Sample preparation for sequencing

Patent metadata

Field	Value
Publication number	US-2021354134-A1
Application number	US-202117236858-A
Country	US
Kind code	A1
Filing date	Apr 21, 2021
Priority date	Apr 22, 2020
Publication date	Nov 18, 2021
Grant date	—

Abstract

Methods and devices for preparing target molecules (e.g., target nucleic acids or target proteins) from a biological sample are provided herein. In some embodiments, methods and devices involve sample lysis, sample fragmentation, enrichment of target molecule(s), and/or functionalization of target molecule(s).

First claim

What is claimed is:

1 . A device for preparing a biological sample for sequencing, wherein the device comprises an automated module configured to receive (i) a lysis cartridge comprising one or more microfluidic channels and configured to intake a biological sample comprising one or more target molecules and produce a lysed sample; and one or more of the cartridges selected from (ii) an enrichment cartridge, (iii) a fragmentation cartridge, and (iv) a functionalization cartridge; wherein (ii), (iii), and (iv) are defined as follows:
(ii) an enrichment cartridge comprises one or more microfluidic channels and is configured to enrich at least one of the one or more target molecules to produce an enriched sample; (iii) a fragmentation cartridge comprises one or more microfluidic channels and is configured to digest or fragment at least one of the one or more target molecules to produce a fragmented sample; and (iv) a functionalization cartridge comprises one or more microfluidic channels and is configured to functionalize a terminal moiety of at least one of the one or more target molecules to form a functionalized sample.

2 . The device of claim 1 , wherein the biological sample is a single cell, mammalian cell tissue, animal sample, fungal sample, plant sample, blood sample, saliva sample, sputum sample, fecal sample, urine sample, buccal swab sample, amniotic sample, seminal sample, synovial sample, spinal sample, or pleural fluid sample.

3 . The device of claim 1 , wherein the one or more target molecules are nucleic acids or proteins.

4 . The device of claim 1 , wherein the one or more microfluidic channels are configured to contain and/or transport fluid(s) and/or reagent(s).

5 . The device of claim 1 , wherein the lysis cartridge comprises reagents that lyse the sample but does not degrade or fragment the one or more target molecules.

6 . The device of claim 1 , wherein the lysis cartridge comprises reagents that promote the one or more target molecules to be at least partially isolated or purified from non-target molecules of the sample.

7 . The device of claim 5 , wherein the reagents comprise detergents, acids, and/or bases.

8 . The device of claim 1 , wherein the one or more microfluidic channels in the lysis cartridge promote shearing of cells and/or tissues.

9 . The device of claim 1 , wherein the lysis cartridge comprises a needle passage that promotes mechanical shearing of cells and/or tissues.

10 . The device of claim 1 , wherein the one or more microfluidic channels in the lysis cartridge comprise a post array.

11 . The device of claim 1 , wherein the lysis cartridge is configured to be heated at an elevated temperature, optionally wherein the elevated temperature is between 20° C. and 60° C.

12 . The device of claim 1 , wherein the module is further configured to receive an enrichment cartridge, optionally wherein the enrichment cartridge is positioned to receive the lysed sample from the lysis cartridge.

13 . The device of claim 1 , wherein the module is further configured to receive a fragmentation cartridge, optionally wherein the fragmentation cartridge is positioned to receive the lysed sample from the lysis cartridge.

14 . The device of claim 1 , wherein the module is further configured to receive a functionalization cartridge, optionally wherein the lysis cartridge and the functionalization cartridge are connected by one or more microfluidic channels.

15 . The device of claim 1 , wherein the device further comprises a sequencing module, optionally wherein the sequencing module performs nucleic acid sequencing or protein sequencing.

16 . A device for preparing one or more target molecules, configured to perform step (i) lyse a biological sample comprising one or more target molecules; and one or more of the following steps selected from (ii), (iii), and (iv),
wherein (ii), (iii), and (iv) are defined as follows:
(ii) enrich at least one of the one or more target molecules and/or at least one non-target molecule;
(iii) fragment the one or more target molecules; and
(iv) functionalize a terminal moiety of the one or more target molecules.

17 . The device of claim 16 , wherein one or more of the steps selected from (i), (ii), (iii), and (iv) are performed in a cartridge.

18 . The device of claim 16 , wherein the one or more steps are performed in the same cartridge.

19 . A method for preparing one or more target molecules, configured to perform step (i) lyse a biological sample comprising one or more target molecules; and one or more of the following steps selected from (ii), (iii), and (iv),
wherein (ii), (iii), and (iv) are defined as follows:
(ii) enrich at least one of the one or more target molecules and/or at least non-target molecule;
(iii) fragment the one or more target molecules; and
(iv) functionalize a terminal moiety of the one or more fragmented target molecules;
wherein one or more of the steps is performed in an automated sample preparation device.

20 . A cartridge for preparing one or more target molecules, configured to perform two or more of the following steps selected from:
(i) lyse a biological sample comprising one or more target molecules; (ii) enrich at least one of the one or more target molecules and/or at least one non-target molecule; (iii) fragment the one or more target molecules; and (iv) functionalize a terminal moiety of the one or more target molecules.

Assignees

• Quantum Si Inc

Inventors

• Rothberg Jonathan M
• Leamon John H
• Schultz Jonathan C
• Millham Michele
• Lv Caixia
• Huang Haidong
• Nani Roger
• Ad Omer
• Reed Brian
• Dyer Matthew
• Boer Robert E

Classifications

• G01N33/6818 Primary

  Sequencing of polypeptides · CPC title

• B01L3/5027

  by integrated microfluidic structures, i.e. dimensions of channels and chambers are such that surface tension forces are important, e.g. lab-on-a-chip · CPC title

• B01L2300/0636

  Integrated biosensor, microarrays · CPC title

• C12Q1/6869

  Methods for sequencing · CPC title

• B01L2300/087

  Multiple sequential chambers · CPC title