Method and system for identifying gene disorder in maternal blood

1 . A method of determining whether a fetus possesses a genetic or congenital disease, comprising:

obtaining a plurality of nucleic acid molecules from a biological sample of a pregnant mother and a biological sample of a father of a pair parenting a fetus;

obtaining maternal genomic DNA (gDNA) sequencing data, maternal cell-free DNA (cfDNA) sequencing data, and paternal gDNA sequencing data of said plurality of nucleic acid molecules using deep next generation sequencing (NGS) of the whole genome or the whole exome;

analyzing said data to identify a first set of sites at which the parents are homozygous for different alleles, and a second set of sites at which at least one of the parents has a mutation associated with a genetic disease, wherein said analyzing comprises identifying in reads covering said first set of sites a first group of reads including only reads that present paternal alleles but no other reads, and a second group including all other reads, and wherein said analyzing is executed by a variant caller;

for each site of said first set, determining a probability that a respective portion of said maternal cfDNA data is derived from said fetus, wherein said determining said probability is based on differences between reads in said first group and reads in said second group in the read fragment size;

classifying each site of said second set according to said probabilities as being either fetal or maternal to genotype said fetus, wherein said classifying comprises calculating a total fetal fraction, constructing a fetal size distribution and a maternal size distribution, binning said fetal size distribution, calculating a fetal fraction for each fragment size bin, wherein said classifying comprises applying a Bayesian procedure, said applying Bayesian procedure comprising using the maternal and/or paternal gDNA sequencing data to calculate each fragment's probability for being fetal, based on the read fragment size, calculating, for at least one site of said second set and at least one fragment at said at least one site, a probability that said fragment is fetal, based on a fetal fraction of a respective fragment size bin to which said fragment belongs, and extracting the genotype at each site that is classified as fetal to genotype said fetus; and

only if said genotyping identifies that the fetus possesses a mutation associated with a genetic or congenital disease:

(i) administering a prenatal or a post-natal treatment for said genetic or congenital disease in an amount effective to prevent or treat said disease, wherein said treatment comprises pharmaceutical based intervention, surgery, genetic therapy, nutritional therapy, or combinations thereof; or

(ii) performing a pregnancy termination.

2 . The method according to claim 1 , wherein said classifying comprises applying a machine learning procedure to said identified sites to genotype said fetus, wherein said applying a machine learning procedure comprises feeding a trained machine learning program with maternal gDNA sequencing data, maternal cfDNA sequencing data, and paternal gDNA sequencing data, wherein the output of the trained machine learning program is classification of sites at which at least one of the parents has a mutation associated with a genetic or congenital disease as being either fetal or maternal; and

wherein the training of the machine learning program comprises feeding the machine learning training program with maternal gDNA sequencing data, maternal cfDNA sequencing data, paternal gDNA sequencing data and fetal gDNA sequencing data for each of a cohort of subjects parenting a genotyped fetus.

3 . The method according to claim 1 , wherein said genetic or congenital disease is a single-gene disorder (SGD) of paternal origin.

4 . The method according to claim 1 , wherein said genetic or congenital disease is a single-gene disorder (SGD) of maternal origin.

5 . The method according to claim 1 , wherein said genetic or congenital disease is characterized by inherited insertions-deletions.

6 . The method according to claim 1 , wherein said genetic or congenital disease is characterized by chromosomal abnormality.

7 . The method according to claim 1 , wherein said genetic or congenital disease is a monogenic disease.

8 . The method according to claim 1 , wherein said genetic or congenital disease is a multigenic disease.

9 . A computer software product, comprising a non-transitory computer readable storage medium in which program instructions are stored, which instructions, when read by a data processor, cause the data processor to receive maternal cfDNA data and paternal cfDNA data of a pair parenting to a fetus and to execute a method of determining whether a fetus possesses a genetic or congenital disease, said method comprising:

obtaining a plurality of nucleic acid molecules from a biological sample of a pregnant mother and a biological sample of a father of a pair parenting a fetus;

obtaining maternal genomic DNA (DNA) sequencing data, maternal cell-free DNA (cfDNA) sequencing data, and paternal gDNA sequencing data of said plurality of nucleic acid molecules using deep next generation sequencing (NGS) of the whole genome or the whole exome;

