# US 2021/0277464 A1 · Methods, devices, and systems for analyte detection and analysis

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- Number: US 2021/0277464 A1
- Document ID: US20210277464A1
- Status: Published application
- Kind: A1
- Application number: 17/308,241
- Filed: 2021-05-05
- Published: 2021-09-09
- Earliest claimed: 2019-03-14
- Assignees: Ultima Genomics, Inc.
- Applicants: Ultima Genomics, Inc.
- Inventors: Nathan BECKETT; Gilad ALMOGY; Nathan CASWELL; Jacob A. WOLF; Kristopher BARBEE; Denis PRISTINSKI; Mark PRATT; Gene POLOVY; Osip SCHWARTZ; Stephanie KUBECKA; Steven MENCHEN; Joseph ANTHONY; Jose Martin SOSA; Phillip You Fai LEE
- Web page: https://patentgrep.com/patent/US20210277464A1

## CPC

- C12Q 1/6874: involving nucleic acid arrays, e.g. sequencing by hybridisation
- G01N 1/312: {for samples mounted on planar substrates}
- C12Q 1/6816: characterised by the detection means (C12Q1/6804 takes precedence)
- G01N 35/1002: {Reagent dispensers}
- C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
- G01N: INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES (measuring or testing apparatus or processes other than immunoassay, involving enzymes or microorganisms C12M, C12Q)

## Abstract

Provided are systems and methods for analyte detection and analysis. A system can comprise an open substrate. The open substrate may be configured to rotate or otherwise move. The open substrate can comprise an array of individually addressable locations, with analytes immobilized thereto. The substrate may be spatially indexed to identify nucleic acid molecules from one or more sources, and/or sequences thereof, with the respective one or more sources. A solution comprising a plurality of probes may be directed across the array to couple at least one of the plurality of probes with at least one of the analytes to form a bound probe. A detector can be configured to detect a signal from the bound probe via scanning of the substrate while minimizing temperature fluctuations of the substrate or optical aberrations caused by bubbles.

## Claims

### Claim 1

A method for dispensing a sample to a substrate surface, comprising: dispensing, via a sample dispenser, a sample solution comprising a plurality of beads onto said substrate surface along a path while said substrate surface and said sample dispenser are in relative motion, wherein said substrate surface comprises a plurality of individually addressable locations that receives and immobilizes said plurality of beads.

### Claim 2 (depends on 1)

The method of claim 1, wherein said substrate surface is substantially planar.

### Claim 3 (depends on 1)

The method of claim 1, wherein said substrate surface is patterned.

### Claim 4 (depends on 3)

The method of claim 3, wherein said substrate surface is patterned using surface chemistry.

### Claim 5 (depends on 1)

The method of claim 1, wherein said path is in a substantially spiral pattern.

### Claim 6 (depends on 5)

The method of claim 5, wherein said sample solution is dispensed onto said substrate surface in said substantially spiral pattern in a radially outward direction with respect to a central axis of said substrate.

### Claim 7 (depends on 5)

The method of claim 5, wherein said sample solution is dispensed onto said substrate surface in said substantially spiral pattern in a radially inward direction with respect to a central axis of said substrate.

### Claim 8 (depends on 5)

The method of claim 5, wherein a path width of said path is greater than a path pitch of said path, wherein said path pitch is a distance between a center of said path at a first position and a center of said path at a second position after one rotation of said substrate surface.

### Claim 9 (depends on 5)

The method of claim 5, wherein a path width of said path is less than a path pitch of said path, wherein said path pitch is a distance between a center of said path at a first position and a center of said path at a second position after one rotation of said substrate surface.

### Claim 10 (depends on 5)

The method of claim 5, wherein a path width of said path is substantially the same as a path pitch of said path, wherein said path pitch is a distance between a center of said path at a first position and a center of said path at a second position after one rotation of said substrate surface.

### Claim 11 (depends on 1)

The method of claim 1, wherein during said dispensing said sample dispenser is moving.

### Claim 12 (depends on 1)

The method of claim 1, wherein during said dispensing said substrate surface is moving.

### Claim 13 (depends on 12)

The method of claim 12, wherein during said dispensing (i) said substrate surface is rotating with respect to a rotational axis and (ii) said sample dispenser is moving with respect to said rotational axis of said substrate surface or said substrate surface is moving such that said rotational axis is moving with respect to said sample dispenser.

### Claim 14 (depends on 13)

The method of claim 13, wherein during said dispensing (i) said substrate surface is rotating with respect to a rotational axis and (ii) said sample dispenser is moving with respect to said rotational axis of said substrate surface and said substrate surface is moving such that said rotational axis is moving with respect to said sample dispenser.

### Claim 15 (depends on 13)

The method of claim 13, wherein said substrate surface is rotating at a rotational frequency of no more than 5 revolutions per minute (rpm).

### Claim 16 (depends on 1)

The method of claim 1, wherein said substrate surface comprises a set of first locations and a set of second locations different from said set of first locations, wherein each first location of said set of first locations has a higher affinity towards immobilizing a bead of said plurality of beads than said set of second locations, wherein said set of first locations comprises said plurality of individually addressable locations.

### Claim 17 (depends on 16)

The method of claim 16, wherein a first location of said set of first locations is not in contact with another first location of said set of first locations on said substrate surface.

### Claim 18 (depends on 17)

The method of claim 17, wherein said set of first locations and said set of second locations are alternating locations on said substrate surface.

### Claim 19 (depends on 16)

The method of claim 16, wherein said set of first locations carries a positive electrostatic charge with affinity towards a negative electrostatic charge, wherein a bead of said plurality of beads comprises a nucleic acid molecule coupled thereto, which nucleic acid molecule carries said negative electrostatic charge.

### Claim 20 (depends on 19)

The method of claim 19, wherein said set of first locations comprises APTMS and wherein said second set of locations comprises HMDS.

### Claim 21 (depends on 1)

The method of claim 1, wherein said plurality of beads comprises a first subset of beads and a second subset of beads, wherein said first subset of beads each comprises a respective template nucleic acid sequence coupled thereto and said second subset of beads does not comprise a template nucleic acid sequence.

### Claim 22 (depends on 21)

The method of claim 21, wherein subsequent to said dispensing said first subset of beads is immobilized to individually addressable locations of said plurality of individually addressable locations and said second subset of beads is not immobilized to said plurality of individually addressable locations.

### Claim 23 (depends on 1)

The method of claim 1, wherein a bead of said plurality of beads comprises a plurality of nucleic acid molecules having sequence identity.

### Claim 24 (depends on 1)

The method of claim 1, wherein said plurality of individually addressable locations comprise at least 50,000,000,000 individually addressable locations.