DNA dabbles

What is Liquid biopsy?? It is a technique for analyzing blood and other bodily fluids, for diagnosing and monitoring diseases.  Because we don't need an invasive procedure, such as surgery, to obtain biofluids, liquid biopsies are non-invasive and painless.  This feature of liquid biopsy makes it useful, when tissue biopsy cannot be used.  An important example of such applications is cancer, where liquid biopsy can be used as a diagnostic and monitoring tool. How is Liquid Biopsy performed? Liquid biopsy analyses can be done on blood as well as other bodily fluids such as urine, saliva or sputum. But, blood samples are the most commonly used samples for testing. A small amount of blood is drawn using a needle and syringe. Cells are separated from the blood and circulating DNA or RNA is extracted from the cell-free blood, or blood components such as plasma or serum. Levels of nucleic acids are commonly measured using techniques such as PCR. Changes in the sequence of nucle...

  Hi readers! Welcome back to another post on cell-free DNA ! This time we will look at another type of change that can occur in DNA – methylation.  Not all genes are expressed in a cell at the same amount at a given time. Some genes are expressed in a lower amount and some are expressed in a higher amount. By gene expression, I mean production of a protein from the gene encoding it. Changes in gene expression which do not affect the DNA sequence are called epigenetic changes .  Methylation is a type of epigenetic change used by the cells to turn off gene expression. It changes a component of the DNA molecule called the nucleotide base. In this event, a methyl group is added to the carbon at the fifth position of a cytosine ring, resulting in the formation of a 5-methylcytosine. Methylation of a gene can block its expression compared to genes that are not methylated. In a cell, addition or removal of methyl groups are used to regulate gene expression.  In cancer, ge...

Hi readers! In today’s post, we will look at mutations that can be detected in cell-free DNA. Mutations are changes in the DNA sequence that can happen due to environmental factors or when DNA is copied. With respect to mutations in cell-free DNA, research has been done primarily in cancer. In cancer, such changes occur in genes that play a role in cell growth and death. During the course of tumor development, a tumor accumulates several mutations. These mutations can be detected in cell-free DNA and this indicates that the cfDNA was released by the tumor. For example, suppose that we isolated cell-free DNA from a breast cancer patient Z and analyzed it for mutations in the PIK3CA gene. PIK3CA gene plays an important role in mediating pathways responsible for growth and survival of the cell. It is the most commonly mutated gene in breast cancer patients, mutations being detected in about 1/3rd of cases. Now, say that Z has a mutation in PIK3CA gene. Now how can this information help u...

 Hi readers and welcome back to my blog post on DNA integrity index! Last time we looked at what DNA integrity index is and how it can be measured. Today, we will look at how DII can be used for diagnosing a disease like cancer. So how can a DII ratio help diagnose cancer?  When we say we use DII ratios for diagnosis, we mean that we are testing whether the values of ratios in patients are different from those in healthy people. Most studies say that the cancer patients have longer fragments than shorter fragments. Healthy people tend to have higher amounts of shorter fragments than longer fragments. So, the amount of long or short fragments of cfDNA in a person determines the DII value for that person. Let’s take a study by Pinzani and colleagues as an example.  In 2011, Pinzani and colleagues tried to find a suitable ratio for diagnosing melanoma. They isolated cell-free DNA from the plasma of 79 melanoma patients and 34 healthy people. They measured DNA fragments of ...

 Earlier we saw how cell-free DNA  is  released into the body fluids . That raises a lot of questions... Does the amount of DNA vary from person-to-person? Can the DNA levels be different in people with diseases than in normal people? Yes, they can be...  For example, in cancer, researchers have measured cfDNA levels using many techniques. Some of them are radioimmunoassay, DNA dipstick, and real-time PCR. Different studies have reported different levels of cfDNA. But in general, cancer patients had higher cfDNA concentration than healthy people. Some studies compared cell-free levels in different cancer types. Of these, lung cancer patients had the highest levels of cell-free DNA. And prostate cancer patients had the lowest levels. So how can this information help in treating disease? To answer this, researchers compared DNA levels with patients' clinical information. They found that patients with bigger tumors had higher cell-free DNA levels. Patients with higher d...

