Detection of genetic abnormalities

• US 10,167,508 B2
• Filed: 02/29/2012
• Issued: 01/01/2019
• Est. Priority Date: 08/06/2010
• Status: Active Grant

• Current Assignee: Roche Molecular Systems (Roche Holding AG)
• Original Assignee: Ariosa Diagnostics Incorporated (Roche Holding AG)
• Inventors: Song, Ken, Oliphant, Arnold, Stuelpnagel, John, Sparks, Andrew
• Primary Examiner(s): Dauner, Joseph G.
• Application Number:
  US13/407,978
• Publication Number:
  US 20120164646A1
• Time in Patent Office: 2,498 Days
• Field of Search: None
• 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: C12Q 2600/158 Expression markers

Abstract

The present invention provides assay systems and related methods for determining genetic abnormalities in mixed samples comprising cell free DNA from both normal and putative genetically atypical cells. Exemplary mixed samples for analysis using the assay systems of the invention include samples comprising both maternal and fetal cell free DNA and samples that contain DNA from normal cells and circulating cancerous cells.

Claims

1. A method for simultaneous detection of a presence or absence of a fetal aneuploidy and a carrier status of a maternal allele in a maternal plasma or serum sample, comprising the steps of:

(a) in a maternal plasma or serum sample comprising maternal and fetal DNA, amplifying two or more selected nucleic acid regions from a first chromosome of interest in the maternal and fetal DNA in the maternal plasma or serum sample with primers complementary to the selected nucleic acid regions from the first chromosome to produce amplified selected maternal and fetal nucleic acid regions in the maternal plasma or serum sample, wherein the amplifying comprises 30 or fewer amplification cycles and the amplified selected maternal and fetal nucleic acid regions from the first chromosome comprise a universal primer binding sequence;

(b) amplifying two or more selected nucleic acid regions from a second chromosome of interest in the maternal and fetal DNA of the maternal plasma or serum sample with primers complementary to the selected nucleic acid regions from the second chromosome to produce amplified selected maternal and fetal nucleic acid regions in the maternal plasma or serum sample, wherein the amplifying comprises 30 or fewer amplification cycles and the amplified selected maternal and fetal nucleic acid regions from the second chromosome comprise a universal primer binding sequence;

(c) amplifying one or more selected nucleic acid regions comprising an allele of interest in the maternal and fetal DNA in the maternal plasma or serum sample with primers complementary to the selected nucleic acid regions comprising the allele of interest to produce amplified selected maternal and fetal nucleic acid regions in the maternal plasma or serum sample, wherein the amplifying comprises 30 or fewer amplification cycles the amplified selected maternal and fetal nucleic acid regions comprising the allele of interest comprise a universal primer binding sequence;

(d) performing universal amplification with universal primers complementary to the universal primer binding sequences, wherein the universal amplification comprises at least 5 cycles, and the amplification steps of (a), (b) and (c) comprise a lower number of amplification cycles than the universal amplification;

(e) detecting the selected maternal and fetal nucleic acid regions from the first and second chromosomes and allele of interest which were amplified with the universal primers in a single sequencing run, wherein detecting the maternal and fetal nucleic acid sequences of the first and second chromosomes is not reliant on detection of any polymorphism within the selected nucleic acid regions from the first and second chromosomes;

(f) quantifying a combined relative frequency for each of the amplified selected maternal and fetal nucleic acid regions from the first and second chromosomes of interest;

(g) comparing the combined relative frequencies of the amplified selected maternal and fetal nucleic acid regions from the first and second chromosomes of interest;

(h) identifying the presence or absence of a statistical variation in the compared combined relative frequencies of the amplified selected maternal and fetal nucleic acid regions of the first chromosome and the combined relative frequencies of the amplified selected maternal and fetal nucleic acid regions of the second chromosome, and identifying the presence of a fetal aneuploidy when the statistical variation is present and identifying the absence of a fetal aneuploidy when a statistical variation is absent; and

(i) determining if the amplified selected maternal and fetal nucleic acid regions from the alleles of interest are detected in a frequency indicative of maternal carrier status of the allele.

2. The method of claim 1, wherein the combined relative frequencies of the amplified selected maternal and fetal nucleic acid regions from each of the first and second chromosomes and the allele of interest are individually quantified, and the combined relative frequencies of the individual amplified selected maternal and fetal nucleic acid regions from the first and second chromosomes are compared.

3. The method of claim 1, wherein the amplified selected maternal and fetal nucleic acid regions from the first and second chromosomes and allele of interest are normalized following detection and prior to quantification.

4. The method of claim 1, wherein the amplified selected maternal and fetal nucleic acid regions from the first and second chromosomes and allele of interest are associated with one or more identifying indices.

5. The method of claim 4, wherein the combined relative frequencies of the amplified selected maternal and fetal nucleic acid regions from the first and second chromosomes and allele of interest are determined through identification of the associated one or more identifying indices.

