Selection of a Platform for Mutation Detection
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Abstract
New mutation detection technologies must keep pace by becoming more cost?effective while offering improved technical sensitivity and higher throughput capacity. In recent years, the number of mutation detection platforms available to the clinical researcher has grown to a point where it is difficult to keep track of all available options as well as their benefits and pitfalls. This unit provides an entry point for a variety of researchers who wish to analyze samples for known or novel mutations and need to determine which platform is most suited for their particular needs. A practical guide is provided in this unit, including a brief overview, information on assay parameters, design and cost considerations, as well as platform flexibility and scalability of the assay. Although the focus here is on applications involving human disease, many of these platforms can be easily adapted to the study of other organisms. Curr. Protoc. Hum. Genet. 56:7.15.1?7.15.30. © 2008 by John Wiley & Sons, Inc.
Keywords: mutation detection; mutation scanning; genotyping
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PDF or HTML at Wiley Online LibraryTable of Contents
- Introduction
- Methods for Direct Mutation Detection
- Methods for Mutation Scanning
- Detection of Constitutional Copy Number Variation
- Methylation Detection
- Acknowledgements
- Literature Cited
- Figures
- Tables
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Figure 7.15.1 Top: The principle of an ARMS assay designed to detect a T/C polymorphism. A and B represent reaction 1 for the T allele. The allele‐specific primer for the T allele binds and can be extended, while the primer specific for the C allele has two mismatches and cannot be extended. C and D show the converse and represent reaction 2 for the C allele. Bottom: The result for three hypothetical samples are shown. Two internal control primer pairs give rise to the top and bottom band in each reaction. View Image -
Figure 7.15.2 (A ) Genotyping results for an SNP present in the VKORC1 gene. Red circles represent patients with homozygous wild‐type genotypes, green triangles represent patients with heterozygous genotypes, blue diamonds represent patients with homozygous mutant genotypes, and grey squares represent negative controls. The sample designated by the X symbol lies outside the acceptable range for genotype calls and was deemed invalid. Representative quantitative PCR results for a homozygous mutant sample (B ), a homozygous wild‐type sample (C ), and a heterozygous sample (D ). View Image -
Figure 7.15.3 The principles of the original (hME; A ) as well as the newer version (iPLEX; B ) of the MassARRAY technology are shown for a hypothetical T/A polymorphism. hME reaction mixes are designed such that a dideoxy nucletotide is incorporated at the first position after the primer when allele 1 is present. For the other allele, the reaction extends for one additional base and terminates at position 2. iPLEX reaction mixes use mass modified nucleotides, which eliminates the need for an extension beyond the first (polymorphic) base. View Image -
Figure 7.15.4 Plating scheme to genotype 32 multiplexes in 12 samples. Samples are first plated onto four 96‐well masterplates in the order shown and then transferred to the 384‐well plate to generate multiple identical sections of 12. View Image -
Figure 7.15.5 Representative DNA sequence chromatograms, as viewed using Mutation Surveyor. The upper chromatogram (pair) in each image represents the forward strand and the lower chromatogram (pair) represents the reverse strand. (The uppermost and lowermost strands are the reference sequences.) (A ) A homozygous missense mutation. (B ) A heterozygous missense mutation. (C ) Scrambled sequence due to a CTTCT deletion. View Image -
Figure 7.15.6 The two left panels show MLPA results generated with the GeneMarker software (Softgenetics). In both cases, an apparent single probe deletion was present (symbolized by the red box). Subsequent sequence analysis of the probe binding sites revealed a heterozygous variant for one (top right) and a heterozygous deletion for the other sample (bottom right, deletion indicated by the brown bar). View Image
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