Granted Patent B2

US 12,435,373 · App. 16/859,655 · Granted Oct 7, 2025

Inventor: Richard P. Rava (Redwood City, CA)

Assignee: VERINATA HEALTH, INC.

C12Q1/6883C12Q1/6827C12Q1/6886C12Q2600/16C12Q2600/172

Abstract

Claims (23)

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.

2. The method of claim 1 , wherein said portion of said mixture of cfDNA has been specifically enriched for polymorphisms to obtain an enriched library.

3. The method of claim 2 , comprising amplification of polymorphic sequences of interest.

4. The method of claim 3 , comprising selecting polymorphic target sequences for amplification prior to sequencing.

5. The method of claim 1 , wherein said sample is unenriched for polymorphic target sequences in said mixture of cfDNA.

6. The method of claim 1 , wherein said multiple fetal polymorphisms are associated with at least one disorder.

7. The method of claim 6 , wherein said at least one disorder is a monogenic disease.

8. The method of claim 6 , wherein said at least one disorder is a polygenic disease.

9. The method of claim 6 , wherein said at least one disorder is cancer.

10. The method of claim 1 , wherein said sample is a blood sample is a plasma sample.

11. The method of claim 1 , wherein the one or more cutoff values associated with the determination of the relative abundance of fetal cfDNA in the maternal sample is about 30% or less of the sequence tag dose.

12. The method of claim 1 , wherein the plurality of sequence tags comprises one or more single nucleotide polymorphisms (SNPs) and/or one or more short tandem repeats (STRs).

13. The method of claim 1 , wherein massively parallel sequencing comprises massively parallel sequencing-by-synthesis with reversible dye terminators.

14. The method of claim 1 , wherein massively parallel sequencing comprises massively parallel sequencing-by-ligation.

Assignments (2)

Continuity (5)

References Cited (368)