Electronic Machine Intelligence Lab (EMIL)

This page is read only. You can view the source, but not change it. Ask your administrator if you think this is wrong.
[[nanoscope:start | Nanoscope Home]]

===== - Biochemical Analysis Instrument =====

Priority: Dec. 1, 2009

• [0006] In many DNA sequencing instruments, individual strands or clonally amplified colonies of limited lengths of DNA are localised to a surface or a bead.  This surface/bead array is usually in a flow cell that enables reagents to be passed across them thus applying chemistries of various types that allow the DNA to be decoded.  The biochemical analysis process within most instruments uses a **step wise cyclical chemistry**, followed by an **imaging stage** to detect the incorporation, annealing or removal of chemically labelled fluorescent probes that enable the DNA under study to be decoded.\\

==== - Problems with Typical Sequencing Instruments [0008]-[0014] ====

==== - Apparatus [0086] - [0089] ====
{{ instrument.png?400}}

• A network of sequencing modules 2.

==== - Sequencing Module [0090] - [] ====
{{module.png?300}}
[0090] The module 2 has a cartridge 10 that is replaceable in the housing 11.  That is the cartridge 10 is loaded into module 2.

=== - Cartridge ===
{{ cartridge1.png?400}}

• [0093] - [0097] The sensor device.\\
• [0098] **Reservoirs** 30 contain the needed chemicals (buffer, lipids, proteins, pre-treatment, sample, etc.)\\
• [0099] **Inlet pumps** 33 pump fluids from reservoirs to the sensor 14.\\
• [0099] **Fluidic system** 31 consisting of **supply channels** 32 connects the inlet pumps to the sensor.\\
• [0099] **Output pump** 34 pumps fluids out of the sensor through **outlet channel** 36 (connected to **waste reservoir** 35 on the bottom).\\
• [0100] **Selector valve** 45 connects the sensor to either the supply or the waste reservoir.\\

{{ cartridge2bot.png?300}}
{{cartridge2.png?300}}
{{wellplate.png?200}}

==== - Three Sensor-on-PCB Alternatives [0148] - [0151] ====
{{ pcb1.png?350}}
• [0148] The sensor device 14 is formed in a chip that is mounted on a PCB 38 and electrically connected to the PCB.  In turn, electrical contacts from the PCB are arranged as an edge connector pad 39.  Inserting the cartridge 10 into the module 2, the contacts 39 make electrical connection to the remainder of the electrical circuit in the module 2.\\
• [0149] In the first possible design 14 is a silicon chip with wells etched into it and electrodes at the bottom of each well.  Through-silicon-vias (TSVs) route the electrodes from the top of the chip (i.e. at the base of the wells) to the bottom of the chip.  This is as discussed in the [[oxforddec192007:start | Dec. 19, 2007 patent]].\\
• [0149] The TSVs at the bottom are solder-bumped to the PCB.
{{oxforddec192007:tsv1.png?340}}
{{ pcb2.png?350}}
• [0149] In turn the PCB connects these wires to **ASICs** 40 on the other side of the PCB.\\
• [0149] The ASICs may include for example an amplifier, a sampling circuit and an ADC.  The **digital output** is supplied from the contacts 39 using for example LVDS.  Alternatively the signal may be provided in amplified analog form with ADC provided within the module.\\
• [0149] The ASICs may also include some components of control circuits for example accepting power and control commands via the contacts in order to set and monitor functioning parameters, including for example current measurement sample rate (1 Hz to 100 kHz) integration capacitors, bit resolution, applied bias voltage.\\
• [0150] The second options is to simply connect the sensor chip directly to the contacts 39 and then use some appropriate ASIC like the [[http://www.flir.com/cvs/cores/view/?id=51965|FLIR ISC 9717]].\\
• [0151] The third option is to fabricate the sensor 14 and ASIC 40 as one device mounted on the PCB 38.
{{isc9717_large.jpg?340}}

==== - Configuration of Module 2 [0152]-[] ====
{{ moduleopen.png?340}}
• [0152] **Internal board** 50 connects to 39 when the cartridge 10 is inserted in the module 2.\\
• [0152] An **embedded computer** 51 is inside the module.\\
• [0152] 50 and 51 are connected by a **PCI data acquisition module** 52.\\
• [0156] The **fluidics actuation unit** 60 on internal board 50 controls the fluidics system 31.\\
• [0157] The **thermal control element** 42 controls the temperature of the cartridge 10.
An example is the [[https://thermal.ferrotec.com/index.php?id=module_detail&mod_id=69|Ferrotec Thermoelectric Module]]. It may be mounted underneath the cartridge.\\
• [0159] The circuits two main functions are **signal processing** and **control**.\\

