SNP Genotyping by Fragment Analysis

Product Literature

• SNaPshot® Multiplex System for SNP genotyping
• 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.