USING THE SIZE OF CELLULAR DNA FRAGMENTS TO DETERMINE COPY NUMBER VARIATIONS

Abstract

The present invention relates to methods for determining copy number variation (CTV) known or suspected to be associated with various medical conditions. In some embodiments, the invention relates to methods for determining copy number variation (CTV) in fetuses using maternal samples containing maternal and fetal cell-free DNA. In some embodiments, the invention relates to methods for determining CTV known or suspected to be associated with various medical conditions. In some embodiments, the invention relates to methods for improving the sensitivity and / or specificity of sequence data analysis by obtaining a parameter associated with fragment size, such as size-weighted coverage or a fraction of fragments falling within a size range.In some embodiments, the parameter associated with fragment size is adjusted to eliminate the bias associated with the GC content within the sample. According to some embodiments, the elimination of the bias associated with the GC content within the sample is based on sequence data corrected to account for the common systematic variation in unaffected training samples. The invention also relates to computer program-type systems and products for evaluating the GC content of sequences of interest.