«« What is DNA? »»
DNA, deoxyribonucleic acid, encodes the information that determines how an organism develops, lives, and reproduces, on a cellular level. Most DNA found in nature has a right-handed double helix conformation, and is composed of the nucleotides adenine (A), thymine (T), cytosine (C), and guanine (G). Genomic DNA, gDNA, which is inherited by offspring, resides in the nucleus of every cell and is tightly packaged as chromosomes. The number of chromosomes present in the nucleus differs between species: humans have 23 pairs of chromosomes, 22 of which are autosomes and the final pair is the sex chromosomes- “X” or “Y”. Dogs have 39 pairs, cats have 19 pairs, horses have 32 pairs, and cattle have 30 pairs of chromosomes. All offspring receive one copy of each pair of chromosomes from their parents, with the sex chromosomes determining the final sex of the organism- “XX” being female and “XY” male.
The two strands of genomic DNA that form the double helix are complementary in nature; the sequence of the second strand can be determined based on the sequence of the first strand, due to the strict base pairing rule where adenine (A) and thymine (T) must pair with each other and cytosine (C) and guanine (G) must pair together. The base pairing rule must be strictly followed to allow for the DNA sequence to be carefully preserved between generations.
Genomic DNA is transcribed in the nucleus into RNA, ribonucleic acid. Messenger RNA, mRNA, is the form of RNA that is carried to the ribosome from the nucleus, where protein synthesis (translation) occurs.
Mitochondrial DNA, mtDNA, is a circular form of DNA that is found in the mitochondria and encodes proteins critical for energy production. mtDNA is maternally inherited which means that all offspring from the same mother will have the same mtDNA, an important note when determining the risk of inheriting disease causing mutations on mtDNA.
Shown is the typical conformation of gDNA found in nature: right handed double helix with ~10-10.6 bases per complete turn. The boxed area is flattened and shown in the center to depict the chemical structure of DNA, including the sugar-phosphate backbone and the nucleotides covalently bound to the deoxyribose of the backbone and bound to the appropriate nucleotide pair on the complementary strand using hydrogen bonding.
«« What causes DNA mutations? »»
Mutations in DNA can occur due to environmental damage or spontaneous errors, such as during replication. UV and x-ray radiation, chemicals, and viral infections are all environmental factors that can cause DNA damage and subsequent mutations. When DNA is damaged by environmental factors the DNA damage response is activated, and a variety of repair enzymes work to fix the DNA damage and restore the DNA to its correct sequence. During DNA replication, proofreading enzymes exist to find when the incorrect base is added to the new DNA strand and work to excise the incorrect base and insert the correct base, according to base pairing rules. Although these mechanisms for DNA repair exist, the repairs are not always perfect, and sometimes DNA damage is missed. When DNA damage and errors persist, they can become permanent mutations that may result in disease development in the organism or its offspring. The majority of novel mutations in an organism are somatic, as opposed to germline, meaning that they are not passed on during reproduction to offspring. Many cancers, for example, are caused by somatic mutations. Germline mutations are those that are present in the germ cells, the cells that give rise to eggs or sperm, and can thus be passed on to future generations through reproduction. At the end of the day, the initial cause of the DNA mutation, whether environmental or spontaneous, is irrelevant to genetic testing, but understanding whether a mutation is somatic or germline in origin is critical for understanding genetic test results in the context of a breeding program.
Common examples of environmental mutagens, from right to left: pesticides, UV radiation, viruses, and x-ray radiation
«« Using WGS to discover unique and complex genetic mutations »»
Whole genome sequencing (WGS) is the most advanced, rigorous, and extensive method of genetic testing available. WGS, as its name suggests, is a method of sequencing the entire genome. Through the use of complex analyzers and software, WGS reads the entire genome and converts it into a format that allows scientists to visualize every single base pair present in the DNA of an organism. Once the whole genome is captured digitally, scientists are able to compare the genomes of unhealthy and healthy animals, to find complex and unique mutations that may be responsible for the presenting genetic disease.
Not all mutations found in an animal’s genome are disease causing or deleterious; therefore, it is critical that analysis of the whole genome be performed carefully by trained geneticists and biochemists to refine the discovered mutations and find the unique mutation(s) likely to be responsible for the animal’s disease state. For example, many mutations are synonymous, meaning that the mutation in the DNA does not result in a change in the final protein sequence, and therefore has no affect on the animal. Nonsynonymous substitution mutations, DNA mutations that change the final protein sequence by altering the nucleotide sequence, are not always disease causing either. These mutations must be carefully filtered to isolate potential disease causing mutations; some of the steps in filtering these mutations include analyzing the affect of the mutation on the secondary and tertiary structure of the protein and determining whether the mutation is present in a critical domain for protein binding or enzymatic activity. Synonymous and nonsynonymous mutations both typically involve mutations in a single nucleotide. It is also possible, however, for mutations to be much larger in scale, with large portions of chromosomes being deleted, for example. These mutations typically result in a vast array of symptoms due to the large number of proteins that are affected, and are thus difficult to clinically diagnose but easily discovered with whole genome sequencing.
MoxxiTech uses our own custom and proprietary software to analyze each animal’s whole genome and determine each animal’s individual risk for a multitude of mutations known to cause disease and to find unique mutations that have yet to be annotated. Further, our highly trained geneticists and biochemists are experts at analyzing mutations to determine whether the mutation(s) are responsible for the presenting disease symptoms or simply DNA polymorphisms.
Examples of common types of DNA mutations in coding regions are shown above. The chosen examples show only single nucleotide changes, but it is possible for multiple mutations to occur on the same strand of DNA or for large numbers of nucleotides to be inserted and/or deleted. Other mutations can occur on the chromosomal level, where large portions of the chromosome are deleted, inverted, or transposed to a different chromosome. Mutations in non-coding regions can also impact the final protein products by affecting protein binding to DNA or DNA modifications (such as methylation), or by altering splice sites. Click Here to read more information about the effects of mutations in noncoding regions, including links to scientific publications, from the NIH.
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