Methods for rapid identification and quantitation of nucleic acid variants

Abstract

There is a need for nucleic acid analysis which is both specific and rapid, and in which no nucleic acid sequencing is required. The present invention addresses this need, among others by providing a method of nucleic acid amplification of overlapping sub-segments of a nucleic acid followed by molecular mass measurement of resulting amplification products by mass spectrometry, and determination of the base compositions of the amplification products.

1 . A method for analyzing a nucleic acid comprising the steps of:
 (a) obtaining a sample comprising nucleic acid for base composition analysis;   (b) selecting at least two primer pairs that will generate overlapping amplification products of at least two sub-segments of the nucleic acid;   (c) amplifying at least two nucleic acid sequences of a region of the nucleic acid designated as a target for base composition analysis using the at least two primer pairs, thereby generating at least two overlapping amplification products;   (d) determining base compositions of the amplification products by;
 (i) measuring molecular masses of one or more of the amplification products generated in step (c) using a mass spectrometer; and 
 (ii) converting one or more of the measured molecular masses to base compositions; 
   (e) comparing one or more of the base compositions with a source of reference base composition data for the nucleic acid sequence; and   (f) identifying the presence of a particular nucleic acid sequence or variant thereof.   
     
     
         2 - 36 . (canceled)