Guides for Sequencing, Fragment and Forensics

What Is Fragment Analysis and Why Is It Still Essential?

Written by SoftGenetics Team | Aug 13, 2025 11:48:48 AM

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.
View full post