Methods for Using Mosaicism in Nucleic Acids Sampled Distal to Their Origin

Patent metadata

Field	Value
Publication number	US-2016122831-A1
Application number	US-201514929075-A
Country	US
Kind code	A1
Filing date	Oct 30, 2015
Priority date	Oct 30, 2014
Publication date	May 5, 2016
Grant date	—

Abstract

Disclosed herein are methods for improving detection and monitoring of human diseases. The methods can be used to provide spatial and/or developmental localization of the source of each differential mutation within the body. The methods can also be used to generate a mutation map of a subject. And the mutation map can be used to monitoring state(s) of health of one or more tissues of a subject.

First claim

What is claimed is:

1 . A method for detecting differential mutations in a blood sample of a subject, comprising:
(a) separating said blood sample into at least a first component that includes cell-free or surface-bound nucleic acid molecules and a second component that includes leukocytes; (b) extracting nucleic acid molecules from said first and second components; (c) independently sequencing extracted nucleic acid molecules from said first and second components; and (d) comparing with a programmed computer processor nucleic acid sequences of said nucleic acid molecules of said first and second components to identify differential mutations.

2 . The method of claim 1 , further comprising (e) identifying a source of said cell-free or surface-bound nucleic acid molecules based on said differential mutations.

3 . The method of claim 2 , further comprising providing a report and/or a therapeutic intervention based on an identification of said source.

4 . The method of claim 2 , wherein said source is identified as a tissue or group of tissues of said subject.

5 . The method of claim 2 , further comprising comparing said differential mutation(s) to a mutation map of said subject to identify said source.

6 . The method of claim 5 , wherein said mutation map is a developmental mutation map or a spatial mutation map.

7 . The method of claim 1 , wherein (d) further comprises identifying variants in nucleic acid molecules of said first component with respect to nucleic acid molecules of said second component.

8 . The method of claim 1 , wherein said nucleic acid molecules of said second component are extracted by disrupting said leukocytes.

9 . The method of claim 1 , wherein said nucleic acid molecules extracted from said first and second components are sequenced in a combined pool.

10 . A method for generating a mutation map of a subject that relates a mutation to a source of said mutation, comprising:
(a) sequencing nucleic acid molecules in nucleic acid samples, which nucleic acid samples are from different tissues of said subject; (b) identifying with a programmed computer processor differential mutations in nucleic acid sequences of said nucleic acid molecules sequenced in (a); and (c) generating in computer memory a relationship between said differential mutations and said different tissues to provide said mutation map of said subject.

11 . The method of claim 10 , wherein said mutation map is a developmental mutation map.

12 . The method of claim 11 , wherein (c) comprises: (i) assigning said differential mutations on a developmental tree; and (ii) generating said developmental mutation map from said developmental tree.

13 . The method of claim 11 , wherein said mutation map is a developmental mutation map that is generated using a hierarchical tree clustering algorithm.

14 . The method of claim 10 , wherein said mutation map is a spatial mutation map.

15 . The method of claim 11 , further comprising providing a report with said developmental mutation map.

16 . The method of claim 10 , wherein (b) comprises identifying variants in said nucleic acid sequences.

17 . The method of claim 10 , wherein said nucleic acid molecules extracted from said biological samples are sequenced in a combined pool.

18 . The method of claim 10 , wherein said sequencing comprises whole genome sequencing, targeted genome sequencing or redundant sequencing.

19 . The method of claim 10 , wherein said nucleic acid samples are obtained from at least one tissue with increased apoptosis.

20 . The method of claim 10 , further comprising obtaining said nucleic acid samples from different tissues of said subject.

21 . The method of claim 20 , further comprising obtaining a nucleic acid sample from blood drawn at a first location of said subject having relatively high concentrations of cell-free nucleic acid molecules from a given tissue and a second location having low concentrations of cell-free nucleic acid molecules from said given tissue.

22 . The method of claim 21 , further comprising identifying mutations specific to said given tissue through differential analysis of nucleic acid sequences generated at said first location and second location.

23 . The method of claim 10 , wherein said different tissues are non-cancerous tissues.

24 . A method for monitoring state(s) of health of one or more tissues of a subject, comprising:
(a) sequencing at least one nucleic acid molecule from a blood sample of said subject to generate a nucleic acid sequence of said at least one nucleic acid molecule; (b) identifying one or more mutations in said nucleic acid sequence; and (c) using a mutation map of said subject in computer memory, identifying with a programmed computer processor a tissue of said subject associated with said nucleic acid molecule based on said one or more mutations identified in (b).

25 . The method of claim 24 , further comprising providing a report with said tissue identified in (c).

26 . The method of claim 24 , wherein said nucleic acid molecule is a cell-free nucleic acid molecule.

27 . The method of claim 24 , further comprising determining a state of health of said tissue by (i) comparing a quantity of said at least one nucleic acid molecule against a reference to identify a relative abundance of said at least one nucleic acid molecule, (ii) aligning said nucleic acid sequence or portion thereof to a genome of said subject to identify a location of said nucleic acid sequence or portion thereof, which location is indicative of said state of health, or (iii) comparing a nucleic acid sequence or portion thereof to a reference to determine an apoptotic pattern, necrotic pattern, or predetermined mutations.

28 . A method of identifying a tissue of origin of a tumor metastasis in a subject, comprising:
(a) sequencing at least one nucleic acid molecule from a tumor metastasis of said subject to generate a nucleic acid sequence of said at least one nucleic acid molecule; (b) identifying one or more mutations in said nucleic acid sequence; and (c) using a mutation map of said subject in computer memory, identifying with a programmed computer processor a tissue of said subject associated with said nucleic acid molecule based on said one or more mutations identified in (b), thereby identifying said tissue of origin.

29 . The method of claim 28 , further comprising treating said subject, wherein said treating comprises administering an anti-cancer agent to said subject that is selected based on said tissue of origin.

30 . The method of claim 28 , wherein said mutation map is a developmental mutation map or a spatial mutation map.

Assignees

• Personalis Inc

Inventors

• West John

Classifications

• C12Q1/6809

  Methods for determination or identification of nucleic acids involving differential detection · CPC title

• G16B45/00

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

• A61K31/7068 Primary

  having oxo groups directly attached to the pyrimidine ring, e.g. cytidine, cytidylic acid · CPC title

• C12Q1/6827

  for detection of mutation or polymorphism · CPC title

• C12Q1/6886 Primary

  for cancer (immunoassay for cancer G01N33/575) · CPC title