DETECTING AND CLASSIFYING COPY NUMBER VARIATION

摘要

The invention provides a method for determining copy number variations (CNV) of a sequence of interest in a test sample that comprises a mixture of nucleic acids that are known or are suspected to differ in the amount of one or more sequence of interest. The method comprises a statistical approach that accounts for accrued variability stemming from process-related, interchromosomal and inter-sequencing variability. The method is applicable to determining CNV of any fetal aneuploidy, and CNVs known or suspected to be associated with a variety of medical conditions. CNV that can be determined according to the method include trisomies and monosomies of any one or more of chromosomes 1-22, X and Y, other chromosomal polysomies, and deletions and/or duplications of segments of any one or more of the chromosomes, which can be detected by sequencing only once the nucleic acids of a test sample.

主权项

1. A method of identifying at least one normalizing sequence or normalizing coverage of a sequence of interest suspected of having a copy number variation in an organism, the method comprising:
(a) providing 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) aligning sequence reads obtained from the qualified samples to a reference sequence including the sequence of interest and thereby providing sequence tags corresponding to the sequence reads; (c) 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) repeatedly calculating 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) 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.