| 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 for classifying a copy number variation in a fetal genome, the method comprising:
(a) sequencing cell free DNA from a maternal test sample obtained from a pregnant woman carrying a fetus to provide sequence reads in an electronic format; (b) aligning the sequence reads to one or more bins from a reference sequence using a computing apparatus and thereby providing sequence tags corresponding to the sequence reads; (c) computationally identifying a number of those sequence tags that are from one or more bins by using a computing apparatus and determining that a first bin of interest in the fetus harbors a copy number variation, wherein the first bin of interest is a first chromosome of interest, and wherein the first chromosome of interest is selected from the group consisting of chromosomes 1-22, X, and Y; (d) calculating a first fetal fraction value by a first method that uses information from the sequence tags from the first bin of interest, wherein calculating the first fetal fraction value comprises (i) calculating a number of sequence tags from the first chromosome of interest and a number of sequence tags from at least one normalizing chromosome sequence to determine a chromosome dose; and (ii) calculating the first fetal fraction value from the chromosome dose, and wherein the first method includes a ploidy assumption that the first bin of interest harbors a complete aneuploidy; (e) calculating a second fetal fraction value by a second method that does not use information from the sequence tags from the first bin of interest; and (f) comparing the first fetal fraction value to the second fetal fraction value and using the comparison to classify the copy number variation of the first bin of interest in the genome of the fetus, and wherein operation (f) classifies the copy number variation into a classification selected from the group consisting of: complete chromosomal duplications, complete chromosomal multiplications, complete chromosomal deletions, partial chromosomal duplications, partial chromosomal multiplications, partial chromosomal deletions, and mosaics. |
