Project:Sex typing with amelogenin

General

The general plan, with thanks to Maria, is: obtain dna samples, extract dna, pcr dna with amelogenin primers, and then run that on agarose gel.

There is still work that could be done, checking the legals, ethics and safety. eg: [1] [2] [3]

I figure we try to arrive at a definitive list of stuff (bill of materials) we need for the experiment, and source the bits we still need, perhaps avoiding unnecessary multiple delivery charges.

There is also a need to figure out how long this will all take and schedule it. The overall duration from start to finish is going to be quite long.

It might help to try out some parts, such as the extraction, before hand, although I don't see how we know whether that works until we run it through the rest. We could practise making gels, running a ladder on them, to figure out mixtures and timings and practise with detecting the dye.

Sampling

Current plan is to sterilise plastic sticks for consenting adult volunteers to rub inside their cheeks. Legally (I am so not a lawyer, and this is not legal advice), reading them a written spiel and getting their verbal agreement with witnesses and seeing them take the sample seems to be sufficient , although the suggestion has been made that a simple signed form might help avoid a possible problem with forgetful witnesses.

cotton swabs are another possible option.

Extraction

There are a number of written protocols out there

[4]

[5]

and a few videos on youtube

This seems to be the typical hackers version [6] which is basically soap to lyse the cells and then meat tenderiser as a protease and separation using alcohol. Reagents are all commonly available, so seems safe enough. will this will work with PCR?

Katherine Aull was boiling hers to get lysis and denature the proteins.

do we also need to do DNA precipitation? [7] why?

The sampling and extraction are crucial steps if the following steps are to work. dna contamination can be amplified in the pcr stage. there is a suggestion that there is an amount of black art in getting this to work well. It might repay the effort to try several different extractions and run them side by side for comparison.

PCR

[8] File:Polymerase.pdf Media:DNA_Ladders.jpg

paper more-or-less at random, Eng 1994 where it gives:

PCR Amplification of the Amelogenin Locus The primers used to amplify the X and Y amelogenin sequences were previously described by Nakahori and colleagues [6]. The primer sequences are as follows: primer AMXY-1F (5'-CTGATGGTTGGCCTCAAGCCTGTG-3') primer AMXY-2R (5'-TAAAGAGATTCATTAACTTGACTG-3') PCR was conducted using the Perkin-Elmer GeneAmp | PCR System 9600 Thermal Cycler. Genomic DNA samples were amplified in a 100 txL reaction volume containing 0.2 mM of each dNTP, 50 mM KCI, 10 mM Tris.HC1 pH 8.3, 4.0 mM MgC12, 120 pmoles of each primer, and 2.5 U Taq polymerase. PCR was run for 30 cycles of 94~ for 1 rain (denature), 65~ for 2 min (anneal), and 72~ for 3 min (extend). Following amplification, the PCR products were analyzed by electrophoresis on 1.2% agarose gels run with 1 X TBE (89 mM Tris borate, 89 mM boric acid, 2 mM EDTA) or 6% nondenaturing polyacryl- amide gels run with 1 X TBE. The gels were stained with ethidium bromide and the fragments were visualized by fluorescence under ultraviolet light.

Andy suggests that we go with the instructions on our polymerase for the PCR.

S4438 (with SYBR green)[9]

D6442 (without)[10]

There is a question mark over whether we need a smaller pippette, or perhaps we can let out some solutions to use a larger volume. Katherine Aull was using syringes.

We need tubes for the thermal cycler.

We have SYBR green to replace the ethidium bromide.

Gel electrophoresis

Eng has

1.2% agarose gels run with 1 X TBE (89 mM Tris borate, 89 mM boric acid, 2 mM EDTA)

If our dye is SYBR Green I then we need blue light (λmax = 497 nm)

It seems we need to manufacture new electrophoresis equipment or has someone taken it to be repaired? I looked into the possibility of making the gel tray as a single bent piece, but the guys I know said they couldn't do it on 5mm acetate.

We are still looking for a better alternative to the copper electrode that gets eaten by the reagents.

It is common to run reference samples (ladders) alongside the samples, so as to see that weight of the sample. would also be handy to calibrate this process first. ladders can be bought, do we already have?

So, we need TAE or TBE for the buffer.

Tris Safety Data Sheet Boric Acid Safety sheet Example COSHH for PCR and gel electrophoresis with TAE

Results

Individuals with deletions such that this test doesn't work on them are extremely rare. So we hope to get correct results for all samples. We discussed blinding the samples to avoid possible bias in interpretation reading the gel, but if we can photograph the gel that could serve that purpose.

It might be nice to do video recording and a write up.

First gel run, Dec 7, 2011

On this date, we had not yet received our PCR tubes, so we were unable to do PCR. Instead, we decided to test our ability to do electrophoresis, using a DNA ladder and SafeWhite stain. We followed the following protocol:

* Agarose, added to buffer, microwaved. 1 gram of agarose to 100ml of tbe: 1% agarose mix will work for 0.4 to 7kb
* cool in a water bath set at 50-55c.
*  add 5 ul of ethidium bromide to gel if using ethidium bromide. If using safewhite add nothing yet
* Add gel to mold: cover sides with masking tape
* Add comb to gel
* Put in fridge for half an hour (or, basically: cool until completely set)
* remove comb.
* prepare sample: 5ul of ladder and 2 ul of safewhite (for the 6x solution)
* add sample to gel tray.
* electrophorese at 100v for 1 hour. Negative terminal closest to DNA
* Visualise under UV at 280-300nm.

The reference I used for this protocol: http://www.biocompare.com/protocols/protocol/318/Agarose-Gel-Electrophoresis.html

Unfortunately we were unable to detect any green glow which would indicate that the DNA in the ladder had bound to the Safewhite.

We resolved to make the next test a simple visualisation test: combine ladder with Safewhite and attempt to visualise under UV.

Future Work

Given that we get this working, it should provide a basis for further experiments. As far as I understand it, it is possible to apply this sort of technique, with appropriate primers, to do detection of SNPs [11] opening up the possibility of testing for something common like RHD or MC1R alleles, and perhaps providing a resource for people who want to genetically test themselves for rarer things a la Katherine Aull (but it is much simpler and cheaper to get such tests run commercially, and there is a difficult ethical case to answer about providing genetic testing without proper expert medical support and interpretation of results).