A combination of different types of next-generation sequencers for analyzing individual genomes may be an efficient means of validating multiple single nucleotide variations calls simultaneously.
121 Recently, Mayba et al developed a pipeline, MBASED to ASE detection, through aggregating information across multiple single nucleotide variation loci to obtain a gene-level ASE.
Multiple nucleotide and amino acid variations can be used as input (Fig. 1).
After careful examination of multiple-sequence alignment, 114 single nucleotide variations were identified.
Multiple sequence alignment analysis revealed that specific nucleotide variations were associated with non-European variants such as African-2 variants.
Even though multiple sequence clusters were identified with single nucleotide variations, most of them were polymorphic within a germplasm line at many loci.
In the 88 unigenes with SFPs, 75% of the sequence variations were SNPs, 10% were multiple nucleotide polymorphisms (adjacent SNPs), and 15% were indels.
However, this approach is consistently biased towards the identification of certain types of other forms of variation such as large insertions, multiple nucleotide polymorphisms (MNP), inversions, translocations and novel sequences and towards the breakpoint resolutions [ 3, 6].
Recently, molecular assays have been developed to further discriminate within subspecies by using pulsed-field gel electrophoresis (PFGE), multiple-locus variable number tandem repeat analysis (MLVA), whole-genome microarrays, and single nucleotide variations (6 – 9 ).
