CONTINUING EDUCATION :: MOLECULAR DIAGNOSTICS


Microsatellites and VNTR typing in clinical settings


By John Brunstein, PhD O


ne application of molecular technology is in what is colloquially referred to as, “DNA fingerprint- ing” or “DNA profiling.” The fingerprint analogy is an apt one, as the method generates a reproducible biometric pattern which is unique to an individual yet provides little or no phenotypic information about the source (gender being the one common exception, as detailed further below). The method also provides data which can be used to calculate relatedness between samples. Beyond its common appearance in fictional- ized (and real) criminal forensics settings, the capabil- ity to link specific trace fragments of human tissue to individuals and to objectively determine relatedness between samples is of real use in anthropological stud- ies and—more to our focus—mundane clinical set- tings. The most common method for DNA profiling


Earning CEUs


See test on page 14 or online at www.mlo-online.com under the CE Tests tab. LEARNING OBJECTIVES


Upon completion of this article, the reader will be able to:


1. Recall the overall biology of microsatellites and the events that take place that lead to random diversity of genetic markers.


2. Discuss the technique involved in VNTR loci evaluation.


3. Describe the clinical applications in which VNTR typing is used.


4. Discuss the benefits of VNTR typing. 8 MAY 2019 MLO-ONLINE.COM


is known as Variable Nucleotide Tandem Repeat (VNTR) typing and will be our present focus.


Terminology


First, some terminology. Within the chromosomes comprising the nuclear DNA of most organisms including humans, there are often intergenic non- coding regions which consist of multiple tandem (head to tail) repeats of a single short (most com- monly 2, 3, 4, or 5 base) element. Examples would be (ATT)n or (GTTAC)n, where the parenthetic set of nucleotides repeats in a row n times. These ele- ments are referred to as microsatellites. The name derives from the dark ages of molecular biology when preparative isolation of DNA included buoy- ant density ultracentrifugation on CsCl gradients. Due to its uniform composition, sheared DNA frag- ments of microsatellite DNA forms small, distinct bands slightly separated from non-repetitive DNA material. When the number of element repeats (n) exceeds about 50, similar but slightly larger unique bands are formed, and these longer elements of similar structure are called minisatellites. To keep things unnecessarily complicated, microsatellites are also sometimes called Short Tandem Repeats (STRs) or Simple Sequence Repeats (SSRs), although this latter term is more frequently applied in plant genetics. Finally, both microsatellites (by any name) and minisatellites are collectively referred to as VNTRs. In practice the terms STR typing, microsatellite typing, and VNTR typing are often used interchangeably—a looseness of terminol- ogy which can sometimes lead to confusion where people look for differences in meaning that aren’t intended.


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