DNA Chip - Genetic Testing of the Future

Lisa Althoff

Copyright 1999

Many, if not most diseases, have their roots in our genes. Genes, through the proteins they encode, determine how efficiently we process foods, how effectively we detoxify poisons, and how vigorously we respond to infections. In the past 20 years, amazing new techniques have allowed scientists to learn a great deal about how genes work and how they are linked to disease. This rapid pace of discovery of genetic factors, responsible for certain diseases, has allowed scientists to genetically test asymptomatic individuals and predict their risk of certain diseases. In this paper, I am going to discuss the following areas pertaining to the topic of genetic testing:

Definition of Genetic Testing

Genetic testing is the analysis of human DNA, RNA, chromosomes, proteins, and certain metabolites in order to detect heritable disease-related genotypes, mutations, phenotypes, or karyotypes for clinical purposes (6). There are several genetic tests currently in use which are used to look for a possible predisposition to certain diseases, as well as to confirm a suspected mutation in an individual or family. These tests vary from newborn screening, with the detection of abnormal or missing gene products to carrier testing, which allows couples to learn if they carry a recessive allele for an inherited disease and thus risk passing that allele onto their children. They can also be used as a predictive gene test, which helps to identify people who are at risk of getting a disease before any symptoms appear (11). The information from genetic tests can help provide people and families with answers to their questions: why did this happen to my child or why do I have to suffer from this disease? Genetic tests also provide scientists with information regarding disease pathogenesis. For instance, by studying the genetic makeup of individuals with breast cancer, scientists can find out what particular mutation in the DNA, or in several genes, is causing the cancer and use that to screen high-risk individuals. Researchers are also taking advantage of genetic tests to find gene mutations that make bacteria or viruses resistant to drugs.

Screening Techniques

The immediate challenge in genetic testing is being able to design an effective mutation analysis method that offers a rapid, accurate, cost-effective, and user-friendly test for scanning several susceptibility genes at once. According to the article in Nature Biotechnology, by Charis Eng and Jan Viig, genetic testing techniques are grouped into two main categories: screening and scanning. Screening methods involve probing specific genes for previously identified mutations. These methods, however, are unrealistic for such diseases which are characterized by a large number of disease-causing mutations that can be virtually anywhere in the gene's coding region or regulatory region (3). For example, in breast cancer, mutations can be found anywhere within the large BRCA1 and BRCA2 genes, two of the many genes that have been implicated in breast cancer (1). Development of a separate DNA probe for each mutation has proven to be too expensive and time consuming to make screening methods feasible.

Scanning methods involve testing the gene or genes having no assumptions about any previous mutations (3). A major limitation in this method is that only the coding regions, splice sites and promoter regions are scanned (3). This excludes mutations within the regulatory regions other than the promoters, introns, as well as other genes whose protein products could potentially interact with the disease-causing gene. Some of the scanning methods include: nucleotide sequencing, tests of molecular phenotype, protein truncation, and just recently DNA chip technology (3). One of the major obstacles in developing successful screening techniques involves the size and complexity of disease related genes.

DNA Chip

Initially developed to enhance genomic sequencing projects, especially the Human Genome Project, DNA chips are finding applications throughout the field of molecular biology (2). Gene scanning techniques that are based on oligonucleotide arrays called DNA chips, provide a rapid method to analyze thousands of genes simultaneously. DNA chips are thus potentially very powerful tools for gaining insight into the complexities of gene expression, detecting genetic variations, making new gene discoveries, fingerprinting and developing new diagnostic tools (7).

The production of DNA chips have evolved along two major pathways: one method uses nucleic acids that have been immobilized on the chip surface sequentially to form oligonucleotides and the other method involves complementary DNA from an individual with a known genetic mutation as a source of prefabricated oligonucleotides (2). In either case, the problem lies with how to attach the nucleic acids or cDNA to the chip.

Chips using nucleic acids are produced using photolithography. Photolithography, according to the Science article by Stephen Fodor, consists of the modification of synthetic linkers, containing photochemically removable protecting groups, attached to a glass substrate, usually a silicon-derivative glass chip. Light is directed at the photolithographic "mask" at specific areas of the chip in order to facilitate the removal of the photoactive groups, yielding 5( hydroxy groups. These modified groups are now capable of binding other nucleotides, generating a highly specific probe, which contains the sequence of a known disease causing genetic mutation.

