Statistical analysis for non-invasive sex chromosome aneuploidy determination

1. A process to calculate a risk of X or Y chromosomal aneuploidy in a maternal blood, serum or plasma sample from a pregnant female comprising fetal and maternal nucleic acids, comprising the steps of:

a) interrogating one or more Y chromosomal loci by hybridizing a first set of two or more sequence-specific oligonucleotide probes to twelve or more non-polymorphic loci, interrogating one or more X chromosomal loci by hybridizing a second set of two or more sequence-specific oligonucleotide probes to twelve or more non-polymorphic loci, and interrogating one or more loci on at least a first autosome by hybridizing a third set of two or more sequence-specific oligonucleotide probes to twelve or more non-polymorphic loci;

b) ligating the hybridized first set of sequence-specific oligonucleotide probes, ligating the hybridized second set of sequence-specific oligonucleotide probes, and ligating the hybridized third set of sequence-specific oligonucleotide probes;

c) amplifying the ligated first set of sequence-specific oligonucleotide probes, amplifying the ligated second set of sequence-specific oligonucleotide probes, and amplifying the ligated third set of sequence-specific oligonucleotide probes;

d) generating, by a computer processor and based on the interrogating of the one or more Y chromosomal loci, the interrogating of the one or more X chromosomal loci, and the interrogating of the one or more loci on at least the first autosome, an estimation of a chromosome frequency for a Y chromosome, an X chromosome and the first autosome;

e) calculating a fetal nucleic acid proportion in the maternal blood, serum or plasma sample by analyzing a frequency of polymorphisms on at least one autosome;

f) calculating, by the computer processor, values of likelihood that the Y chromosome is present in no copies, one copy or two or more copies in the maternal blood, serum or plasma sample using the calculated fetal nucleic acid proportion;

g) generating, by the computer processor, a calculated risk of aneuploidy of the Y chromosome in the maternal blood, serum or plasma sample by comparing the values of likelihood to a first mathematic model assuming no copies of the Y chromosome, a second mathematic model assuming one copy of the Y chromosome, and a third mathematic model assuming two or more copies of the Y chromosome;

h) calculating, by the computer processor, values of likelihood that the X chromosome is present in one copy, two copies or three or more copies in the maternal blood, serum or plasma sample using the calculated fetal nucleic acid proportion; and

i) generating, by the computer processor, a calculated risk of aneuploidy of the X chromosome in the maternal blood, serum or plasma sample by comparing the values of likelihood to a first mathematic model assuming one copy of the X chromosome, a second mathematic model assuming two copies of the X chromosome, and a third mathematic model assuming three or more copies of the X chromosome.

2. The process of claim 1 , wherein the X or Y chromosomal aneuploidy is a fetal aneuploidy.

3. The process of claim 1 , wherein at least ten or more polymorphic loci are interrogated.

4. The process of claim 3 , wherein at ten or more polymorphic loci on at least two autosomes are interrogated.

5. The process of claim 4 , wherein a fetal nucleic acid proportion in the maternal blood, serum or plasma sample is calculated by analyzing the frequency of polymorphisms from at least two autosomes.

6. The process of claim 4 , wherein at least ten or more polymorphic loci on at least three autosomes are interrogated.

7. The process of claim 6 , wherein the fetal nucleic acid proportion in the maternal blood, serum or plasma sample is calculated by analyzing the frequency of polymorphisms from at least three autosomes.

8. The process of claim 1 , wherein at least 24 loci are interrogated on each of the X chromosome, the Y chromosome and the at least one autosome.

9. The process of claim 8 , wherein at least 32 loci are interrogated on each of the X chromosome, the Y chromosome and the at least one autosome.

10. The process of claim 9 , wherein each locus is measured at least 100 times.

11. The method of claim 1 , wherein at least 96 polymorphic loci are measured to calculate the percent fetal nucleic acid proportion.

12. The process of claim 2 , wherein the calculated risk of fetal aneuploidy is adjusted using extrinsic information on prior risk.

