US 12,205,674 B2
System and method for determining genetic relationships between a sperm provider, oocyte provider, and the respective conceptus
John Burke, Reno, NV (US); Brian Rhees, Reno, NV (US); Joshua David Blazek, Houston, TX (US); and Michael Jon Large, Houston, TX (US)
Assigned to CooperSurgical, Inc., Trumbull, CT (US)
Filed by CooperSurgical, Inc., Trumbull, CT (US)
Filed on Jun. 19, 2020, as Appl. No. 16/906,965.
Claims priority of provisional application 62/865,130, filed on Jun. 21, 2019.
Prior Publication US 2020/0402616 A1, Dec. 24, 2020
Int. Cl. G16B 30/10 (2019.01); C12Q 1/6883 (2018.01); G16B 10/00 (2019.01); G16B 20/10 (2019.01); G16B 20/20 (2019.01)
CPC G16B 30/10 (2019.02) [G16B 20/10 (2019.02); G16B 20/20 (2019.02); C12Q 1/6883 (2013.01); C12Q 2600/156 (2013.01); G16B 10/00 (2019.02)] 5 Claims
 
1. A method for determining the genetic relationship of a preimplantation conceptus with a sperm provider and oocyte provider, comprising:
receiving low-coverage conceptus, sperm provider, and oocyte provider sequence data, wherein the sequence data is between 0.001× and 10×;
aligning the received sequence data to a reference genome;
identifying single nucleotide polymorphisms (SNPs) in the sperm provider, oocyte provider, and conceptus sequence data;
imputing missing gaps in the sperm provider sequence data and the oocyte provider sequence data using an imputation reference;
calculating a paternal consistency score (scorep) between the sperm provider and the conceptus, wherein calculating the paternal consistency score includes using the following formula:
scorep=(Ncp×Nn/(NSNP×NC)) wherein Ncp is the number of SNPs consistent between conceptus and sperm provider, Nn is the number of novel SNPs observed in the conceptus, NSNP is the number of SNPs observed in the conceptus, sperm provider, and oocyte provider, and NC is the number of SNPs consistent with either of the sperm provider and oocyte provider;
calculating a maternal consistency score (scorem) between the oocyte provider and conceptus, wherein calculating the maternal consistency score includes using the following formula:
scorem=(Ncm×Nn/(NSNP×Nc)) wherein Ncm is the number of SNPs consistent between conceptus and oocyte provider, Nn is the number of novel SNPs observed in the conceptus, NSNP is the number of SNPs observed in the conceptus, sperm provider, and oocyte provider, and Nc is the number of SNPs consistent with either of the sperm provider and oocyte provider;
classifying the sperm provider and/or the oocyte provider as related to the conceptus if the paternal consistency score and/or the maternal consistency score exceeds a predetermined threshold; and
rejecting the preimplantation conceptus as a candidate for implantation if the sperm provider and/or the oocyte provider is not classified as related to the preimplantation conceptus.