The other method, described in the DNA Chips and Microassays website, uses purified single-stranded cDNA from an individual with a known genetic disease, requiring the use of touch or fine micropipetting, to spot the cDNA onto the surface of the chip. The cDNA immobilizes on the chip through covalent bonds, due to the positively charged surface, produced by amino silane or polylysine (2). For both types of chips, a potential DNA target sequence, from an asymptomatic individual, is fluorescently tagged and allowed to interact with the probes. Hybridization will occur at complementary sequences between the two samples resulting in a fluorescent image, which is then scanned by a laser beam and analyzed by a computer. The intensity of fluorescent light varies with the strength of the hybridization, thus providing a quantitative 'snapshot' of gene expression (7).

This approach, requiring only minute consumption of chemical reagents and minute preparations of biological samples, can scan more than 400,000 probes placed on a single chip measuring 1.28cm X 1.28cm in size (7). As of now, specific chips are available for as little as $100, but could cost over thousands of dollars, once custom-made chips are available (2). In the future, attempts to design chips using the computer, instead of doing it by hand, will greatly speed up the process allowing companies to make custom chips in one day, as opposed to months, which would lower the cost of production. Consequently, DNA chips could probably sell for about $50, providing access to scientists regardless of their funding situation (10).

Ethical Considerations

The ability to pinpoint genetic mutations that predispose a person to a disease has generated a firestorm of controversy within the medical establishment and in the general public. Raising serious ethical issues, the decision to have a genetic test deserves careful preparation and thought. A natural division amongst all people, regarding specific issues, is to be either for or against the topic in discussion. Unfortunately, genetic testing is not that simple.

Genetic testing has been slow to achieve popularity, partly due to the likelihood of obtaining meaningful data. When there are so many genes interacting together within any given disease, how could one test possibly be able to examine every pathway that could lead to a potential disease? Scientists have produced DNA chips with the capability of containing 20-30,000 different probes per square centimeter (2). This means, virtually all genetic sequences pertaining to a particular disease could be formatted on one DNA chip. This technology could greatly reduce health care costs by reducing the number of visits to the doctor or perhaps even a specialist, by cutting back on the number of useless diagnostic tests, by reducing the amount of needless pharmaceutical prescriptions, or because the chip has a shelf life of up to several months, there should not be a need to throw out expired chips. With the DNA chips intricate design, even hard to find genes found in mRNA species are able to be detected (7).

DNA chips sound simple in concept, but generating probes on a solid array surface requires considerable expertise and "technical wizardry" (2). At present, DNA chips are much too expensive and limited in application, because their use requires prior knowledge of gene sequences and any interactions with other genes, in order to be available for use in medical practices. DNA chip making is a complex process and most of the labor is usually done by high tech and fairly expensive robotics.

Critics of genetic testing believe it is unethical due to the lack of comprehension in the test results. A positive outcome can effect a person's life in important ways: allowing for earlier detection, the possibility of prevention, or the ability to make personal medical and lifestyle decisions. On the other hand, a positive test could also result in potential employment discrimination, ineligibility for health insurance coverage or higher premiums, as well as in physical and psychological strain. The decision is especially wrenching for persons confronted with a disease that can be neither prevented nor cured. For these reasons, many groups and individuals oppose genetic testing. In contrast, advocates believe these concerns can be minimized if potential consumers are educated about the limits of tests and their potential consequences through genetic counseling.

Public Policy

Before genetic tests become publicly available, specialists and society at large, need to come to terms with major technical, ethical, and economic concerns. These issues need to be addressed in carefully conducted research programs. Genetic discrimination is perhaps the most critical issue involved in genetic testing; the idea of discriminating against someone due to there genetic makeup is a very new concept. According to the National Action Plan on Breast Cancer (NAPBC) fact sheet, some protection from discrimination by employers is offered through the Americans with Disabilities Act (ADA), where recently the Equal Employment Opportunity Commission (EEOC) expanded the definition of "disabled" to include individuals who carry genes that put them at higher risk for genetic disorders.

