US 2014/0193818 A1 · PARTITION DEFINED DETECTION METHODS

Abstract

Methods are disclosed for resolving measurement problems such problems in measuring chromosomal copy number. Some disclosed methods involve first selecting a primary assay element characteristic to partition. Such characteristic may be a source of experimental variability such as the GC content of measured DNA sequences. Additionally, the disclosed methods may employ an abundance or copy number function to transform the assay element frequencies into an abundance, dose, copy number score, or the like. In some cases, the disclosed methods estimate an amount of certain fetal DNA in a sample. The methods can further compare the estimated amount to a measured amount of fetal DNA in the sample. The comparison can be used to determine the fetal sex or aneuploidy.

Claims46

Dependent claims

A method of detecting aneuploidy or sex in a fetus, the method comprising:

(a) extracting DNA from the blood of an individual carrying the fetus;
(b) mapping segments of the extracted DNA to a reference genome comprising a chromosome of interest;
(c) partitioning substrings of the reference genome into a plurality of partition levels based on a source of variability that biases chromosome abundance measurements;
(d) calculating an expected number of segments mapped to the chromosome of interest using (i) the number of substrings in the chromosome of interest in each partition level, and (ii) the number of substrings in the reference genome in each partition level;
and
(e) detecting aneuploidy or sex in the fetus by comparing an actual number of segments mapped to the chromosome of interest against the expected number of segments mapped to the chromosome of interest.

3 more elements

Dependencies are inferred from the claim text.

Partition defined detection methods

Life of this patent

Partition defined detection methods

Life of this patent

Abstract

Claims46