US-12623224-B2 - Integrated optoelectronic read head and fluidic cartridge useful for nucleic acid sequencing

US12623224B2US 12623224 B2US12623224 B2US 12623224B2US-12623224-B2

Abstract

A detection apparatus having a read head including a plurality of microfluorometers positioned to simultaneously acquire a plurality of the wide-field images in a common plane; and (b) a translation stage configured to move the read head along a substrate that is in the common plane. The substrate can be a flow cell that is included in a cartridge, the cartridge also including a housing for (i) a sample reservoir, (ii) a fluidic line between the sample reservoir and the flow cell; (iii) several reagent reservoirs in fluid communication with the flow cell, (iv) at least one valve configured to mediate fluid communication between the reservoirs and the flow cell; and (v) at least one pressure source configured to move liquids from the reservoirs to the flow cell. The detection apparatus and cartridge can be used together or independent of each other.

Inventors

Dale Buermann
John A. Moon
Bryan Crane
Mark Wang
Stanley S. Hong
Jason Harris
Matthew Hage
Mark J. Nibbe

Assignees

ILLUMINA, INC.

Dates

Publication Date: 20260512
Application Date: 20221229

Claims (6)

1 . A fluidics cartridge, comprising: a flow cell comprising an optically transparent surface, an inlet port and an outlet port; and a housing comprising a material that is optically opaque, wherein the housing holds: a plurality of reagent reservoirs in fluid communication with the flow cell via the inlet port of the flow cell and via the outlet port of the flow cell; a valve; first fluidic lines respectively connecting each of the plurality of reagent reservoirs to the valve; a second fluidic line connecting the valve to the inlet port of the flow cell; a pump to move a fluid from at least one of the plurality of reagent reservoirs to the flow cell and from the flow cell back to the at least one of the plurality of reagent reservoirs; a third fluidic line connecting the outlet port of the flow cell to the pump; a second valve to control fluid flow from the flow cell to each of the plurality of reagent reservoirs; a fourth fluidic line connecting the pump to the second valve; and fifth fluidic lines respectively connecting each of the plurality of reagent reservoirs to the second valve; wherein an optically transparent window interrupts the housing, and wherein the optically transparent surface is positioned in the optically transparent window.
2 . The fluidics cartridge as defined in claim 1 , further comprising: a waste reservoir; and a sixth fluidic line connecting the waste reservoir to the second valve.
3 . A fluidics cartridge, comprising: a flow cell comprising an optically transparent surface, an inlet port and an outlet port; and a housing comprising a material that is optically opaque, wherein the housing holds: a plurality of reagent reservoirs in fluid communication with the flow cell via the inlet port of the flow cell; a plurality of supplemental reservoirs in fluid communication with the flow cell via the outlet port of the flow cell; a first valve; first fluidic lines respectively connecting each of the plurality of reagent reservoirs to the first valve; a second fluidic line connecting the first valve to the inlet port of the flow cell; a second valve; a pump to move a fluid from at least one of the plurality of reagent reservoirs to the flow cell and from the flow cell to one of the plurality of supplemental reservoirs; a third fluidic line connecting the outlet port of the flow cell to the pump; a fourth fluidic line connecting the pump to the second valve; and fifth fluidic lines respectively connecting each of the plurality of supplemental reservoirs to the second valve; wherein an optically transparent window interrupts the housing, and wherein the optically transparent surface is positioned in the optically transparent window.
4 . The fluidics cartridge as defined in claim 3 , further comprising: a waste reservoir; and a sixth fluidic line connecting the waste reservoir to the second valve.
5 . The fluidics cartridge as defined in claim 3 wherein: the plurality of supplemental reservoirs are fluidically connected to the first valve; and the first valve includes dedicated ports to deliver used liquids from each of the plurality of supplemental reservoirs to the flow cell.
6 . The fluidics cartridge as defined in claim 3 , further comprising a third valve fluidically connected to the plurality of supplemental reservoirs to respectively deliver used liquids from each of the plurality of supplemental reservoirs to the flow cell.

