Simulating multiplexed SNP discovery rates using base-specific cleavage and mass spectrometry

Motivation: Single Nucleotide Polymorphisms (SNPs) are believed to contribute strongly to the genetic variability in living beings, and SNP and mutation discovery are of great interest in today's Life Sciences. A comparatively new method to discover such polymorphisms is based on base-specific cleavage, where resulting cleavage products are analyzed by mass spectrometry (MS). One particular advantage of this method is the possibility of multiplexing the biochemical reactions, i.e. examining multiple genomic regions in parallel. Simulations can help estimating the performance of a method for polymorphism discovery, and allow us to evaluate the influence of method parameters on the discovery rate, and also to investigate whether the method is well suited for a certain genomic region. Results: We show how to efficiently conduct such simulations for polymorphism discovery using base-specific cleavage and MS. Simulating multiplexed polymorphism discovery leads us to the problem of uniformly drawing a multiplex. Given a multiset of natural numbers we want to uniformly draw a subset of fixed cardinality so that the elements sum up to some fixed total length. We show how to enumerate multiplex layouts using dynamic programming, which allows us to uniformly draw a multiplex.