Processes for calculating phased fetal genomic sequences
First Claim
Patent Images
1. A process for determining the phased composition in a fetal heritable genomic region from a maternal sample comprising maternal DNA and fetal DNA, the process comprising the steps of:
- isolating cell-free nucleic acids from the maternal sample comprising the maternal DNA and the fetal DNA, wherein the cell-free nucleic acids comprise selected nucleic acid regions;
interrogating the selected nucleic acid regions in the fetal heritable genomic region using oligonucleotides to amplify the selected nucleic acid regions, the oligonucleotides comprising universal amplification sequences;
applying the amplified selected nucleic acid regions to an array-based pull-out detection system to identify informative loci corresponding to a heritable genomic region of interest;
providing, to a computer processor, phased sequence information from at least one corresponding parental heritable genomic region;
identifying, by the computer processor, five or more informative loci in the fetal DNA corresponding to a heritable genomic region of interest from the phased sequence information of the at least one corresponding parental heritable genomic region;
calculating, by the computer processor, a paternal contribution of the heritable genomic region of interest using the phased sequence information of the five or more informative loci;
calculating, by the computer processor, the maternal contribution of the heritable genomic region of interest by comparing the paternal contribution of the heritable genomic region of interest to the selected nucleic acid regions in the fetal heritable genomic region; and
generating, by the computer processor, a prediction of a likely phased composition of the heritable genomic region of interest in the fetal DNA using the maternal and paternal contributions of the heritable genomic region of interest.
2 Assignments
0 Petitions
Accused Products
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.
-
Citations
13 Claims
-
1. A process for determining the phased composition in a fetal heritable genomic region from a maternal sample comprising maternal DNA and fetal DNA, the process comprising the steps of:
-
isolating cell-free nucleic acids from the maternal sample comprising the maternal DNA and the fetal DNA, wherein the cell-free nucleic acids comprise selected nucleic acid regions; interrogating the selected nucleic acid regions in the fetal heritable genomic region using oligonucleotides to amplify the selected nucleic acid regions, the oligonucleotides comprising universal amplification sequences; applying the amplified selected nucleic acid regions to an array-based pull-out detection system to identify informative loci corresponding to a heritable genomic region of interest; providing, to a computer processor, phased sequence information from at least one corresponding parental heritable genomic region; identifying, by the computer processor, five or more informative loci in the fetal DNA corresponding to a heritable genomic region of interest from the phased sequence information of the at least one corresponding parental heritable genomic region; calculating, by the computer processor, a paternal contribution of the heritable genomic region of interest using the phased sequence information of the five or more informative loci; calculating, by the computer processor, the maternal contribution of the heritable genomic region of interest by comparing the paternal contribution of the heritable genomic region of interest to the selected nucleic acid regions in the fetal heritable genomic region; and generating, by the computer processor, a prediction of a likely phased composition of the heritable genomic region of interest in the fetal DNA using the maternal and paternal contributions of the heritable genomic region of interest. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13)
-
Specification
-
- Resources
Litigation Campaign Assessment
Thank you for your request. You will receive a custom alert email when the Litigation Campaign Assessment is available.
×
-
Current AssigneeRoche Molecular Systems Inc (Roche Holding AG)
-
Original AssigneeAriosa Diagnostics Incorporated (Roche Holding AG)
-
InventorsStuelpnagel, John, Struble, Craig, Wang, Eric
-
Primary Examiner(s)Lin, Jerry
-
Application NumberUS13/898,239Publication NumberTime in Patent Office2,185 DaysField of Search702 20US Class CurrentCPC Class CodesG16B 20/00 ICT specially adapted for f...G16B 20/20 Allele or variant detection...