=== - Signal Processing Function [0160] - [0175] ===
• [0160] Signal processing is distributed between the internal board 50 and the embedded processor 51.\\
{{ moduleblock.png?500}}
• [0161] The sensor device is connected to a **switch arrangement** as described in [[oxfordapr202009a:start | Apr. 20, 2009 patent]].  As before, there are more well electrodes 22 than **detection channels** 65.\\
• [0162] Alternatively the switch arrangement 62 may be provided and controlled separately from the ASIC 40.\\

{{detectionchan.png?200}}

• [0163] The ASIC 40 provides an **array of detection channels** 65.\\
• [0164] The charge amplifier 66 integrates the current supplied thereto from the well 21 to provide an output representative of the charge supplied in successive integration periods.\\
• [0164] Each channel has an ADC as well (it seems).

{{ embedded.png?500}}

• [0165] The FPGA 72 on the internal board 50 includes a buffer arranged to buffer the digital signals from each detection channel 65 before supply via the PCI data acquisition module 52 to the embedded computer 51.\\
• [0166] Alternatively some readout chip on 50 could be feeding the FPGA.\\
• [0168] The embedded computer 51 processes the digital data from each channel.  51 includes a **processing module** 73 implemented in software that includes a **pipeline** 74 in respect of each channel.\\
• [0169] The pipeline 74 processes the raw output data representing the measured electrical signal to produce output data representing the results of the biochemical analysis in respect of the corresponding channel.  Interactions between the nanopore and the sample cause characteristic changes in the electrical current that are recognizable events.  Thus, the pipeline 74 detects those events and generates output data that is event data representing those events.  Examples of such processing are disclosed in the [[oxfordfeb202007:start | Feb. 20, 2007 patent]].\\
• [0169] The **output data** that is event data may in the simplest case represent only the fact that the event has occurred, but more typically includes other information about the event, for example the **magnitude and period of the event**.\\
• [0170] Additionally, the pipeline may classify the event and output data may represent the classification of the event.  In the context of poly nucleotide measurements this may be referred to as **base calling**.\\
• [0171] The pipeline also produces output data that is **quality data** representative of the quality of the output data that represents the results of the biochemical analysis.  This may represent a probability of the detection and/or classification of the events being incorrect.\\
• [0174] The processing module 73 may also derive and store quality control metrics representing parameters of the biochemical analysis itself.\\
• [0175] Could also do some of the pipeline work on the FPGA 72 on the internal board 50.\\

=== - The Control Function [0176]-[0203] ===
• [0176] The control function is distributed between the internal board 50 and embedded computer 51.\\
• [0177] The control function includes a **controller** 58, for example a [[http://www.arm.com/products/processors/cortex-m/cortex-m3.php|Cortex M3 microcontroller]], provided on the internal board 50.\\
• [0178] Controller 50 itself controlled by **control module** 80 implemented in embedded computer 51.  50 and 80 communicate via RS232 81.\\
• [0201] The analysis apparatus 13 (where is this 13?!?!?!) may contain **control DNA** spiked into real samples.  Data from the control DNA can be used to adjust and refine the algorithms.

==== - Cluster of Modules [0204] - [0243] ====

==== - Manner of Module Networking [0244] - [0251] ====

==== - Implementation Examples [0252] - [0260] ====

==== - Specifics on Sequencing Example 1 [0261] - [0275] ====

==== - Details of Biochemical Analysis that can be Performed [0276] - [0298] ====

• [0282] nanopore-assisted sequencing by hydridisation; strand sequencing; and exonuclease-nanopore sequencing\\
• [0284]  External circuitry can then perform measurements of DNA passing through each and every nanopore in the array **without the synchronization of base addition** to each nanopore in the array, i.e. each nanopore is free to process a single DNA strand independently of every other, for example as disclosed in [[oxforddec192007:start | Dec. 19, 2007 patent]].\\
• [0284] Having processes one strand, each nanopore is also then free to begin processing a subsequent strand.\\