Category Archives: DNA

Alternate Titles: deoxyribonucleic acid

DNA, abbreviation of deoxyribonucleic acid, organic chemical of complex molecular structure that is found in all prokaryotic and eukaryotic cells and in many viruses. DNA codes genetic information for the transmission of inherited traits.

A brief treatment of DNA follows. For full treatment, see genetics: DNA and the genetic code.

The chemical DNA was first discovered in 1869, but its role in genetic inheritance was not demonstrated until 1943. In 1953 James Watson and Francis Crick determined that the structure of DNA is a double-helix polymer, a spiral consisting of two DNA strands wound around each other. Each strand is composed of a long chain of monomer nucleotides. The nucleotide of DNA consists of a deoxyribose sugar molecule to which is attached a phosphate group and one of four nitrogenous bases: two purines (adenine and guanine) and two pyrimidines (cytosine and thymine). The nucleotides are joined together by covalent bonds between the phosphate of one nucleotide and the sugar of the next, forming a phosphate-sugar backbone from which the nitrogenous bases protrude. One strand is held to another by hydrogen bonds between the bases; the sequencing of this bonding is specifici.e., adenine bonds only with thymine, and cytosine only with guanine.

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genetics : DNA and the genetic code

The configuration of the DNA molecule is highly stable, allowing it to act as a template for the replication of new DNA molecules, as well as for the production (transcription) of the related RNA (ribonucleic acid) molecule. A segment of DNA that codes for the cells synthesis of a specific protein is called a gene.

DNA replicates by separating into two single strands, each of which serves as a template for a new strand. The new strands are copied by the same principle of hydrogen-bond pairing between bases that exists in the double helix. Two new double-stranded molecules of DNA are produced, each containing one of the original strands and one new strand. This semiconservative replication is the key to the stable inheritance of genetic traits.

Within a cell, DNA is organized into dense protein-DNA complexes called chromosomes. In eukaryotes, the chromosomes are located in the nucleus, although DNA also is found in mitochondria and chloroplasts. In prokaryotes, which do not have a membrane-bound nucleus, the DNA is found as a single circular chromosome in the cytoplasm. Some prokaryotes, such as bacteria, and a few eukaryotes have extrachromosomal DNA known as plasmids, which are autonomous, self-replicating genetic material. Plasmids have been used extensively in recombinant DNA technology to study gene expression.

The genetic material of viruses may be single- or double-stranded DNA or RNA. Retroviruses carry their genetic material as single-stranded RNA and produce the enzyme reverse transcriptase, which can generate DNA from the RNA strand. Four-stranded DNA complexes known as G-quadruplexes have been observed in guanine-rich areas of the human genome.

More here:
DNA | Facts & Structure | Britannica.com

Isabel Rojas

Identity is an interesting concept. For the most part we like to believe that we define our own identity. The truth is a lot goes into defining our identity. And what it comes down to is what we accept as our own. The more we know about ourselves, our own experiences, our families past and heritage, and so on - the more our own identity changes and evolves and becomes further defined in our minds and accepted as our own. I have a lot of thoughts and experiences around this topic that have caused my own identity do grow and evolve over time. Here is a snap shot:

I was born in NYC, the youngest of 5 kids. My parents and three older siblings were born in Bogota, Colombia. My family migrated to NYC in the late 70s looking for a better life. After my brother and I were born in the early 80s my parents had begun to realize what a dangerous city it was at that time and decided to head back to Colombia. They worked hard to build a 3 story building where we would live, work, and rent out space. It was a 3 year process. But sadly Colombia at that time was worsening. Bomb threats throughout the city and in front of our new building became too much for my family. We made the trip back to NYC and a year later drove to Salt Lake City where we have lived for about 27 years.

People look at me and often wonder what I am.

People look at me and often wonder what I am. It is often both entertaining and frustrating when people attempt to find out where I am from. My name implies Hispanic/Latino and considering that is the largest ethnic/minority population in Utah its a pretty safe guess. However, when Im with my Polynesian friends people think Im Hawaiian or a mix of Polynesian and something else. In fact in high school I MCd a Polynesian dance group because I could pull off the look. When I travel my friend have told me that they like having me around because I blend in just about anywhere. I recently attended a Nepali church service and had a few people ask me what part of Nepal I was from. Its fun when people assume I am from a different culture/heritage then I am. And I have to admit its kind of entertaining watching people try to skirt around the inquiry as to where I am from.

I identify myself as Colombian, But the sad thing is that when I go to Colombia some family members consider me North American because I was born in the U.S. However, in the U.S. I am defined as Hispanic/Latino in just about every form of paper work I fill out, by associates, friends, and strangers. I often weave in and out of the wonderful experience of growing up straddling two worlds and cultures and the feeling of being neither from here nor there. There is a constant pull between how other identify and define me and how I chose to define and accept myself, my heritage, my culture, and the unknown history that somehow contributes to who I am.

As my dad and I have begun to explore our genealogy the past 7 years or so, weve found that our family is largely from Spain which is no big surprise. My mom is white; her mother was also fair skinned with grayish blue eyes. Some of her cousins that live in Colombia are blond and blue eyed. But that isnt rare in Colombia, let alone south/central america. Colombians have a wide range of ethnicities and consequently a lot of racial discrimination. The Spanish influence is very much present and often people can easily say how many generations back are from Spain. My dad also suspects we have German ancestry somewhere back there.

I received an AncestryDNA kit a few years ago for my birthday. My friend knew I had been working on family history and thought I should give it a shot. Since then Ive had my mother and grandmother on my fathers side tested as well. What surprised me the most in my results was that Im 35% Native American, 5% African, and 29% from the Iberian Peninsula. This has drastically broadened the way I think about my identity and heritage. I feel a sense of connectedness with those areas of the world now and am now anxious to dig deeper and see how far back our records can go. In a less personal sense, I feel like information like this can have a great influence on how people think and treat each other. My grandmother, who took pride in being of pure blood, meaning Spanish, would have completely rejected the notion that Im 5% African, and likely would have blamed it on my fathers side.

There is great power in understanding our deepest heritage and history and in giving ourselves permission to connect with others through that heritage and knowledge. Its liberating in many ways.

Like many who work on their family history, our family had a few lines where we were really struggling to find more information. My 2nd great-grandfather was a mystery ancestor on one of those lines. We could not pin him to a specific census, nor could we find any information about his arrival in the United States. We did however believe he came from Jewish descent.

