Amplicon Sequencing
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In
molecular biology Molecular biology is the branch of biology that seeks to understand the molecular basis of biological activity in and between cells, including biomolecular synthesis, modification, mechanisms, and interactions. The study of chemical and phys ...
, an amplicon is a piece of DNA or
RNA Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation and expression of genes. RNA and deoxyribonucleic acid ( DNA) are nucleic acids. Along with lipids, proteins, and carbohydra ...
that is the source and/or product of amplification or
replication Replication may refer to: Science * Replication (scientific method), one of the main principles of the scientific method, a.k.a. reproducibility ** Replication (statistics), the repetition of a test or complete experiment ** Replication crisi ...
events. It can be formed artificially, using various methods including
polymerase chain reaction The polymerase chain reaction (PCR) is a method widely used to rapidly make millions to billions of copies (complete or partial) of a specific DNA sample, allowing scientists to take a very small sample of DNA and amplify it (or a part of it) ...
s (PCR) or
ligase chain reaction The ligase chain reaction (LCR) is a method of DNA amplification. The ligase chain reaction (LCR) is an amplification process that differs from PCR in that it involves a thermostable ligase to join two probes or other molecules together which can t ...
s (LCR), or naturally through
gene duplication Gene duplication (or chromosomal duplication or gene amplification) is a major mechanism through which new genetic material is generated during molecular evolution. It can be defined as any duplication of a region of DNA that contains a gene ...
. In this context, ''amplification'' refers to the production of one or more copies of a genetic fragment or target sequence, specifically the amplicon. As it refers to the product of an amplification reaction, ''amplicon'' is used interchangeably with common laboratory terms, such as "PCR product." Artificial amplification is used in
research Research is "creative and systematic work undertaken to increase the stock of knowledge". It involves the collection, organization and analysis of evidence to increase understanding of a topic, characterized by a particular attentiveness t ...
, forensics, and
medicine Medicine is the science and Praxis (process), practice of caring for a patient, managing the diagnosis, prognosis, Preventive medicine, prevention, therapy, treatment, Palliative care, palliation of their injury or disease, and Health promotion ...
for purposes that include detection and quantification of
infectious agents In biology, a pathogen ( el, πάθος, "suffering", "passion" and , "producer of") in the oldest and broadest sense, is any organism or agent that can produce disease. A pathogen may also be referred to as an infectious agent, or simply a ger ...
, identification of human remains, and extracting
genotypes The genotype of an organism is its complete set of genetic material. Genotype can also be used to refer to the alleles or variants an individual carries in a particular gene or genetic location. The number of alleles an individual can have in a ...
from human hair. Natural
gene duplication Gene duplication (or chromosomal duplication or gene amplification) is a major mechanism through which new genetic material is generated during molecular evolution. It can be defined as any duplication of a region of DNA that contains a gene ...
plays a major role in
evolution Evolution is change in the heritable characteristics of biological populations over successive generations. These characteristics are the expressions of genes, which are passed on from parent to offspring during reproduction. Variation ...
. It is also implicated in several forms of human cancer including
primary mediastinal B cell lymphoma Primary mediastinal B-cell lymphoma, abbreviated PMBL, is a rare type of lymphoma that forms in the mediastinum (the space in between the lungs) and predominantly affects young adults. It is a subtype of diffuse large B-cell lymphoma; however, it ...
and
Hodgkin's lymphoma Hodgkin lymphoma (HL) is a type of lymphoma, in which cancer originates from a specific type of white blood cell called lymphocytes, where multinucleated Reed–Sternberg cells (RS cells) are present in the patient's lymph nodes. The condition w ...
. In this context the term ''amplicon'' can refer both to a section of
chromosomal A chromosome is a long DNA molecule with part or all of the genetic material of an organism. In most chromosomes the very long thin DNA fibers are coated with packaging proteins; in eukaryotic cells the most important of these proteins are ...
DNA that has been excised, amplified, and reinserted elsewhere in the
genome In the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding ...
, and to a fragment of extrachromosomal DNA known as a
double minute Double minutes are small fragments of extrachromosomal DNA, which have been observed in a large number of human tumors including breast, lung, ovary, colon, and most notably, neuroblastoma. They are a manifestation of gene amplification as a result ...
, each of which can be composed of one or more
gene In biology, the word gene (from , ; "... Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' or ''gender'') can have several different meanings. The Mendelian gene is a b ...
s. Amplification of the genes encoded by these amplicons generally increases
transcription Transcription refers to the process of converting sounds (voice, music etc.) into letters or musical notes, or producing a copy of something in another medium, including: Genetics * Transcription (biology), the copying of DNA into RNA, the fir ...
of those genes and ultimately the volume of associated
protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respon ...
s.