6. The method of claim 1, wherein the amplified selected maternal and fetal nucleic acid regions from the first and second chromosomes and allele of interest are quantified by counting each nucleic acid region an average of at least 500 times.

7. The method of claim 1, wherein the method is performed with maternal plasma.

8. The method of claim 1, wherein the number of amplification cycle using the universal primers is 20 cycles or more.

9. The method of claim 1, wherein the number of amplification cycle using the primers complementary to the selected nucleic acid regions is 5-30.

15. The method of claim 1, wherein the method is performed with maternal plasma.

24. The method of claim 1, wherein the method is performed with maternal plasma.

10. A method for simultaneous detection of a presence or absence of a fetal aneuploidy and a maternal genetic alteration in a locus associated with a heritable disease in a maternal plasma or serum sample comprising the steps of:

(a) in a maternal plasma or serum sample comprising maternal and fetal DNA, amplifying two or more selected nucleic acid regions from a first chromosome of interest in the maternal and fetal DNA in the maternal plasma or serum sample with primers complementary to the selected nucleic acid regions from the first chromosome to produce amplified selected maternal and fetal nucleic acid regions in the maternal plasma or serum sample, wherein the amplifying comprises 30 or fewer amplification cycles, and the amplified selected maternal and fetal nucleic acid regions from the first chromosome comprise a universal primer binding sequence;

(b) amplifying two or more selected nucleic acid regions from a second chromosome of interest in the maternal and fetal DNA in the maternal plasma or serum sample with primers complementary to the selected nucleic acid regions from the second chromosome to produce amplified selected maternal and fetal nucleic acid regions in the maternal plasma or serum sample, wherein the amplifying comprises 30 or fewer amplification cycles and the amplified selected maternal and fetal nucleic acid regions from the second chromosome comprise a universal primer binding sequence;

(c) amplifying one or more selected nucleic acid regions comprising all or part of a locus associated with a heritable disease in the maternal and fetal DNA with primers complementary to the selected nucleic acid regions comprising the allele of interest to produce amplified selected maternal and fetal nucleic acid regions in the maternal plasma or serum sample, wherein the amplifying comprises 30 or fewer amplification cycles and the amplified selected maternal and fetal nucleic acid regions comprising the allele of interest comprise a universal primer binding sequence;

(d) performing universal amplification with universal primers complementary to the universal primer binding sequences, wherein the universal amplification comprises at least 5 cycles, and the amplification steps of (a), (b) and (c) comprise a lower number of amplification cycles than the universal amplification;

(e) detecting the selected maternal and fetal nucleic acid regions from the first and second chromosomes and the locus associated with a heritable trait which were amplified with the universal primers by counting each nucleic acid region an average of at least 100 times in a single sequencing run, wherein detecting the amplified selected maternal and fetal nucleic acid sequences from the first and second chromosomes is not reliant on detection of any polymorphism within the selected nucleic acid regions from the first and second chromosomes;

(f) quantifying a combined relative frequency for each of the amplified selected maternal and fetal nucleic acid regions from the first and second chromosomes of interest;

(g) comparing the combined relative frequency of the amplified selected maternal and fetal nucleic acid regions from the first and second chromosomes of interest;

(h) identifying the presence or absence of a statistical variation in the compared combined relative frequencies of the amplified selected maternal and fetal nucleic acid regions of the first chromosome and the combined relative frequencies of the amplified selected maternal and fetal nucleic acid regions of the second chromosome indicative of the presence or absence of fetal aneuploidy, and identifying the presence of a fetal aneuploidy when the statistical variation is present and identifying the absence of a fetal aneuploidy when a statistical variation is absent; and

(i) determining if the amplified selected maternal and fetal nucleic acid regions corresponding to a heritable disease are detected and identifying a presence of the heritable disease in the one or more amplified selected maternal and fetal nucleic acid region comprising all or part of a locus associated with a heritable disease when the amplified selected maternal and fetal nucleic acid regions corresponding to the heritable disease are detected and identifying the absence of the heritable disease in the one or more amplified selected maternal and fetal nucleic acid region comprising all or part of a locus associated with a heritable disease when the amplified selected maternal and fetal nucleic acid regions corresponding to the heritable disease are not detected.

11. The method of claim 10, wherein the amplified selected maternal and fetal nucleic acid regions from the first and second chromosomes and the locus associated with a heritable trait are normalized following detection and prior to quantification.

12. The method of claim 10, wherein the amplified selected maternal and fetal nucleic acid regions from the first and second chromosomes and the locus associated with a heritable trait are associated with one or more identifying indices.

13. The method of claim 12, wherein the combined relative frequency of the amplified selected maternal and fetal nucleic acid regions from the first and second chromosomes and the locus associated with a heritable trait are determined through identification of the associated one or more identifying indices.

14. The method of claim 10, wherein the amplified selected maternal and fetal nucleic acid regions from the first and second chromosomes and the locus associated with a heritable trait are quantified by counting each nucleic acid region an average of at least 500 times.

