Capillary Electrophoresis for Clinical Research Environments

Because you can’t afford to get it wrong

Due to its high accuracy and fast, simple workflow, capillary electrophoresis (CE) is a foundational technology for clinical research applications. With resolution down to a single base pair, CE can be used for research pertaining to the identification and characterization of both known and unknown diseases. CE can be used for both Sanger sequencing and fragment analysis. Sanger sequencing is useful for both targeted sequencing and confirmation analysis. Fragment analysis is a useful method for multiplexing, investigating variants, SNPs, or size analysis.

Featured fragment analysis applications for clinical research

Research of tandem repeat disorders

With high resolution and low sample input requirements, fragment analysis is an excellent tool for researching repeat expansion. Examples include:

  • Research of CGG repeats in Fragile X syndrome (1)
  • FLT3-ITD mutations in AML (2)
  • CTG repeats in the DMPK gene in myotonic dystrophy type 1 (3)

White Paper: The SeqStudio Genetic Analyzer simplifies the analysis of triplet repeat expansions with AmplideX PCR/CE reagents

Copy number variant research

CE is an accurate and cost-effective method for researching copy number variants (CNVs). CNVs in certain genes can be associated with onset and severity of disease. For example:

  • In spinal muscular atrophy (SMA), severity is modulated by the SMN2 copy number (4)
  • NPD1/NPD2 CNVs can influence the inherited

Microsatellite instability

Microsatellite instability (MSI) is the accumulation of insertion or deletion errors at microsatellite repeat sequences in cancer cells. With its high accuracy,  fragment analysis is an excellent tool for the measurement of MSI in oncology research. MSI can be found in many cancer types including colorectal, gastric, and endometrial cancer.

Exploring deletion and duplication mutations

With high accuracy and low sample input, CE is a good choice for researching detection of deletions and duplications of exons. Examples include:

  • Investigation of aneuploidy related disorders (6)
  • PMS2 and PMS2CL genes in the investigation of lynch syndrome (7)
  • Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD) (8)
  • SHANK3 gene involved in Phelan-McDermid syndrome (9)

Webinar: Multivariate analysis using targeted sequence interrogation

Multiplexed PCR for pathogen research

CE allows the targeting of multiple pathogens simultaneously without splitting samples. Turnaround time is significantly faster than culture methods. Targets include:

  • Multiple respiratory infections including RNA viruses
  • Meningitis, encephalitis, and sepsis to find the causative agent
  • Multiplexed bacterial infection for joint applications

Featured Sanger sequencing applications for clinical research

Infectious disease and drug resistance research

Many viruses, most notably HIV, develop resistance mutations. Sanger sequencing can quickly and reliably help explore mutations associated with drug resistance. For example:

  • In drug resistant HIV, mutations can be found in the protease, reverse transcriptase, and other regions (10)
  • For HPV- genotyping and identification of resistance mutations

Web page: HIV resistance testing

Cancer associated genes

Many cancer-related mutations are found in small regions of DNA. Sanger sequencing is widely used for its accuracy. Examples of genes studied include:

  • BRCA1
  • EGFR
  • KRAS
  • NRAS
  • BRAF

Confirmation of NGS and CRISPR gene editing

Sanger sequencing by CE is widely used for its  sequencing accuracy. It can be used to verify sequence in many clinical research applications, including:

  • Next-generation sequencing (NGS)
  • CRISPR
  • mRNA vaccines and therapeutics

Genetic analyzers

Applied Biosystems genetic analyzers are a trusted standard for Sanger sequencing and fragment analysis by CE.

Low to high throughput—get a quote for a genetic analyzer that meets your genetic testing needs.

Citations

1. CarrierMax FMR1 Reagent KitHIV-1 Drug Resistance Testing

2. Research Protocol Guide: FLT3-ITD mutation detection using capillary electrophoresis

3. Fragment Analysis in Neuroscience: A Flexible Tool for Addressing Multiple Questions

4. Ratni, Hasane et al. “Discovery of Risdiplam, a Selective Survival of Motor Neuron-2 ( SMN2) Gene Splicing Modifier for the Treatment of Spinal Muscular Atrophy (SMA).” Journal of medicinal chemistry vol. 61,15 (2018): 6501-6517. doi:10.1021/acs.jmedchem.8b00741

5. Natalie Hammond, et al, "Identification and characterization of protein interactions with the major Niemann–Pick type C disease protein in yeast reveals pathways of therapeutic potential", Genetics, Volume 225, Issue 1, September 2023, iyad129, https://doi.org/10.1093/genetics/iyad129

6. Brochure: Aneuploidy Detection by QF-PCR  of STR Markers on the  Applied Biosystems 3500xL Genetic Analyzer

7. Andini, K. D., et al, S. W. (2023). PMS2-associated Lynch syndrome: Past, present and future. Frontiers in oncology, 13, 1127329. https://doi.org/10.3389/fonc.2023.1127329

8. https://www.mda.org/disease/duchenne-muscular-dystrophy/research

9. Uchino, Shigeo, and Chikako Waga. SHANK3 as an autism spectrum disorder-associated gene. Brain & development vol. 35,2 (2013): 106-10. doi:10.1016/j.braindev.2012.05.013

10. Flyer: Enhancing the science in the global fight to end HIV

For Research Use Only. Not for use in diagnostic procedures.