Structure

Amplicons in general are
direct repeat Direct repeats are a type of genetic sequence that consists of two or more repeats of a specific sequence. In other words, the direct repeats are nucleotide sequences present in multiple copies in the genome. Generally, a direct repeat occurs when a ...
(head-to-tail) or
inverted repeat An inverted repeat (or IR) is a single stranded sequence of nucleotides followed downstream by its reverse complement. The intervening sequence of nucleotides between the initial sequence and the reverse complement can be any length including zero. ...
(head-to-head or tail-to-tail) genetic sequences, and can be either linear or circular in structure. Circular amplicons consist of imperfect inverted duplications annealed into a circle and are thought to arise from precursor linear amplicons. During artificial amplification, amplicon length is dictated by the experimental goals.


Technology

Analysis of amplicons has been made possible by the development of amplification methods such as
PCR PCR or pcr may refer to: Science * Phosphocreatine, a phosphorylated creatine molecule * Principal component regression, a statistical technique Medicine * Polymerase chain reaction ** COVID-19 testing, often performed using the polymerase chain r ...
, and increasingly by cheaper and more high-throughput technologies for DNA sequencing or
next-generation sequencing Massive parallel sequencing or massively parallel sequencing is any of several high-throughput approaches to DNA sequencing using the concept of massively parallel processing; it is also called next-generation sequencing (NGS) or second-generation s ...
, such as
ion semiconductor sequencing Ion semiconductor sequencing is a method of DNA sequencing based on the detection of hydrogen ions that are released during the polymerization of DNA. This is a method of "sequencing by synthesis", during which a complementary strand is built bas ...
, popularly referred to as the brand of the developer, Ion Torrent. DNA sequencing technologies such as next-generation sequencing have made it possible to study amplicons in
genome biology ''Genome Biology'' is a peer-reviewed open access scientific journal covering research in genomics. It was established in 2000 and is published by BioMed Central. The chief editor is currently Andrew Cosgrove ( BioMed Central, New York). Abstrac ...
and
genetics Genetics is the study of genes, genetic variation, and heredity in organisms.Hartl D, Jones E (2005) It is an important branch in biology because heredity is vital to organisms' evolution. Gregor Mendel, a Moravian Augustinian friar worki ...
, including cancer genetics research,International Cancer Genome Consortium Official Website
/ref>
phylogenetic In biology, phylogenetics (; from Greek φυλή/ φῦλον [] "tribe, clan, race", and wikt:γενετικός, γενετικός [] "origin, source, birth") is the study of the evolutionary history and relationships among or within groups o ...
research, and
human genetics Human genetics is the study of inheritance as it occurs in human beings. Human genetics encompasses a variety of overlapping fields including: classical genetics, cytogenetics, molecular genetics, biochemical genetics, genomics, population gen ...
.National Human Genome Research Institute
/ref> For example, using the
16S rRNA 16S rRNA may refer to: * 16S ribosomal RNA 16 S ribosomal RNA (or 16 S rRNA) is the RNA component of the 30S subunit of a prokaryotic ribosome ( SSU rRNA). It binds to the Shine-Dalgarno sequence and provides most of the SSU structure. The ...
gene, which is part of every bacterial and archaeal genome and is highly conserved, bacteria can be taxonomically classified by comparison of the amplicon sequence to known sequences. This works similarly in the fungal domain with the
18S rRNA 18S may refer to: *18S ribosomal RNA 18S ribosomal RNA (abbreviated 18S rRNA) is a part of the ribosomal RNA. The S in 18S represents Svedberg units. 18S rRNA is an SSU rRNA, a component of the eukaryotic ribosomal small subunit (40S). 18S rRNA ...
gene as well as the
ITS1 Internal transcribed spacer (ITS) is the spacer DNA situated between the small-subunit ribosomal RNA (rRNA) and large-subunit rRNA genes in the chromosome or the corresponding transcribed region in the polycistronic rRNA precursor transcript. I ...
non-coding region. Irrespective of the approach used to amplify the amplicons, some technique must be used to quantitate the amplified product.Stanley, J. (2002). Essentials of Immunology & Serology by Jacqueline Stanley. Albany, NY: Delmar. Generally, these techniques incorporate a capture step and a detection step, although how these steps are incorporated depends on the individual
assay An assay is an investigative (analytic) procedure in laboratory medicine, mining, pharmacology, environmental biology and molecular biology for qualitatively assessing or quantitatively measuring the presence, amount, or functional activity of ...
. Examples include the Amplicor HIV-1 Monitor Assay (
RT-PCR Reverse transcription polymerase chain reaction (RT-PCR) is a laboratory technique combining reverse transcription of RNA into DNA (in this context called complementary DNA or cDNA) and amplification of specific DNA targets using polymerase chai ...
), which has the capacity to recognize
HIV The human immunodeficiency viruses (HIV) are two species of '' Lentivirus'' (a subgroup of retrovirus) that infect humans. Over time, they cause acquired immunodeficiency syndrome (AIDS), a condition in which progressive failure of the immu ...
in
plasma Plasma or plasm may refer to: Science * Plasma (physics), one of the four fundamental states of matter * Plasma (mineral), a green translucent silica mineral * Quark–gluon plasma, a state of matter in quantum chromodynamics Biology * Blood plas ...
; the HIV-1 QT ( NASBA), which is used to measure plasma
viral load Viral load, also known as viral burden, is a numerical expression of the quantity of virus in a given volume of fluid, including biological and environmental specimens. It is not to be confused with viral titre or viral titer, which depends on the ...
by amplifying a segment of the HIV RNA; and
transcription mediated amplification Transcription-mediated amplification (TMA) is an isothermal (does not change the nucleic acid temperature), single-tube nucleic acid amplification system utilizing two enzymes, RNA polymerase and reverse transcriptase. "Amplification" means crea ...
, which employs a hybridization protection assay to distinguish ''
Chlamydia trachomatis ''Chlamydia trachomatis'' (), commonly known as chlamydia, is a bacterium that causes chlamydia, which can manifest in various ways, including: trachoma, lymphogranuloma venereum, nongonococcal urethritis, cervicitis, salpingitis, pelvic infl ...
'' infections. Various detection and capture steps are involved in each approach to assess the amplification product, or amplicon. With amplicon sequencing the high number of different amplicons resulting from amplification of a usual sample are concatenated and sequenced. After quality control classification is done by different methods, the counts of identical taxa representing their relative abundance in the sample.


