Detecting and classifying copy number variation

A computer program product comprising a non-transitory computer readable medium storing program code that, when executed by one or more processors of a computer system, causes the computer system to determine a normalizing sequence of a sequence of interest, said program code comprising:

• (a) code for obtaining sequence reads generated using a nucleic acid sequencer from a plurality of qualified samples for the sequence of interest, wherein the qualified samples are known to have a normal copy number of the sequence of interest;
• (b) code for aligning the sequence reads to a reference genome including the sequence of interest and thereby providing sequence tags corresponding to the sequence reads;
• (c) code for identifying a number of those sequence tags that are from the sequence of interest and identifying a number of those sequence tags that are from a plurality of potential normalizing sequences;
• (d) code for repeatedly determining sequence doses for the sequence of interest using the number of sequence tags for the sequence of interest and the number of sequence tags for the plurality of potential normalizing sequences;
• and
• (e) code for selecting the normalizing sequence, alone or in a combination with one or more other potential normalizing sequences, giving sequence doses for the sequence of interest having:
• (i) the smallest variability among two or more of the qualified samples, (ii) the greatest differentiability between two or more of the qualified samples and one or more affected samples known to have a copy number variation of the sequence of interest, (iii) the smallest variability and the greatest differentiability, or (iv) a combination of small variability and large differentiability.

A system comprising one or more processors, system memory, and one or more computer-readable storage media having stored thereon instructions for execution on said processor to:

• (a) receive sequence reads obtained using a nucleic acid sequencer from a plurality of qualified samples for a sequence of interest, wherein the qualified samples are known to have a normal copy number of the sequence of interest;
• (b) align the sequence reads to a reference genome including the sequence of interest and thereby providing sequence tags corresponding to the sequence reads;
• (c) identify a number of those sequence tags that are from the sequence of interest and identifying a number of those sequence tags that are from a plurality of potential normalizing sequences;
• (d) repeatedly determine sequence doses for the sequence of interest using the number of sequence tags for the sequence of interest and the number of sequence tags for the plurality of potential normalizing sequences;
• and
• (e) select a normalizing sequence, alone or in a combination with one or more other potential normalizing sequences, giving sequence doses for the sequence of interest having:
• (i) the smallest variability among two or more of the qualified samples, (ii) the greatest differentiability between two or more of the qualified samples and one or more affected samples known to have a copy number variation of the sequence of interest, (iii) the smallest variability and the greatest differentiability, or (iv) a combination of small variability and large differentiability.