Identifying a de novo fetal mutation from a maternal biological sample

Abstract

Systems, methods, and apparatus for determining a fractional concentration of fetal DNA in a biological sample are provided. The biological sample may be enriched for nucleic acid molecules in a target region. A plurality of nucleic acid molecules from the enriched biological sample may be sequenced specific to the target region. One or more first loci may be determined. The fetal genome is heterozygous at each first loci such that the fetal genome has a respective first and second allele at that first loci. The maternal genome is homozygous at each first loci such that the maternal genome. For at least one of the first loci, a first number of counts of the respective first allele and a second number of counts of the respective second allele may be determined. The fractional concentration may be determined based on the first and second numbers.

What is claimed is: 
     
         1 . A method of determining a fractional concentration of fetal DNA in a biological sample taken from a female pregnant with a fetus, the fetus having a father and a mother being the pregnant female, wherein the biological sample contains a mixture of maternal and fetal nucleic acids, the method comprising:
 enriching the biological sample obtained from the pregnant female for nucleic acid molecules in a target region;   sequencing a plurality of nucleic acid molecules from the enriched biological sample to obtain sequencing results, the sequencing being specific to the target region, wherein the sequencing results are analyzed to:
 identify a location of the nucleic acid molecule in the target region of the human genome; and 
 determine a respective allele of the nucleic acid molecule; 
   determining one or more first loci, wherein the fetal genome is heterozygous at each first loci such that the fetal genome has a respective first and second allele at that first loci, and wherein a maternal genome is homozygous at each first loci such that the maternal genome has two of the respective second allele at that first loci, the first allele being different than the second allele;   for at least one of the first loci:
 determining a first number P of counts of the respective first allele and a second number Q of counts of the respective second allele; and 
   determining the fractional concentration based on the first and second numbers.   
     
     
         2 . The method of  claim 1 , wherein determining the one or more first loci includes:
 determining the paternal genome is homozygous for the respective first allele at each loci of the one or more first loci and determining the maternal genome is homozygous for the respective second allele at the same locus.   
     
     
         3 . The method of  claim 1 , wherein determining a specific locus to be the one or more first loci includes:
 determining a cutoff value for a number of predicted counts of the respective first allele at the specific locus, the cutoff value predicting whether the maternal genome is homozygous and the fetal genome is heterozygous, wherein the cutoff value is determine based on a statistical distribution of numbers of counts for different combinations of homozygosity and heterozygosity at the specific locus;   based on the analysis of the sequencing results, detecting the respective first and second allele at the specific locus;   determining a number of actual counts of the respective first allele based on the sequencing of the plurality of nucleic acid molecules from the biological sample; and   determining the specific locus is one of the first loci when the number of actual counts is less than the cutoff value.   
     
     
         4 . The method of  claim 3 , wherein determining the cutoff value includes determining a statistical distribution for a maximum and a minimum fractional concentration. 
     
     
         5 . The method of  claim 4 , wherein the statistical distribution is a Poisson distribution. 
     
     
         6 . The method of  claim 4 , wherein the maximum and the minimum fractional concentration depend on the length of the pregnancy. 
     
     
         7 . The method of  claim 1 , wherein enriching the biological sample comprises performing solution phase capture, microarray capture, or targeted amplification. 
     
     
         8 . The method of  claim 1 , wherein sequencing the plurality of nucleic acid molecules comprises sequencing both ends of each nucleic acid molecule of the plurality of nucleic acid molecules. 
     
     
         9 . The method of  claim 1 , wherein sequencing the plurality of nucleic acid molecules comprises random sequencing of the enriched biological sample. 
     
     
         10 . The method of  claim 1 , further comprising:
 determining the number of molecules to be analyzed at a first locus of the one or more first loci using an assumed value of fractional concentration of fetal DNA and a target probability of detecting the respective first allele at the first locus.   
     
