Processes for calculating phased fetal genomic sequences
AssigneeAriosa Diagnostics, Inc.
InventorsJohn Stuelpnagel, Craig Struble, Eric Wang
Life of this patent
Estimating the term…
Abstract
The present invention provides processes for calculating phased genomic sequences of the fetal genome using fetal DNA obtained from a maternal sample. The processes and systems of the present invention utilize novel technological and computational approaches to detect fetal genomic sequences and determine the phased heritable genomic sequences. The invention could be used, e.g., to identify in utero deleterious mutations carried by the parents and inherited by a fetus within a particular heritable genomic region.
Claims27
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A computer-implemented process for determining the phased composition in a fetal heritable genomic region, comprising the steps of:
- providing phased sequence information from the maternal and paternal genome on at least one corresponding heritable genomic region;
- masking sequence information on loci that are indistinguishable between the maternal and paternal genome;
- providing empirical sequence information on five or more informative loci from a maternal sample corresponding to the heritable genomic region;
- calculating the predicted paternal contribution of the heritable genomic region to the fetus based on the empirically identified paternal sequences of the five or more informative loci;
- calculating the predicted maternal contribution of the heritable genomic region to the fetus based on the ratio of empirically identified sequences in the maternal sample;
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- providing a likelihood value of the fetal heritable genomic region contributed by the maternal and/or paternal source based on the predicted maternal and paternal contributions of the heritable genomic region to the fetus.
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A computer-implemented process to calculate a value of likelihood for a fetal heritable genomic region, comprising:
- providing maternal and paternal sequence information for a heritable genomic region;
- providing empirical sequence information from a heritable genomic region within a maternal sample, wherein the sequence information is obtained from the maternal sample using massively parallel sequencing;
- identifying at least five informative loci within the maternal and paternal heritable genomic region;
- calculating a value of the likelihood of the heritable genomic region inherited by the fetus from the father based on the informative loci and the empirical sequence information;
- identifying at least five loci which are maternally and paternally heterozygous;
- calculating a value of the likelihood of the heritable genomic region inherited by the fetus from the mother based on value of the likelihood of the heritable genomic region inherited by the fetus from the father and the empirical sequence information on the loci which are maternally and paternally heterozygous.
Dependencies are inferred from the claim text.