13. The process of claim 2 , wherein a risk of X chromosome aneuploidy is calculated utilizing XFF.

14. The process of claim 2 , wherein a risk of Y chromosome aneuploidy is calculated utilizing YFF.

15. The process of claim 1 , wherein calculating the values of likelihood that the Y chromosome is present in no copies, one copy or two or more copies in the maternal blood, serum or plasma sample and calculating values of likelihood that the X chromosome is present in one copy, two copies or three or more copies in the maternal blood, serum or plasma sample is performed by bootstrap sampling.

16. The process of claim 1 , wherein the calculating a risk step is performed using a log 10 odds ratio.

17. A process to calculate a risk of an X chromosomal aneuploidy in a maternal blood, serum or plasma sample comprising fetal and maternal nucleic acids, wherein the process steps are performed on a computer, comprising the steps of:

a) interrogating one or more X chromosomal loci by hybridizing a first set of two or more sequence-specific oligonucleotide probes to twelve or more non-polymorphic loci;

b) interrogating one or more polymorphic loci on at least a first autosome by hybridizing a second set of two or more sequence-specific oligonucleotide probes to twelve or more non-polymorphic loci;

c) ligating the hybridized first set of sequence-specific oligonucleotide probes and ligating the hybridized second set of sequence-specific oligonucleotide probes;

d) amplifying the ligated first set of sequence-specific oligonucleotide probes and amplifying the ligated second set of sequence-specific oligonucleotide probes;

e) estimating a chromosome frequency for an X chromosome and the first autosome;

f) calculating a fetal nucleic acid proportion in the maternal blood, serum or plasma sample by analyzing a frequency of polymorphic loci on at least one autosome;

g) calculating values of likelihood that the X chromosome is present in one copy, two copies or more than two copies in the maternal blood, serum or plasma sample using the calculated fetal nucleic acid proportion; and

h) calculating a risk of aneuploidy of the X chromosome in the maternal blood, serum or plasma sample by comparing the values of likelihood to a first mathematic model assuming one copy of the X chromosome, a second mathematic model assuming two copies of the X chromosome, and a third mathematic model assuming three copies of the X chromosome.

18. The process of claim 17 , wherein the X chromosomal aneuploidy is a fetal aneuploidy.

19. The process of claim 18 , further comprising determining whether the fetal nucleic acid proportion in the maternal blood, serum or plasma sample is adequate to reliably perform analysis.

20. The process of claim 17 , wherein at least ten or more polymorphic loci are interrogated.

21. The process of claim 20 , wherein at least ten or more polymorphic loci on at least two autosomes are interrogated.

22. The process of claim 21 , wherein a fetal nucleic acid proportion in the maternal blood, serum or plasma sample is calculated by analyzing the frequency of polymorphic loci from at least two autosomes.

23. The process of claim 22 , wherein at least ten or more polymorphic loci on at least three autosomes are interrogated.

24. The process of claim 23 , wherein the fetal nucleic acid proportion in the maternal blood, serum or plasma sample is calculated by analyzing the frequency of polymorphisms from at least three autosomes.

25. The process of claim 17 , wherein at least 24 loci are interrogated on the X chromosome.

26. The process of claim 25 , wherein at least 32 loci are interrogated on each of the X chromosome and the at least one autosome.

27. The process of claim 25 , wherein each locus is measured at least 20 times.

28. The method of claim 17 , wherein at least 96 polymorphic loci are measured to calculate the fetal nucleic acid proportion.

29. The process of claim 18 , wherein the calculated risk of fetal aneuploidy is adjusted using extrinsic information on prior risk.

30. The process of claim 18 , wherein a risk of X chromosome aneuploidy is calculated utilizing XFF.

31. The process of claim 14 , wherein the YFF calculation comprises a YFF value that is used to determine the presence of more than two copies of the Y chromosome in the fetal nucleic acid.

32. The process of claim 18 , wherein the fetus does not have a Y chromosome when the YFF value is less than zero.