US 8,195,415 B2 · Noninvasive diagnosis of fetal aneuploidy by sequencing

Abstract

Disclosed is a method to achieve digital quantification of DNA (i.e., counting differences between identical sequences) using direct shotgun sequencing followed by mapping to the chromosome of origin and enumeration of fragments per chromosome. The preferred method uses massively parallel sequencing, which can produce tens of millions of short sequence tags in a single run and enabling a sampling that can be statistically evaluated. By counting the number of sequence tags mapped to a predefined window in each chromosome, the over- or under-representation of any chromosome in maternal plasma DNA contributed by an aneuploid fetus can be detected. This method does not require the differentiation of fetal versus maternal DNA. The median count of autosomal values is used as a normalization constant to account for differences in total number of sequence tags is used for comparison between samples and between chromosomes.

Claims17

Dependent claims

A method of testing for an abnormal distribution of a specified chromosome portion in a mixed sample of normally and abnormally distributed chromosome portions obtained from a subject, comprising:

(a) sequencing DNA from the mixed sample to obtain sequences from multiple chromosome portions, wherein said sequences comprise a number of sequence tags of sufficient length of determined sequence to be assigned to a chromosome location within a genome;
(b) assigning the sequence tags to corresponding chromosome portions including at least the specified chromosome by comparing the determined sequence of the sequence tags to a reference genomic sequence;
(c) determining values for numbers of sequence tags mapping to chromosome portions by using a number of windows of defined length within normally and abnormally distributed chromosome portions to obtain a first value and a second value therefrom;
and
(d) using the values from step (c) to determine a differential, between the first value and the second value, which is determinative of whether or not the abnormal distribution exists.

2 more elements

Dependencies are inferred from the claim text.

Noninvasive diagnosis of fetal aneuploidy by sequencing

Life of this patent

Noninvasive diagnosis of fetal aneuploidy by sequencing

Life of this patent

Abstract

Claims17