Nucleic acid-based tests for prenatal gender determination

• US 8,709,726 B2
• Filed: 03/10/2009
• Issued: 04/29/2014
• Est. Priority Date: 03/11/2008
• Status: Expired due to Fees

• Current Assignee: Sequenom Incorporated (Laboratory Corporation Of America Holdings)
• Original Assignee: Sequenom Incorporated (Laboratory Corporation Of America Holdings)
• Inventors: Oeth, Paul Andrew, Mahboubi, Payam, Lee, Min Seob
• Primary Examiner(s): Benzion, Gary
• Assistant Examiner(s): THOMAS, DAVID C
• Application Number:
  US12/401,493
• Publication Number:
  US 20090317817A1
• Time in Patent Office: 1,876 Days
• Field of Search: None
• US Class Current: 435/6.12
• CPC Class Codes: C12Q 1/6879 for sex determination
• CPC Class Codes: C12Q 2600/16 Primer sets for multiplex assays

Abstract

Provided herein are compositions, processes and kits for noninvasive, early determination of fetal sex from, and/or amount of fetal nucleic acid in, an extracellular nucleic acid sample from a pregnant female. Such compositions, processes and kits are useful for detection of low genomic copy numbers of male fetal nucleic acid in a high copy number background of female nucleic acid, thereby determining the sex of a fetus and/or amount of fetal nucleic acid in a sample.

Claims

1. A method for identifying the presence or absence of Y-chromosome nucleic acid in extracellular nucleic acid from a pregnant female, which comprises:

(a) contacting under amplification conditions extracellular nucleic acid from a pregnant female with three or more primer sets selected from the group consisting of;

2. The method of claim 1, wherein the extracellular nucleic acid is deoxyribonucleic acid (DNA).

3. The method of claim 1, wherein the extracellular nucleic acid is ribonucleic acid (RNA).

4. The method of claim 1, wherein the extracellular nucleic acid is contacted with one or more first primer and corresponding second primer selected from the group consisting of:

5. The method of claim 1, wherein detecting the presence or absence of the amplification products comprises contacting under extension conditions amplification products with an extension oligonucleotide selected from the group consisting of:

6. The method of claim 4, wherein detecting the presence or absence of the amplification products comprises contacting under extension conditions amplification products with an extension oligonucleotide selected from the group consisting of:

7. The method of claim 5, wherein the extended extension oligonucleotides are detected by mass spectrometry.

8. The method of claim 6, wherein the extended extension oligonucleotides are detected by mass spectrometry.

9. The method of claim 1, wherein the extracellular nucleic acid is from blood serum.

10. The method of claim 1, wherein the extracellular nucleic acid is from blood plasma.

11. The method of claim 1, which further comprises determining the sex of the fetus based on the presence or absence of Y-chromosome nucleic acid, whereby the presence of Y-chromosome nucleic acid determines the fetus is male.

12. The method of claim 1, wherein the first primers or second corresponding primers or the first primers and second corresponding primers include universal tag sequences.

13. The method claim 1, wherein the extracellular nucleic acid is contacted with four or more of the primer sets.

14. The method claim 1, wherein the extracellular nucleic acid is contacted with five or more of the primer sets.

15. The method claim 1, wherein the extracellular nucleic acid is contacted with six or more of the primer sets.

16. The method claim 1, wherein the extracellular nucleic acid is contacted with seven or more of the primer sets.

17. The method claim 1, wherein the extracellular nucleic acid is contacted with eight of the primer sets.

18. The method of claim 17, which further comprises contacting the extracellular nucleic acid with a control primer set under amplification conditions and detecting the presence or absence of a control amplification product from the control primer set, wherein the control primers of the control primer set can hybridize to the maternal nucleic acid.

19. The method of claim 18, wherein the control primers of the control primer set hybridize to a nucleotide sequence that encodes or controls the expression of an albumin protein.

20. The method of claim 19, wherein the control primer set comprises the following control primers:

21. The method of claim 18, wherein detecting the presence or absence of the control amplification product comprises contacting under extension conditions each control amplification product with a control extension oligonucleotide and detecting extended control extension oligonucleotide.

22. The method of claim 21, wherein the control extension oligonucleotide has the nucleotide sequence GCAGTGTCCATTTGAAGAT (SEQ ID NO:

71).

23. A kit that comprises three or more primer sets selected from the group consisting of:

24. The kit of claim 23, comprising eight of the primer sets.

27. The kit of claim 23, wherein the 5′

tag sequence comprises a universal primer sequence.

25. A method for determining the amount of fetal nucleic acid in a sample of extracellular nucleic acid from a pregnant female, which comprises:

(a) contacting under amplification conditions extracellular nucleic acid from a pregnant female with three or more primer sets selected from the group consisting of;

26. The method of claim 25, wherein detecting the amount of the amplification products comprises contacting under extension conditions amplification products with an extension oligonucleotide selected from the group consisting of: