Single Nucleotide Polymorphisms, SNPs, 2023

     Single nucleotide polymorphisms, or SNPs, are Genetic DNA variants.  SNPs predict an individual’s response to drugs, susceptibility to environmental factors, and uncovers the risk of developing diseases. SNPs can also be used to track the insurance of disease-associated genetic variants within families.

     SNPs occur normally throughout a person’s DNA. They occur almost once in every 1,000 nucleotides on average, which means there are roughly 4 to 5 million SNPs in a person's genome. These variations occur in many individuals; to be classified as a SNP, a variant is found in at least 1 percent of the population. Scientists have found more than 600 million SNPs in populations around the world.

     SNPs research is known as Genotyping. Genotyping is a laboratory process in which an individual’s germline DNA is analyzed for SNPs. Genotyping differs from sequencing in which all of the nucleotides comprising a specific length of DNA are assessed.  Genotyping is used in a number of sectors.  The most important sectors are clinical research, clinical diagnostics and agriculture.

     An example of the use of Genotyping in clinical research is for the purpose of Precision Medicine.  This form of medicine uses information about a person’s own genes or proteins to prevent, diagnose, or treat disease.  One sort of Precision Medicine is "targeted therapy to treat HER2-positive breast cancer cells by tumor marker testing." PMC

     An example of the use of Genotyping in clinical diagnostics is to treat Antimicrobial Resistance.  This Resistance is the developed within a disease-causing microbe. A resistant microbe has the ability to survive exposure to an antimicrobial agent that was previously an effective treatment.  Antimicrobial Resistance initiates through mutation or gene transfer.

     An example of the use of Genotyping in agriculture is to identify potential genes to improve crop and livestock breeding programs. Breeding complex traits and minor genetic effects with high-density markers is Genotyping.  Each trait-related locus is associated with at least one marker for the purpose of choosing top-ranked lines based on individuals' genomic estimated breeding values.

     SNPs research occurs with a genotyper.  "Kmer-based Alignment-free Graph Genotyper, or KAGE, is a new genotyper for SNPs and short indels that builds on recent ideas of alignment-free genotyping from Malva and PanGenie for computationally efficiency. KAGE implements two novel ideas for utilizing all previously known haplotype information from repositories such as the "1000 Genomes Project" in order to improve genotyping accuracy, and speed." BMC, Genome Biology 

     SNPs are found in the DNA. They can act as biological markers, helping scientists locate genes that are associated with disease. When SNPs occur within a gene or in a regulatory region near a gene, they may play a more direct role in disease by affecting the gene’s functions. Research continues to identify SNPs associated with complex diseases such as heart disease, diabetes, and cancer.

CANCER

“About 1,660,290 new cancer cases are expected to be diagnosed in 2013, and in 2013 about 580,350 Americans are projected to die of cancer, almost 1,600 people a day. Cancer remains the second most common cause of death in the US, accounting for nearly 1 of every 4 deaths. (http://www.cancer.org/index) ”

 

     This statistic isn’t very detailed either.  There are several different types of cancer; none of which diminish the uninviting reality of the disease.

 

 

     You might ask: “Well, what is cancer?”

     Cancer is defined as a malignancy.  This malignancy is an abnormal growth of cells.  “The growth and differentiation of cells in the body are normally strictly controlled.  Thus, with few exceptions, cells in the adult body are largely quiescent.  However, for a variety of reason, a cell may be made to proliferate uncontrollably to form a tumor (Wiley Asia Student Ed.  FUNDAMENTALS OF BIOCHEMISTRY. Voet 2006).” This unwanted growth that damages healthy organs is the uncontrolled malignancy.  The growth then continues to spread toward other healthy organs.  Cancer symptoms vary widely based on the type of cancer. Cancer treatment could include chemotherapy, radiation, and/or surgery.

     The best way to treat cancer is through early detection.  The diagnosis begins with routine self-exam or physical exams. “If the diagnosis is positive (cancer is present), other tests are performed to provide specific information about the cancer. This essential follow-up phase of diagnosis is called staging. The most important thing doctors need to know is whether cancer has spread from one area of the body to another. If the initial diagnosis is negative for cancer and symptoms persist, further tests may be needed. If the biopsy is positive for cancer, be sure to seek a confirming opinion by a doctor who specializes in cancer treatment before any treatment is started (http://www.webmd.com/cancer/default.htm).”

