Assay systems for genetic analysis

• US 10,131,937 B2
• Filed: 11/10/2011
• Issued: 11/20/2018
• Est. Priority Date: 08/06/2010
• Status: Active Grant

• Current Assignee: Roche Molecular Systems Inc (Roche Holding AG)
• Original Assignee: Ariosa Diagnostics Incorporated (Roche Holding AG)
• Inventors: Sparks, Andrew, Oliphant, Arnold, Zahn, Jacob, Song, Ken, Stuelpnagel, John
• Primary Examiner(s): Dauner, Joseph G.
• Application Number:
  US13/293,419
• Publication Number:
  US 20130004950A1
• Time in Patent Office: 2,567 Days
• Field of Search: None
• CPC Class Codes: C12Q 1/6809 Methods for determination or identification of nucleic acids involving differential detection
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6862 Ligase chain reaction [LCR]
• CPC Class Codes: C12Q 2525/155 incorporating/generating a new priming site
• CPC Class Codes: C12Q 2525/161 incorporating target specific and non-target specific sites
• CPC Class Codes: C12Q 2533/107 Probe or oligonucleotide ligation
• CPC Class Codes: C12Q 2535/131 Allele specific probes
• CPC Class Codes: C12Q 2565/514 characterised by the use of the arrayed oligonucleotides as identifier tags, e.g. universal addressable array, anti-tag or tag complement array
• CPC Class Codes: C12Q 2565/543 characterised by the use of two or more capture oligonucleotide primers in concert, e.g. bridge amplification

Abstract

The present invention provides assays systems and methods for detection of chromosomal abnormalities and status of single loci associated with monogenic or polygenic traits in a sample containing nucleic acids from a maternal and a fetal source.

Claims

1. A method for detecting a fetal copy number variation in a maternal plasma or serum sample comprising fetal and maternal cell-free DNA, the method comprising:

(a) obtaining the maternal plasma or serum sample comprising fetal and maternal cell-free DNA;

(b) hybridizing (i) a first set of at least 24 and less than 2000 pairs of fixed sequence oligonucleotides with (ii) the fetal and maternal cell-free DNA in the maternal plasma or serum sample, wherein the percent fetal DNA is less than 25% of the sample, wherein the oligonucleotides of each pair are complementary to regions flanking a non-polymorphic locus within a first chromosome or a portion of the first chromosome, and wherein the melting temperatures (T_ms) of first fixed sequence oligonucleotides of each of the pairs of the first set vary in a range of two degrees centigrade;

(c) hybridizing (i) a second set of at least 24 and less than 2000 pairs of fixed sequence oligonucleotides with (ii) the fetal and maternal cell-free DNA in the maternal plasma or serum sample, wherein the percent fetal DNA is less than 25% of the sample, wherein the oligonucleotides of each pair are complementary to regions flanking a non-polymorphic locus within a second chromosome or a portion of the second chromosome and wherein the T_ms of first fixed sequence oligonucleotides of each of the pairs of the second set vary in a range of two degrees centigrade;

(d) extending the regions between the hybridized oligonucleotides of the first and second sets of fixed sequence oligonucleotide pairs with a polymerase and dNTPs to create hybridized adjacent extended oligonucleotides spanning the non-polymorphic loci in the first and second nucleic acid regions of interest;

(e) ligating the hybridized adjacent extended oligonucleotides to produce ligation products;

(f) amplifying the ligation products to produce amplification products, wherein an average number of amplification products per locus is greater than 100;

(g) detecting the amplification products at least an average of 100 times to count the relative frequency of each non-polymorphic locus within the first and second nucleic acid regions of interest; and

(h) detecting a fetal copy number variation of the first nucleic acid region of interest in the maternal serum or plasma sample relative to the second nucleic acid region of interest.

2. The method of claim 1, wherein the fetal copy number variation is a fetal chromosomal aneuploidy.

3. The method of claim 1, wherein the fixed sequence oligonucleotides of the first and second sets comprise universal primer regions.

4. The method of claim 3, wherein the universal primer regions are used in sequence determination of the amplification products.

5. The method of claim 3, wherein the fixed sequence oligonucleotides of each set comprises at least one universal primer region, wherein the at least one universal primer region of the first set of fixed sequence oligonucleotides differs from the at least one universal primer region of the second set of fixed sequence oligonucleotides.

6. The method of claim 1, wherein one or both of the fixed sequence oligonucleotides in each pair comprises at least one index.

7. The method of claim 6, wherein the amplification products are detected by sequencing the at least one index.

8. The method of claim 6, wherein the at least one index comprises a locus index.

9. The method of claim 6, wherein the at least one index comprises both a sample index and a locus index, and wherein the sample index and the locus index are on different fixed sequence oligonucleotides in a pair.