analyzing said data to identify a first set of sites at which the parents are homozygous for different alleles, and a second set of sites at which at least one of the parents has a mutation associated with a genetic disease, wherein said analyzing comprises identifying in reads covering said first set of sites a first group of reads including only reads that present paternal alleles but no other reads, and a second group including all other reads, and wherein said analyzing is executed by a variant caller;

for each site of said first set, determining a probability that a respective portion of said maternal cfDNA data is derived from said fetus, wherein said determining said probability is based on differences between reads in said first group and reads in said second group in the read fragment size;

classifying each site of said second set according to said probabilities as being either fetal or maternal to genotype said fetus, wherein said classifying comprises calculating a total fetal fraction, constructing a fetal size distribution and a maternal size distribution, binning said fetal size distribution, calculating a fetal fraction for each fragment size bin, wherein said classifying comprises applying a Bayesian procedure, said applying Bayesian procedure comprising using the maternal and/or paternal gDNA sequencing data to calculate each fragment's probability for being fetal, based on the read fragment size, calculating, for at least one site of said second set and at least one fragment at said at least one site, a probability that said fragment is fetal, based on a fetal fraction of a respective fragment size bin to which said fragment belongs, and extracting the genotype at each site that is classified as fetal to genotype said fetus; and

only if said genotyping identifies that the fetus possesses a mutation associated with a genetic or congenital disease:

(i) administering a prenatal or a post-natal treatment for said genetic or congenital disease in an amount effective to prevent or treat said disease, wherein said treatment comprises pharmaceutical based intervention, surgery, genetic therapy, nutritional therapy, or combinations thereof; or

(ii) performing a pregnancy termination.

10 . A system for fetal genotyping, comprising: an input circuit receiving maternal cell-free DNA (cfDNA) data and paternal (cfDNA) data of a pair parenting to a fetus; a data processor configured for analyzing said data to identify sites at which the parents are homozygous for executing a method of determining whether a fetus possesses a genetic or congenital disease, said method comprising:

obtaining a plurality of nucleic acid molecules from a biological sample of a pregnant mother and a biological sample of a father of a pair parenting a fetus;

obtaining maternal genomic DNA (gDNA) sequencing data, maternal cell-free DNA (cfDNA) sequencing data, and paternal gDNA sequencing data of said plurality of nucleic acid molecules using deep next generation sequencing (NGS) of the whole genome or the whole exome;

analyzing said data to identify a first set of sites at which the parents are homozygous for different alleles, and a second set of sites at which at least one of the parents has a mutation associated with a genetic disease, wherein said analyzing comprises identifying in reads covering said first set of sites a first group of reads including only reads that present paternal alleles but no other reads, and a second group including all other reads, and wherein said analyzing is executed by a variant caller;

for each site of said first set, determining a probability that a respective portion of said maternal cfDNA data is derived from said fetus, wherein said determining said probability is based on differences between reads in said first group and reads in said second group in the read fragment size;

classifying each site of said second set according to said probabilities as being either fetal or maternal to genotype said fetus, wherein said classifying comprises calculating a total fetal fraction, constructing a fetal size distribution and a maternal size distribution, binning said fetal size distribution, calculating a fetal fraction for each fragment size bin, wherein said classifying comprises applying a Bayesian procedure, said applying Bayesian procedure comprising using the maternal and/or paternal gDNA sequencing data to calculate each fragment's probability for being fetal, based on the read fragment size, calculating, for at least one site of said second set and at least one fragment at said at least one site, a probability that said fragment is fetal, based on a fetal fraction of a respective fragment size bin to which said fragment belongs, and extracting the genotype at each site that is classified as fetal to genotype said fetus; and

only if said genotyping identifies that the fetus possesses a mutation associated with a genetic or congenital disease:

(i) administering a prenatal or a post-natal treatment for said genetic or congenital disease in an amount effective to prevent or treat said disease, wherein said treatment comprises pharmaceutical based intervention, surgery, genetic therapy, nutritional therapy, or combinations thereof; or

(ii) performing a pregnancy termination.

11 . The method of claim 1 wherein said variant caller is selected from a group consisting of Genome Analysis Toolkit (GATK) or Freebayes.