Genetic Testing

John Van Hemert
2/9/2006

What is Genetic Testing?

Genetic testing is a medical procedure that inspects a patient’s genes for changes in genes, chromosomes and proteins, which indicate certain genetic disorders and diseases. There more than 900 different genetic tests which require a variety of techniques. Genetic tests are a voluntary practice. They are considered “consultancy” more than medicine because they are not 100% accurate and insurance rarely covers genetic testing.

Why Test Genes?

Many conditions ranging from baldness to diabetes to cancer are inherited. Other conditions occur because of affected genes that mutate. There is a long list of types of genetic tests, which indicate the reasons for testing:

  1. Newborn screening – newborn infants are testes immediately after birth in order to identify and treat genetic disorders early in life.
  2. Diagnostic – genetic tests are performed in order to confirm a diagnosis based on symptoms. Results are used in treatment decisions.
  3. Carrier – testing for genes that cause genetic disorders manifesting only when joined with another copy of the same mutation.
  4. Prenatal – testing of the fetus for suspected genetic disorders in order to make pregnancy decisions.
  5. Preimplantation – a kind of quality control for assisted reproductive procedures; embryos are tested for disorder-causing mutations.
  6. Predictive/Presymptomatic – these tests are used to detect genetic mutations that cause suspected diseases later in life. An example of this would be a young woman testing for mutations that cause breast cancer because older generations of women in her family have had breast cancer.
  7. Forensic – these tests are meant to identify victims of crimes or catastrophe and to detect biological relationships.

Computing for Genetic Testing

Genetics is a relatively new and quickly growing science. It is a data-rich practice and state-of-the-art computing has only recently developed to the point at which it can process all of this data. Further, the ideal storage techniques for genetic data have yet to be invented. Bioinformatics, the marriage of molecular genetics computer science (not to mention a large identity with statistics and mathematics), has produced significant advances in genetics and genetic testing. See the chapter on bioinformatics.

ESTs

Computer science brought to genetics the “divide and conquer” paradigm. This means the application of distributed processing and storage for the huge amount of genetic data produced by the most basic of experiments. An Expressed Sequence Tag (EST) is a small segment of a DNA segment. Scientists split up a genome into hundreds or thousands of ESTs, process each separately and reconstruct the full code. The problem is that when the ESTs are split apart, there is no direct way of knowing their original order. Complicated algorithms and statistical models are used to determine the correct order.


Genomics - The Pasteur Institute

Microarrays

Microarrays are to modern bioinformatics as shovels are to archaeology; they are a cheap and extensively used tool for discovery. Even after an entire genome code is discovered, the meaning of the code is unknown, like knowing syntax without knowing semantics. The next step, therefore, is to somehow observe individual genes in controlled conditions to see how they react and discover the function of specific codes. Previously, scientists were able to observe only a few genes at one time in experiments. Microarrays allow for the observation of thousands of genes at one time. A microarray holds thousands of genes on a small chip, much like a processor chip holds transistors. The genes can be observed easily during experiments. For example, take a scientist who wishes to find the genes responsible for a sunflower’s reaction to drought. She would deprive one sunflower of water and provide plenty of water for a control sunflower. Then, the scientist would create a microarray of each sunflower’s genes and observe the differences on the two microarrays to see which genes were “activated.” After experiments are performed for every conceivable condition of the sunflower, a corresponding function can be known for every piece of its DNA code.



Microarray Overview - The Wellcome Trust Center for Human Genetics

What can be tested?

There are over 900 genetic disorders that can be tested. To see what diseases are caused by which genes, visit the Chromosome Map at the National Center for Biotechnology Information.

Issues

Genetic testing brings up several questions and issues. For instance, consider the world in a few years when a genetic test for any and all diseases is little more expensive than a pregnancy test. You and your friend, whose family has a slight history of cystic fibrosis, are both interviewing for a job. The interview includes complimentary glasses of purified water. Your friend is clearly more qualified. One week later, to your surprise, you are offered the job. How can this be? What you did not see at the interview was that the employer saved the glasses that you and your friend drank from during the interview. The company ran genetic tests on the handful of live cells in the traces of saliva you left on the glasses. The tests revealed that your friend is likely to suffer cystic fibrosis while you show no signs of genetic disorders. This is known as genetic discrimination and it will become more and more prevalent in the years to come.

How can an employer do such a thing? How can they not? General Motors spends more money on health care for its employees than it spends on steel. Health care will become a target for strategic cost-cutting and that includes avoiding expensive employees. Genetic testing will add a new dimension to health as we know it. It provides a quantitative, concrete diagnosis of future health. Genetic testing will prove to be the most significant development in medicine since the advent of surgery itself.

Sources and related articles

Genomics and Medical Devices: A New Paradigm for Health Care
ESTs Factsheet
Gene Testing - National Cancer Institute
Gene Testing - Human Genome Project
Genetic Testing - Lawrence Berkeley Laboratory
Genetic Testing - Medicine Plus