US 12,322,509 B2
Methods and related aspects for analyzing chromosome number status
Daniel Ariad, Pikesville, MD (US); Rajiv McCoy, Baltimore, MD (US); and Manuel Viotti, San Francisco, CA (US)
Assigned to THE JOHNS HOPKINS UNIVERSITY, Baltimore, MD (US)
Appl. No. 18/035,811
Filed by THE JOHNS HOPKINS UNIVERSITY, Baltimore, MD (US)
PCT Filed Nov. 5, 2021, PCT No. PCT/US2021/058219
§ 371(c)(1), (2) Date May 8, 2023,
PCT Pub. No. WO2022/098980, PCT Pub. Date May 12, 2022.
Claims priority of provisional application 63/190,033, filed on May 18, 2021.
Claims priority of provisional application 63/111,037, filed on Nov. 8, 2020.
Prior Publication US 2023/0307130 A1, Sep. 28, 2023
Int. Cl. G16H 50/20 (2018.01); G16B 20/10 (2019.01); G16B 20/20 (2019.01); G16B 40/20 (2019.01)
CPC G16H 50/20 (2018.01) [G16B 20/10 (2019.02); G16B 20/20 (2019.02); G16B 40/20 (2019.02)] 20 Claims
OG exemplary drawing
 
1. A method of conducting genetic testing of a test subject prior to transferring the test subject to a maternal patient, the method comprising:
obtaining a biopsy comprising one or more cells from the test subject, wherein the test subject comprises a preimplantation embryo;
producing a set of sequencing reads from nucleic acids obtained the biopsy;
selecting, by a computer, sequencing reads obtained from the test subject that comprise nucleic acid variants within defined genomic windows to produce sets of observed test subject nucleic acid variants;
obtaining, by the computer, joint allele frequencies and/or linkage disequilibrium patterns of corresponding nucleic acid variants observed in a reference subject population to produce sets of reference subject joint allele frequency and/or linkage disequilibrium pattern data;
classifying the chromosome number status of the test subject as at least likely euploid using the sets of observed test subject nucleic acid variants and the sets of reference subject joint allele frequency and/or linkage disequilibrium pattern data, wherein classifying the chromosome number status of the test subject comprises determining at least one likelihood ratio of two competing ploidy hypotheses; and,
transferring the test subject to the maternal patient, wherein the test subject is transferred in utero of the maternal patient.