Patent ID: 9411937
Filing Date: 2016-08-09
CPC Classification: C12Q,G16B,G16H

Claim Text:
1. A method for identifying and classifying a copy number variation in a genome of a mother or a fetus, the method comprising: (a) receiving sequence reads from fetal and maternal cell-free nucleic acids of a maternal test sample obtained from the mother carrying the fetus, wherein the sequence reads are provided 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 the computing apparatus and determining that a first bin of interest harbors a copy number variation; (d) calculating a fetal fraction value by a method that uses information from the number of sequence tags from the first bin of interest, wherein the method includes a ploidy assumption that the genome of the fetus has a complete aneuploidy within the first bin of interest; (e) comparing the fetal fraction value to a first threshold obtained based on maternal training samples, wherein the maternal training samples are obtained from pregnant mothers known to have an aneuploidy within the first bin of interest; and (f) determining whether said copy number variation resides in the genome of the mother or in the genome of the fetus based on the comparison of (e).