Applications compendium for Sanger sequencing and fragment analysis
An online collection of innovative application notes and articles focused on capillary electrophoresis workflows
Presented below is a collection of application notes and protocols describing selected applications utilizing Sanger sequencing and fragment analysis techniques on Applied Biosystems capillary electrophoresis genetic analyzers. Our customers and Applied Biosystems scientists have contributed to the articles in this collection. We hope that reading about their work will help guide your current research and spark ideas for other innovative applications.
The 3500 Series Genetic Analyzer
- Fungal DNA sequencing from laser capture microdissection samples
- SNP Gentyping Using SNaPshot® Multiplex Kit and 3500 Series Genetic Analyzer
- Resequencing Workflow for MLH1 and MSH2 Variant Analysis Application Note
- Development of a Workflow to Detect Sequence Variants in the BRCA1 and BRCA2 Genes
- ISSR Genotyping of Endangered Plants Using an Optimized Workflow
- Development of an Interlaboratory-Verified Sequencing Workflow for KRAS Variant Identification
- Aneuploidy Detection by QF-PCR of STR Markers on the Applied Biosystems 3500xL Genetic Analyzer
- DNA Resequencing Analysis of X-linked Variants Using the Applied Biosystems 3500xL Genetic Analyzer
- Uniparental disomy (UPD) analysis of chromosome 15 (3.2MB)
- High coverage gene expression profiling on the Applied Biosystems® 3500xL Genetic Analyzer (1.6MB)
- BigDye® Direct Cycle Sequencing Kit simplifies workflow for characterizing melanoma mutations in research samples
Cell and Gene Therapy
BAC Fingerprinting
- Sizing of Large DNA Fragments Generated by BAC Fingerprinting on Capillary Electrophoresis System
- BAC Fingerprinting on the Applied Biosystems 3730/3730xl DNA Analyzer
Cancer
- Resequencing Workflow for MLH1 and MSH2 Variant Analysis Application Note
- Development of a Workflow to Detect Sequence Variants in the BRCA1 and BRCA2 Genes
Copy Number Analysis
- Gene Copy Number analysis using semi-quantitative multiplex PCR-based assay on capillary electrophoresis systems
- Aneuploidy Detection by QF-PCR of STR Markers on the Applied Biosystems 3500xL Genetic Analyzer
Epigenetics and Methylation
- Three Optimized Workflows for CpG Island Methylation Profiling
- Methylation Analysis by Bisulfite Sequencing: Chemistry, Products and Protocols from Applied Biosystems
- Application Note: MethylSeq Direct workflow: a fast method for DNA methylation analysis.
Genetic Disorders
- Aneuploidy Detection by QF-PCR of STR Markers on the Applied Biosystems 3500xL Genetic Analyzer
- DNA Resequencing Analysis of X-linked Variants Using the Applied Biosystems 3500xL Genetic Analyzer
Gene Expression Profiling
Genotyping
- SNP Gentyping Using SNaPshot® Multiplex Kit and 3500 Series Genetic Analyzer
- ISSR Genotyping of Endangered Plants Using an Optimized Workflow
Microsatellite (STR) Analysis
- Aneuploidy Detection by QF-PCR of STR Markers on the Applied Biosystems 3500xL Genetic Analyzer
- Uniparental disomy (UPD) analysis of chromosome 15 (3.2 MB)
Mutation Detection
- Equivalent Performance of the Applied Biosystems™ 3500 and SeqStudio™ Flex Genetic Analyzer CE Systems for AmplideX® Gene Variant Analysis
- Detection and Quantification of Sequence Variants from Sanger Sequencing Traces
- Genotyping KRAS and BRAF Mutations in Paraffin-embedded Samples for Cancer Research
- Resequencing Workflow for MLH1 and MSH2 Variant Analysis Application Note
- Single Strand Conformation Polymorphism (SSCP) Analysis Application Note
- Development of a Workflow to Detect Sequence Variants in the BRCA1 and BRCA2 Genes
