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I am not by any means a biologist - so go easy.

What would be a method for determining whether or not a patient has cancer based only on a genomic sequence?

Update Thanks for the help in revising the questions.

  1. What information is extractable once a genome has been sequenced?

  2. Is it possible to derive whether or not a person has cancer based only on the genome which was sequenced? i.e. Are there anomalies to look out for to detect the cancer.

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To make it clear: you want to know 1. What info it's possible to get from sequencing; 2. Does sequecing make any impact on the genome? –  Pgibas Jan 31 at 22:24
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For the second question: You want to know, if its possible to make a decision if a person has a cancer only based on their DNA sequence? –  Chris Feb 1 at 9:07
    
@Chris - Yes i think you've hit the nail on the head. –  Aiden Strydom Feb 1 at 21:40
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2 Answers 2

up vote 2 down vote accepted

Answering your question 2:

Is it possible to derive whether or not a person has cancer based only on the genome which was sequenced? i.e. Are there anomalies to look out for to detect the cancer.

I would say no. The problem with mutations is that we still don't know exactly what mutations are needed for a cell to become a primary tumor cell. There are anomalies, but we know these in fully developed tumors. I can give an example (I need to explain a bit wider for it) to show this:

The expression of genes is dependent on many different signals, some come from the outside of the cell (for example from growth factors) and they are passed down into the nucleus along so called signal transduction pathways. For melanoma (skin cancer) mutations in some key elements of this pathways are pretty often mutated, for example we find mutations in one kinase (an enzyme that phosphorylates other proteins) in about 60% of the cases. This kinase is called Braf and it carries a mutations in amino acid 600 changing it from valine to glutamic acid (so call Braf-V600E). This makes the kinase permanently active (also when she shouldn't be activated due to a missing signal) which derugulates otherwise pretty tightly controlled gene expression.

The problem with the Braf-V600E mutation is that this is not only found in melanoma cells, but also in benign nevi. Only that these are usually senescent (meaning that they do not divide and only sit on the skin) and harmless. Most of them never transform into melanoma, but some do and here we don't know why. Obviously cells need to pick up other mutations on their way to become cancer cells and there are quite some possibilities for that.

Cancer is a pretty complex disease, which is under high selection pressure: Cells need to evade the immune system and also be able to survive, proliferate and differentiate. Whole genome sequencing has opened a door to understand cancers better and also to diagnose them better in terms of treatment, but I don't think you can really do this only on the base of a sequence, since there a too many possibilities to bring up false positive (and also negative) results. Its possible that the Cancer genome project will change this, but I am doubtful about it.

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Thank you - more than insightful it was helpful. Unfortunately the answer doesn't boast well for my research. Again, i have a much better understanding of my issue and different ways to look at it - Thanks. –  Aiden Strydom Feb 3 at 22:27
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When sequencing a human's (i hope im stating this correctly) genome is there a difference between the genome before and after the patient is found to have developed some sort of cancer.

If you are asking if cancer cells have an altered genome as compared to the rest of the organism, yes, this usually is the case.

What would be a method for determining whether or not a patient has cancer based only on a genomic-sequence.

If you scrape some cheek cells to do DNA sequencing, you will know what the sequence is in those cheek cells, and you can figure that most of the cells in the rest of the body have that same sequence. But if some, say, brain cells have acquired genetic errors causing them to start going haywire, that won't magically change the DNA in your cheek cells.

A genetic predisposition could be identified...if scientists had determined one. For instance, Angelina Jolie got a double mastectomy because both her family history and her genetics strongly indicated that she would get breast cancer otherwise.

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Thanks. I have a slightly better idea of what i am asking. –  Aiden Strydom Jan 31 at 23:33
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In some cancers its even different between different stages of the tumor cells (tumors are not homogeneous). –  Chris Feb 1 at 9:06
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