Non-invasive fetal sex determination

• US 9,994,897 B2
• Filed: 03/08/2013
• Issued: 06/12/2018
• Est. Priority Date: 03/08/2013
• Status: Active Grant

• Current Assignee: Roche Molecular Systems (Roche Holding AG)
• Original Assignee: Ariosa Diagnostics Incorporated (Roche Holding AG)
• Inventors: Struble, Craig, Oliphant, Arnold, Wang, Eric
• Primary Examiner(s): Riggs, II, Larry D
• Application Number:
  US13/790,642
• Publication Number:
  US 20140256572A1
• Time in Patent Office: 1,922 Days
• Field of Search: None
• CPC Class Codes: C12Q 1/6879 for sex determination
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers

Abstract

The present invention provides methods for non-invasive determination of sex in a fetus or of Y chromosomal frequency abnormalities—indicative of aneuploidy or sex mosaicisms in a fetus—by detecting and determining the relative contribution genetic sequences from the Y chromosome in view of the percent fetal contribution in a maternal mixed sample.

Claims

1. A method for measuring a risk for Y chromosomal frequency abnormalities in a fetus comprising the steps of:

(a) annealing sets of two fixed sequence oligonucleotides specific to selected non-polymorphic nucleic acid regions on the Y chromosome and to polymorphic and non-polymorphic selected nucleic acid regions on at least one non-Y chromosome in maternal samples comprising maternal and fetal nucleic acids, wherein a portion of each of the two fixed sequence oligonucleotides is complementary to one of the selected non-polymorphic or polymorphic nucleic acid regions, at least one of the two fixed sequence oligonucleotides specific to the non-polymorphic nucleic acid regions comprises a locus index, at least one of the two fixed sequence oligonucleotides specific to the polymorphic nucleic acid regions comprises an allele index, at least one of the two fixed sequence oligonucleotides per set comprises an amplification universal primer sequence, and wherein the oligonucleotides specific to the polymorphic selected nucleic acid regions on the at least one non-Y chromosome in the maternal and fetal nucleic acids are specific for different alleles in the selected polymorphic nucleic acid region;

(b) annealing bridging oligonucleotides to the selected non-polymorphic and polymorphic nucleic acid regions, wherein the bridging oligonucleotides hybridize between the two fixed sequence oligonucleotides of each set;

(c) ligating the fixed sequence oligonucleotides and bridging oligonucleotides;

(d) selectively amplifying the selected nucleic acid regions from the Y chromosome and the at least one non-Y chromosome to generate amplified selected nucleic acid regions using the universal primer sequence, wherein distinct labels are incorporated into the amplification products, wherein at least eight selected nucleic acid regions from the Y chromosome and the at least one non-Y chromosome are amplified;

(e) hybridizing the amplification products to an array;

(f) measuring a percent of fetal nucleic acids in the maternal samples by quantifying the selected polymorphic nucleic acid regions from the at least one non-Y chromosome by imaging the array and quantifying the labels specific for the different alleles in each selected polymorphic nucleic acid regions, where the maternal nucleic acids are homozygous for one allele and the fetal nucleic acids are heterozygous; and

(g) measuring a probability that the fetus is a normal male fetus and the risk for Y chromosomal frequency abnormalities by (i) quantifying the selected non-polymorphic nucleic acid regions from the Y chromosome by imaging the array and quantifying the labels and (ii) quantifying the selected non-polymorphic nucleic acid regions from the at least one non-Y chromosome by imaging the array and quantifying the labels, wherein the fetus is a normal male fetus if the non-polymorphic nucleic acid regions on the Y chromosome contribute no more than 1/46^th of the percent of fetal nucleic acids in the maternal samples and the fetus is at risk for Y chromosomal frequency abnormalities if the non-polymorphic nucleic acid regions on the Y chromosome contribute 1/23^rd or more of the percent of fetal nucleic acids in the maternal samples.

2. The method of claim 1 wherein at least forty-eight selected nucleic acid regions from the Y chromosome and the at least one non-Y chromosome are amplified.

3. The method of claim 2, wherein at least ninety-six selected nucleic acid regions from the Y chromosome and the at least one non-Y chromosome are amplified.

4. The method of claim 1, wherein the Y chromosomal frequency abnormality arises from a Y chromosome aneuploidy, a Y chromosome mosaicism of the fetus or sample contamination.

5. The method of claim 1, wherein selected nucleic acid regions from at least two non-Y chromosomes are selectively amplified, sequenced and quantified.