     
         11 . The method of  claim 1 , further comprising:
 for a specific locus:
 comparing counts of the respective first allele to a cutoff value, and 
 categorizing, using the comparison of the counts to the cutoff value, the locus as a locus where the mother is homozygous in the first allele and the fetus is heterozygous; the mother is heterozygous and the fetus is heterozygous; or the mother is heterozygous and the fetus is homozygous. 
   
     
     
         12 . The method of  claim 1 , wherein the fractional concentration is determined as 2×P/(P+Q). 
     
     
         13 . The method of  claim 1 , wherein P and Q are determined for a plurality of first loci, and where the fractional concentration f is determined as 
       
         
           
             
               
                 f 
                 = 
                 
                   
                     
                       ∑ 
                       
                         i 
                         = 
                         1 
                       
                       n 
                     
                     
                       2 
                       ⁢ 
                       
                         P 
                         i 
                       
                     
                   
                   
                     
                       ∑ 
                       
                         i 
                         = 
                         1 
                       
                       n 
                     
                     
                       ( 
                       
                         
                           P 
                           i 
                         
                         + 
                         
                           Q 
                           i 
                         
                       
                       ) 
                     
                   
                 
               
               , 
             
           
         
       
       where p i  is the first number for the ith first loci and q i  is the second number for the ith first loci. 
     
     
         14 . A computer product comprising a non-transitory computer readable medium storing a plurality of instructions that when executed control a computer system to determine a fractional concentration of fetal DNA in a biological sample taken from a female pregnant with a fetus, the fetus having a father and a mother being the pregnant female, wherein the biological sample contains a mixture of maternal and fetal nucleic acids, the instructions comprising:
 receiving sequencing results of a sequencing of a plurality of nucleic acid molecules from an enriched biological sample, the enriched biological sample being enriched for nucleic acid molecules in a target region, the sequencing being specific to the target region, wherein the sequencing results are analyzed to:
 identify a location of the nucleic acid molecule in the target region of the human genome; and 
 determine a respective allele of the nucleic acid molecule; 
   determining one or more first loci, wherein the fetal genome is heterozygous at each first loci such that the fetal genome has a respective first and second allele at that first loci, and wherein a maternal genome is homozygous at each first loci such that the maternal genome has two of the respective second allele at that first loci, the first allele being different than the second allele;   for at least one of the first loci:
 determining a first number P of counts of the respective first allele and a second number Q of counts of the respective second allele; and 
   determining the fractional concentration based on the first and second numbers.   
     
     
         15 . A system comprising:
 the computer product of  claim 14 ; and   one or more processors for executing instructions stored on the computer readable medium.   
     
     
         16 . A system comprising:
 an enrichment system configured to enrich a biological sample for nucleic acid molecules in a target region to form an enriched biological sample;   a sequencing device configured to sequence a plurality of nucleic molecules in the enriched biological sample; and   a computer system comprising:
 a computer product comprising a non-transitory computer readable medium storing a plurality of instructions that when executed control a computer system to determine a fractional concentration of fetal DNA in the biological sample taken from a female pregnant with a fetus, the fetus having a father and a mother being the pregnant female, wherein the biological sample contains a mixture of maternal and fetal nucleic acids, the instructions comprising:
 receiving sequencing results from the sequencing device of a sequencing of a plurality of nucleic acid molecules from the enriched biological sample from the enrichment system, the enriched biological sample being enriched for nucleic acid molecules in the target region, the sequencing being specific to the target region, wherein the sequencing results are analyzed to: 
 identify a location of the nucleic acid molecule in the target region of the human genome; and 
 determine a respective allele of the nucleic acid molecule; 
 determining one or more first loci, wherein the fetal genome is heterozygous at each first loci such that the fetal genome has a respective first and second allele at that first loci, and wherein a maternal genome is homozygous at each first loci such that the maternal genome has two of the respective second allele at that first loci, the first allele being different than the second allele; 
 for at least one of the first loci:
 determining a first number P of counts of the respective first allele and a second number Q of counts of the respective second allele; and 
 determining the fractional concentration based on the first and second numbers; and 
 
 one or more processors for executing instructions stored on the computer readable medium.