Applications

PCR can be used to determine sex from a human DNA sample. The
loci Locus (plural loci) is Latin for "place". It may refer to: Entertainment * Locus (comics), a Marvel Comics mutant villainess, a member of the Mutant Liberation Front * ''Locus'' (magazine), science fiction and fantasy magazine ** '' Locus Award ...
of
Alu element An Alu element is a short stretch of DNA originally characterized by the action of the '' Arthrobacter luteus (Alu)'' restriction endonuclease. ''Alu'' elements are the most abundant transposable elements, containing over one million copies d ...
insertion is selected, amplified and evaluated in terms of size of the fragment. The sex assay utilizes AluSTXa for the
X chromosome The X chromosome is one of the two sex-determining chromosomes ( allosomes) in many organisms, including mammals (the other is the Y chromosome), and is found in both males and females. It is a part of the XY sex-determination system and XO se ...
, AluSTYa for the
Y chromosome The Y chromosome is one of two sex chromosomes ( allosomes) in therian mammals, including humans, and many other animals. The other is the X chromosome. Y is normally the sex-determining chromosome in many species, since it is the presence or a ...
, or both AluSTXa and AluSTYa, to reduce the possibility of error to a negligible quantity. The inserted chromosome yields a large fragment when the homologous region is amplified. The males are distinguished as having two DNA amplicons present, while females have only a single amplicon. The kit adapted for carrying out the method includes a pair of primers to amplify the locus and optionally polymerase chain reaction reagents. LCR can be used to diagnose
tuberculosis Tuberculosis (TB) is an infectious disease usually caused by ''Mycobacterium tuberculosis'' (MTB) bacteria. Tuberculosis generally affects the lungs, but it can also affect other parts of the body. Most infections show no symptoms, in w ...
. The sequence containing protein
antigen In immunology, an antigen (Ag) is a molecule or molecular structure or any foreign particulate matter or a pollen grain that can bind to a specific antibody or T-cell receptor. The presence of antigens in the body may trigger an immune response. ...
B is targeted by four
oligonucleotide Oligonucleotides are short DNA or RNA molecules, oligomers, that have a wide range of applications in genetic testing, research, and forensics. Commonly made in the laboratory by solid-phase chemical synthesis, these small bits of nucleic acids ...
primers—two for the
sense strand In genetics, a sense strand, or coding strand, is the segment within double-stranded DNA that carries the translatable code in the 5′ to 3′ direction, and which is complementary to the antisense strand of DNA, or template strand, which do ...
, and two for the antisense strand. The primers bind adjacent to one another, forming a segment of double stranded DNA that once separated, can serve as a target for future rounds of replication. In this instance, the product can be detected via the microparticle enzyme immunoassay (MEIA).


See also

*
DNA polymerase A DNA polymerase is a member of a family of enzymes that catalyze the synthesis of DNA molecules from nucleoside triphosphates, the molecular precursors of DNA. These enzymes are essential for DNA replication and usually work in groups to create ...
*
High Resolution Melt High Resolution Melt (HRM) analysis is a powerful technique in molecular biology for the detection of mutations, polymorphisms and epigenetic differences in double-stranded DNA samples. It was discovered and developed by Idaho Technology and ...
*
Melting curve analysis Melting curve analysis is an assessment of the dissociation characteristics of double-stranded DNA during heating. As the temperature is raised, the double strand begins to dissociate leading to a rise in the absorbance intensity, hyperchromicity ...
*
Molecular biology Molecular biology is the branch of biology that seeks to understand the molecular basis of biological activity in and between cells, including biomolecular synthesis, modification, mechanisms, and interactions. The study of chemical and phys ...


References


Further reading

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External links

{{DEFAULTSORT:Amplicon DNA Genetics techniques Molecular biology Biotechnology Polymerase chain reaction Laboratory techniques Molecular biology techniques