- Development of an Interlaboratory-Verified Sequencing Workflow for KRAS Variant Identification
- Development of a resequencing workflow for variant analysis in the APC gene (1MB)
- BigDye® Direct Cycle Sequencing Kit simplifies workflow for characterizing melanoma mutations in research samples
- BigDye® sequencing reagents for rapid detection of mutations in non-small cell lung carcinoma research samples
Plants, Animals, and Agriculture
Resequencing
- ABRF 2011 - A New Sequencing Primer and Workflow Increase 5' Resolution and Throughput on HLA Sequencing
- Resequencing Workflow for MLH1 and MSH2 Variant Analysis Application Note
- Development of a Workflow to Detect Sequence Variants in the BRCA1 and BRCA2 Genes
- Development of an Interlaboratory-Verified Sequencing Workflow for KRAS Variant Identification
- DNA Resequencing Analysis of X-linked Variants Using the Applied Biosystems 3500xL Genetic Analyzer
- Development of a resequencing workflow for variant analysis in the APC gene (1MB)
- BigDye® Direct Cycle Sequencing Kit simplifies workflow for characterizing melanoma mutations in research samples
Capillary electrophoresis webinars
A complete workflow for human cell line authentication
Dr. Steve Jackson, Product applications, Thermo Fisher Scientific
Application of capillary electrophoresis in rare and inherited disease testing
Dr Farshad Niri, Alberta Precision Laboratories
Case Studies of Microsatellite Instability Analysis and KRAS Variant Detection in Colorectal Cancer
Shawn Fahl, PhD, VP Lab Operations Cell Services & R&D Biospecimens, Discovery Life Sciences
Jelena Feenstra, PhD, Senior Manager Global Scientific Communication, Thermo Fisher Scientific
Detection of Low-Level Somatic Mutations in FFPE Samples Using Sanger Sequencing
Luca Quagliata, PhD, Senior Director, University Hospital Basel
Enabling neurological disease research via DNA fragment analysis
Gary Latham, PhD, Senior Vice President Research and Development, Asuragen
Genetic analysis for mRNA sequence confirmation and identity testing
Dr. Steve Jackson, Product applications, Thermo Fisher Scientific
Genome editing workflow facilitated by the Thermo Fisher Scientific portfolio solution
Dr. Steve Jackson, Product applications, Thermo Fisher Scientific
Multivariate Analysis Using Targeted Sequence Interrogation
Dr. Jeremy Stuart, Chief Scientific Officer of Precision Genetics
Overview of key applications on the SeqStudio Genetic Analyzer
Dr. Steve Jackson, Product applications, Thermo Fisher Scientific
Targeted Sequence Analysis to Propel Biopharmaceutic Development
Edgar Schreiber, PhD, Sr. Staff Product Applications Specialist, Thermo Fisher Scientific
Understanding how Sanger sequencing & fragment analysis are powering infectious disease research today
Dr. Archana Gupta,Staff Scientist, Thermo Fisher Scientific
Utility of Fragment Analysis in the Era of NGS-based Clinical Research
Dr. Somak Roy, Associate Professor Division of Pathology, Director of Molecular and Genomic Pathology Services, Cincinnati Children's Hospital Medical Center
Dr. Steve Jackson, Product applications, Thermo Fisher Scientific
Capillary electrophoresis blog posts
- Smart Deep Basecaller (SDB)– an AI solution for improving Sanger sequencing basecalling
- Fragment Analysis in Neuroscience: A Flexible Tool for Addressing Multiple Questions
- mRNA therapies: current landscape and future possibilities
- Unlocking the potential of mRNA for the future treatment of rare diseases
- Fragment Analysis: Versatility that Fuels Cancer Research
- Double-Stranded DNA Quality Control Using Capillary Electrophoresis
- Comparing Microsatellite Instability Marker Panels to Unlock Precision Medicine for Lynch Syndrome Patients
- Multiplex PCR Coupled with Fragment Analysis
