Book Chapter10.1007/978-1-61779-228-1_11
Genotyping with Sequenom.
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TL;DR: Sequenom's MassARRAY(®) genotyping platform is a powerful and flexible method for assaying up to a few thousand markers and up to thousands of individuals for polymorphisms in populations for which cost-efficient high-throughput arrays are nonexistent.
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Abstract: Often in evolutionary genetics research, one needs to analyze polymorphisms in populations for which cost-efficient high-throughput arrays are nonexistent, either because the species is not a model organism or because the populations have been subjected to such specific conditions that their base variation is almost unique. In this situation, custom-made genotyping assays are required. Sequenom's MassARRAY(®) genotyping platform is a powerful and flexible method for assaying up to a few thousand markers and up to thousands of individuals. It is based on distinguishing allele-specific primer extension products by mass spectrometry (MALDI-TOF). Most stages of the experimental protocol reflect adaptations of established PCR protocols to multiplexing, which allows the simultaneous amplification and detection of multiple markers per reaction.
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TL;DR: The increasing amounts of sequence data able to be generated using next-generation sequencing technologies have produced a vast expansion in the rate of discovery of polymorphisms, with single nucleotide polymorphisms (SNPs) predominating as the marker of choice.
46
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George Ayodo,Alkes L. Price,Alon Keinan,Arthur Ajwang,Michael F. Otieno,Alloys S. S. Orago,Nick Patterson,David Reich +7 more
TL;DR: An association study of putative resistance variants in 471 severe malaria cases and 474 controls from the Luo in Kenya empirically demonstrates that combining association analysis with evidence of natural selection can increase power to detect risk variants by orders of magnitude.