Hi and welcome back! In the last few posts, we looked at the basics of cell-free DNA and how it reaches the bloodstream from the cells.  We saw that both living and dying cells can release DNA into body fluids. Now, you must be wondering, "what does cell-free DNA do after it comes out of the cell?" "Is there a purpose for cells releasing DNA?" Many researchers have searched for answers to these very questions. They probed for clues to cell-free DNA biology. Whether cell-free DNA can play a role in disease? Whether cell-free DNA can be used in general body functions? Can cell-free DNA perhaps help in defense against infection or disease? Or maybe it can pass along signals from one cell to another? In the coming posts, we will look at the answers to some of these questions. We will learn what researchers have understood about cell-free DNA biology until now.   In the beginning few posts, we also talked about cell-free DNA being used for diagnosis of disease. So how...

 Welcome back reader! Today, we will look at how DNA reaches the bloodstream. There are two ways by which cells release DNA. One is when living cells release DNA under certain conditions such as stress or as defense. This is called as active release of DNA. Second, when cells die, they release their contents into the surroundings. This is called passive release of DNA.  Now, how can a cell actively release DNA into blood? There are many processes by which living cells can release DNA.  First is phagocytosis. Phagocytosis is a process by which white blood cells eat dead or infected cells and bacteria to protect the body from infection. Some of the types of white blood cells that usually do phagocytosis are monocytes, macrophages and neutrophils. Second is NETosis vital. Now imagine a man is fishing. What would he do if he wants to catch a large amount of fish at once? Throw a net, right? In the same way, neutrophils throw NETs to catch any bacteria or similar microbes that...

  My last post gave you a glimpse into the basics of circulating nucleic acids. Today, we will look at circulating cell-free DNA (cfDNA).  Live or dying cells can release DNA into the blood stream. In case of diseases, it can be released by normal as well as diseased cells. Persons with infectious diseases may have viral DNA in their blood. Likewise, during pregnancy, fetal DNA can be detected in the mother's blood. But a large part of cell-free DNA arises from normal cells in case of diseases and from maternal cells, in case of pregnancy. But, the genetic and the epigenetic markers the DNA carries is different from the normal cells. So, researchers try to diagnose disease or fetal abnormalities based on these changes. For example, cancer cells contain mutations in specific genes.  These can be detected in cell-free DNA. In this case, the DNA containing the mutation is specific to the tumor and is thus called  "circulating tumor DNA (ctDNA)".  Now,  there ...

  Welcome to another post on liquid biopsy ! Today we are going to look at circulating nucleic acids. We all have heard of nucleic acids at some point in our life. Nucleic acids contain genetic instructions that make an organism grow and develop. DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are the main classes of nucleic acids. They are present in all cells of an organism. Then what are circulating nucleic acids??? Sometimes the cells release these nucleic acids into the blood or other body fluids. Since blood is more commonly studied, when we talk about “circulation“, we are mostly talking about blood, unless it is mentioned otherwise. Because these nucleic acids are present in the blood circulation, they are called circulating nucleic acids . Because these nucleic acids are present outside the cell, they are also called cell-free nucleic acids , like cell-free DNA or cell-free RNA.  In 1948, Mandel and Mattais reported for the first time that nucleic acids are pre...

  Hi! Thanks for visiting DNADabbles, a blog about all things related to genetics and genomics.  Our blog is a place where we will share our insights on the world of Molecular biology and Human Genetics. We will be writing about different genetic topics and how they relate to human health, as well as various applications in society. The topics of the  blogs will range from genetic testing and disorders to medical applications of DNA sequencing. We will start with a series of posts on liquid biopsy. In future posts, we will explain what liquid biopsy means, and its  importance in managing disease, in a simple and easy-to-understand way. More on that in the next post!  We are excited to begin this journey with you and look forward to your feedback along the way!   Please post any comments or questions you might have in the comments section below!