Video: 5 Criteria for Selecting a Lab for Genetic Testing
There are a variety of clinical laboratory testing methods in use, each with its different applications, strengths, and limitations. Different types of genomic variation require different methodologies to detect them. Specific clinical applications may sometimes require the use of multiple methodologies to be comprehensive, sometimes used in parallel, other times sequentially. With technological advances, current methodologies may be supplanted with newer ones because they are faster, cheaper, and/or higher throughput. In general, the following guide will be useful for matching the methodology to the type of variation it can detect, and providing practical advice for the use of genomic testing modalities. First, we would like to clarify some terms commonly used for testing.
TARGETED (GENOTYPING) VERSUS NONTARGETED METHODS
Targeted methods typically referred to as genotyping, analyze only specific, known DNA variants while nontargeted methods are more comprehensive and allow for the discovery of new DNA variants. In other words, one must already know what genetic variant one is looking for in the case of a targeted genotyping test, usually because the variant is a known cause of the disease. An example would be the factor V Leiden variant that confers an increased risk of thrombosis. Advantages of targeted genotyping are the lower cost and more rapid turnaround time. A disadvantage is that targeted tests may miss detecting genetic changes that are not suspected a priori.
Laboratory tests range from measuring a single analyte to a group of analytes to the entire complement of analytes (for DNA, this is the whole genome). Terminology that captures multiplex or genome-wide analysis includes panels, array, and microarray.
The following are descriptions of commonly used technologies in genomic medicine.
Karyotyping is a nontargeted cytogenetic technique used to detect chromosomal numerical variants (aneuploidies), large copy number variants (deletions or insertions), and structural variants across the genome (translocations, inversions). As such, a karyotype can be a screening test, looking for any change in the chromosomes that might cause a disease, or a diagnostic test, analyzing for a particular trisomy, for example.
A variety of tissues can be analyzed by karyotyping, including blood (i.e., lymphocytes), fibroblasts (usually from a skin biopsy), amniocytes (from amniocentesis), chorionic villi, products of conception, and tumor cells. Cells are captured during mitosis when the chromosomes are condensed, and the chromosomes are chemically fixed, stained, and then spread out on a slide. The most commonly used stain is Giemsa, also called GTG or G-banding. This staining labels some regions of the chromosomes darker (usually rich in A and T bases, generally indicating less gene-rich areas) and lighter areas (richer in G and C, usually with more genes). Images of the chromosomes from single cells ...