Differences

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--- geneonyxmar302012:start [2015/05/06 02:06] – magiero
+++ geneonyxmar302012:start [2015/05/06 03:53] (current) – magiero
@@ Line 24: / Line 24: @@
 • FIG. 6 shows the configuration that is typically used during ISFET-based sequencing for SNP detection.
-[[fig6.png]]
+{{ 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.\\