Molecular Diagnostics – An Introduction

March 10, 2014 at 12:54 pm Leave a comment

Molecular Diagnostics (also known as nucleic acid based diagnostics) studies the composition of an individual’s genetic material – i.e. our DNA – in order to arrive at conclusions that have medical implications. The reason this science that is still in its infancy is hailed by many as the next frontier of medicine is that it is far more precise than previous methods, faster by several orders of magnitude – often giving results in hours vs. the weeks required by conventional tests, and can give results with far lower sample quantities. Additionally, it can sometimes give information that is simply not available from any other test.

Some kinds of molecular diagnostic tests help understand the likelihood of a patient responding positively to a particular medication, others help identify mutations that predict the probability of a healthy individual developing certain ailments in the future, yet others help conclusively identify the ailment at the root of troublesome symptoms so that the cause could be treated properly.

Basics of the science underlying the technique :

(note – those uninterested in a basic biology lesson can skip this section)

The cornerstone of molecular diagnostics is the identification of pathogenic mutations in an individual’s genetic material, i.e. their DNA.

Our DNA is made up of a sequence of pieces called genes. Each gene is made up of a series of bases (Adenosine,Thymine,Cytosine,Guanine, commonly written as A,T,C and G) in a certain order. These bases and the precise locations on the gene at which they are present are a molecular code that carries information required for making all the functional molecules – RNA and proteins – required by us. These proteins, once synthesised, are responsible for our characteristics – whether it’s the colour of our eyes and skin, our blood group, our tendency to gain weight quickly, or male-pattern baldness etc. Thus the bases and the sequence of their location on the genes are responsible for our heritable traits.

Small changes in the sequence of bases on a gene – such as substitution of one base for another, or omission or repetition of a small segment, can change the gene’s function and manifest as a difference, say in physical appearance etc. You can think of these bases on the gene as letters on this page that occur in a certain order to form words and sentences. Occasionally, a typographical error – a missing alphabet, a duplication, or a wrong substitution may occur, some do not matter much and we can still read the words and unnerstand them, but others may gargle (garble) the meaning of a word or sentence.

Similarly, most variations are harmless, but some can make the gene faulty; for instance, a particular protein may not be produced properly, or produced in the wrong amounts or not produced at all; such variations that make the gene’s operations faulty are called mutations. These mutations are the signposts that molecular diagnostics searches for and draws conclusions from. Thus the science is based on being able to recognise and map the structure of each gene, and identify mutations in them, as well as the knowledge of those mutations that affect our metabolic processes / physiology. This is not as easy a task as it sounds as human genes have from a few hundred up to two million bases on them (yes, really !) and you have to know and locate the specific mutation that is responsible for the effect under consideration.

(For further information on structure of the DNA, you can read the following :

What is a Genome

What is DNA 

What is a gene

How genes work 

Mutations and health

What is a gene mutation and how does it occur 

Inheriting genetic conditions )

 

Some Scenarios in which a molecular diagnostic test could be used :

Therapy support and therapy monitoring :

Determining probable response rates to certain therapies and their appropriateness for use in specific patients. In doing so, molecular diagnostics enables more personalised / individualised therapies, either with the goal of minimising harmful side-effects and / or judging how well individuals will respond to a planned course of treatment and whether they should go in for it.

This DNA-based approach to treatment, known as pharmacogenomics, is already in use in combating certain cancers.  Chemotherapy is prohibitively expensive and often has extremely painful side-effects, and not all patients respond equally well to a medication or cocktail of medications; getting the combination right often involves an initial trial-and-error phase, a frustrating and physically tortuous time for the patient. In the case of certain types of cancer, molecular diagnostics can help predict a patient’s response to a medication, thus avoiding much trauma – both emotional and physical, and saving time and money.

Take breast cancer, for instance. One of the medications used to avoid a recurrence after radiation therapy or chemotherapy is the drug Herceptin from Genentech. Now about 20-30% of breast cancer patients exhibit an over-expression of the Her2/neu gene and only these patients benefit from treatment with Herceptin.  A molecular diagnostic test to check for presence of the mutation of Her2/neu gene helps identify those that would benefit from the treatment; thus it costs about Rs. 15,000-20,000 to figure out whether a treatment running into lakhs of rupees will actually benefit someone. This is the personalised approach to medicine rather than the one-size-fits-all-with-the-same-ailment approach.

 

Early Detection Testing :

Detecting the presence of pathogens through detection of their RNA or DNA.

Using a molecular diagnostic test, diseases caused by a virus – think HIV and AIDS, HPV and cervical cancer, Hepatitis B, Hepatitis C etc. – could be quickly and reliably diagnosed well before the initial symptoms appear, thus giving physicians a longer treatment window and the patient a chance of earlier treatment and earlier return to good health. In these instances, the tests checks whether the RNA of the virus (ahem, which is significantly different from our DNA) can be detected in the patient’s tissue / sputum / blood sample sent for testing.

These tests can be used to detect other pathogens such as bacteria too. Consider the traditional diagnostic tests for TB which is caused by bacteria (Mycobacterium Tuberculosis). The current battery of tests include the Mantoux tuberculin skin test, a tissue culture, a sputum test, a chest X-Ray and a blood test; in spite of conducting all of these, there is a chance of getting a false positive or false negative result when the results are available a few weeks later. On the contrary, one molecular diagnostic test can confirm not just the presence of TB but also identify the genetic mutations in the bacterium and identify the strain of the bacterium responsible for the symptoms and which drugs it is resistant to, all this within a few hours.

Valuable info indeed in this era of multi-drug resistant TB (MDR-TB), when making a fast and accurate diagnosis of the type of TB infection a patient may have is the most important step to curing a patient.

 

Predisposition testing :

Analysing the probability of an individual developing certain genetically inherited diseases.

Such tests, done for risk analysis of cystic fibrosis, breast cancer and other hereditary diseases, can help understand whether an individual has a higher probability of developing an ailment than the general population. These are not definitive tests, in that they cannot predict whether an individual will get the ailment in future, they can only tell us that an individual has a higher or lower probability than the general population does of getting the ailment. Hence, there is still a lot of debate about whether such information is beneficial for an individual or not, whether it makes them worry unnecessarily about factors which they have no control over.

For instance, consider the BRCA1 and BRCA2 genes that belong to a class of genes known as tumour suppressor. A woman who has inherited a harmful mutation in BRCA1 or BRCA2 is about five times more likely to develop breast cancer than a woman who does not have such a mutation.

In a family with a history of breast or ovarian cancer, it may be informative to analyse a tissue sample of a patient (sufferer of breast cancer) and identify which harmful mutations are present; then other family members can be tested to find out if they also have the same mutation and their probability of developing breast cancer later can be computed. However, while a negative result can rule out breast cancer and bring a sense of relief, a positive test result only provides information about a person’s probability of developing cancer in future. It cannot tell whether an individual will definitely develop cancer; not all women who inherit a harmful BRCA1 or BRCA2 mutation will develop breast or ovarian cancer.

Note : Common medical problems such as heart disease, diabetes, and obesity do not have a single genetic cause—they are likely associated with the effects of multiple genes in combination with lifestyle and environmental factors, in such cases, genetics has a smaller, more complex role to play. More on this and other matters in another post.

  •  Zenobia Driver

(with a lot of assistance from assorted secondary sources)

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Entry filed under: Health & Wellness, Healthcare. Tags: , , , , .

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