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First off, I'm new to bioinformatics and I am learning about DNA sequencing.

Let's say that I knew that a specific region of a genome which contained information about a disease (whether it a person had the disease or not).

It would make sense that we would only want to sequence that part of the genome in order to make a detector for this disease.

Would it be possible to 'cut-out' this region of the genome and only sequence that part (so we don't have to sequence the entire thing)? If not, how would we sequence only this part of the genome (it doesn't make sense to sequence the other parts as they don't give us information).

Thanks in advance.

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  • $\begingroup$ Yes, it's possible to sequence a certain region. Probably the most straightforward method would be PCR amplification. $\endgroup$ – canadianer Oct 26 '14 at 1:46
  • $\begingroup$ I have been doing a little researching, and I also found something called 'Targeted Resequencing', do you know whether this has anything to do with PCR amplification? $\endgroup$ – Luke Oct 26 '14 at 1:59
  • $\begingroup$ Resequencing is basically sequencing something that has already been sequenced. This means that instead of assembling all of your sequence reads from scratch, you can just align them to the reference sequence (the entire human genome has been sequenced). Targeted resequencing means your sequencing a specific region, such as a gene. The targeting can be done by PCR or by other methods. $\endgroup$ – canadianer Oct 26 '14 at 3:32
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Yes, it is possible to sequence a specific region of the genome. The method, as you mentioned, is called targeted sequencing. Resequencing is basically sequencing something that has already been sequenced. This means that instead of assembling all of your sequence reads from scratch, you can just align them to the reference sequence (in your case, the entire human genome has been sequenced). Targeted resequencing means you're sequencing a specific region, such as a gene. This requires concentration of the specific DNA you wish to sequence and can be done by PCR amplification (using primers that flank your desired sequence) or hybridisation (using probes complementary to your desired sequence that are fixed to a surface), among other methods.

For information on methods for enriching a DNA sequence, give this a read:

Mamanova, L. et al. Target-enrichment strategies for next-generation sequencing. Nat. Methods. 7, 111-118 (2010).

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  • $\begingroup$ So, let me get this straight: we PCR amplify the region of interest. Then use straight forward DNA sequencing on the PCR'd region? $\endgroup$ – Luke Oct 26 '14 at 14:07
  • $\begingroup$ Yes, basically. $\endgroup$ – canadianer Oct 26 '14 at 16:37

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