Electronic Machine Intelligence Lab (EMIL)

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===== - ISFET Array for Detecting a Single Nucleotide Polymorphism =====

Priority: Mar 30, 2012

(from WO 2013/144580 A1)

==== - Technical Field ====

==== - Background ====

• 99.9% of the code is similar among the human population and it is the remaining 0.1% that makes the differences.\\ 
• Single Nucleotide Polymorphism is a single mutation of a gene that can be found in more than 1% of a population.\\
• How to detect if a particular sequence is in the genome?  If a primer attaches then it matches and it can be extended.  This extension of a primer on the target releases pyrophosphate and H+ ions [3]. Therefore, by detecting whether the acidity in the analyte has increased or not, it is possible to determine whether extension has occurred or not; and consequently whether the designed sequence was matched or not.\\
• …the presently used platform for ISFETs has made them power and memory intensive.\\
• The presently used platforms are required to process large amounts of data in order to provide a yes/no answer saying a particular polymorphism is detected in the target DNA or not. These intensive requirements are mainly due to the existence of sources of error that need to be cancelled out in the measurement.

==== - ISFETs in SNP Detection ====

• The use of an ISFET in sequencing and SNP detection relies on the fact that hydrogen ions are released as a result of hydrolysis of pyrophosphate, a by-product of the extension of primer/probe strands on target DNA strands when they match\\
• rather than taking an absolute measurement of the pH, detection of its change is enough to be able to determine whether the designed probe with a known sequence matches with the target. Therefore, having a REFET that is used to detect all non-ideal signals and subsequently cancel them out from a working ISFET in a differential configuration, can provide for a reliable monitoring of the pH change [11, 12]\\
• Consequently, the REFET is exposed to a mixture of non-extendable (i.e. non-matching) primer with nucleotides, enzymes and target DNA strands to provide the same condition as for the working ISFET except the pH change [13].\\
• FIG. 6 shows the configuration that is typically used during ISFET-based sequencing for SNP detection.

{{ fig6.png?400}}

==== - Existing Technology ====

• Toumazou is beating up on his 2010 ISSCC paper ("A multichannel DNA SoC for rapid point-of-care gene detection,").\\
• Drawbacks of the ISSCC system are:
  * Small pH changes and sensitivity (Ideal is 59 mV/pH and in practice pH drops by one unit or less).
  * Single REFET
  * Reference Electrode
  * Monitoring/Tracking the Reaction
  * ISFET Interface
  * Analogue to Digital Converters (ADCs) (a 10-bit ADC for **each** ISFET in array!!!)

==== - Summary ====

In my words\\

• You have four small chambers (per "feature"?), each containing, A,C,G,T, respectively.\\
• In each of these chambers you pump your target DNA and a primer (and some enzyme).\\
• With this we are looking for a SNP in the n+1 position of the target.\\
• Ostensibly the primer (of length n) binds to the DNA at the predetermined spot (defined by the sequence of the primer itself).\\
• The chamber containing the nt that complements the SNP (in the n+1 position) will then undergo a hydrolisis reaction that drops the pH and is detected by an ISFET.\\
• The ISFET's (one per chamber) are **cleverly interfaced** (__this is basically the invention__) to four differential amps (based on knowledge of allele possibilities in mammals) which produce signal combinations such that the type of SNP encountered can be identified.\\
• This arrangement reduces the effect of offsets and the need for extensive, high-resolution sampling.

==== - Detailed Description ====

{{fig8a.png?300 }}
{{ fig8b.png?300 }}

=== - New Differential Scheme (REFET-Less) ===

•  Instead of measuring each ISFET signal, a differential measurement is calculated while the signal is also amplified at the point of measurement.\\
{{ fig9.png?200}}
• This can ease the work of an ADC, but more advantageously an ADC may not even be required.\\
• …each chamber (A, T, C, G) has two ISFETs\\
• Each ISFET provides one of the input pair transistors in a differential amplifier. Four differential amplifiers are used (X, Y, Z, W).\\
• The ISFETs are wired in a way that one of the two ISFETs of a chamber makes the non-inverting input of an amplifier and the other one creates the inverting one in another amplifier. In this configuration, the previously known design of an interface with several buffers and offset-cancelling circuits has been replaced with single simple differential amplifiers.\\
• In this method, and with this configuration, there is no need for a separate REFET as the common non-ideal signals are cancelled out by the differential measurements.\\
• An embodiment has been described that uses differential amplifiers to provide the differential measurement. However, other components can be used in place of differential amplifiers. For example, rather than take the difference in voltages (as is the case for differential amplifiers), it is possible to transform the signal into currents and then subtract currents from each other. This is carried out using trans-conductance amplifiers in place of the differential amplifiers. A further alternative is to use comparators in place of the differential amplifiers. The term “difference detectors” can be used to cover all suitable components. Difference detectors can be seen as “subtractors”, which substract one input from another to find the difference between the two.\\

=== -  A DNA Gate Array ===

=== - A REFET-Less DNAGA ===

=== - A Sample Scenario ===

==== - Summary ====

• Novel methods have been discussed that overcome the difficulties that are experienced with current ISFET-based sequencing and SNP detection chips, in particular power and memory.\\