With this DNA cousin match, weve been able to add a generation to our family tree.

Shortly thereafter, we were contacted by another Ancestry member who used the AncestryDNA kit. He was the descendant of our mystery ancestor and as it turns out, was the 2nd cousin once removed of my father. He was able to point us to the correct 1860 census for the family where we were able discover other family members, and we should now be able to trace their family back to France. So with this DNA cousin match, weve been able to add a generation to our family tree, as well as identify several siblings and their spouses. For immigration research, its so much easier to find a town of origin when youre looking at an entire family who came over rather than just one individual, so Im really excited about the prospects.

In December of 2012 I received an AncestryDNA kit as a gift from my brother-in-law who was hoping to help me learn more about my roots as I was adopted.

More recently, an Ancestry employee was describing the AncestryDNA test to a potential investor and suggested he take the test to experience it. He did, and when his test results came back he was surprised to discover he was related to me either through a grandfather or great-grandfather. He did not recognize my name and when he shared the results with his father Greg, Greg was inspired to take the test as well. Greg's results indicated that I was a possible first cousin, and so he sent me a message.

This has opened a new chapter in my lifeand it is a most welcome life interruption.'

In May of 2014 (less than two years after taking my own test), I received that letter from Greg. We eventually confirmed that we were half-brothers. While Greg's father was my father as well, my birth mother was in her early 20s when she was pregnant with me and had not informed my father. Within days of Gregs letter, I discovered my half-brother and half-sister that I had never met.

Unfortunately, both of my biological parents have since passed away. But instead, I now have connected with my half-siblings Greg and Carole, his half-nephews and niece (Gregs three sons and daughter), and their families. Ive had the most heartwarming embrace from my new brother, sister, and their kids. This has opened a new chapter in my lifeand it is a most welcome "life interruption." I look forward to meeting my family in person in December 2014.

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DNA Tests for Ethnicity & Genealogical DNA testing

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Where can I find DNA testing in Buffalo, New York?

A-DNA is one of the possible double helical structures which DNA can adopt. A-DNA is thought to be one of three biologically active double helical structures along with B-DNA and Z-DNA. It is a right-handed double helix fairly similar to the more common B-DNA form, but with a shorter, more compact helical structure whose base pairs are not perpendicular to the helix-axis as in B-DNA. It was discovered by Rosalind Franklin, who also named the A and B forms. She showed that DNA is driven into the A form when under dehydrating conditions. Such conditions are commonly used in to form crystals, and many DNA crystal structures are in the A form. The same helical conformation occurs in double-stranded RNAs, and in DNA-RNA hybrid double helices.

A-DNA is fairly similar to B-DNA given that it is a right-handed double helix with major and minor grooves. However, as shown in the comparison table below, there is a slight increase in the number of base pairs (bp) per turn (resulting in a smaller twist angle), and smaller rise per base pair (making A-DNA 20-25% shorter than B-DNA). The major groove of A-DNA is deep and narrow, while the minor groove is wide and shallow.

Dehydration of DNA drives it into the A form, and this apparently protects DNA under conditions such as the extreme desiccation of bacteria.[1] Protein binding can also strip solvent off of DNA and convert it to the A form, as revealed by the structure of a rod-shaped virus.[2]

It has been proposed that the motors that package double-stranded DNA in bacteriophages exploit the fact that A-DNA is shorter than B-DNA, and that conformational changes in the DNA itself are the source of the large forces generated by these motors.[3] In this model, ATP hydrolysis is used to drive protein conformational changes that alternatively dehydrate and rehydrate the DNA, and the DNA shortening/lengthening cycle is coupled to a protein-DNA grip/release cycle to generate the forward motion that moves DNA into the capsid.

Read this article:
A-DNA - Wikipedia, the free encyclopedia

Deoxyribonucleic Acid (DNA)

We all know that elephants only give birth to little elephants, giraffes to giraffes, dogs to dogs and so on for every type of living creature. But why is this so?

The answer lies in a molecule called deoxyribonucleic acid (DNA), which contains the biological instructions that make each species unique. DNA, along with the instructions it contains, is passed from adult organisms to their offspring during reproduction.

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In organisms called eukaryotes, DNA is found inside a special area of the cell called the nucleus. Because the cell is very small, and because organisms have many DNA molecules per cell, each DNA molecule must be tightly packaged. This packaged form of the DNA is called a chromosome.

During DNA replication, DNA unwinds so it can be copied. At other times in the cell cycle, DNA also unwinds so that its instructions can be used to make proteins and for other biological processes. But during cell division, DNA is in its compact chromosome form to enable transfer to new cells.

Researchers refer to DNA found in the cell's nucleus as nuclear DNA. An organism's complete set of nuclear DNA is called its genome.

Besides the DNA located in the nucleus, humans and other complex organisms also have a small amount of DNA in cell structures known as mitochondria. Mitochondria generate the energy the cell needs to function properly.

In sexual reproduction, organisms inherit half of their nuclear DNA from the male parent and half from the female parent. However, organisms inherit all of their mitochondrial DNA from the female parent. This occurs because only egg cells, and not sperm cells, keep their mitochondria during fertilization.

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DNA is made of chemical building blocks called nucleotides. These building blocks are made of three parts: a phosphate group, a sugar group and one of four types of nitrogen bases. To form a strand of DNA, nucleotides are linked into chains, with the phosphate and sugar groups alternating.

The four types of nitrogen bases found in nucleotides are: adenine (A), thymine (T), guanine (G) and cytosine (C). The order, or sequence, of these bases determines what biological instructions are contained in a strand of DNA. For example, the sequence ATCGTT might instruct for blue eyes, while ATCGCT might instruct for brown.

The complete DNA instruction book, or genome, for a human contains about 3 billion bases and about 20,000 genes on 23 pairs of chromosomes.

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DNA contains the instructions needed for an organism to develop, survive and reproduce. To carry out these functions, DNA sequences must be converted into messages that can be used to produce proteins, which are the complex molecules that do most of the work in our bodies.

Each DNA sequence that contains instructions to make a protein is known as a gene. The size of a gene may vary greatly, ranging from about 1,000 bases to 1 million bases in humans. Genes only make up about 1 percent of the DNA sequence. DNA sequences outside this 1 percent are involved in regulating when, how and how much of a protein is made.