 

Cancer research is ongoing.  The cure isn’t far away.  We keep praying.  New developments are constantly on the horizon.  A recent headline on www.newscientist.com read, Antibody wakes up T-cells to make cancer vanish , 17:07 04 June 2013 by Andy Coghlan

 

 

     With this progress researchers learned how to wake up otherwise slumbering T-cells.  The T-cells are dosing off and permitting unrecognized cells to proliferate.  Full functioning T-cells will instantly recognize and destroy foreign material in the body.  Tumor cells became wise to that fact, though.  Tumor cells evolved and masked themselves with a sprout surface molecule called a ligand.  Ligands bind.  On tumor cells, the ligand binds and activates a receptor on the T-cell called PD-1.  The PD-1 receptor is an almost perfect mask.  The T-cells can’t recognize foreign material.  The immune system continues to produce tissues with the cancer as if everything were normal.  The abovementioned antibodies can unmask the cancer cell by blocking the ligand’s interaction with PD-1 ligand.  Then, certainly, the T-cells can resume destroying the foreign material eradicating the cancer.  Research Lambrolizumab, and Nivolumab for more details.

     One day the only subject that springs to mind on the term CANCER is the astrological sign.

 

Keeping a strong body healthy

The proper function of proteins in the body is very essential to health.  The proteins also have to have a functional structure and cellular integrity.  Getting old keeps humans from being young and healthy, obviously.  Our body ages because various organisms are always subject to attack causing diseases and viruses.  Disease causing agents are termed pathogens.  Pathogens will penetrate the protective layer, the skin, and then move on towards the first line of defense.  Mucous membranes are the first line of defense.  Once the pathogens break through the mucous membranes they are labeled foreign invaders and will subsequently be destroyed by the immune system.

The human body is a model for a city that is always at war.  If the city isn’t reconstructed it will crumble.  What types of defense will a city utilize in the midst of a war?

The human body has two types of immunity:

                -Cellular immunity and humoral immunity

Coming straight out of the bone marrow we introduce antibody.  Antibodies are proteins that are mediated against viral attacks.  “The immune response is triggered by the presence of a foreign macromolecule, often a protein or carbohydrate, known as an antigen” (Voet, Fundamentals of Biochemistry 2006).  B cells produce antibodies, which as we recently said, mature in the bone marrow.  Pay attention to B cells.  B cells flaunt immunoglobulins on their exteriors.  Immunoglobulins snatch foreign invaders, and lock them in the B cells where they are broken and degraded.  The broken antigen is then placed on display.  The circulating antibodies become antigen specific.  The antibodies fluidly mark antigens for destruction.  Some B cells are short-lived.  They survive for a couple of days.  Some B cells live from many weeks to many years.  These potent B cells are called memory B cells. 

“…tolerance…”

Memory B cells mount a secondary response.  This response is more accurate and much faster than the primary response mentioned earlier.

“…sensitivity…”

The immunoglobulins themselves also create a diverse group of proteins.  The differences between the sub classes of immunoglobulins are: different amounts of heavy chains, and various subunits.  “These subunits associate by disulfide bonds and noncovalent interactions to form a roughly Y-shaped symmetric molecule with the formula (LH)₂” (Voet, Fundamentals of Biochemistry 2006).  We have: IgM, IgA, IgG, IgE, and IgD.  We can use an example in accordance with Rheumatology International journal (Novel mutations of MVK gene in Japanese family members affected with hyperimmunoglobulinemia D and periodic fever syndrome, Mizuno 2011).  IgD expression begins when the B cell leaves the bone marrow headed to peripheral lymphoid tissues.  IgD functions to signal B cell activation.  When IgD is unavailable, at abnormally low serum levels, HIDs (hyperimmunoglobulinemia D syndrome) results.

The proper functioning of proteins such as IgD keeps humans healthy.  If IgD does its job acceptably,  by activating  B cells to destroy antigens, the primary and secondary defenses will keep us healthy.  We will continue to get old.  We don’t have to be undesirably broken down and unhealthy, though.