Screening for genetic defects

Now that scientists have mapped the human genome, computers can be used to detect genetic defects.
Screening for genetic diseases existed before the application of computers. Family histories were used, together with a knowledge of inheritance patterns and statistics, to determine the likelihood of a couple having offspring with genetic disorders such as sickle cell anaemia.
Some genetic disorders such as phenylketonuria have had simple chemical detection tests available for some time. Once detected, careful control of diet prevents mental retardation, demonstrating the value of detecting the presence of a genetic disease before any symptoms have appeared.
What the computer adds to the screening process is the power to compare very long genetic sequences (i.e. sequences of base pairs) against the human genome in a way that would be far too time consuming (and therefore expensive) to be carried out by hand. Once a particular gene and type of defect has been identified, it becomes possible to develop a test to find out whether a patient has that genetic defect well before any signs of it appear.
Genetic tests are used for several reasons, including:

• prenatal diagnostic testing;
  
• testing to predict adult-onset disorders such as Huntington's and Alzheimer's disease;
  
• forensic and identity testing.
  

Example 5 Breast cancer and genetics

Breast cancer is one of the commonest cancers in women (it occurs in men as well, albeit rarely). The success of treatment following early diagnosis led to a great deal of research in ways of identifying the cancer in the population at large. Some time before the mapping of the human genome it was already known that between 10 and 15 per cent of breast cancers are familial in origin (i.e. groups of related individuals show a greater than average tendency to develop the disease).
Following the mapping of the human genome, it was determined that about one-third of familial cancers are attributable to defects in two genes known as BRCA1 and BRCA2. Now there is a genetic test to determine whether or not a woman whose family history includes a high incidence of breast cancer is carrying these defective genes. If she is, her risk of developing breast cancer over her lifetime is between 56 and 85 percent; and she has a greater than average probability of developing ovarian cancer.
However, there is little point in having a test if there are not corresponding means of providing help. In the case of breast cancer, increased frequency in screening can help detect the cancer at an early stage (and thereby increase the effectiveness of treatment). More controversial is the preventive removal of breast tissues, which imposes a heavy emotional and physical burden without being completely effective. As with so many technological developments, there are costs associated with their use.

It is hoped that using information related to the human genome will lead to ways in which genetic defects can be corrected or their effects lessened.
There are a number of genetic databases that can be accessed over the internet. Using them to detect defects involves searching enormous databases containing genetic sequences which requires huge computational effort.
This case study on DNA has illustrated three main points:

1. DNA data is coded in a very simple way (with just four letters of the alphabet);
   
2. such a simple code can still generate complex, multiple structures;
   
3. searching such a structure is a time-consuming task.
   

SAQ 6

How can a simple code, such as the DNA bases, become such a complex problem for computing?

Answer

Although the code is simple, the bases combine in very complex structures called genes (analogous to words in a language) that can be combined into more complex structures called chromosomes (analogous to a volume of a large encyclopedia). Searching for a particular genetic defect in the genetic structure of the human being is not a trivial task. Apart from the size of the search, there are likely to be many instances of the same combination of base pairs (just as searching for the word ‘king’ in the collected works of Shakespeare would yield a large number of hits, including some false ones such as ‘lurking’).