Description

CROSS-REFERENCE TO RELATED APPLICATIONS This application is a continuation of co-pending U.S. application Ser. No. 16/735,001, filed Jan. 6, 2020, which itself is a continuation of U.S. application Ser. No. 15/594,413, filed May 12, 2017, which itself is a division of U.S. application Ser. No. 14/335,117, filed Jul. 18, 2014, now U.S. Pat. No. 9,650,669, which is itself a division of U.S. application Ser. No. 13/766,413, filed Feb. 13, 2013, now U.S. Pat. No. 9,193,996, which itself is based on, and claims the benefit of, U.S. Provisional Application No. 61/619,784, filed Apr. 3, 2012, each of which is incorporated herein by reference in its entirety. BACKGROUND Embodiments of the present disclosure relate generally to apparatus and methods for fluidic manipulation and optical detection of samples, for example, in nucleic acid sequencing procedures. Our genome provides a blue print for predicting many of our inherent predispositions such as our preferences, talents, susceptibility to disease and responsiveness to therapeutic drugs. An individual human genome contains a sequence of over 3 billion nucleotides. Differences in just a fraction of those nucleotides impart many of our unique characteristics. The research community is making impressive strides in unraveling the features that make up the blue print and with that a more complete understanding of how the information in each blue print relates to human health. However, our understanding is far from complete and this is hindering movement of the information from research labs to the clinic where the hope is that one day each of us will have a copy of our own personal genome so that we can sit down with our doctor to determine appropriate choices for a healthy lifestyle or a proper course of treatment. The current bottleneck is a matter of throughput and scale. A fundamental component of unraveling the blue print for any given individual is to determine the exact sequence of the 3 billion nucleotides in their genome. Techniques are available to do this, but those techniques typically take many days and thousands upon thousands of dollars to perform. Furthermore, clinical relevance of any individual's genomic sequence is a matter of comparing unique features of their genomic sequence (i.e. their genotype) to reference genomes that are correlated with known characteristics (i.e. phenotypes). The issue of scale and throughput becomes evident when one considers that the reference genomes are created based on correlations of genotype to phenotype that arise from research studies that typically use thousands of individuals in order to be statistically valid. Thus, billions of nucleotides can eventually be sequenced for thousands of individuals to identify any clinically relevant genotype to phenotype correlation. Multiplied further by the number of diseases, drug responses, and other clinically relevant characteristics, the need for very inexpensive and rapid sequencing technologies becomes ever more apparent. What is needed is a reduction in the cost of sequencing that drives large genetic correlation studies carried out by research scientists and that makes sequencing accessible in the clinical environment for the treatment of individual patients making life changing decisions. Embodiments of the invention set forth herein satisfy this need and provide other advantages as well. BRIEF SUMMARY The present disclosure provides a detection apparatus that includes (a) a carriage including a plurality of microfluorometers, wherein each of the microfluorometers has an objective configured for wide-field image detection, wherein the plurality of microfluorometers is positioned to simultaneously acquire a plurality of the wide-field images in a common plane, and wherein each of the wide-field images is from a different area of the common plane; (b) a translation stage configured to move the carriage in at least one direction parallel to the common plane; and (c) a sample stage configured to hold a substrate in the common plane. This disclosure further provides a method of imaging a substrate, including the steps of (a) providing a substrate including fluorescent features on a surface; (b) acquiring a plurality of wide-field images of a first portion of the surface using a plurality of microfluorometers, wherein each of the microfluorometers acquires a wide-field image from a different location of the surface, wherein the plurality of microfluorometers are affixed to a carriage; and (c) translating the carriage in a direction parallel to the surface and repeating (b) for a second portion of the surface. The method can use any of the apparatus set forth elsewhere herein, but need not be so limited in all embodiments. Also provided is a fluidics cartridge that includes (a) a flow cell having an optically transparent surface, an inlet and an outlet; and (b) a housing made of a material that is optically opaque and impermeable to aqueous liquids, wherein the housing holds: