Genetic Testing Techniques

Polymerase chain reaction (PCR) is a common technique for making numerous copies of short DNA sections from a very small sample of genetic material. This process is called “amplifying” DNA and it enables specific genes or regions of interest to be detected or measured. This method is often used to copy DNA so it can be sequenced or analyzed with other techniques. It is often used to help look for genetic variants known to cause certain diseases, such as those associated with cancer or genetic disorders.

DNA sequencing refers to determining the order of bases [adenine (A), thymine (T), cytosine (C) and guanine (G)] that make up DNA. Sequencing allows clinicians to determine if a gene or the region that regulates a gene (regulatory region of DNA) contains changes, or variants, linked to a disorder.

Sanger sequencing (single gene)

For many years, Sanger sequencing has been the gold standard for clinical DNA sequencing to look at single genes or a few genes at a time. It relies on a special chemical that marks each DNA nucleotide with a different colored fluorescent dye, depending on which A, T, C, or G base it carries. This is the same technique that was used in the Human Genome Project. Sanger sequencing is reliable, but it can only read one short section of DNA from one patient at a time.

Next-generation sequencing (NGS) (whole exome sequencing and whole genome sequencing)

When the Human Genome Project was completed in 2003, it took over a decade to finalize the sequence of a single person’s genome using Sanger sequencing. Today there are much faster sequencing technologies that can perform the same task in a few days. These are collectively called next-generation sequencing (NGS) technologies. They are fast because they sequence millions of small DNA fragments in parallel (at the same time). NGS techniques can be used to look at the estimated 22,000 genes that code for the production of proteins. The protein-coding sections of genes are called exons and all of them together are called the exome. All of the genes, both the coding and non-coding portions of the genes, along with the areas between the genes, is called the genome. When NGS is used to evaluate the entire exome or genome, it is called whole exome sequencing or whole genome sequencing, respectively.

NGS is widely available now. Many commercial and academic laboratories currently use NGS for medical purposes and more are adopting the technology as time goes on. For instance, whole exome sequencing or whole genome sequencing can be used to evaluate individuals with a personal or family history that suggest a predisposition to breast cancer and ovarian cancer. Several genes can be evaluated at the same time to determine whether gene variants are present that would increase risk of these cancers. However, once a variant has been identified within a family, other members are tested for that specific variant, rather than the panel of genes.

Results from NGS must always be interpreted carefully. In evaluating whole exomes or whole genomes, NGS can identify many more genetic changes than older techniques that sequence individual or select genes, but the significance of the changes is not always understood. Many times, genetic changes that are detected are not able to point to an identifiable disorder. That’s why, when considering or undergoing genetic testing, it is important to seek help from a genetics expert or genetic counselor to understand test results, implications of the results, or risk of passing genetic disorders to any children.

Everyone has 23 pairs of chromosomes, which include 22 pairs of autosomes and one pair of sex chromosomes. The science that relates to the study of these chromosomes is referred to as “cytogenetics.” Trained cytogeneticists examine the number, shape, and staining pattern of these structures using special technologies. In this way, they can detect extra chromosomes, missing chromosomes, missing or extra pieces of chromosomes, or rearranged chromosomes.

Chromosome Analysis (Karyotyping)

Karyotyping begins with placing cells on glass slides and separating whole chromosomes from the nuclei of the cells. The slides are stained with special dyes and examined under a microscope. Then, pictures are taken of the chromosomes on the slides, and the picture is cut into pieces, so the chromosome pairs can be arranged and matched. Each chromosome pair is assigned a special number (from 1 to 22, then X and Y) that is based on its staining pattern and size.

Examining a person’s whole chromosomes, called karyotyping, can diagnose a wide array of disorders. Down syndrome, in which an individual has an extra chromosome 21, can be determined by karyotyping studies. When there are three chromosomes in one group instead of a pair, it is referred to as a “trisomy.” Missing chromosomes can also be detected, as in the case of Turner syndrome, in which a female has only a single X chromosome. When there is only one chromosome instead of a pair, it is referred to as a “monosomy.”

