Titlebook: Genotyping; Methods and Protocol Stefan J. White,Stuart Cantsilieris Book 2017 Springer Science+Business Media New York 2017 DNA.Taqman-bas

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Targeted Locus Amplification and Next-Generation Sequencing, In combination with next-generation sequencing, TLA enables the complete sequencing and haplotyping of targeted regions of interest. Here we outline the basis of TLA, together with a detailed protocol of the technique.

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,The MassARRAY? System for Targeted SNP Genotyping, capable of efficiently genotyping tens to hundreds of SNPs are still crucial for many aspects of this work, including replication of associations. The Agena Bioscience MassARRAY System is one such platform. Here, we provide a guide to using the MassARRAY System, from assay design, through mass spectrometry, to generation of genotype data.

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Genotyping Multiallelic Copy Number Variation with Multiplex Ligation-Dependent Probe Amplification. Multiplex ligation-dependent probe amplification (MLPA) is a PCR-based approach that allows copy number determination of up to 50 genomic loci in a single reaction. In this chapter, we outline the basic protocol, with a particular emphasis on the appropriate approach to accurately genotype multiallelic copy numbers.

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Quantitative DNA Analysis Using Droplet Digital PCR,ts allows the precise quantification of a given sequence. In this chapter we briefly outline the basis of ddPCR, and describe two different applications using the Bio-Rad QX200 system: genotyping copy number variation and quantification of Illumina sequencing libraries.

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Full-Length Mitochondrial-DNA Sequencing on the PacBio RSII,In this setup we first generate long-range PCR products for two partially overlapping 7.7 and 9.2 kb MT DNA-specific amplicons, add sample-specific barcodes, and sequence these on the PacBio RSII system to obtain full-length MT DNA sequences for genotyping/haplotyping purposes.

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