- SARS-CoV-2 Omicron Variant Surveillance
- Sanger Sequencing & NGS for SARS-CoV-2 Omicron Variant Surveillance
- The Role of Capillary Electrophoresis (CE) in Drug Development
- Sanger Sequencing for Quality Control in AAV Vector Production
- Life on the Edge: Using Genetic Analysis to Track Beluga Whales in a Changing Arctic
- SARS-CoV-2 Surveillance: Sanger Sequencing Tools for Any Region of the SARS-CoV-2 Genome
- Gene Editing by CRISPR/Cas9 and The Importance of Sanger Sequencing To Power Edit Confirmation
- Using Sanger Sequencing and Fragment Analysis to Detect COVID-19 in India: An Interview with Dr. Ashwin Dalal
- The Precision and Simplicity of Fragment Analysis Helps Protect and Conserve the Ocean’s Top Predator
- Breast Cancer Disparity Among African American Women: Insights Powered by Sanger Sequencing
- New Avian Viruses Discovered with the Help of Sanger Sequencing
- Sanger Sequencing and Fragment Analysis Help Improve Clinical Outcomes of Acute Lymphoblastic Leukemia (ALL) in Pediatric Patients
- Using Sanger Sequencing to Detect Drug Resistance Mutations in HIV in Zambia
- SeqStudio Sanger Sequencing for Cooler Inherited Disease Research
- Capillary Electrophoresis (CE) or Next-Generation Sequencing (NGS) for STR Analysis?
- Guide to Sanger Sequencing by Capillary Electrophoresis: From Education to Application
- Determining Oncology Allele Frequency by Sanger Sequencing with FFPE Preserved Samples
- How to Generate High Quality Sanger Sequencing Data
- Messy Sanger Sequencing Reads near the Primer?
- When Do I Use Sanger Sequencing vs NGS?
- Sanger Sequencing by Resources
- How Does Sanger Sequencing Work?
- Sanger Sequencing Applications
- Sanger Sequencing Bioinformatics
- Designing a 27-plex PCR for fragment analysis
- Fragment Analysis
- Sanger Sequencing Foundations
The 3500 Series Genetic Analyzer
- Fungal DNA sequencing from laser capture microdissection samples
- SNP Gentyping Using SNaPshot® Multiplex Kit and 3500 Series Genetic Analyzer
- Resequencing Workflow for MLH1 and MSH2 Variant Analysis Application Note
- Development of a Workflow to Detect Sequence Variants in the BRCA1 and BRCA2 Genes
- ISSR Genotyping of Endangered Plants Using an Optimized Workflow
- Development of an Interlaboratory-Verified Sequencing Workflow for KRAS Variant Identification
- Aneuploidy Detection by QF-PCR of STR Markers on the Applied Biosystems 3500xL Genetic Analyzer
- DNA Resequencing Analysis of X-linked Variants Using the Applied Biosystems 3500xL Genetic Analyzer
- Uniparental disomy (UPD) analysis of chromosome 15 (3.2MB)
- High coverage gene expression profiling on the Applied Biosystems® 3500xL Genetic Analyzer (1.6MB)
- BigDye® Direct Cycle Sequencing Kit simplifies workflow for characterizing melanoma mutations in research samples
Cell and Gene Therapy
BAC Fingerprinting
- Sizing of Large DNA Fragments Generated by BAC Fingerprinting on Capillary Electrophoresis System
- BAC Fingerprinting on the Applied Biosystems 3730/3730xl DNA Analyzer
Cancer
- Resequencing Workflow for MLH1 and MSH2 Variant Analysis Application Note
- Development of a Workflow to Detect Sequence Variants in the BRCA1 and BRCA2 Genes
Copy Number Analysis
- Gene Copy Number analysis using semi-quantitative multiplex PCR-based assay on capillary electrophoresis systems
- Aneuploidy Detection by QF-PCR of STR Markers on the Applied Biosystems 3500xL Genetic Analyzer
Epigenetics and Methylation
- Three Optimized Workflows for CpG Island Methylation Profiling
- Methylation Analysis by Bisulfite Sequencing: Chemistry, Products and Protocols from Applied Biosystems
- Application Note: MethylSeq Direct workflow: a fast method for DNA methylation analysis.
