomy, and other assays relevant in disease diagnostics or genetic screening.
Chimerism monitoring and mixed-cell population analysis: Sensitive tracking of donor/recipient markers or contamination, with consistent and automated workflows.
Modern genetic research and diagnostics demand precise, reliable, and efficient analysis of capillary electrophoresis (CE) data. Laboratories often face challenges such as manual allele calling, inconsistent reporting, and complex workflows across diverse assays.
SoftGenetics provides two complementary software solutions - GeneMarker® and ChimerMarker®, designed to streamline workflows, improve consistency, and support high-quality scientific outcomes.
GeneMarker® integrates multiple functions — fragment analysis, quality control, allele calling, and reporting — into a single platform. By eliminating the need to switch between different tools, GeneMarker® reduces errors and saves time. Its intuitive interface enables both novice and expert users to navigate complex analyses efficiently, making it ideal for high-throughput or routine lab workflows.
ChimerMarker® complements this by specializing in chimerism analysis, particularly for monitoring hematopoietic stem cell transplants (HSCT). It streamlines detection of donor and recipient DNA mixtures, automatically analyzing post-transplant samples and generating clear, actionable reports. Both platforms together simplify post-genotyping workflows, ensuring accurate, reproducible results from multiple assay types.
GeneMarker® automates peak detection, sizing, binning, and allele calling for CE-based assays, reducing human error and speeding up analysis. Its built-in quality control alerts identify saturated peaks and other anomalies. For specialized assays like repeat expansions, copy number variations, and methylation analysis, GeneMarker® converts raw fragment data into meaningful metrics automatically.
ChimerMarker® offers automated chimerism quantification by analyzing STR or SNP profiles from donor and recipient samples. The software calculates chimerism percentages, highlights significant deviations, and flags samples that require follow-up. This automation reduces variability between operators and ensures precise post-transplant monitoring.
GeneMarker® supports a wide range of CE-based assays, including:
MLPA and MS-MLPA
Microsatellite instability (MSI)
Loss of heterozygosity (LOH)
STR analysis
Aneuploidy testing
Fragile X repeat expansions
ChimerMarker® focuses on chimerism detection, compatible with CE platforms for STR and SNP analysis. Together, both platforms allow labs to process a broad spectrum of genetic assays, from standard genotyping to specialized post-transplant monitoring, all within validated, integrated software.
GeneMarker® improves reporting speed and consistency by enabling users to save templates and analysis settings. Automated QC and peak detection reduce variability, and exportable reports (PDF, text, spreadsheet, images) support regulatory and research documentation.
ChimerMarker® complements this by automatically generating chimerism reports, highlighting donor/recipient ratios and trends over time. Shared templates and panels across labs promote reproducibility and standardization, ensuring that results are consistent regardless of operator or site.
Both GeneMarker® and ChimerMarker® are designed for usability:
Biologist-friendly interfaces reduce training needs
Customizable panels and advanced settings accommodate research and diagnostic applications
User management and audit trails support compliance in regulated environments
High-throughput analysis options streamline large datasets
These features make both platforms suitable for routine laboratory workflows, complex research projects, and clinical diagnostics.
GeneMarker® and ChimerMarker® are widely adopted in research and clinical labs worldwide. They feature robust quality control, compatibility with multiple CE platforms, and extensive technical support from SoftGenetics. Detailed documentation, webinars, and application notes ensure laboratories can implement workflows confidently and maintain compliance with scientific and regulatory standards.
SoftGenetics’ GeneMarker® and ChimerMarker® together transform post-genotyping and chimerism workflows. By combining automation, broad assay support, intuitive interfaces, and reliable reporting, they help laboratories reduce manual work, standardize procedures, and achieve faster, more accurate, and reproducible results.
Whether performing routine genotyping or post-transplant monitoring, these software solutions provide the tools labs need to optimize efficiency and scientific outcomes.
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