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Detailed method of genotyping is given in Text S1.
High resolution melting is a new method of genotyping and variant scanning that can be seamlessly appended to PCR amplification.
The high prevalence of genetic diseases resulting from gross deletions has highlighted a need for a quick, simple, and reliable method of genotyping these mutations.
Therefore pyrosequencing was used as an alternative method of genotyping some SNPs.
On the other hand, Raafat et al. (2015) found that STAT4 polymorphism was not associated with an increased risk of SLE in Egyptian females; this may be attributed to the difference in the method of genotyping that was performed by the real-time PCR allelic discrimination technique in the previous study.
This became the sole method of genotyping within the established colony following confirmation that the PCR assay recapitulated results obtained by Southern blotting.
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The development of relatively cheap and high throughput methods of genotyping and phenotyping plants offers the opportunity to explore local germplasm more thoroughly than before and should accelerate the identification of sources of genetic variation suitable for breeding.
This may include employing other methods of genotyping such as sequencing, and new assays which may help to evaluate possible method related confounding factors in allele scoring to determine genotype phenotype association [54] [55].
Two independent methods of genotyping namely DHPLC and sequencing will be combined as was done previously [ 81- 84].
The heterogeneity may attribute to the confounding factors due to case definition, sample size and methods of genotyping.
Whereas such PCR chimeras are easy to identify with Sanger sequencing of multiple clones from PCR amplicons, less rigorous methods of genotyping polyploids based on sizing of PCR-amplified fragments (e.g., SSRs) are likely to have a high error rate due to the incidence of such artifacts.
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