What is fragment analysis used for?

Fragment analysis is used to determine the sizes of DNA fragments, with applications in STR analysis, mutation detection, microsatellite analysis, and other genetic testing applications.

How does fragment analysis differ from sequencing?

Fragment analysis determines fragment sizes but doesn't provide sequence information, while sequencing identifies the actual nucleotide sequence. Fragment analysis is often faster and more cost-effective for certain applications.

What software is used for fragment analysis?

SoftGenetics' GeneMarker software is specifically designed for fragment analysis, providing automated sizing, allele calling, and quality assessment for various fragment analysis applications.

What Is Fragment Analysis and Why Is It Still Essential?

Fragment analysis is a cornerstone of genetic research and diagnostics, allowing precise sizing of DNA fragments through capillary electrophoresis (CE). While high-throughput sequencing dominates headlines, fragment analysis remains unmatched in speed, simplicity, and cost for specific use cases like STR genotyping, kinship, MSI, LOH, MLPA and microsatellite analysis.

What Is Fragment Analysis?

Fragment analysis involves fluorescently labeled PCR products separated via CE. The output—an electropherogram—shows distinct peaks representing fragment sizes.

Applications include:

- STR genotyping for forensics, identity testing and chimerism monitoring post-BMT
- Microsatellite instability (MSI) and genotyping detection in tumor/normal comparisons
- LOH (Loss of Heterozygosity) detection in tumor/normal comparisons
- MLPA, AFLP, Trisomy, Fragile X and other Repeat Expansions

Comparison Table

	Fragment Analysis	Next-Gen Sequencing (NGS)
Output	Fragment size (bp)	Full nucleotide sequence
Ideal Use	STRs, microsatellites	SNPs, indels, structural variants
Cost per sample	Low	Higher
Time to result	<2 hours	1–3 days
Required infrastructure	CE + software	Library prep + sequencer + pipeline

For Expert Users

Advanced researchers can extract even more from fragment data using:

Allelic ladder normalization to reduce run-to-run drift
In-silico panel editing for custom markers or rare variant detection
Multiplexed panels with dye balancing to increase throughput
Quantitative LOH and MSI analysis using ratio-based allele peak comparison
MLPA and MS-MLPA analysis of deletions/duplications and methylation

GeneMarker® supports custom panel development, size standard calibration, and locked audit trails for regulated environments.

Why It Still Matters in 2025

Despite NGS advances, CE remains essential for:

Validated forensic workflows
High-confidence STR and SSR calls
Screening large sample sets quickly
Applications where base-level resolution is unnecessary or overkill

How SoftGenetics Helps

GeneMarker®: high-performance sizing, binning, and allele calling plus embedded post-genotyping modules (MLPA/MS-MLPA, Aneuploidy, MSI, LOH…)
GeneMarker®HID: forensic-ready STR interpretation with mixture detection, database comparison, and visual QC tools
ChimerMarker®: Accurate, rapid genotyping, chimerism and MCC data analysis with documented time savings of up to 85%

Start your journey with a free 35-day trial of SoftGenetics software and experience the difference in variant detection analysis.