16. The method of claim 10, wherein the number of amplification cycle using the universal primers is 20 cycles or more.

17. The method of claim 10, wherein the number of amplification cycle using the primers complementary to the selected nucleic acid regions is 5-30.

18. A method for simultaneous detection of a presence or absence of a fetal aneuploidy and a fetal carrier status in a maternal plasma or serum sample, comprising the steps of:

(a) in a maternal plasma or serum sample comprising maternal and fetal DNA, amplifying two or more selected nucleic acid regions from a first chromosome of interest in the maternal and fetal DNA in the maternal plasma or serum sample with primers complementary to the selected nucleic acid regions from the first chromosome to produce amplified selected maternal and fetal nucleic acid regions that in the maternal plasma or serum sample, wherein the amplifying comprises 30 or fewer amplification cycles and the amplified selected maternal and fetal nucleic acid regions from the first chromosome comprise a universal primer binding sequence;

(b) amplifying two or more selected nucleic acid regions from a second chromosome of interest in the maternal and fetal DNA in the maternal plasma or serum sample with primers complementary to the selected nucleic acid regions from the second chromosome to produce amplified selected maternal and fetal nucleic acid regions in the maternal plasma or serum sample, wherein the amplifying comprises 30 or fewer amplification cycles and the amplified selected maternal and fetal nucleic acid regions from the second chromosome comprise a universal primer binding sequence;

(c) amplifying one or more selected nucleic acid regions comprising an allele of interest in the maternal and fetal DNA in the maternal plasma or serum sample with primers complementary to the selected nucleic acid regions comprising the allele of interest to produce amplified selected maternal and fetal nucleic acid regions in the maternal plasma or serum sample, wherein the amplifying comprises 30 or fewer amplification cycles and the amplified selected maternal and fetal nucleic acid regions comprising the allele of interest comprise a universal primer binding sequence;

(d) performing universal amplification with universal primers complementary to the universal primer binding sequences, wherein the universal amplification comprises at least 5 cycles, and the amplification steps of (a), (b) and (c) comprise a lower number of amplification cycles than the universal amplification;

(e) detecting the selected maternal and fetal nucleic acid regions from the first and second chromosomes and allele of interest which were amplified with the universal primers by counting each nucleic acid region an average of at least 100 times in a single sequencing run, wherein detecting the amplified selected maternal and fetal nucleic acid sequences from the first and second chromosomes is not reliant on detection of any polymorphism within the selected nucleic acid regions from the first and second chromosomes;

(f) quantifying a combined relative frequency of the amplified selected maternal and fetal nucleic acid regions from the first and second chromosomes of interest;

(g) comparing the combined relative frequencies of the amplified selected maternal and fetal nucleic acid regions from the first and second chromosomes of interest;

(h) identifying the presence or absence of a statistical variation in the compared combined relative frequencies of the amplified selected maternal and fetal nucleic acid regions of the first chromosome and the combined relative frequencies of the amplified selected maternal and fetal nucleic acid regions of the second chromosome indicative of the presence or absence of a fetal aneuploidy, and identifying the presence of a fetal aneuploidy when the statistical variation is present and identifying the absence of a fetal aneuploidy when a statistical variation is absent;

(i) determining if the amplified selected maternal and fetal nucleic acid regions from the allele of interest are detected in a frequency indicative of fetal inheritance of the allele.

19. The method of claim 18, wherein the combined relative frequencies of the amplified selected maternal and fetal nucleic acid regions from each of the first and second chromosomes and the allele of interest are individually quantified, and the combined relative frequencies of the individual amplified selected maternal and fetal nucleic acid regions from the first and second chromosomes are compared.

20. The method of claim 18, wherein the amplified selected maternal and fetal nucleic acid regions from the first and second chromosomes and allele of interest are normalized following detection and prior to quantification.

21. The method of claim 18, wherein the amplified selected maternal and fetal nucleic acid regions from the first and second chromosomes and allele of interest are associated with one or more identifying indices.

22. The method of claim 21, wherein the combined relative frequencies of the amplified selected maternal and fetal nucleic acid regions from the first and second chromosomes and allele of interest are determined through identification of the associated one or more identifying indices.

23. The method of claim 18, wherein the amplified selected maternal and fetal nucleic acid regions from the first and second chromosomes and allele of interest are quantified by counting each nucleic acid region an average of at least 500 times.

25. The method of claim 18, wherein the allele of interest is putatively associated with a Robertsonian translocation.

26. The method of claim 18, wherein the locus is putatively associated with a Robertsonian translocation.

27. The method of claim 18, wherein the allele of interest is putatively associated with a Robertsonian translocation.

28. The method of claim 18, wherein the number of amplification cycle using the universal primers is 20 cycles or more.

29. The method of claim 18, wherein the number of amplification cycle using the primers complementary to the selected nucleic acid regions is 5-30.