Several public policy measures have been taken in the hopes of preventing genetic discrimination by health insurance companies. After four years of discord, eleven states have now passed bills that would bar health insurance companies from using genetic tests as the sole reason to deny or cut coverage or to charge higher premiums (8). People should not be punished for a hereditary predisposition that may or may not make them sick in the future. Congress in 1995, forbade group health policies in the workplace from denying coverage based on genetic tests (8). The Health Insurance Portability and Accountability Act of 1996 mandated that genetic test results alone cannot be treated as a pre-existing condition and group medical plans cannot force any person to pay a higher premium than people of equal status, based solely on genetic test results (5). These laws are definitely a step in the right direction, however, as genetic testing increases in use, more legislation unquestionably will be needed to fully protect at-risk individuals.

Personal opinion

Before researching the topic of genetic testing, I really did not have a solid viewpoint on the topic. I was in favor of some of the aspects pertaining to genetic testing, such as using the concept to study genes and their functions, while against the procedure at the same time. Now that I have delved into the topic, I am dead set against performing genetic tests on individuals just to find out if they are carriers of a mutated gene.

At first, the general public will think of genetic testing as a noble, technical advancement in science, one in which the knowledge gained from these tests could help prevent such painful genetic diseases, such as cystic fibrosis, many of the cancers or storage diseases. When they think of genetic testing, they will have someone in mind who is near and dear to their hearts, who is suffering from a genetic disease, which cannot be effectively treated. These people are the ones in favor of genetic testing, in order to find the disease-causing mutation, which in the future would help gain insight into genetic therapy. This would be fine, if the genetic research would stop there. However, if scientists can find out what causes genetic diseases, why not try to prevent them from ever occurring, by genetically engineering a disease-free human. Scientists could potentially produce a human race that could live well past a century. The world's population has already approximately doubled since the 1950's, how many more people can the Earth support before another mass extinction occurs and wipes out the entire ecosystem. I believe that everyone was put on this Earth for a purpose, whether that means they have to suffer from an illness and die at an early age or they lead a healthy life and live to be one hundred years of age. I consider a true test of the existence of evolution, when we have the knowledge and technical aspects to greatly enhance the human race, but have the common sense and morality to restrain ourselves.


1. All About Breast Cancer Genes. Obtained from the WWW:http://www.lbl.gov/Education/ELSI/cancer-genes.html
2. DNA Chips and Microassays. Obtained from the WWW:http://sciborg.uwaterloo.ca/~bpbobech.welcome.html
3. Eng, Charis and Jan Viig. 1997. Genetic Testing: The problems and the promise. Nature Biotechnology 15:422-426.
4. Fodor, Stephen, P.A. 1997. Massively Parallel Genomics. Science 277:394-395.
5. Health Insurance Portability and Accountability Act of 1996. Obtained from the WWW:http//www.hcfa.gov/regs/HIPAACER.htm
6. Holtzman, Neil A., M.D., MPH and Michael S. Watson, Ph.D. Promoting Safe and Effective Genetic Testing in the United States. Obtained from the WWW:http://www.nhgri.nih.gov/ELSI/TFGT_final/
7. ISB News Report. Obtained from the WWW:http://gophisb.biochem.vt.edu/news/1997/news97.sep.html#sep9701
8. LaMendola, Bob. Lawmakers: Genetic testing alone should not impact health coverage. Obtained from the WWW:http://www.sun-sentinel.com/news/2939.html
9. NAPBC Fact Sheet: "Genetic Testing for Breast Cancer Risk: It's Your Choice: Obtained from the WWW:http://www.oncolink.upenn.edu/disease/breast/genetics/napbc/napbc-fact.html
10. Singh-Gasson, Sangeet et al. 1999. Maskless fabrication of light-directed oligonucleotide microarrays using a digital micromirror array. Nature Biotechnology 17:974-978.
11. U.S. Department of Health and Human Services. Understanding Gene Testing. Obtained from the WWW:http://www.accessexcallence.org/AE/AEPC/NIH/index.html

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