Cell-free DNA in diagnostic testing: DNA integrity index

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 In my last post, we looked at how concentration of cell-free DNA can be used as a biomarker for cancer. Today, we will look at another attribute of cell-free DNA: its integrity index. 

what is DNA integrity index


First, how are the amounts of DNA measured? Usually, researchers use a technique called real-time PCR to measure the concentration of the DNA fragments. Now, PCR or polymerase chain reaction is a technique by which researchers create many copies of a DNA sequence. In short, during PCR, we add short DNA sequences called primers. We then select a gene sequence that we want to make copies of. We then use primers that bind to our gene of interest. An enzyme called DNA polymerase uses the gene sequence as a template. It extends the primers to create copies of the template DNA sequence. Real-time PCR is different from the standard PCR technique in that the number of copies of DNA are measured as they are created. Usually, fluorescent dyes are added which bind to the newly created DNA copies. A detector then monitors the fluorescence of the dyes. From this fluorescence, a researcher calculates the amount of DNA copies. 

A point to be noted here is that we can decide the size of the fragment we want to measure. Now DNA integrity is a ratio of long fragments of DNA versus the short fragments. So we will first measure the amounts of long DNA fragments and the amounts of short DNA fragments. Then, we divide the amount of long fragments by the amount of short fragments. This gives us a ratio called a DNA integrity index. 



So now we know what is DNA integrity index and how it is measured. Many studies have tried to use DII to create a test for cancer diagnosis. But what are the lengths of fragments measured to calculate DII? That is a question researchers are still trying to find an answer for. Different studies tested different fragments sizes and ratios. For example, one study tested a long fragment size of 300 bases and short fragment size of 60 bases. Another study by Pinzani and colleagues compared different ratios and found that a ratio of 180/67 was very suitable for diagnostic testing.

But irrespective of the fragment size used, the integrity index of DNA in cancer patients was found to be different from that in normal people. For instance, one study found that longer fragments are present at smaller amounts while small fragments are present in larger amounts. 

But what ratio is used and whether DII is suitable for diagnostic testing remains to be seen...In my next post, we will look at an example of how DII can be used for diagnosing cancer. See you next time!

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