Genetic Disorders
- Aneuploidy Detection by QF-PCR of STR Markers on the Applied Biosystems 3500xL Genetic Analyzer
- DNA Resequencing Analysis of X-linked Variants Using the Applied Biosystems 3500xL Genetic Analyzer
Gene Expression Profiling
Genotyping
- SNP Gentyping Using SNaPshot® Multiplex Kit and 3500 Series Genetic Analyzer
- ISSR Genotyping of Endangered Plants Using an Optimized Workflow
Microsatellite (STR) Analysis
- Aneuploidy Detection by QF-PCR of STR Markers on the Applied Biosystems 3500xL Genetic Analyzer
- Uniparental disomy (UPD) analysis of chromosome 15 (3.2 MB)
Mutation Detection
- Equivalent Performance of the Applied Biosystems™ 3500 and SeqStudio™ Flex Genetic Analyzer CE Systems for AmplideX® Gene Variant Analysis
- Detection and Quantification of Sequence Variants from Sanger Sequencing Traces
- Genotyping KRAS and BRAF Mutations in Paraffin-embedded Samples for Cancer Research
- Resequencing Workflow for MLH1 and MSH2 Variant Analysis Application Note
- Single Strand Conformation Polymorphism (SSCP) Analysis Application Note
- Development of a Workflow to Detect Sequence Variants in the BRCA1 and BRCA2 Genes
- Development of an Interlaboratory-Verified Sequencing Workflow for KRAS Variant Identification
- Development of a resequencing workflow for variant analysis in the APC gene (1MB)
- BigDye® Direct Cycle Sequencing Kit simplifies workflow for characterizing melanoma mutations in research samples
- BigDye® sequencing reagents for rapid detection of mutations in non-small cell lung carcinoma research samples
Plants, Animals, and Agriculture
Resequencing
- ABRF 2011 - A New Sequencing Primer and Workflow Increase 5' Resolution and Throughput on HLA Sequencing
- Resequencing Workflow for MLH1 and MSH2 Variant Analysis Application Note
- Development of a Workflow to Detect Sequence Variants in the BRCA1 and BRCA2 Genes
- Development of an Interlaboratory-Verified Sequencing Workflow for KRAS Variant Identification
- DNA Resequencing Analysis of X-linked Variants Using the Applied Biosystems 3500xL Genetic Analyzer
- Development of a resequencing workflow for variant analysis in the APC gene (1MB)
- BigDye® Direct Cycle Sequencing Kit simplifies workflow for characterizing melanoma mutations in research samples
Capillary electrophoresis webinars
A complete workflow for human cell line authentication
Dr. Steve Jackson, Product applications, Thermo Fisher Scientific
Application of capillary electrophoresis in rare and inherited disease testing
Dr Farshad Niri, Alberta Precision Laboratories
Case Studies of Microsatellite Instability Analysis and KRAS Variant Detection in Colorectal Cancer
Shawn Fahl, PhD, VP Lab Operations Cell Services & R&D Biospecimens, Discovery Life Sciences
Jelena Feenstra, PhD, Senior Manager Global Scientific Communication, Thermo Fisher Scientific
Detection of Low-Level Somatic Mutations in FFPE Samples Using Sanger Sequencing
Luca Quagliata, PhD, Senior Director, University Hospital Basel
Enabling neurological disease research via DNA fragment analysis
Gary Latham, PhD, Senior Vice President Research and Development, Asuragen
Genetic analysis for mRNA sequence confirmation and identity testing
Dr. Steve Jackson, Product applications, Thermo Fisher Scientific
Genome editing workflow facilitated by the Thermo Fisher Scientific portfolio solution
