Methods of determining tissues and/or cell types giving rise to cell-free dna, and methods of identifying a disease or disorder using same

Patent metadata

Field	Value
Publication number	US-2023212672-A1
Application number	US-202217805656-A
Country	US
Kind code	A1
Filing date	Jun 6, 2022
Priority date	Jul 25, 2014
Publication date	Jul 6, 2023
Grant date	—

Abstract

The present disclosure provides methods of determining one or more tissues and/or cell-types contributing to cell-free DNA (“cfDNA”) in a biological sample of a subject. In some embodiments, the present disclosure provides a method of identifying a disease or disorder in a subject as a function of one or more determined more tissues and/or cell-types contributing to cfDNA in a biological sample from the subject.

First claim

1 . A method of identifying a clinical condition in a test subject, the method comprising:
(a) obtaining sequences of at least a portion of cfDNA present in a test sample from the test subject, wherein the sequences have endpoints and the sequences are mappable to genomic locations; (b) calculating a test sample value of the frequency of sample cfDNA endpoints at one or more genomic locations, wherein the frequency of the sample cfDNA endpoints is a function of the number of endpoints and the number of sequenced molecules mappable to the genomic locations; (c) comparing the test sample value with a first reference value calculated from the frequency of cfDNA endpoints obtained from the sequences of cfDNA molecules obtained from a first reference sample, wherein the frequency of the cfDNA endpoints is a function of the number of endpoints and the number of sequenced molecules mappable to the genomic locations; wherein the first reference sample is obtained from a person known to have the presence or the absence of the clinical condition, and (d) identifying or diagnosing the presence or absence of the clinical condition based on at least the comparing step.

2 . The method of claim 1 , wherein the first reference sample is obtained from a person known to have the clinical condition.

3 . The method of claim 1 , wherein the first reference sample is obtained from a person known to not have the clinical condition.

4 . The method of claim 2 , further comprising the steps of:
comparing the value of frequency of the sample cfDNA endpoints with a second reference value calculated from the cfDNA endpoints obtained from the sequences of cfDNA obtained from a second reference sample and wherein the frequency of the endpoints are a function of the number of endpoints and the number of sequenced molecules mappable to the defined genomic location, wherein the second reference sample is obtained from a person known to not have the clinical condition.

5 . The method of claim 4 , wherein identifying or diagnosing the presence or absence of the clinical condition comprises determining if the test sample value is more similar to the first reference value or the second reference value.

6 . The method of claim 5 , wherein the clinical condition is cancer.

7 . The method of claim 5 , wherein the genomic location comprises a transcription factor binding site.

8 . The method of claim 5 , wherein the genomic location comprises a CTCF binding site.

9 . The method of claim 6 , wherein the cfDNA sequenced comprises DNA derived from hematopoietic cells and non-hematopoietic cells, wherein at least a portion of the non-hematopoietic cells are tumor cells.

10 . The method of claim 8 , wherein test values and reference values are calculated for a plurality of genomic locations.

11 . The method of claim 8 , wherein the cfDNA is sequenced on a massively parallel DNA sequencer.

12 . The method of claim 5 , wherein the genomic locations comprise a plurality of separate genomic locations and separate test values and reference values for each genomic location.

13 . The method of claim 12 , wherein test frequency values and the reference frequency values are compared for a plurality of genomic locations.

14 . The method of claim 8 , wherein the test frequency values and the reference frequency values are calculated at a single genomic coordinate resolution level.

15 . The method of claim 5 , wherein test frequency values and the reference frequency values are calculated at a single genomic coordinate resolution for a plurality of single base locations within the genomic locations.

16 . The method of claim 14 , wherein test frequency values and reference frequency values are calculated at a single genomic coordinate resolution for a plurality of single base locations within the genomic locations.

17 . The method of claim 15 , wherein test frequency values and reference frequency values are compared for a plurality of genomic locations.

18 . The method of claim 16 , wherein test frequency values and reference frequency values are compared for a plurality of genomic locations.

Assignees

• Univ Washington

Inventors

• Shendure Jay
• Snyder Matthew
• Kircher Martin

Classifications

• G16B30/00

  ICT specially adapted for sequence analysis involving nucleotides or amino acids · CPC title

• G16B45/00

  ICT specially adapted for bioinformatics-related data visualisation, e.g. displaying of maps or networks · CPC title

• G16B20/20

  Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection · CPC title

• C12Q1/6881 Primary

  for tissue or cell typing, e.g. human leukocyte antigen [HLA] probes · CPC title

• G16B40/00

  ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding · CPC title