US 12,435,373 B2
Identification of polymorphic sequences in mixtures of genomic DNA
Richard P. Rava, Redwood City, CA (US)
Assigned to VERINATA HEALTH, INC., San Diego, CA (US)
Filed by VERINATA HEALTH, INC., San Diego, CA (US)
Filed on Apr. 27, 2020, as Appl. No. 16/859,655.
Application 16/859,655 is a continuation of application No. 13/009,718, filed on Jan. 19, 2011, granted, now 10,662,474.
Application 13/009,718 is a continuation in part of application No. 12/958,347, filed on Dec. 1, 2010, abandoned.
Claims priority of provisional application 61/360,837, filed on Jul. 1, 2010.
Claims priority of provisional application 61/296,358, filed on Jan. 19, 2010.
Prior Publication US 2020/0291478 A1, Sep. 17, 2020
This patent is subject to a terminal disclaimer.
Int. Cl. C12Q 1/6883 (2018.01); C12Q 1/6827 (2018.01); C12Q 1/6886 (2018.01)
CPC C12Q 1/6883 (2013.01) [C12Q 1/6827 (2013.01); C12Q 1/6886 (2013.01); C12Q 2600/16 (2013.01); C12Q 2600/172 (2013.01)] 14 Claims
 
1. A method for identifying multiple fetal polymorphisms in a fetal genome of a blood sample obtained from a pregnant woman comprising a mixture of cfDNA of a fetal and a maternal genome, said method comprising steps:
(a) performing massively parallel sequencing of amplicons obtained from said mixture of cfDNA, thereby obtaining a plurality of sequence tags;
(b) mapping the sequences of said plurality of sequence tags to the sequences of multiple reference polymorphisms, to identify sequence tags mapped to each of said multiple reference polymorphisms;
(c) for each of said multiple reference polymorphisms:
(i) quantifying mapped sequence tags that map to a first allele of the reference polymorphism to obtain sequence tag density for the first allele;
(ii) quantifying mapped sequence tags that map to the second allele of the reference polymorphism to obtain a sequence tag density for the second allele;
(iii) determining a sequence tag dose from the ratio of the sequence tag density for the first allele and the sequence tag density for the second allele;
(iv) comparing the sequence tag dose to a determination of the relative abundance of fetal cfDNA in the maternal sample; and
(v) classifying an allele as a fetal polymorphism when the sequence tag dose is less than one or more cutoff values associated with the determination of the relative abundance of fetal cfDNA in the maternal sample;
wherein the identification of fetal polymorphisms originating from the fetal genome in the mixture is performed without genotyping the maternal alleles in a maternal sample that is substantially free of fetal nucleic acids.