Noninvasive diagnosis of fetal aneuploidy by sequencing

• US 10,669,585 B2
• Filed: 06/28/2016
• Issued: 06/02/2020
• 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): Brown, Mindy G
• Application Number:
  US15/195,135
• Publication Number:
  US 20170029890A1
• Time in Patent Office: 1,435 Days
• Field of Search: None
• 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 testing for a fetal aneuploidy 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 about 20-100 bp, to be assigned to a chromosome location within a genome;

(b) aligning the sequence tags to corresponding chromosome portions including at least the specified chromosome;

(c) counting a number of sequence tags mapping to chromosome portions by counting sequence tags within a number of windows of defined length within chromosome portions presumed to be normally distributed to obtain a first value and within chromosome portions that are possibly abnormally distributed to obtain a second value therefrom; and

(d) using the values from step (c) to calculate a differential between the first value and the second value, wherein a statistically significant differential as determined by a t-test and as represented by a t statistic outside −

3.09 to 3.09 indicates that an abnormal distribution of a specified chromosome portion exists, thereby identifying a fetal aneuploidy.

2. The method of claim 1, wherein calculating the differential includes the step of calculating a normalized sequence tag density of the specified DNA chromosome portion and a normalized sequence tag density of another DNA chromosome portion in said mixed sample, wherein all autosomes are used to calculate the normalized sequence tag density.

3. The method of claim 1 wherein the sequencing is massively parallel sequencing.

4. The method of claim 1 wherein the fetal aneuploidy is an aneuploidy of at least one of chromosome 13, 18 and 21.

5. The method of claim 1 wherein the step of aligning sequence tags to corresponding chromosome portions allows one nucleotide mismatch.

6. The method of claim 1 wherein the sequence tags are about 25-100 bp in length.

7. The method of claim 1 wherein at least about 1 million sequence tags are obtained.

8. The method of claim 1 further comprising the step of calculating a normalized sequence tag density of the specified DNA chromosome portion and a normalized sequence tag density of another DNA chromosome portion in said mixed sample.

9. The method of claim 1 wherein the calculating a differential includes the step of calculating a normalized sequence tag density of the specified DNA chromosome portion and a normalized sequence tag density of another DNA chromosome portion in said mixed sample, wherein all autosomes are used to calculate the normalized sequence tag density.

10. The method of claim 1 further comprising the step of measuring over-and under-representation of a chromosome by calculating a sequence tag density for each chromosome in the sample, namely chromosomes 1-22, X and also chromosome Y if present.

17. The method of claim 1 wherein the sequencing is massively parallel sequencing.

11. A method of testing for a fetal aneuploidy in a mixed sample of normally and abnormally distributed DNA molecules, comprising:

(a) sequencing DNA in said sample by massively parallel sequencing to obtain a number of sequence tags

(b) mapping said sequence tags to specific chromosome portions, each chromosomal portion being comprised in a non-overlapping sliding window of a predetermined length;

(c) counting numbers of sequence tags mapped to each sliding window on at least each autosome;

(d) calculating a mean of said numbers for each autosome and a second mean for at least all autosomes;

(e) calculating a normalized value from all autosomes, using said second mean;

wherein a statistically significant difference as determined by a t-test among normalized values among autosomes indicates the presence of an abnormally distributed autosomal chromosome portion of interest, and wherein said statistically significant difference is represented by a t statistic outside −

3.09 to 3.09, thereby identifying a fetal aneuploidy.

12. The method of claim 11 further comprising the step of calculating a relationship between numbers of sequence tags and GC content associated with sequence tags in a given window and correcting for a higher or lower number of reads resulting from a change in GC content.

13. The method of claim 11 further comprising the step of calculating a normalized value for chromosome X and, if present, Y.

14. The method of claim 11 wherein said mapping includes mapping sequences with one nucleotide mismatch.

15. A method of identifying genetically altered DNA in a mixed sample of normal and genetically altered DNA from a tumor 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 about 20-100 bp, to be assigned to a chromosome location within a genome;

(b) aligning the sequence tags to corresponding chromosome portions including at least the specified chromosome;

(c) counting a number of sequence tags mapping to chromosome portions by counting sequence tags within a number of windows of defined length within chromosome portions presumed to be normally distributed to obtain a first value and within chromosome portions that are possibly abnormally distributed to obtain a second value therefrom; and

(d) using the values from step (c) to calculate a differential between the first value and the second value, wherein a statistically significant differential as determined by a t-test and as represented by a t statistic outside −

3.09 to 3.09 identifies the presence of genetically altered DNA in the tumor.

16. The method of claim 15, wherein calculating the differential includes the step of calculating a normalized sequence tag density of the specified DNA chromosome portion and a normalized sequence tag density of another DNA chromosome portion in said mixed sample, wherein all autosomes are used to calculate the normalized sequence tag density.

18. The method of claim 15, wherein the step of aligning sequence tags to corresponding chromosome portions allows one nucleotide mismatch.

19. The method of claim 15, wherein the sequence tags are about 25-100 bp in length.

20. The method of claim 15, wherein at least about 1 million sequence tags are obtained.

21. The method of claim 15, further comprising the step of calculating a normalized sequence tag density of the specified DNA chromosome portion and a normalized sequence tag density of another DNA chromosome portion in said sample.

22. The method of claim 15, wherein the calculating a differential includes the step of calculating a normalized sequence tag density of the specified DNA chromosome portion and a normalized sequence tag density of another DNA chromosome portion in said mixed sample, wherein all autosomes are used to calculate the normalized sequence tag density.

23. A method of identifying genetically altered DNA in a mixed sample of normal and genetically altered DNA from a tumor obtained from a subject, comprising:

(a) sequencing DNA in said sample by massively parallel sequencing to obtain a number of sequence tags

(b) mapping said sequence tags to specific chromosome portions, each chromosomal portion being comprised in a non-overlapping sliding window of a predetermined length;

(c) counting numbers of sequence tags mapped to each sliding window on at least each autosome;

(d) calculating a mean of said numbers for each autosome and a second mean for at least all autosomes;

(e) calculating a normalized value from all autosomes, using said second mean;

wherein a statistically significant difference as determined by a t-test among normalized values among autosomes indicates the presence of an abnormally distributed autosomal chromosome portion of interest, and wherein said statistically significant difference represented by a t statistic outside −

3.09 to 3.09 identifies the presence of genetically altered DNA in the tumor.

24. The method of claim 23, further comprising the step of calculating a relationship between numbers of sequence tags and GC content associated with sequence tags in a given window and correcting for a higher or lower number of reads resulting from a change in GC content.

25. The method of claim 23, further comprising the step of calculating a normalized value for chromosome X and, if present, Y.

26. The method of claim 23, wherein said mapping includes mapping sequences with one nucleotide mismatch.