Dr. Steve Jackson, Product applications, Thermo Fisher Scientific
Multivariate Analysis Using Targeted Sequence Interrogation
Dr. Jeremy Stuart, Chief Scientific Officer of Precision Genetics
Overview of key applications on the SeqStudio Genetic Analyzer
Dr. Steve Jackson, Product applications, Thermo Fisher Scientific
Targeted Sequence Analysis to Propel Biopharmaceutic Development
Edgar Schreiber, PhD, Sr. Staff Product Applications Specialist, Thermo Fisher Scientific
Understanding how Sanger sequencing & fragment analysis are powering infectious disease research today
Dr. Archana Gupta,Staff Scientist, Thermo Fisher Scientific
Utility of Fragment Analysis in the Era of NGS-based Clinical Research
Dr. Somak Roy, Associate Professor Division of Pathology, Director of Molecular and Genomic Pathology Services, Cincinnati Children's Hospital Medical Center
Dr. Steve Jackson, Product applications, Thermo Fisher Scientific
Capillary electrophoresis blog posts
- Smart Deep Basecaller (SDB)– an AI solution for improving Sanger sequencing basecalling
- Fragment Analysis in Neuroscience: A Flexible Tool for Addressing Multiple Questions
- mRNA therapies: current landscape and future possibilities
- Unlocking the potential of mRNA for the future treatment of rare diseases
- Fragment Analysis: Versatility that Fuels Cancer Research
- Double-Stranded DNA Quality Control Using Capillary Electrophoresis
- Comparing Microsatellite Instability Marker Panels to Unlock Precision Medicine for Lynch Syndrome Patients
- Multiplex PCR Coupled with Fragment Analysis
- SARS-CoV-2 Omicron Variant Surveillance
- Sanger Sequencing & NGS for SARS-CoV-2 Omicron Variant Surveillance
- The Role of Capillary Electrophoresis (CE) in Drug Development
- Sanger Sequencing for Quality Control in AAV Vector Production
- Life on the Edge: Using Genetic Analysis to Track Beluga Whales in a Changing Arctic
- SARS-CoV-2 Surveillance: Sanger Sequencing Tools for Any Region of the SARS-CoV-2 Genome
- Gene Editing by CRISPR/Cas9 and The Importance of Sanger Sequencing To Power Edit Confirmation
- Using Sanger Sequencing and Fragment Analysis to Detect COVID-19 in India: An Interview with Dr. Ashwin Dalal
- The Precision and Simplicity of Fragment Analysis Helps Protect and Conserve the Ocean’s Top Predator
- Breast Cancer Disparity Among African American Women: Insights Powered by Sanger Sequencing
- New Avian Viruses Discovered with the Help of Sanger Sequencing
- Sanger Sequencing and Fragment Analysis Help Improve Clinical Outcomes of Acute Lymphoblastic Leukemia (ALL) in Pediatric Patients
- Using Sanger Sequencing to Detect Drug Resistance Mutations in HIV in Zambia
- SeqStudio Sanger Sequencing for Cooler Inherited Disease Research
- Capillary Electrophoresis (CE) or Next-Generation Sequencing (NGS) for STR Analysis?
- Guide to Sanger Sequencing by Capillary Electrophoresis: From Education to Application
- Determining Oncology Allele Frequency by Sanger Sequencing with FFPE Preserved Samples
- How to Generate High Quality Sanger Sequencing Data
- Messy Sanger Sequencing Reads near the Primer?
- When Do I Use Sanger Sequencing vs NGS?
- Sanger Sequencing by Resources
- How Does Sanger Sequencing Work?
- Sanger Sequencing Applications
- Sanger Sequencing Bioinformatics
- Designing a 27-plex PCR for fragment analysis
- Fragment Analysis
- Sanger Sequencing Foundations