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DNA's instructions are used to make proteins in a two-step process. First, enzymes read the information in a DNA molecule and transcribe it into an intermediary molecule called messenger ribonucleic acid, or mRNA.

Next, the information contained in the mRNA molecule is translated into the "language" of amino acids, which are the building blocks of proteins. This language tells the cell's protein-making machinery the precise order in which to link the amino acids to produce a specific protein. This is a major task because there are 20 types of amino acids, which can be placed in many different orders to form a wide variety of proteins.

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The Swiss biochemist Frederich Miescher first observed DNA in the late 1800s. But nearly a century passed from that discovery until researchers unraveled the structure of the DNA molecule and realized its central importance to biology.

For many years, scientists debated which molecule carried life's biological instructions. Most thought that DNA was too simple a molecule to play such a critical role. Instead, they argued that proteins were more likely to carry out this vital function because of their greater complexity and wider variety of forms.

The importance of DNA became clear in 1953 thanks to the work of James Watson, Francis Crick, Maurice Wilkins and Rosalind Franklin. By studying X-ray diffraction patterns and building models, the scientists figured out the double helix structure of DNA - a structure that enables it to carry biological information from one generation to the next.

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Scientist use the term "double helix" to describe DNA's winding, two-stranded chemical structure. This shape - which looks much like a twisted ladder - gives DNA the power to pass along biological instructions with great precision.

To understand DNA's double helix from a chemical standpoint, picture the sides of the ladder as strands of alternating sugar and phosphate groups - strands that run in opposite directions. Each "rung" of the ladder is made up of two nitrogen bases, paired together by hydrogen bonds. Because of the highly specific nature of this type of chemical pairing, base A always pairs with base T, and likewise C with G. So, if you know the sequence of the bases on one strand of a DNA double helix, it is a simple matter to figure out the sequence of bases on the other strand.

DNA's unique structure enables the molecule to copy itself during cell division. When a cell prepares to divide, the DNA helix splits down the middle and becomes two single strands. These single strands serve as templates for building two new, double-stranded DNA molecules - each a replica of the original DNA molecule. In this process, an A base is added wherever there is a T, a C where there is a G, and so on until all of the bases once again have partners.

In addition, when proteins are being made, the double helix unwinds to allow a single strand of DNA to serve as a template. This template strand is then transcribed into mRNA, which is a molecule that conveys vital instructions to the cell's protein-making machinery.

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Last Updated: June 16, 2015

Excerpt from:
Genome - Deoxyribonucleic Acid (DNA)

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DNA - The New York Times

DNA (Deoxyribonucleic acid), of the shape of a double helix, found in the nucleus of a cell, is where genetic information is encoded and transferred. It has all the instructions needed for the development and functioning of an organism. DNA segments are known as genes. DNA research is a very complex scientific study which aids in finding complicated evolutionary information in humans and animals. It is a vast topic that has aided theories and discoveries in many diverse areas. The articles given below present DNA research in clearer light. They also tell you about the structure and composition of DNA, and also about DNA sequencing and replication.

What Does a Mutagen Mean in Biology?

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Nucleoside and nucleotide are commonly used terms with regards to the molecular and structural components of the nucleic acids, DNA and RNA. They are often used interchangeably, however, they are quite distinct entities. This...

Plasmids: Functions, Types, and Uses

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The terms 'adenine' and 'adenosine' are often used interchangeably, to refer to each other, however they differ with respect to their chemical structure and the other biomolecules that they interact with. This article compares...

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Originally posted here:
DNA | Buzzle.com

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People in New York shared their opinions about Paternity Testing

Do you personally know of anyone who has undergone paternity/maternity testing?

Yes: 59%

No: 34%

Unsure: 6%

Have you undergone paternity or maternity testing?

Yes: 19%

No: 78%

Rather not say: 1%

What was the reason that you underwent paternity/maternity testing?

Ordered by the court to prove I was/was not the parent: 37%

For my own proof that I was/was not the parent: 20%

To prove to the mother/father/child that I was/was not the parent: 20%

Other: 10%

Rather not say: 10%

Have any of your immediate family members ever undergone paternity/maternity testing?

Yes: 23%

No: 68%

Unsure: 8%

Please rate your level of agreement/disagreement with the following statement: It is a violation of constitutional rights and/or human rights for a court to order a person to undergo a paternity/maternity test.

Completely disagree: 33%

Mostly disagree: 13%

Neither agree or disagree: 31%

Mostly agree: 9%

Completely agree: 11%

Regarding the results of paternity/maternity tests, how well do you trust the results?

Completely distrust: 12%

Distrust: 4%

Unsure whether they are trustworthy or not: 26%

Trust: 42%

Completely trust: 14%

Source: Survey.com

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DNA Testing Buffalo NY - dna testing, Buffalo NY about dna ...

Forensic scientists analyze biological evidence to help solve a variety of crimes. These analyses can show that biological materials from a specific individual was found at a crime scene, can help inform how a victim may have died, and can even bring identity to unknown human remains found in advanced stages of decomposition. Forensic biology is used to determine what types of biological stains, such as blood or semen, are left at a crime scene and to link those stains to individuals through DNA analysis.

Partnership with Applied Genetics Group We work closely with the NIST Applied Genetics Group, which focuses on developing standards and technology to support the use of DNA testing in human identification. For example, with the Applied Genetics Group, we helped develop Standard Reference Material for DNA profiling to ensure that forensic laboratories produce consistent results. We also supported their research to enable forensic scientists to obtain DNA profiles from items that have previously been unsuccessful in yielding DNA results using conventional DNA analysis markers. This has enabled more information to be entered into DNA databases, which is useful when attempting to provide leads in unsolved crimes with degraded evidence and establishing the identity of victims after a mass disaster. In addition, we supported the Applied Genetics Group efforts to improve the processes used to evaluate evidence items that contain DNA mixtures and their research to speed up the forensic DNA analysis process.

Technical Working Group on Biological Evidence PreservationThe proper long-term storage and preservation of biological evidence has become increasingly newsworthy as states throughout the U.S. enact legislation allowing post-conviction DNA testing of evidence. In August 2010, we partnered with the National Institute of Justice to lead the Technical Working Group on Biological Evidence Preservation, which examines current policies, procedures, and practices in biological evidence collection, storage, and preservation. The primary objective of the working group was to establish best practices, based in science, to reduce the premature destruction and degradation of biological evidence, thus ensuring its availability for future analysis.

