Clinical Genomics 101: Biological Samples
Any clinical testing workflow begins by collecting a biological sample from each patient; for genomic testing, this means collecting DNA from a patient’s cells. There are a number of different ways in which genetic material can be collected and the choice of which technique is used is typically decided by a variety of factors. Once collected, samples need to be processed and stored, before being prepared for testing.
DNA and RNA reside in almost every cell of the body and so can be collected from a range of different tissues. Peripheral blood and bone marrow are relatively frequently used DNA sources, and blood, tissue, cells, saliva, and faecal matter are all used to gather both DNA and RNA samples. In general, the most common DNA collection method is buccal swabbing, which collects small saliva sample from the inner cheek. This technique is primarily used because of its simple and non-invasive nature, which minimises the time required and the trauma for the patient.
Buccal swabbing is not always the most suitable technique, however. While a saliva sample can provide information about a patient’s overall genome, it does not always provide insight into the genetic mutations that have caused disease at a specific site in the body. The most frequent example of this is the development of a cancerous tumour, which will carry mutations that cannot be detected via buccal swabbing. In such cases, it may instead be necessary to perform a tissue biopsy to selectively collect diseased cells to investigate their genomes.
Due to their invasive nature, tissue biopsies will typically only be performed when a patient is suspected of having localised cells that carry harmful mutations. While the technique is commonly associated with cancer diagnosis, biopsies are also frequently used to investigate the condition of specific organs or tissues, such as in the case of kidney disease or during fertility testing.
The nature of the biopsy used is largely determined by the location of the cells necessary for testing. Cells that are growing near the surface of the skin can usually be gathered by skin biopsies, but deeper tissues need to be collected via either needle or surgical biopsies.
Incisional Biopsies – A shallow incision is made and a small amount of tissue is collected from just below the skin.
Excisional Biopsies – An entire area of suspicion, such as a mole that has changed colour or shape, is removed from the surface of the skin.
Punch Biopsies – A specialised circular tool bores through the skin to collect a sample containing skin cells and tissue from just below the surface of the skin.
Shave Biopsies – A sharp tool, typically a scalpel, is used to scrape tissue from the surface of the skin.
Fine Needle Aspirations – A very thin needle is inserted into the region of interest and a small sample is drawn into a syringe.
Core Needle Biopsies – A needle that is larger than those used in fine needle aspirations is inserted through the skin into the region of interest. The wider needle allows for a larger sample to be collected.
Vacuum-Assisted Biopsies – A specialised needle is inserted into th region of interest and suction is used to draw a sample. The vacuum technology enables a larger sample to be collected, or for multiple samples to be drawn from the same site without multiple injections.
Image-Guided Biopsies – As an advanced version of other needle biopsies for deep tissue collection, image guidance is used to ensure that the needle reaches the correct site. CT scans, X-rays, MRI’s, Ultrasounds, and Fluoroscopies have all been used as imaging techniques.
Bone Marrow Aspirations – A needle is used to collect a fluid sample from a patient’s bone marrow. This technique is frequently combined with bone marrow biopsies.
Laparoscopic Biopsies – A surgical incision is made and a thin, flexible tube with a light and a camera is inserted into the body. When the camera detects the tissue of interest, forceps can be used to collect a small sample.
Endoscopic Biopsies – A thin, flexible tube with a light and a camera is inserted into the body via the mouth. When the camera detects the tissue of interest, forceps can be used to collect a small sample.
Bone Marrow Biopsies – A solid sample of bone marrow is collected from patient’s bones, typically from the pelvic bone. This technique is frequently combined with bone marrow aspirations.
Tissue biopsies are a very useful tool for identifying what genetic changes have taken place in diseased tissues, as they provide a DNA sample from the affected area. Unfortunately, there are problems too. The immediate issue is that some of these tests are very invasive in nature, in particular, those which require surgical intervention.
As a result, a patient who has undergone this sample collection will then need a recovery period which can be especially distressing for patients who are already ill. Another concern arises when the area of interest is deep within the body or in an area that is largely inaccessible, such as the brain.
When this is the case, collecting a tissue sample can be impossible, or presents too high a risk for the test to be considered worthwhile, and the patient cannot be biopsied. As a result, tissue biopsies are an insufficient… Download the full guide to learn more.