Statistical analysis for non-invasive sex chromosome aneuploidy determination

Abstract

The present invention provides methods for non-invasive determination of X and/or Y chromosomal abnormalities indicative of aneuploidy or sex mosaicisms in a maternal sample by detecting and determining the relative contribution of genetic sequences from the X chromosome and/or the Y chromosome in the maternal sample.

1 - 33 . (canceled) 
     
     
         34 . A process to calculate a risk of 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 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 and ligating the hybridized third set of sequence-specific oligonucleotide probes;   c) amplifying the ligated first 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 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 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.   
     
     
         35 . The process of  claim 34 , wherein the Y chromosomal aneuploidy is a fetal aneuploidy. 
     
     
         36 . The process of  claim 34 , wherein at least ten or more polymorphic loci are interrogated. 
     
     
         37 . The process of  claim 36 , wherein at least ten or more polymorphic loci on at least two autosomes are interrogated. 
     
     
         38 . The process of  claim 37 , 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 two autosomes. 
     
     
         39 . The process of  claim 37 , wherein at least ten or more polymorphic loci on at least three autosomes are interrogated. 
     
     
         40 . The process of  claim 38 , 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. 
     
     
         41 . The process of  claim 34 , wherein at least 24 loci are interrogated on each of the Y chromosome and the at least one autosome. 
     
     
         42 . The process of  claim 41 , wherein at least 32 loci are interrogated on each of the Y chromosome and the at least one autosome. 
     
     
         43 . The process of  claim 42 , wherein each locus is measured at least 100 times. 
     
     
         44 . The method of  claim 34 , wherein at least 96 polymorphic loci are measured to calculate the percent fetal nucleic acid proportion. 
     
     
         45 . The process of  claim 34 , wherein the calculated risk of fetal aneuploidy is adjusted using extrinsic information on prior risk. 
     
     
         46 . The process of  claim 34 , wherein a risk of Y chromosome aneuploidy is calculated utilizing YFF. 
     
     
         47 . The process of  claim 34 , 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 is performed by bootstrap sampling. 
     
     
         48 . The process of  claim 34 , wherein the calculating a risk step is performed using a log 10 odds ratio. 
     
     
         49 . A process to calculate a risk of an Y 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 Y 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 Y 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 Y 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 Y 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 Y chromosome, a second mathematic model assuming two copies of the Y chromosome, and a third mathematic model assuming three copies of the Y chromosome.   
     
     
         50 . The process of  claim 49 , wherein the Y chromosomal aneuploidy is a fetal aneuploidy. 
     
     
         51 . The process of  claim 50 , further comprising determining whether the fetal nucleic acid proportion in the maternal blood, serum or plasma sample is adequate to reliably perform analysis. 
     
     
         52 . The process of  claim 49 , wherein at least ten or more polymorphic loci are interrogated. 
     
     
         53 . The process of  claim 49 , wherein at least ten or more polymorphic loci on at least two autosomes are interrogated. 
     
     
         54 . The process of  claim 49 , 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. 
     
     
         55 . The process of  claim 49 , wherein at least ten or more polymorphic loci on at least three autosomes are interrogated. 
     
     
         56 . The process of  claim 55 , 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. 
     
     
         57 . The process of  claim 49 , wherein at least 24 loci are interrogated on the Y chromosome. 
     
     
         58 . The process of  claim 49 , wherein at least 32 loci are interrogated on each of the Y chromosome and the at least one autosome. 
     
     
         59 . The process of  claim 49 , wherein each locus is measured at least 20 times. 
     
     
         60 . The method of  claim 52 , wherein at least 96 polymorphic loci are measured to calculate the fetal nucleic acid proportion. 
     
     
         61 . The process of  claim 49 , wherein the calculated risk of fetal aneuploidy is adjusted using extrinsic information on prior risk. 
     
     
         62 . The process of  claim 49 , wherein a risk of Y chromosome aneuploidy is calculated utilizing YFF. 
     
     
         63 . The process of  claim 62 , 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.