6. The method of claim 5, wherein selected nucleic acid regions from at least four non-Y chromosomes are selectively amplified, sequenced and quantified.

7. The method of claim 6 wherein selected nucleic acid regions from at least six non-Y chromosomes are selectively amplified, sequenced and quantified.

8. The method of claim 1, wherein the at least one non-Y chromosome is selected from chromosome 13, 18 or 21.

9. The method of claim 1, wherein at least one of the fixed oligonucleotides comprises at least one sample index.

10. The method of claim 9, wherein before the selective amplification step the maternal samples are in different vessels for the reactions, and after the selective amplification step the maternal samples are pooled.

11. The method of claim 1, wherein at least one of the fixed oligonucleotides further comprises a locus index and a sample index, where the locus index and sample index are located on a same fixed sequence oligonucleotide in a set.

12. The method of claim 1, wherein at least one of the fixed oligonucleotides further comprises a locus index and a sample index, where the locus index and sample index are located on different fixed sequence oligonucleotides in a set.

13. The method of claim 1, wherein at least one of the fixed sequence oligonucleotides interrogating the polymorphic selected nucleic acid regions in the at least one non-Y chromosome comprises an allele index.

14. The method of claim 1, where the DNA is selectively amplified in a single vessel.

15. The method of claim 1, where the selected nucleic acid regions are each counted an average of at least five times.

16. The method of claim 15, where the selected nucleic acid regions are each counted an average of at least 250 times.

25. The method of claim 1, wherein both fixed sequence oligonucleotides comprise a universal primer sequence.

17. A method for measuring the risk of Y chromosomal frequency abnormalities in a fetus comprising the steps of:

(a) obtaining at least five maternal samples comprising maternal and fetal nucleic acids;

(b) placing each of the maternal samples in a separate reaction vessel;

(c) annealing sets of two fixed sequence oligonucleotides specific to selected nucleic acid regions on the Y chromosome and to polymorphic and non-polymorphic selected nucleic acid regions on at least two non-Y chromosomes to the maternal and fetal nucleic acids, wherein at least one of the fixed sequence oligonucleotides comprises a sample index;

(d) selectively amplifying the selected nucleic acid regions from the Y chromosome and the at least two non-Y chromosomes to generate amplified selected nucleic acid regions;

(e) pooling the at least five maternal samples into a single reaction vessel;

(f)sequencing the amplified selected nucleic acid regions;

(g) using software executed on a computer, quantifying the sequenced nucleic acid regions;

(h) using software executed on a computer, determining a frequency of the quantified selected nucleic acid regions from the Y chromosome and the at least two non-Y chromosomes;

(i)(using software executed on a computer, measuring a percent of fetal nucleic acids in the maternal sample by measuring the frequency of the quantified polymorphic selected nucleic acid regions from the at least two non-Y chromosomes; and

(j) using software executed on a computer, measuring the probability that the fetus is a normal male fetus and the risk for Y chromosomal frequency abnormalities in the fetus by (i) quantifying the frequency of the selected nucleic acid regions from the Y chromosome; and

(ii) quantifying the non-polymorphic selected nucleic acid regions from the at least two non-Y chromosomes, wherein the fetus is a normal male fetus if the nucleic acid regions on the Y chromosome contribute no more than 1/46^th of the percent of fetal nucleic acids in the maternal sample and the fetus is at risk for Y chromosomal frequency abnormalities if the nucleic acid regions on the Y chromosome contribute 1/23^rd or more of the percent fetal nucleic acids in the maternal sample.

18. The method of claim 17, wherein at least one of the fixed oligonucleotides comprises at least one additional index.

19. The method of claim 18, wherein the at least one index comprises a locus index.

20. The method of claim 19, wherein the measuring the frequency of the quantified nucleic acid regions from the Y chromosome and the at least two non-Y chromosomes step is performed by hybridization to an array.

21. The method of claim 18, where the locus index and sample index are located on a same fixed sequence oligonucleotide in a set.

22. The method of claim 18, where the locus index and sample index are located on different fixed sequence oligonucleotides in a set.

23. The method of claim 17, wherein at least one of the fixed sequence oligonucleotides interrogating the polymorphic selected nucleic acid regions in the at least two non-Y chromosome comprises an allele index.

24. The method of claim 17, wherein the sets of oligonucleotide primers further comprise a bridging oligonucleotide.