Development of SNP islands and application of SNP islands in genomic analysis

A system for determining a location in a nucleic acid sequence for which to design one or more primers, comprising:

• a processor;
• and
• memory storing instructions that, when executed by the processor, cause the system to:
• receive a nucleic acid sequence from one or more DNA samples;
• scan the nucleic acid sequence from the one or more DNA samples and determine locations of a plurality of single-nucleotide polymorphisms (SNPs) in the sequence;
• scan the nucleic acid sequence from the one or more DNA samples to locate a first region, a second region, and a third region, wherein the second region includes a plurality of SNP locations that satisfy a first predefined criteria, and wherein the first and third regions flank the second region;
• determine a location within one of the first and third regions for which to design a primer for amplification of a region of the nucleic acid sequence that includes the plurality of SNP locations that satisfy the first predefined criteria, wherein the determination comprises selecting a location that minimizes a likelihood of a primer designed for amplification of the second region of the nucleic acid sequence that includes the plurality of SNP locations that satisfy the first predetermined criteria amplifying the nucleic acid sequence outside of the second region;
• generate a primer for the determined location;
• amplify the determined location using the generated primer to generate a plurality of amplicons for the one or more DNA samples;
• and
• sequence and aligning each amplicon of the plurality of amplicons to generate one or more representations of each DNA sample of the one or more DNA samples, wherein generating one or more representations of each DNA sample includes generating and storing in a memory of a computing device one or more sequence alignment maps for each DNA sample.

A non-transitory computer readable storage medium storing instructions that, when executed by a system comprising a processor, cause the system to:

• receive a nucleic acid sequence from one or more DNA samples;
• scan the nucleic acid sequence from the one or more DNA samples and determine locations of a plurality of single-nucleotide polymorphisms (SNPs) in the sequence;
• scan the nucleic acid sequence from the one or more DNA samples to locate a first region, a second region, and a third region, wherein the second region includes a plurality of SNP locations that satisfy a first predefined criteria, and wherein the first and third regions flank the second region;
• determine a location within one of the first and third regions for which to design a primer for amplification of a region of the nucleic acid sequence that includes the plurality of SNP locations that satisfy the first predefined criteria, wherein the determination comprises selecting a location that minimizes a likelihood of a primer designed for amplification of the second region of the nucleic acid sequence that includes the plurality of SNP locations that satisfy the first predetermined criteria amplifying the nucleic acid sequence outside of the second region;
• generate a primer for the determined location;
• amplify the determined location using the generated primer to generate a plurality of amplicons for the one or more DNA samples;
• and
• sequence and aligning each amplicon of the plurality of amplicons to generate one or more representations of each DNA sample of the one or more DNA samples, wherein generating one or more representations of each DNA sample includes generating and storing in a memory of a computing device one or more sequence alignment maps for each DNA sample.