10. The method of claim 1, wherein step (g) is performed by high throughput sequencing.

11. The method of claim 1, wherein the amplification products are detected on an array.

12. A method for detecting a fetal chromosomal aneuploidy of a first chromosome in a maternal plasma or serum sample comprising fetal and maternal cell-free DNA, the method comprising:

(a) obtaining the maternal plasma or serum sample comprising fetal and maternal cell-free DNA;

(b) hybridizing (i) a first set of at least 24 and less than 2000 pairs of fixed sequence oligonucleotides with (ii) the fetal and maternal cell-free DNA in the maternal plasma or serum sample, wherein the percent fetal DNA is less than 25% of the sample, wherein the oligonucleotides of each pair are complementary to regions flanking a non-polymorphic locus within a first chromosome or a portion of the first chromosome, and wherein the melting temperatures (T_ms) of first fixed sequence oligonucleotides of each of the pairs of the first set vary in a range of two degrees centigrade;

(c) hybridizing (i) a second set of at least 24 and less than 2000 pairs of fixed sequence oligonucleotides with (ii) the fetal and maternal cell-free DNA in the maternal plasma or serum sample, wherein the percent fetal DNA is less than 25% of the sample, wherein the oligonucleotides of each pair are complementary to regions flanking a non-polymorphic locus within a second chromosome or a portion of the second chromosome and wherein the T_ms of first fixed sequence oligonucleotides of each of the pairs of the second set vary in a range of two degrees centigrade;

(d) extending the regions between the hybridized oligonucleotides of the first and second sets of fixed sequence oligonucleotide pairs with a polymerase and dNTPs to create hybridized adjacent extended oligonucleotides spanning the non-polymorphic loci in the first and second chromosomes of interest;

(e) ligating the hybridized adjacent extended oligonucleotides to produce ligation products;

(f) amplifying the ligation products to produce amplification products, wherein an average number of amplification products per locus is greater than 100;

(g) detecting the amplification products at least an average of 100 times to count the relative frequency of each non-polymorphic locus within the first and second chromosomes of interest; and

(h) detecting a fetal chromosomal aneuploidy of the first chromosome in the maternal serum or plasma sample if the relative frequencies of the first and second chromosome of interest vary statistically.

13. The method of claim 12, wherein the fixed sequence oligonucleotides of the first and second sets comprise universal primer regions.

14. The method of claim 13, wherein the universal primer regions are used in sequence determination of the amplification products.

15. The method of claim 12, wherein one or both of the fixed sequence oligonucleotides in each pair comprises at least one index.

16. The method of claim 15, wherein the amplification ligation products are detected by sequencing the at least one index.

17. The method of claim 15, wherein the at least one index comprises a locus index.

18. The method of claim 15, wherein the at least one index comprises a sample index.

19. The method of claim 15, wherein the at least one index comprises both a sample index and a locus index, and wherein the sample index and the locus index are present on the same fixed oligonucleotide in a set.

20. The method of claim 15, wherein the at least one index comprises both a sample index and a locus index, and wherein the sample index and the locus index are on different fixed sequence oligonucleotides within a pair.

21. The method of claim 12, wherein the amplification products are detected on an array.

22. A method for detecting a fetal chromosomal aneuploidy of a first chromosome in a maternal plasma or serum sample comprising fetal and maternal cell-free DNA, the method comprising:

(a) obtaining the maternal plasma or serum sample comprising fetal and maternal cell-free DNA;

(b) hybridizing (i) a first set of at least 24 and less than 2000 pairs of fixed sequence oligonucleotides with (ii) the fetal and maternal cell-free DNA in the maternal plasma or serum sample, wherein the percent fetal DNA is less than 25% of the sample, wherein the oligonucleotides of each pair are complementary to regions flanking a non-polymorphic locus within a first chromosome or a portion of the first chromosome, wherein the melting temperatures (T_ms) of first fixed sequence oligonucleotides of each of the pairs of the first set vary in a range of two degrees centigrade, and wherein at least one of the fixed sequence oligonucleotides in each pair of the first set of fixed sequence oligonucleotides comprises a locus index;

(c) hybridizing (i) a second set of at least 24 and less than 2000 pairs of fixed sequence oligonucleotides with (ii) the fetal and maternal cell-free DNA in the maternal plasma or serum sample, wherein the percent fetal DNA is less than 25% of the sample, wherein the oligonucleotides of each pair are complementary to regions flanking a non-polymorphic locus within a second chromosome or a portion of the second chromosome, wherein the T_ms of first fixed sequence oligonucleotides of each of the pairs of the second set vary in a range of two degrees centigrade, and wherein at least one of the fixed sequence oligonucleotides in each pair of the second set of fixed sequence oligonucleotides comprises a locus index;

(d) extending the regions between the hybridized oligonucleotides of the first and second sets of fixed sequence oligonucleotide pairs with a polymerase and dNTPs to create hybridized adjacent extended oligonucleotides spanning the non-polymorphic loci in the first and second chromosomes of interest;

(e) ligating the hybridized adjacent extended oligonucleotides to produce ligation products;

(f) amplifying the ligation products to produce amplification products, wherein an average number of amplification products per locus is greater than 100;

(g) detecting the amplification products at least an average of 100 times to count the relative frequency of each non-polymorphic locus within the first and second chromosomes of interest; and

(h) detecting a fetal chromosomal aneuploidy of the first chromosome in the maternal serum or plasma sample if the relative frequencies of the first and second chromosome of interest vary statistically.

23. The method of claim 22, wherein the amplification products are detected on an array.

24. The method of claim 23, wherein the amplification products are detected on an array via the locus index.