Fragment Analysis Fundamentals
Novice or expert—learn the basics of fragment analysisFragment analysis applications are those in which fluorescent fragments of DNA (produced by PCR using primers designed for a specific interrogation task) are separated using capillary electrophoresis and sized by comparison to a size standard.  Most fragment analysis applications have simplified workflows—straightforward sample preparation (without the purification required for sequencing samples), ability to multiplex, and applications can all be separated using the same capillary electrophoresis (CE) polymer. The video gives an overview of the fragment analysis workflow and introduces you to some of the applications you can develop on our CE instruments. The step-by-step guide gives a generalized look at fragment analysis. For application-specific step-by-step guides go here. |
Step-by-Step Guide to General Fragment Analysis
 DNA extraction is a critical first step in the experimental workflow of Fragment analysis. The overall quality of the fragment analyzed can be significantly affected by characteristics of the sample itself, and the method chosen for nucleic acid extraction. Ideal methods will vary depending on the source or tissue type, how it was obtained from its source, and how the sample was handled or stored prior to extraction. Recommended Products: |
Product Literature
- Protocol: ABI PRISM® SNaPshot® Multiplex System
- Quick Reference Card: ABI PRISM® SNaPshot® Multiplex System
- User Bulletin: Using SNaPshot® on the 3730/3730xl DNA Analyzers and the 3130/3130xl Genetic Analyzers
- Application Note: BAC Fingerprinting on the Applied Biosystems 3730/3730xl DNA Analyzer (3 MB)
- Getting Started Guide: GeneMapper® Software Version 4.0 and SNaPshot® Kit Analysis (3.71 MB)
References
SNP Analysis
- Species Identification within Lactobacillus Plantarum
Rapid identification of Lactobacillus plantarum group using the SNaPshot minisequencing assay.
Publication: Syst Appl Microbiol. 2011 Dec;34(8):586-9.
Authors: Huang CH, Chang MT, Huang MC, Lee FL. - Sub Species Identification in Tigers
The development and validation of a single SNaPshot multiplex for tiger species and subspecies identification-Implications for forensic purposes.
Publication: Forensic Sci Int Genet. 2011 Jun 30.
Authors: Kitpipit T, Tobe SS, Kitchener AC, Gill P, Linacre A. - Tracking Cows and Their Products
SNPmplexViewer–toward a cost-effective traceability system.
Publication: BMC Res Notes. 2011 May 23;4:146.
Authors: Seroussi Y, Shirak A, Seroussi E. - Identification: Differentiating drug and non-drug forms of cannabis
Differentiation of drug and non-drug Cannabis using a single nucleotide polymorphism (SNP) assay.
Publication: Forensic Sci Int. 2011 Apr 15;207(1-3):193-7. Epub 2010 Oct 30.
Authors: Rotherham D, Harbison SA. - Identifying Species in M. Tuberculosis Complex
Identification and genotyping of Mycobacterium tuberculosis complex species by use of a SNaPshot Minisequencing-based assay.
Publication: J Clin Microbiol. 2010 May;48(5):1758-66. Epub 2010 Mar 10.
Authors: Bouakaze C, Keyser C, de Martino SJ, Sougakoff W, Veziris N, Dabernat H, Ludes B. - Blood Typing
Detection of blood group genes using multiplex SNaPshot method.
Publication: Transfusion. 2009 Apr;49(4):740-9. Epub 2009 Jan 2.
Authors: Palacajornsuk P, Halter C, Isakova V, Tarnawski M, Farmar J, Reid ME, Chaudhuri A. - Selective Breeding in Horses
Identification of horse chestnut coat color genotype using SNaPshot.
Publication: BMC Res Notes. 2009 Dec 16;2:255.
Authors: Rendo F, Iriondo M, Manzano C, Estonba A. - Wheat Breeding
Insertion site-based polymorphism markers open new perspectives for genome saturation and marker-assisted selection in wheat.
Publication: Plant Biotechnol J. 2010 Feb;8(2):196-210.
Authors: Paux E, Faure S, Choulet F, Roger D, Gauthier V, Martinant JP, Sourdille P, Balfourier F, Le Paslier MC, Chauveau A, Cakir M, Gandon B, Feuillet C. - Mitochondrial SNPs Screening
A new method for analysis of mitochondrial DNA point mutations and assess levels of heteroplasmy.
Publication: Biochem Biophys Res Commun (2006) 342(2): 387-393.
Authors: Cassandrini, D., M. G. Calevo, et al. - Species identification within Lactobacillus casei
Application of the SNaPshot minisequencing assay to species identification in the Lactobacillus casei group.
Publication: Mol Cell Probes. 2011 Aug;25(4):153-7.
Authors: Huang CH, Chang MT, Huang MC, Lee FL. - Validation of Heteroplasmy after Next Generation Sequencing
Detecting heteroplasmy from high-throughput sequencing of complete human mitochondrial DNA genomes.
Publication: The American Journal of Human Genetics 2010, 87(2), 237-249.
Authors: Li M, Schonberg A, Schaefer M, et al. - Mitochondrial Variants
Mitochondrial variants in schizophrenia, bipolar disorder, and major depressive disorder.
Publication: PLoS One (2009)4(3): e4913.
Authors: Rollins, B., M. V. Martin, et al. - SNP Screening
A SNaPshot assay for the rapid and simple detection of four common hotspot codon mutations in the PIK3CA gene.
Publication: BMC Research Notes 2009, 2:66
Authors: Hurst, D C,Zuiverloon, TCM, Hafner, C, Zwarthoff, EC et al. - Loss of Heterozygosity
Multiplex SNaPshot Genotyping for Detecting Loss of Heterozygosity in the Mismatch-Repair Genes MLH1 and MSH2 in Microsatellite-Unstable Tumors.
Publication: Clin Chem 54(11): 1844-1854 (2008)
Authors: Bujalkova, M., K. Zavodna, et al. - Anitretroviral Resitance Mutation
Pre-screening HIV-1 reverse transcriptase resistance mutations in subtype B patients using a novel multiplex primer extension assay.
Publication: Curr HIV Res (2009) 7(4): 398-409.
Authors: Jakobsen, M. R., A. Aggerholm, et al. - Asses Meat Performance in Pigs
SNaPshot minisequencing and a panel of candidate genes for complex routine testing of meat performance traits in pigs.
Publication: Anim Biotechnol. 2007;18(2):109-15.
Authors: Civánová K, Knoll A. - Degraded DNA
Developing multiplexed SNP assays with special reference to degraded DNA templates.
Publication: Nature Protocols 2006;1(3):1370-8
Authors: Sanchez, JJ. & Endicott, P. - Pathogen Resistance
Single nucleotide polymorphism and haplotypes in the IL10 region associated with HCV clearance
Publication: Genes Immun. 2005 Jun;6(4):347-57.
Authors: Oleksyk TK, Thio CL, Truelove AL, Goedert JJ, Donfield SM, Kirk GD, Thomas DL, O'Brien SJ, Smith MW. - Mitochondrial SNPs Screening
Mitochondrial DNA mutations in patients with postlingual, nonsyndromic hearing impairment
Publication: European Journal of Human Genetics (2005) 13, 26−33.
Authors: Jacobs HT, Hutchin TP, Käppi T, Gillies G, et al. - Scrapie Susceptability Screening
Primer extension assay for prion protein genotype determination in sheep.
Publication: Molecular and Cellular Probes (2004), 18(1), 33-37.
Authors: Vaccari G, Conte M, Morelli L, Di Guardo G, et al. - Gene Alterations in Carcinogenesis
Role of COX-2, thromboxane A2 synthase, and prostaglandin I2 synthase in papillary thyroid carcinoma growth.
Publication: Mod Pathol. 2005 Feb;18(2):221-7.
Authors: Kajita S, Ruebel KH, Casey MB, Nakamura N et al. - Arabidopsis Marker
Establishment of a high-efficiency SNP-based framework marker set for Arabidopsis.
Publication: Plant J. 2003 Oct;36(1):122-40.
Authors: Törjék O, Berger D, Meyer RC, Müssig C, Schmid KJ, Rosleff Sörensen T, Weisshaar B, Mitchell-Olds T, Altmann T. - SNP Validation in Immunity
Single nucleotide polymorphisms and haplotypes in the IL10 region associated with HCV clearance.
Authors: Oleksyk TK, Thio CL, Truelove AL, Goedert JJ, et al.
SNP Quantification
- Quantitative Mutant Measurement
Putative precursor cancer cells in human colorectal cancer tissue.
Publication: Int J Clin Exp Pathol (2009)2(2): 154-162
Authors: Goranova, T. E., M. Ohue, et al. - Allele-specific Gene Expression
Cis-acting variation in the expression of a high proportion of gene in human brain.
Publication: Hum Genet. 2003 Jul;113(2):149-53. Epub 2003 May 1.
Authors: Bray NJ, Buckland PR, Owen MJ, O'Donovan MC. - Allele-specific Gene Expression
Allelic variation in human gene expression
Publication: Curr Opin Oncol. 2004 Jan;16(1):39-43.
Authors: Yan H, Zhou W. - Quantitative SNP Allele Frequency Measurement
Universal, robust, highly quantitative SNP allele frequency measurement in DNA pools.
Publication: Hum Genet. 2002 May;110(5):471-8. Epub 2002 Mar 23.
Authors: Norton N, Williams NM, Williams HJ, Spurlock G et al.
BAC Fingerprinting
- High-throughput Fingerprinting of Bacterial Artificial Chromosomes
High-throughput fingerprinting of bacterial artificial chromosomes using
Publication: Genomics 82 (2003) 378–389
Authors: Ming-Cheng Luo, Carolyn Thomas, Frank M. You, Joseph Hsiao
Methylation
- Detecting Methylation Status
Capillary electrophoretic analysis of methylation status in CpG-rich regions by single-base extension of primers modified with N6-methoxy-2,6-diaminopurine
Publication: Analytical Biochemistry Volume 380, Issue 1, 1 September 2008, Pages 13-20.
Authors: Boyd, V.L. et al. - Methylation Status
Single nucleotide extension technology for quantitative site-specific evaluation of metC/C in GC-rich regions.
Publication: Nucleic Acids Res (2005) 33(10): e95.
Authors: Kaminsky, Z. A., A. Assadzadeh, et al.
