Noninvasive diagnosis of fetal aneuploidy by sequencing

• US 9,353,414 B2
• Filed: 01/30/2014
• Issued: 05/31/2016
• Est. Priority Date: 09/20/2008
• Status: Active Grant

• Current Assignee: Board of Trustees of the Leland Stanford Junior University (Stanford University)
• Original Assignee: Board of Trustees of the Leland Stanford Junior University (Stanford University)
• Inventors: Fan, Hei-Mun Christina, Quake, Stephen R.
• Primary Examiner(s): Joike, Michele K
• Assistant Examiner(s): Brown, Mindy G
• Application Number:
  US14/168,714
• Publication Number:
  US 20140329691A1
• Time in Patent Office: 852 Days
• Field of Search: None
• US Class Current: 1/1
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: G01N 2800/387 Down syndrome; Trisomy 18; Trisomy 13
• CPC Class Codes: G01N 33/48 Biological material, e.g. blood, urine G01N33/02, G01N33/26, G01N33/44, G01N33/46 take precedence; Haemocytometers counting blood corpuscules distributed over a surface by scanning the surface G06M11/02

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.

Claims

1. A method of determining the presence or absence of a fetal chromosomal abnormality in a maternal serum or plasma sample comprising a mixture of fetal and maternal DNA, comprising the steps of:

a) obtaining maternal and fetal DNA from said sample;

b) sequencing a plurality of specific predefined subchromosomal sequences of the maternal and fetal DNA from step a) to obtain a plurality of sequence tags aligning to the subchromosomal sequences, wherein said subchromosomal sequences are from a first chromosome being tested for the fetal chromosomal abnormality and from at least one second chromosome that is euploid, said at least one second chromosome being different than from said first chromosome; and

wherein said plurality of subchromosomal sequences cover only a portion of said first chromosome and only a portion of said at least one second chromosome;

c) assigning the plurality of sequence tags to their corresponding predefined subchromosomal sequences;

d) determining a number of sequence tags aligning to the predefined subchromosomal sequences of said first chromosome and a number of sequence tags aligning to the predefined subchromosomal sequences of said at least one second chromosome while accounting for variations in G/C content of the preselected subchromosomal sequences; and

e) comparing the numbers from step d) to determine the presence of absence of said fetal chromosomal abnormality.

2. The method of claim 1 wherein said fetal chromosomal abnormality is a fetal aneuploidy.

3. The method of claim 2 wherein said fetal chromosomal abnormality is a fetal chromosomal microdeletion or microduplication.

4. The method of claim 3 wherein said microdeletion or microduplication is a 22q11 deletion.

5. The method of claim 2, wherein the sequence tags that originate from the first chromosome are a specified number of nucleotides in length.

6. The method of claim 1, wherein the DNA molecules of the maternal sample have been selected for sequences less than a predetermined number of nucleotides.

7. The method of claim 2, wherein the fetal aneuploidy is a chromosome 21 aneuploidy and wherein said first chromosome is chromosome 21.

8. The method of claim 2, wherein the fetal aneuploidy is a chromosome 18 aneuploidy and wherein said first chromosome is chromosome 18.

9. The method of claim 2, wherein the fetal aneuploidy is chromosome 13 aneuploidy and the wherein said first chromosome is chromosome 13.

10. The method of claim 2, wherein said fetal aneuploidy is sex chromosomal aneuploidy, and wherein said first chromosome is chromosome X or chromosome Y.

11. The method of claim 1 wherein the comparing of step e) comprises calculating a ratio of the number of sequence tags aligning to the preselected subsequences of said first chromosome to the number of sequence tags aligning to the preselected subsequences of said at least one second chromosome.