The Technical Working Group on Biological Evidence Preservation has released The Biological Evidence Preservation Handbook: Best Practices for Evidence Handlers. The Handbook addresses packaging and storage, tracking and chain of custody, and disposition of biological evidence. For more information on the Handbook and the working group, visit the Technical Working Group on Biological Evidence Preservation's page.

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Biology/DNA

DNA sequencing is the process of determining the precise order of nucleotides within a DNA molecule. It includes any method or technology that is used to determine the order of the four basesadenine, guanine, cytosine, and thyminein a strand of DNA. The advent of rapid DNA sequencing methods has greatly accelerated biological and medical research and discovery.

Knowledge of DNA sequences has become indispensable for basic biological research, and in numerous applied fields such as medical diagnosis, biotechnology, forensic biology, virology and biological systematics. The rapid speed of sequencing attained with modern DNA sequencing technology has been instrumental in the sequencing of complete DNA sequences, or genomes of numerous types and species of life, including the human genome and other complete DNA sequences of many animal, plant, and microbial species.

The first DNA sequences were obtained in the early 1970s by academic researchers using laborious methods based on two-dimensional chromatography. Following the development of fluorescence-based sequencing methods with a DNA sequencer,[1] DNA sequencing has become easier and orders of magnitude faster.[2]

DNA sequencing may be used to determine the sequence of individual genes, larger genetic regions (i.e. clusters of genes or operons), full chromosomes or entire genomes. Sequencing provides the order of individual nucleotides present in molecules of DNA or RNA isolated from animals, plants, bacteria, archaea, or virtually any other source of genetic information. This information is useful to various fields of biology and other sciences, medicine, forensics, and other areas of study.

Sequencing is used in molecular biology to study genomes and the proteins they encode. Information obtained using sequencing allows researchers to identify changes in genes, associations with diseases and phenotypes, and identify potential drug targets.

Since DNA is an informative macromolecule in terms of transmission from one generation to another, DNA sequencing is used in evolutionary biology to study how different organisms are related and how they evolved.

The field of metagenomics involves identification of organisms present in a body of water, sewage, dirt, debris filtered from the air, or swab samples from organisms. Knowing which organisms are present in a particular environment is critical to research in ecology, epidemiology, microbiology, and other fields. Sequencing enables researchers to determine which types of microbes may be present in a microbiome, for example.

Medical technicians may sequence genes (or, theoretically, full genomes) from patients to determine if there is risk of genetic diseases. This is a form of genetic testing, though some genetic tests may not involve DNA sequencing.

DNA sequencing may be used along with DNA profiling methods for forensic identification and paternity testing.

The canonical structure of DNA has four bases: thymine (T), adenine (A), cytosine (C), and guanine (G). DNA sequencing is the determination of the physical order of these bases in a molecule of DNA. However, there are many other bases that may be present in a molecule. In some viruses (specifically, bacteriophage), cytosine may be replaced by hydroxy methyl or hydroxy methyl glucose cytosine.[3] In mammalian DNA, variant bases with methyl groups or phosphosulfate may be found.[4][5] Depending on the sequencing technique, a particular modification may or may not be detected, e.g., the 5mC (5 methyl cytosine) common in humans may or may not be detected.[6]

Deoxyribonucleic acid (DNA) was first discovered and isolated by Friedrich Miescher in 1869, but it remained understudied for many decades because proteins, rather than DNA, were thought to hold the genetic blueprint to life. This situation changed after 1944 as a result of some experiments by Oswald Avery, Colin MacLeod, and Maclyn McCarty demonstrated that purified DNA could change one strain of bacteria into another type. This was the first time that DNA was shown capable of transforming the properties of cells.

In 1953 James Watson and Francis Crick put forward their double-helix model of DNA which depicted DNA being made up of two strands of nucleotides coiled around each other, linked together by hydrogen bonds, in a spiral configuration. Each strand they argued was composed of four complementary nucleotides: adenine (A), cytosine (C), guanine (G) and thymine (T) and was oriented in opposite directions. Such a structure they proposed allowed each strand to reconstruct the other and was central to the passing on of hereditary information between generations.[7]

The foundation for sequencing DNA was first laid by the work of Fred Sanger who by 1955 had completed the sequence of all the amino acids in insulin, a small protein secreted by the pancreas. This provided the first conclusive evidence that proteins were chemical entities with a specific molecular pattern rather than a random mixture of material suspended in fluid. Sanger's success in sequencing insulin greatly electrified x-ray crystallographers, including Watson and Crick who by now were trying to understand how DNA directed the formation of proteins within a cell. Soon after attending a series of lectures given by Fred Sanger in October 1954, Crick began to develop a theory which argued that the arrangement of nucleotides in DNA determined the sequence of amino acids in proteins which in turn helped determine the function of a protein. He published this theory in 1958.[8]

RNA sequencing was one of the earliest forms of nucleotide sequencing. The major landmark of RNA sequencing is the sequence of the first complete gene and the complete genome of Bacteriophage MS2, identified and published by Walter Fiers and his coworkers at the University of Ghent (Ghent, Belgium), in 1972[9] and 1976.[10]

The first method for determining DNA sequences involved a location-specific primer extension strategy established by Ray Wu at Cornell University in 1970.[11] DNA polymerase catalysis and specific nucleotide labeling, both of which figure prominently in current sequencing schemes, were used to sequence the cohesive ends of lambda phage DNA.[12][13][14] Between 1970 and 1973, Wu, R Padmanabhan and colleagues demonstrated that this method can be employed to determine any DNA sequence using synthetic location-specific primers.[15][16][17]Frederick Sanger then adopted this primer-extension strategy to develop more rapid DNA sequencing methods at the MRC Centre, Cambridge, UK and published a method for "DNA sequencing with chain-terminating inhibitors" in 1977.[18]Walter Gilbert and Allan Maxam at Harvard also developed sequencing methods, including one for "DNA sequencing by chemical degradation".[19][20] In 1973, Gilbert and Maxam reported the sequence of 24 basepairs using a method known as wandering-spot analysis.[21] Advancements in sequencing were aided by the concurrent development of recombinant DNA technology, allowing DNA samples to be isolated from sources other than viruses.

