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I'm currently reading about radiation hybrid mapping with a TSP (traveling salesman problem) application in order to find an ordering of the genetic markers (i'm a mathematics student) and was wondering about the usefulness of the procedure. If the end result determines the proximity of certain genetic markers then we can draw inferences about genes which are in close proximity to each other and genes which are separated with a larger distance. I'm wondering for certain set of genes if they are closely related distance wise then are the properties for the genes often related to each other? I believe there are also genes which are dependent upon having other genes in close proximity in order to function properly if I am not mistaken. Is this true?

I'm also curious as to what we may say if we have for instance two genes which are separated by large distance? May this be related to the fact that the farther away two genes are the more they act like they are unlinked?

Any help is appreciated.

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One might say that this question is too basic for this list, and I feel that it must have been asked before in some form, but I can’t locate an example. So here is a short answer.

First, it should be mentioned that Radiation Hybrid Mapping is an old technique which, judging by the brevity of the entry in Wikipedia, is little used today. The main reason for this is the availability of the genomic sequencing. It may make a good example for algorithms, but that’s probably about it.

However, the basic question is still valid, “Does human gene proximity suggest interaction, and lack of proximity not?”

At one time it was thought that this might be so because of the clustering of bacterial genes e.g. involved in a single metabolic pathway in operons. However, this is generally not the case in higher eukaryotes like humans. A good example is the locations of the genes for the two subunits of adult human haemoglobin which associate in the tetrameric protein α2β2. The gene for the α subunit is located on chromosome 11, whereas that for the β subunit is located on chromosome 16. Another example is the genes for the approx. 80 proteins that assemble into the protein-synthesizing organelle, the ribosome. This 1998 paper (which, incidentally, used radiation hybrids) concluded:

Though functionally related and coordinately expressed, the 75 mapped genes are widely dispersed: Both sex chromosomes and at least 20 of the 22 autosomes carry one or more rp genes.

So, although there may be counter-examples, no general conclusions about human genes can be drawn from mapping alone.

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  • $\begingroup$ Thank you very much for your answer. I was wondering in relation to genomic sequencing which also seems very much to be a quickly evolving field what are the most popular used techniques today? I assume cost and efficacy very much play a role here. $\endgroup$
    – PianoMath
    Mar 6 at 13:37
  • $\begingroup$ @PianoMath — That's another question. Depends what question you are asking in your research. $\endgroup$
    – David
    Mar 6 at 18:42

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