Genotyping Methods and Protocols

This volume covers the latest techniques used to study single nucleotide polymorphisms (SNP) genotyping, such as Sanger sequencing, qPCR, Nanopore sequencing, and PACE. The chapters in this book cover topics such as SNP nomenclature, databases, and significance of SNPs in various fields; PCR-based techniques like HRM and CD-PCR; isothermal amplification methodologies; high-throughput methods like FCS-based SNP genotyping; and guidance of data analysis, emphasizing the importance of quality control, statistical analysis, and visualization. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Cutting-edge and thorough, Genotyping: Methods and Protocols is a valuable resource for both new and experienced researchers who want to gain a deeper understanding of genotyping and its myriad of applications.

An assay for Variable Fragment Length Allele-Specific Genotyping.- Digital PCR-Based Genotyping: A Precision Approach to HCMV Drug Resistance.- Digital PCR Genotyping of Pepino Mosaic Virus.- Isothermal Amplification Techniques: An Emerging Tool for On-Site Detection of Phytopathogens in Field Conditions.- Loop-Mediated Isothermal Amplification (LAMP) Genotyping for Presence-Absence Determination of Gene of Interest in Test Samples.- RPA Workflow for Sex Determination Genotyping in a Diecious Plant.- Sex Genotyping by Flow Cytometry.- High Throughput Genotyping by CD-PCR.- Probe-Based qPCR Workflow Using Fast Nucleic Acid Sampling and Molecular Genotyping in a Diecious Plant.- Probe-Based RTqPCR Workflow for Dual Interrogation of Virus/Viroid Genotype in Molecular Diagnostics Multiplex.- Haplotype and Presence-Absence Variation Analysis using High Resolution Melting (HRM) Analysis for Genotyping Genes of Interest.- PCR Allele Competitive Extension (PACE) Workflow for Genotyping by SNP Identification.- The Power of Short Tandem Repeat (STR) Analysis for Analysis of Genetic Differences and Genotype Identification.- Targeted Amplicon Genotyping by Sanger Sequencing.- Long-Range Targeted Nanopore Ligation Sequencing Workflow for Targeted Amplicon Sequencing of Secondary Metabolite Gene.- Double Digest Restriction-Site Associated DNA Sequencing (ddRAD-Seq).- The Fast and Accurate Enrichment of Canid Excrement for Species* and Other Analyses (FAECES*) Method for Noninvasive Genotyping of Field-Collected Canid Scat.