Methods and systems for identification of spinal muscular atrophy

A method for identifying a genetic signature(s) associated with spinal muscular atrophy (SMA) in a nucleic acid sample of a subject, comprising:

• (a) in a single vessel, providing a reaction mixture comprising said nucleic acid sample of said subject, a polymerizing enzyme and a probe set, which probe set comprises (i) a first probe that has sequence specificity for an SMN1 gene at a first locus of said nucleic acid sample, (ii) a second probe that has sequence specificity for an SMN2 gene at said first locus, (iii) a third probe that has sequence specificity for said SMN1 or SMN2 gene at a second locus of said nucleic acid sample, which second locus is different than said first locus, and (iv) a fourth probe that has sequence specificity for a genetic aberration of said SMN1 gene at said second locus;
• (b) subjecting said reaction mixture in said single vessel to conditions sufficient to generate a plurality of amplicons corresponding to said first locus and said second locus;
• (c) detecting said plurality of amplicons;
• and
• (d) based at least in part on said plurality of amplicons detected in (c), (i) identify said genetic signature(s) associated with SMA, with an accuracy of at least 90%.

A system for identifying a genetic signature(s) associated with SMA in a nucleic acid sample of a subject, comprising:

• a single vessel configured to contain a reaction mixture comprising said nucleic acid sample of said subject, a polymerizing enzyme and a probe set, which probe set comprises (i) a first probe that has sequence specificity for an SMN1 gene at a first locus of said nucleic acid sample, (ii) a second probe that has sequence specificity for an SMN2 gene at said first locus, (iii) a third probe that has sequence specificity for said SMN1 or SMN2 gene at a second locus of said nucleic acid sample, which second locus is different than said first locus, and (iv) a fourth probe that has sequence specificity for a genetic aberration of said SMN1 gene at said second locus;
• a detector operatively coupled to said single vessel;
• and
• one or more computer processors operatively coupled to said single vessel, wherein said one or more computer processors are individually or collectively programmed to (i) subject said reaction mixture in said single vessel to conditions sufficient to generate a plurality of amplicons corresponding to said first locus and said second locus;
• (ii) use said detector to detect said plurality of amplicons;
• and (iii) based at least in part on said plurality of amplicons detected in (ii), identify a genetic signature(s) associated with SMA with an accuracy of at least 90%.