Sometimes, a piece of a chromosome will break off and attach to another chromosome. When this happens, it is referred to as a “translocation” or “rearrangement.” For example, chronic myelogenous leukemia (CML) is a disease caused by a translocation in which a part of chromosome 9 breaks off and attaches itself to chromosome 22 (BCRABL-1 fusion gene). Another example is Burkitt lymphoma, in which a piece of chromosome 8 attaches to chromosome 14. These chromosomal translocations cause disease because the broken piece usually attaches to the new chromosome near a special gene that then becomes activated and helps to produce tumor cells. Translocations can sometimes be seen under the microscope if a special stain is used via karyotyping.

Fluorescence in situ hybridization (FISH)

A special technique commonly called FISH for short can be used to view changes in chromosomes that result from genetic variations. A gene segment in a chromosome can be made to “light up” or fluoresce when it is bound by a special probe. By using more than one probe at once, cytogeneticists can compare to see if the probes are located in their normal positions or if they have moved to a new location on a different chromosome, or if there are more or fewer copies of a probe than in a normal cell.

Genetic changes in some cancers can be detected using this method. For instance, FISH is one of the methods used to determine increased copy number (amplification) of the gene ERBB2 (also known as HER2) in breast cancer. There are many other applications of FISH technology as well, such as detecting chromosomal deletions, in which a certain part of a chromosome is completely missing. In this case, the chromosome segment will not fluoresce compared to a normal set of chromosomes.

Microarray testing is a technique that is used for a wide variety of purposes. In diagnostic testing, microarrays may be used to determine whether an individual’s DNA contains a duplication, a deletion, or large stretches of identical DNA which can sometimes cause disease. Like karyotyping, microarray testing looks at all of the chromosomes at once, but it can detect changes that are smaller than either karyotyping or FISH can detect.

Microarrays are made up of thousands of short, synthetic, single-stranded DNA sequences attached to a solid surface like a bead or a chip. The DNA sequences comprise the normal gene being examined as well as different versions of that gene that have been found in humans. The DNA in a person’s sample is processed and labeled with a fluorescent dye and added to the microarray. The resulting pattern of fluorescence is examined and interpreted. Specific points along every chromosome is examined to see if there is any additional or missing chromosomal information. For example, a duplication would indicate that there is one more copy of the chromosome information than normal and a deletion is one less copy than normal.

Microarrays may also include additional information collected from single nucleotide polymorphisms (SNPs). Although these SNPs don’t actually tell us sequencing information (i.e. they don’t allow for determination of which base, A, T, C or G, is present) they are able to identify which pair of bases is present (A&T or C&G) at any specific location. This additional information helps determine whether there are any regions on the chromosomes that appear identical (which not typical since one chromosome is maternally inherited and one is paternally inherited). If there is an autosomal recessive disease gene within this region and there is a disease -causing variant present, it will be present in both copies, and thus expected to cause the autosomal disorder associated with that gene.

Chromosomal microarrays are considered a first-tier test for individuals with developmental delays, intellectual disabilities, autism spectrum disorders or multiple birth defects, and is recommended in lieu of a karyotype.

Gene expression profiling looks at which genes are turned on or off in cells. Gene expression is the process of making specific proteins from the information contained in the genes. Different tissues express different sets of genes based on their role in the body. The information from the gene is used to make a template for building RNA. RNA then undergoes specific modifications to create the protein required by the cell. Gene expression tests evaluate the RNA in a person’s tissue sample to determine which genes are actively making proteins.

For example, gene expression profiling is now available for breast cancer. These tests evaluate the products (RNA) of specific groups of genes in malignant breast tumors to predict prognosis, recurrence, and spread (metastasis) of the cancer, as well as to guide treatment. They are ultimately aimed at developing a personalized approach to patient care and breast cancer therapy.