The first full DNA genome to be sequenced was that of bacteriophage X174 in 1977.[22]Medical Research Council scientists deciphered the complete DNA sequence of the Epstein-Barr virus in 1984, finding it contained 172,282 nucleotides. Completion of the sequence marked a significant turning point in DNA sequencing because it was achieved with no prior genetic profile knowledge of the virus.[23]

A non-radioactive method for transferring the DNA molecules of sequencing reaction mixtures onto an immobilizing matrix during electrophoresis was developed by Pohl and co-workers in the early 1980s.[24][25] Followed by the commercialization of the DNA sequencer "Direct-Blotting-Electrophoresis-System GATC 1500" by GATC Biotech, which was intensively used in the framework of the EU genome-sequencing programme, the complete DNA sequence of the yeast Saccharomyces cerevisiae chromosome II.[26]Leroy E. Hood's laboratory at the California Institute of Technology announced the first semi-automated DNA sequencing machine in 1986.[27] This was followed by Applied Biosystems' marketing of the first fully automated sequencing machine, the ABI 370, in 1987 and by Dupont's Genesis 2000[28] which used a novel fluorescent labeling technique enabling all four dideoxynucleotides to be identified in a single lane. By 1990, the U.S. National Institutes of Health (NIH) had begun large-scale sequencing trials on Mycoplasma capricolum, Escherichia coli, Caenorhabditis elegans, and Saccharomyces cerevisiae at a cost of US$0.75 per base. Meanwhile, sequencing of human cDNA sequences called expressed sequence tags began in Craig Venter's lab, an attempt to capture the coding fraction of the human genome.[29] In 1995, Venter, Hamilton Smith, and colleagues at The Institute for Genomic Research (TIGR) published the first complete genome of a free-living organism, the bacterium Haemophilus influenzae. The circular chromosome contains 1,830,137 bases and its publication in the journal Science[30] marked the first published use of whole-genome shotgun sequencing, eliminating the need for initial mapping efforts.

By 2001, shotgun sequencing methods had been used to produce a draft sequence of the human genome.[31][32]

Several new methods for DNA sequencing were developed in the mid to late 1990s and were implemented in commercial DNA sequencers by the year 2000.

On October 26, 1990, Roger Tsien, Pepi Ross, Margaret Fahnestock and Allan J Johnston filed a patent describing stepwise ("base-by-base") sequencing with removable 3' blockers on DNA arrays (blots and single DNA molecules).[33] In 1996, Pl Nyrn and his student Mostafa Ronaghi at the Royal Institute of Technology in Stockholm published their method of pyrosequencing.[34]

On April 1, 1997, Pascal Mayer and Laurent Farinelli submitted patents to the World Intellectual Property Organization describing DNA colony sequencing.[35] The DNA sample preparation and random surface-PCR arraying methods described in this patent, coupled to Roger Tsien et al.'s "base-by-base" sequencing method, is now implemented in Illumina's Hi-Seq genome sequencers.

Lynx Therapeutics published and marketed "Massively parallel signature sequencing", or MPSS, in 2000. This method incorporated a parallelized, adapter/ligation-mediated, bead-based sequencing technology and served as the first commercially available "next-generation" sequencing method, though no DNA sequencers were sold to independent laboratories.[36]

In 2004, 454 Life Sciences marketed a parallelized version of pyrosequencing.[37] The first version of their machine reduced sequencing costs 6-fold compared to automated Sanger sequencing, and was the second of the new generation of sequencing technologies, after MPSS.[38]

The large quantities of data produced by DNA sequencing have also required development of new methods and programs for sequence analysis. Phil Green and Brent Ewing of the University of Washington described their phred quality score for sequencer data analysis in 1998.[39]

Allan Maxam and Walter Gilbert published a DNA sequencing method in 1977 based on chemical modification of DNA and subsequent cleavage at specific bases.[19] Also known as chemical sequencing, this method allowed purified samples of double-stranded DNA to be used without further cloning. This method's use of radioactive labeling and its technical complexity discouraged extensive use after refinements in the Sanger methods had been made.

Maxam-Gilbert sequencing requires radioactive labeling at one 5' end of the DNA and purification of the DNA fragment to be sequenced. Chemical treatment then generates breaks at a small proportion of one or two of the four nucleotide bases in each of four reactions (G, A+G, C, C+T). The concentration of the modifying chemicals is controlled to introduce on average one modification per DNA molecule. Thus a series of labeled fragments is generated, from the radiolabeled end to the first "cut" site in each molecule. The fragments in the four reactions are electrophoresed side by side in denaturing acrylamide gels for size separation. To visualize the fragments, the gel is exposed to X-ray film for autoradiography, yielding a series of dark bands each corresponding to a radiolabeled DNA fragment, from which the sequence may be inferred.[19]

The chain-termination method developed by Frederick Sanger and coworkers in 1977 soon became the method of choice, owing to its relative ease and reliability.[18][40] When invented, the chain-terminator method used fewer toxic chemicals and lower amounts of radioactivity than the Maxam and Gilbert method. Because of its comparative ease, the Sanger method was soon automated and was the method used in the first generation of DNA sequencers.

Sanger sequencing is the method which prevailed from the 1980s until the mid-2000s. Over that period, great advances were made in the technique, such as fluorescent labelling, capillary electrophoresis, and general automation. These developments allowed much more efficient sequencing, leading to lower costs. The Sanger method, in mass production form, is the technology which produced the first human genome in 2001, ushering in the age of genomics. However, later in the decade, radically different approaches reached the market, bringing the cost per genome down from $100 million in 2001 to $10,000 in 2011.[41]

Large-scale sequencing often aims at sequencing very long DNA pieces, such as whole chromosomes, although large-scale sequencing can also be used to generate very large numbers of short sequences, such as found in phage display. For longer targets such as chromosomes, common approaches consist of cutting (with restriction enzymes) or shearing (with mechanical forces) large DNA fragments into shorter DNA fragments. The fragmented DNA may then be cloned into a DNA vector and amplified in a bacterial host such as Escherichia coli. Short DNA fragments purified from individual bacterial colonies are individually sequenced and assembled electronically into one long, contiguous sequence. Studies have shown that adding a size selection step to collect DNA fragments of uniform size can improve sequencing efficiency and accuracy of the genome assembly. In these studies, automated sizing has proven to be more reproducible and precise than manual gel sizing.[42][43][44]

The term "de novo sequencing" specifically refers to methods used to determine the sequence of DNA with no previously known sequence. De novo translates from Latin as "from the beginning". Gaps in the assembled sequence may be filled by primer walking. The different strategies have different tradeoffs in speed and accuracy; shotgun methods are often used for sequencing large genomes, but its assembly is complex and difficult, particularly with sequence repeats often causing gaps in genome assembly.

