Method and system for estimating whether a female is pregnant based on a blood sample

Abstract

A method for estimating whether a female is pregnant, said method comprising measuring allele presences (D) for a plurality of genetic markers of at least one chromosome, different from the X and Y chromosome, in a sample of cell-free DNA from a potentially pregnant female; each allele presence representing the presence at a genetic marker of at least one of: a reference allele of maternal or foetal origin, and an alternative allele of maternal or foetal origin; based on said measured allele presences, determining a homozygous fraction (F ho ) thereof which is associated with purely homozygous genetic markers; and estimating whether the female is pregnant based on said fraction.

1 . A method for estimating whether a female is pregnant, said method comprising:
 measuring allele presences (D) for a plurality of genetic markers of at least one chromosome, different from the X and Y chromosome, in a sample of cell-free DNA from a potentially pregnant female; each allele presence representing the presence at a genetic marker of at least one of: a reference allele of maternal or foetal origin or an alternative allele of maternal or fetal origin;   determining a homozygous fraction (F ho ) thereof which is associated with purely homozygous genetic markers based on said measured allele presences and   estimating whether the female is pregnant based on said homozygous fraction, wherein the estimating comprises:   estimating that the female is pregnant if the homozygous fraction is below a first predetermined value; and   estimating that the female is not pregnant if the homozygous fraction is above a second predetermined value, wherein the first and second predetermined value may be the same or wherein the second predetermined value may be larger than the first predetermined value.   
     
     
         2 . The method of  claim 1 , wherein the determining of the homozygous fraction comprises:
 calculating a corresponding number of allele frequencies for said plurality of genetic markers based on said measured allele presences for the plurality of genetic markers; and   determining as the homozygous fraction the fraction of said measured allele presences for which the allele frequency is 0 or 1 within a predetermined error margin.   
     
     
         3 . (canceled) 
     
     
         4 . The method of  claim 1 , further comprising:
 determining a heterozygous fraction (F he ) thereof which is associated with heterozygous genetic markers based on said measured allele presences; and   wherein the estimating comprises:   estimating whether the female is pregnant based on the homozygous fraction and said heterozygous fraction.   
     
     
         5 . The method of  claim 4 , further comprising:
 calculating a threshold value as a function of the heterozygous fraction;   wherein the estimating comprises:   estimating that the female is pregnant if the homozygous fraction is below the calculated threshold value; and   estimating that the female is not pregnant if the homozygous fraction is above the calculated threshold value.   
     
     
         6 . The method of  claim 1 , wherein the first and second threshold are a constant value which has been determined empirically. 
     
     
         7 . The method of  claim 1 , wherein determining a homozygous fraction (F ho ) which is associated with purely homozygous genetic markers comprises:
 calculating a corresponding number of allele frequencies for said plurality of genetic markers based on said measured allele presences for the plurality of genetic markers; and   determining read counts in function of the allele frequency for said plurality of genetic markers;   selecting a portion of the read counts; and   determining a homozygous fraction (F ho ) of said selected portion, which is associated with purely homozygous genetic markers.   
     
     
         8 . The method of  claim 1 , wherein the measuring and determining steps are performed for a batch comprising a plurality of samples of the female; wherein for each sample of the batch, the homozygous fraction is calculated; and
 wherein the estimating is further based on said homozygous fraction of each sample.   
     
     
         9 . The method of  claim 1 , wherein the sample is maternal blood, plasma, urine, cerebrospinal fluid, serum, saliva or is transcervical lavage fluid. 
     
     
         10 . The method of  claim 1 , wherein said measuring step comprises at least one of the following: polymerase chain reaction (PGR), ligase chain reaction, nucleic acid sequence based amplification (NASBA), and/or branched DNA methods. 
     
     
         11 . A system for estimating whether a female is pregnant, said system comprising:
 a measurement device configured for measuring allele presences (D) for a plurality of genetic markers of at least one chromosome, different from the X and Y chromosome, in a sample of cell-free DNA from a potentially pregnant female; each allele presence representing the presence at a genetic marker of at least one of: a reference allele of maternal or foetal origin, or an alternative allele of maternal or foetal origin;   a determining module configured for determining, based on said measured allele presences, a homozygous fraction (F ho ) thereof which is associated with purely homozygous genetic markers;   an estimating module configured for estimating whether the female is pregnant based on said fraction.   
     
     
         12 . The system of  claim 11 , wherein the determining module is configured for:
 calculating a corresponding number of allele frequencies for said plurality of genetic markers based on said measured allele presences;   determining as the homozygous fraction the fraction of said measured allele presences for which the allele frequency is 0 or 1 within a predetermined error margin.   
     
     
         13 . The system of  claim 11 , wherein the estimating module is configured for:
 estimating that the female is pregnant if the homozygous fraction is below a first predetermined value; and   estimating that the female is not pregnant if the homozygous fraction is above a second predetermined value, wherein the first and second predetermined value may be the same or wherein the second predetermined value may be larger than the first predetermined value.   
     
     
         14 . The system of  claim 11 , wherein the determining module is further configured for:
 determining a heterozygous fraction (F he ) thereof which is associated with heterozygous genetic markers based on said measured allele presences; and   wherein the estimating module is further configured for:   estimating whether the female is pregnant based on the homozygous fraction and said heterozygous fraction.   
     
     
         15 . The system of  claim 13 , wherein the determining module is further configured for: calculating a threshold value as a function of the heterozygous fraction; and
 wherein the estimating module is further configured for:   estimating that the female is pregnant if the homozygous fraction is below the calculated threshold value; and   estimating that the female is not pregnant if the homozygous fraction is above the calculated threshold value.   
     
     
         16 . The system of  claim 11 , wherein the measurement device and determining module are configured to perform the measuring and determining for a batch comprising a plurality of samples, wherein for each sample of the batch, the homozygous fraction is calculated; and
 wherein the estimating module is configured for estimating whether the female is pregnant based on said homozygous fraction of each sample.   
     
     
         17 . The system of  claim 11 , wherein the measurement device is configured to measure allele presences using at least one of the following: polymerase chain reaction (PCR), ligase chain reaction, nucleic acid sequence based amplification (NASBA), and/or branched DNA methods. 
     
     
         18 . A computer program comprising computer-executable instructions to perform, when the program is run on a computer, at least the step of estimating of the method of  claim 1 . 
     
     
         19 . A digital data storage medium encoding a machine-executable program of instructions to perform at least the step of estimating of  claim 1 . 
     
     
         20 . The method of  claim 7 , comprising selecting a portion of the read counts in which the read counts with the highest and/or the lowest values are removed. 
     
     
         21 . The method of  claim 5 , wherein the threshold value is 0.5-0.75.