High-resolution and non-invasive fetal sequencing
AssigneesThe General Hospital Corporation, The Broad Institute, Inc.
InventorsMichael E. Talkowski, Harrison Brand, Christopher Whelan
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Abstract
Provided herein are computer-implemented methods for assigning maternal or fetal origin to one or more genetic variants in cell free DNA (cfDNA) from a sample from a pregnant mammal, preferably a pregnant human, using a probabilistic model for assigning maternal or fetal origin to genetic variants in DNA from a sample obtained from a pregnant mammal, wherein the model assigns maternal or fetal origin based on a combination of fetal fraction and DNA fragment size.
Claims16
A computer-implemented method for assigning maternal or fetal origin to one or more genetic variants in cell free DNA (cfDNA) from a sample from a pregnant mammal, preferably a pregnant human, the method comprising:
- (a) accessing, from memory, a probabilistic model for assigning maternal or fetal origin to genetic variants in DNA from a sample obtained from a pregnant mammal, wherein the model assigns maternal or fetal origin based on a combination of fetal fraction and/or DNA fragment size and other sequencing features;
- (b) inputting, into the model, a set of values representing one or more genetic variants detected in the cfDNA from a peripheral blood sample from a pregnant mammal, wherein the values include empirically determined sequence information, e.g., ratio of different bases in the read, and DNA fragment size information, e.g, a rank sum statistic, for each genetic variant;
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- (c) assigning, using the model, maternal or fetal origin for the one or more genetic variants.
Dependencies are inferred from the claim text.