Most sequencing approaches use an in vitro cloning step to amplify individual DNA molecules, because their molecular detection methods are not sensitive enough for single molecule sequencing. Emulsion PCR[45] isolates individual DNA molecules along with primer-coated beads in aqueous droplets within an oil phase. A polymerase chain reaction (PCR) then coats each bead with clonal copies of the DNA molecule followed by immobilization for later sequencing. Emulsion PCR is used in the methods developed by Marguilis et al. (commercialized by 454 Life Sciences), Shendure and Porreca et al. (also known as "Polony sequencing") and SOLiD sequencing, (developed by Agencourt, later Applied Biosystems, now Life Technologies).[46][47][48]

Shotgun sequencing is a sequencing method designed for analysis of DNA sequences longer than 1000 base pairs, up to and including entire chromosomes. This method requires the target DNA to be broken into random fragments. After sequencing individual fragments, the sequences can be reassembled on the basis of their overlapping regions.[49]

Another method for in vitro clonal amplification is bridge PCR, in which fragments are amplified upon primers attached to a solid surface[35][50][51] and form "DNA colonies" or "DNA clusters". This method is used in the Illumina Genome Analyzer sequencers. Single-molecule methods, such as that developed by Stephen Quake's laboratory (later commercialized by Helicos) are an exception: they use bright fluorophores and laser excitation to detect base addition events from individual DNA molecules fixed to a surface, eliminating the need for molecular amplification.[52]

Next-generation sequencing applies to genome sequencing, genome resequencing, transcriptome profiling (RNA-Seq), DNA-protein interactions (ChIP-sequencing), and epigenome characterization.[53] Resequencing is necessary, because the genome of a single individual of a species will not indicate all of the genome variations among other individuals of the same species.

The high demand for low-cost sequencing has driven the development of high-throughput sequencing (or next-generation sequencing) technologies that parallelize the sequencing process, producing thousands or millions of sequences concurrently.[54][55] High-throughput sequencing technologies are intended to lower the cost of DNA sequencing beyond what is possible with standard dye-terminator methods.[38] In ultra-high-throughput sequencing as many as 500,000 sequencing-by-synthesis operations may be run in parallel.[56][57][58]

The first of the next-generation sequencing technologies, massively parallel signature sequencing (or MPSS), was developed in the 1990s at Lynx Therapeutics, a company founded in 1992 by Sydney Brenner and Sam Eletr. MPSS was a bead-based method that used a complex approach of adapter ligation followed by adapter decoding, reading the sequence in increments of four nucleotides. This method made it susceptible to sequence-specific bias or loss of specific sequences. Because the technology was so complex, MPSS was only performed 'in-house' by Lynx Therapeutics and no DNA sequencing machines were sold to independent laboratories. Lynx Therapeutics merged with Solexa (later acquired by Illumina) in 2004, leading to the development of sequencing-by-synthesis, a simpler approach acquired from Manteia Predictive Medicine, which rendered MPSS obsolete. However, the essential properties of the MPSS output were typical of later "next-generation" data types, including hundreds of thousands of short DNA sequences. In the case of MPSS, these were typically used for sequencing cDNA for measurements of gene expression levels.[36]

The Polony sequencing method, developed in the laboratory of George M. Church at Harvard, was among the first next-generation sequencing systems and was used to sequence a full E. coli genome in 2005.[71] It combined an in vitro paired-tag library with emulsion PCR, an automated microscope, and ligation-based sequencing chemistry to sequence an E. coli genome at an accuracy of >99.9999% and a cost approximately 1/9 that of Sanger sequencing.[71] The technology was licensed to Agencourt Biosciences, subsequently spun out into Agencourt Personal Genomics, and eventually incorporated into the Applied Biosystems SOLiD platform. Applied Biosystems was later acquired by Life Technologies, now part of Thermo Fisher Scientific.

A parallelized version of pyrosequencing was developed by 454 Life Sciences, which has since been acquired by Roche Diagnostics. The method amplifies DNA inside water droplets in an oil solution (emulsion PCR), with each droplet containing a single DNA template attached to a single primer-coated bead that then forms a clonal colony. The sequencing machine contains many picoliter-volume wells each containing a single bead and sequencing enzymes. Pyrosequencing uses luciferase to generate light for detection of the individual nucleotides added to the nascent DNA, and the combined data are used to generate sequence read-outs.[46] This technology provides intermediate read length and price per base compared to Sanger sequencing on one end and Solexa and SOLiD on the other.[38]

Solexa, now part of Illumina, was founded by Shankar Balasubramanian and David Klenerman in 1998, and developed a sequencing method based on reversible dye-terminators technology, and engineered polymerases.[72] The terminated chemistry was developed internally at Solexa and the concept of the Solexa system was invented by Balasubramanian and Klenerman from Cambridge University's chemistry department. In 2004, Solexa acquired the company Manteia Predictive Medicine in order to gain a massivelly parallel sequencing technology invented in 1997 by Pascal Mayer and Laurent Farinelli.[35] It is based on "DNA Clusters" or "DNA colonies", which involves the clonal amplification of DNA on a surface. The cluster technology was co-acquired with Lynx Therapeutics of California. Solexa Ltd. later merged with Lynx to form Solexa Inc.

In this method, DNA molecules and primers are first attached on a slide or flow cell and amplified with polymerase so that local clonal DNA colonies, later coined "DNA clusters", are formed. To determine the sequence, four types of reversible terminator bases (RT-bases) are added and non-incorporated nucleotides are washed away. A camera takes images of the fluorescently labeled nucleotides. Then the dye, along with the terminal 3' blocker, is chemically removed from the DNA, allowing for the next cycle to begin. Unlike pyrosequencing, the DNA chains are extended one nucleotide at a time and image acquisition can be performed at a delayed moment, allowing for very large arrays of DNA colonies to be captured by sequential images taken from a single camera.

