Identifying a de novo fetal mutation from a maternal biological sample

A method of identifying a de novo mutation in a genome of an unborn fetus of a pregnant female, the fetus having a father and a mother being the pregnant female, the father having a paternal genome and the mother having a maternal genome, the method comprising:

• performing a random sequencing of a plurality of nucleic acid molecules from a biological sample obtained from the pregnant female to obtain sequence reads of the plurality of nucleic acid molecules, wherein the biological sample contains a mixture of cell-free maternal and fetal nucleic acids, and wherein the sequencing of a nucleic acid molecule is paired-end sequencing that provides a pair of sequences corresponding to both ends of the nucleic acid molecule;
• receiving the sequence reads at a computer system;
• identifying, by the computer system, a location of each of the plurality of nucleic acid molecules in a human genome using the sequence reads of the plurality of nucleic acid molecules, wherein identifying the location of a nucleic acid molecule in the human genome includes mapping the pair of sequences corresponding to both ends of the nucleic acid molecule to the human genome;
• for each of at least a portion of the locations, determining, by the computer system, one or more maternal sequences in the maternal genome and one or more paternal sequences in the paternal genome at the location;
• identifying, by the computer system, a first sequence in the sequence reads of the plurality of nucleic acid molecules at a first location that is not present in the determined maternal or paternal sequences at the first location;
• determining, by the computer system, a first fractional concentration of the first sequence in the biological sample at the first location using the sequence reads corresponding to the first location;
• determining, by the computer system, a second fractional concentration of a second sequence in the biological sample at a second location using the sequence reads corresponding to the second location, the second sequence being inherited by the fetus from the father at the second location, wherein the second sequence is present in the paternal genome at the second location and not present in the maternal genome at the second location;
• classifying, by the computer system, the first sequence as a de novo mutation at the first location in a fetal genome of the fetus if the first and second fractional concentrations are about the same;
• and
• when the first sequence is classified as the de novo mutation:
• outputting, by the computer system, classification information identifying the first sequence as being the de novo mutation at the first location as a result of receiving the sequence reads from the sequencing of the plurality of nucleic acid molecules from the biological sample obtained from the pregnant female.