SNP Genotyping at home - lab protocol?

[Mike Petersen]

Hi everybody,
let´s say I would like to do a genotyping at home. Does anybody know how to do that?
Is there anything like a lab protocol?
So for example I´m looking for a special SNP like the lactose intolerance SNP (http://www.snpedia.com/index.php/Rs4988235)
I know, I could do a test with a gene chip with a company like 23andme.
But just for my interest: Is there any way to find out a special SNP in the DIY-way at home?
Get the DNA, isolate it, do the PCR to amplify but what to do next?

Thank you in advance

Mike

[Kermit Henson]

You need to sequence the gene. Sanger is a cheap way to do that, but you will have to look for some company. After that, you compare your sequence withsome database. But to be sure about theresults, you have to use controls during your dna extraction and pcr amplification, and check them also by sanger.
Before Sanger, remember that you have to clean your sample.

If the mutation that you are looking for is enough big (lets say normal gene size is 1kb and mutated gene size is 0,7kb) you could check it by agarose electrophoresis, after PCR. But is not the usual case in human genetics

[scoc...@gmail.com]

My worry is seq error on dirty samples. Either the signal drops too soon, like barely 300bp in, or a robot error. Scanning for a single bp change may need more than a single pass.

Sebastian S. Cocioba
CEO & Founder
New York Botanics, LLC
Plant Biotech R&D

---

From: Kermit Henson
Sent: ‎10/‎22/‎2014 2:38 AM
To: diy...@googlegroups.com
Subject: [DIYbio] SNP Genotyping at home - lab protocol?

You need to sequence the gene. Sanger is a cheap way to do that, but you will have to look for some company. After that, you compare your sequence withsome database. But to be sure about theresults, you have to use controls during your dna extraction and pcr amplification, and check them also by sanger.
Before Sanger, remember that you have to clean your sample.

If the mutation that you are looking for is enough big (lets say normal gene size is 1kb and mutated gene size is 0,7kb) you could check it by agarose electrophoresis, after PCR. But is not the usual case in human genetics

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[j boogie]

Amplify the gene in question and use a quantitative realtime PCR assay and look for differences in high resolution melt curve vs control. 

Or, drink 3 glasses of milk, wait a couple months on lactose free diet, and drink some of the lactose-free stuff. Then analyse your feelings? That is the old school way, the gut feeling. That and tallying those in your lineage who have it, and arriving at a conclusion that is, if not empirical, at least probable in a Bayesian sense.

I would recommend the 23andme sequencing, I got mine done. As long as you are comfortable with the reported error rate- which could be diminished with repeat sequencing and some sort of alignment algorithm. Otherwise you are talking a lot of work and access to expensive hardware.