Decoupling the enzymatic reaction and the image capture allows for optimal throughput and theoretically unlimited sequencing capacity. With an optimal configuration, the ultimately reachable instrument throughput is thus dictated solely by the analog-to-digital conversion rate of the camera, multiplied by the number of cameras and divided by the number of pixels per DNA colony required for visualizing them optimally (approximately 10 pixels/colony). In 2012, with cameras operating at more than 10MHz A/D conversion rates and available optics, fluidics and enzymatics, throughput can be multiples of 1 million nucleotides/second, corresponding roughly to 1 human genome equivalent at 1x coverage per hour per instrument, and 1 human genome re-sequenced (at approx. 30x) per day per instrument (equipped with a single camera).[73]

Applied Biosystems' (now a Life Technologies brand) SOLiD technology employs sequencing by ligation. Here, a pool of all possible oligonucleotides of a fixed length are labeled according to the sequenced position. Oligonucleotides are annealed and ligated; the preferential ligation by DNA ligase for matching sequences results in a signal informative of the nucleotide at that position. Before sequencing, the DNA is amplified by emulsion PCR. The resulting beads, each containing single copies of the same DNA molecule, are deposited on a glass slide.[74] The result is sequences of quantities and lengths comparable to Illumina sequencing.[38] This sequencing by ligation method has been reported to have some issue sequencing palindromic sequences.[70]

Ion Torrent Systems Inc. (now owned by Life Technologies) developed a system based on using standard sequencing chemistry, but with a novel, semiconductor based detection system. This method of sequencing is based on the detection of hydrogen ions that are released during the polymerisation of DNA, as opposed to the optical methods used in other sequencing systems. A microwell containing a template DNA strand to be sequenced is flooded with a single type of nucleotide. If the introduced nucleotide is complementary to the leading template nucleotide it is incorporated into the growing complementary strand. This causes the release of a hydrogen ion that triggers a hypersensitive ion sensor, which indicates that a reaction has occurred. If homopolymer repeats are present in the template sequence multiple nucleotides will be incorporated in a single cycle. This leads to a corresponding number of released hydrogens and a proportionally higher electronic signal.[75]

DNA nanoball sequencing is a type of high throughput sequencing technology used to determine the entire genomic sequence of an organism. The company Complete Genomics uses this technology to sequence samples submitted by independent researchers. The method uses rolling circle replication to amplify small fragments of genomic DNA into DNA nanoballs. Unchained sequencing by ligation is then used to determine the nucleotide sequence.[76] This method of DNA sequencing allows large numbers of DNA nanoballs to be sequenced per run and at low reagent costs compared to other next generation sequencing platforms.[77] However, only short sequences of DNA are determined from each DNA nanoball which makes mapping the short reads to a reference genome difficult.[76] This technology has been used for multiple genome sequencing projects and is scheduled to be used for more.[78]

Heliscope sequencing is a method of single-molecule sequencing developed by Helicos Biosciences. It uses DNA fragments with added poly-A tail adapters which are attached to the flow cell surface. The next steps involve extension-based sequencing with cyclic washes of the flow cell with fluorescently labeled nucleotides (one nucleotide type at a time, as with the Sanger method). The reads are performed by the Heliscope sequencer.[79][80] The reads are short, averaging 35 bp.[81] In 2009 a human genome was sequenced using the Heliscope, however in 2012 the company went bankrupt.[82]

SMRT sequencing is based on the sequencing by synthesis approach. The DNA is synthesized in zero-mode wave-guides (ZMWs) small well-like containers with the capturing tools located at the bottom of the well. The sequencing is performed with use of unmodified polymerase (attached to the ZMW bottom) and fluorescently labelled nucleotides flowing freely in the solution. The wells are constructed in a way that only the fluorescence occurring by the bottom of the well is detected. The fluorescent label is detached from the nucleotide upon its incorporation into the DNA strand, leaving an unmodified DNA strand. According to Pacific Biosciences (PacBio), the SMRT technology developer, this methodology allows detection of nucleotide modifications (such as cytosine methylation). This happens through the observation of polymerase kinetics. This approach allows reads of 20,000 nucleotides or more, with average read lengths of 5 kilobases.[65][83] In 2015, Pacific Biosciences announced the launch of a new sequencing instrument called the Sequel System, with 1 million ZMWs compared to 150,000 ZMWs in the PacBio RS II instrument.[84][85]

DNA sequencing methods currently under development include reading the sequence as a DNA strand transits through nanopores,[86][87] and microscopy-based techniques, such as atomic force microscopy or transmission electron microscopy that are used to identify the positions of individual nucleotides within long DNA fragments (>5,000 bp) by nucleotide labeling with heavier elements (e.g., halogens) for visual detection and recording.[88][89] Third generation technologies aim to increase throughput and decrease the time to result and cost by eliminating the need for excessive reagents and harnessing the processivity of DNA polymerase.[90]

This method is based on the readout of electrical signals occurring at nucleotides passing by alpha-hemolysin pores covalently bound with cyclodextrin. The DNA passing through the nanopore changes its ion current. This change is dependent on the shape, size and length of the DNA sequence. Each type of the nucleotide blocks the ion flow through the pore for a different period of time. The method has a potential of development as it does not require modified nucleotides, however single nucleotide resolution is not yet available.[91]

Two main areas of nanopore sequencing in development are solid state nanopore sequencing, and protein based nanopore sequencing. Protein nanopore sequencing utilizes membrane protein complexes -Hemolysin and MspA (Mycobacterium Smegmatis Porin A), which show great promise given their ability to distinguish between individual and groups of nucleotides.[92] In contrast, solid-state nanopore sequencing utilizes synthetic materials such as silicon nitride and aluminum oxide and it is preferred for its superior mechanical ability and thermal and chemical stability.[93] The fabrication method is essential for this type of sequencing given that the nanopore array can contain hundreds of pores with diameters smaller than eight nanometers.[92]

The concept originated from the idea that single stranded DNA or RNA molecules can be electrophoretically driven in a strict linear sequence through a biological pore that can be less than eight nanometers, and can be detected given that the molecules release an ionic current while moving through the pore. The pore contains a detection region capable of recognizing different bases, with each base generating various time specific signals corresponding to the sequence of bases as they cross the pore which are then evaluated.[93] When implementing this process it is important to note that precise control over the DNA transport through the pore is crucial for success. Various enzymes such as exonucleases and polymerases have been used to moderate this process by positioning them near the pores entrance.[94]

Oxford Nanopore Technologies, a United Kingdom-based startup company, is currently developing products using nanopore sequencing. These products include the MinION, a handheld sequencer capable of generating more than 150 megabases of sequencing data in one run. The MinION is not yet available to the public and has been found to produce numerous errors, though further study may alleviate the issue.[95][96]

Another approach uses measurements of the electrical tunnelling currents across single-strand DNA as it moves through a channel. Depending on its electronic structure, each base affects the tunnelling current differently, allowing differentiation between different bases.[97]

The use of tunnelling currents has the potential to sequence orders of magnitude faster than ionic current methods and the sequencing of several DNA oligomers and micro-RNA has already been achieved.[98]

Sequencing by hybridization is a non-enzymatic method that uses a DNA microarray. A single pool of DNA whose sequence is to be determined is fluorescently labeled and hybridized to an array containing known sequences. Strong hybridization signals from a given spot on the array identifies its sequence in the DNA being sequenced.[99]

This method of sequencing utilizes binding characteristics of a library of short single stranded DNA molecules (oligonucleotides), also called DNA probes, to reconstruct a target DNA sequence. Non-specific hybrids are removed by washing and the target DNA is eluted.[100] Hybrids are re-arranged such that the DNA sequence can be reconstructed. The benefit of this sequencing type is its ability to capture a large number of targets with a homogenous coverage.[101] A large number of chemicals and starting DNA is usually required. However, with the advent of solution-based hybridization, much less equipment and chemicals are necessary.[100]

Mass spectrometry may be used to determine DNA sequences. Matrix-assisted laser desorption ionization time-of-flight mass spectrometry, or MALDI-TOF MS, has specifically been investigated as an alternative method to gel electrophoresis for visualizing DNA fragments. With this method, DNA fragments generated by chain-termination sequencing reactions are compared by mass rather than by size. The mass of each nucleotide is different from the others and this difference is detectable by mass spectrometry. Single-nucleotide mutations in a fragment can be more easily detected with MS than by gel electrophoresis alone. MALDI-TOF MS can more easily detect differences between RNA fragments, so researchers may indirectly sequence DNA with MS-based methods by converting it to RNA first.[102]

The higher resolution of DNA fragments permitted by MS-based methods is of special interest to researchers in forensic science, as they may wish to find single-nucleotide polymorphisms in human DNA samples to identify individuals. These samples may be highly degraded so forensic researchers often prefer mitochondrial DNA for its higher stability and applications for lineage studies. MS-based sequencing methods have been used to compare the sequences of human mitochondrial DNA from samples in a Federal Bureau of Investigation database[103] and from bones found in mass graves of World War I soldiers.[104]

Early chain-termination and TOF MS methods demonstrated read lengths of up to 100 base pairs.[105] Researchers have been unable to exceed this average read size; like chain-termination sequencing alone, MS-based DNA sequencing may not be suitable for large de novo sequencing projects. Even so, a recent study did use the short sequence reads and mass spectroscopy to compare single-nucleotide polymorphisms in pathogenic Streptococcus strains.[106]

In microfluidic Sanger sequencing the entire thermocycling amplification of DNA fragments as well as their separation by electrophoresis is done on a single glass wafer (approximately 10cm in diameter) thus reducing the reagent usage as well as cost.[107] In some instances researchers have shown that they can increase the throughput of conventional sequencing through the use of microchips.[108] Research will still need to be done in order to make this use of technology effective.

This approach directly visualizes the sequence of DNA molecules using electron microscopy. The first identification of DNA base pairs within intact DNA molecules by enzymatically incorporating modified bases, which contain atoms of increased atomic number, direct visualization and identification of individually labeled bases within a synthetic 3,272 base-pair DNA molecule and a 7,249 base-pair viral genome has been demonstrated.[109]

This method is based on use of RNA polymerase (RNAP), which is attached to a polystyrene bead. One end of DNA to be sequenced is attached to another bead, with both beads being placed in optical traps. RNAP motion during transcription brings the beads in closer and their relative distance changes, which can then be recorded at a single nucleotide resolution. The sequence is deduced based on the four readouts with lowered concentrations of each of the four nucleotide types, similarly to the Sanger method.[110] A comparison is made between regions and sequence information is deduced by comparing the known sequence regions to the unknown sequence regions.[111]

A method has been developed to analyze full sets of protein interactions using a combination of 454 pyrosequencing and an in vitro virus mRNA display method. Specifically, this method covalently links proteins of interest to the mRNAs encoding them, then detects the mRNA pieces using reverse transcription PCRs. The mRNA may then be amplified and sequenced. The combined method was titled IVV-HiTSeq and can be performed under cell-free conditions, though its results may not be representative of in vivo conditions.[112]

The success of a DNA sequencing protocol is dependent on the sample preparation. A successful DNA extraction will yield a sample with long, non-degraded strands of DNA which require further preparation according to the sequencing technology to be used. For Sanger sequencing, either cloning procedures or PCR are required prior to sequencing. In the case of next generation sequencing methods, library preparation is required before processing.[113]

With the advent of next generation sequencing, Illumina and Roche 454 methods have become a common approach to transcriptomic studies (RNAseq). RNA can be extracted from tissues of interest and converted to complimentary DNA (cDNA) using reverse transcriptasea DNA polymerase that synthesizes a complimentary DNA based on existing strands of RNA in a PCR-like manner.[114] Complimentary DNA can be processed the same way as genomic DNA, allowing the expression levels of RNAs to be determined for the tissue selected.[115]

In October 2006, the X Prize Foundation established an initiative to promote the development of full genome sequencing technologies, called the Archon X Prize, intending to award $10 million to "the first Team that can build a device and use it to sequence 100 human genomes within 10 days or less, with an accuracy of no more than one error in every 100,000 bases sequenced, with sequences accurately covering at least 98% of the genome, and at a recurring cost of no more than $10,000 (US) per genome."[116]

Each year the National Human Genome Research Institute, or NHGRI, promotes grants for new research and developments in genomics. 2010 grants and 2011 candidates include continuing work in microfluidic, polony and base-heavy sequencing methodologies.[117]

The sequencing technologies described here produce raw data that needs to be assembled into longer sequences such as complete genomes (sequence assembly). There are many computational challenges to achieve this, such as the evaluation of the raw sequence data which is done by programs and algorithms such as Phred and Phrap. Other challenges have to deal with repetitive sequences that often prevent complete genome assemblies because they occur in many places of the genome. As a consequence, many sequences may not be assigned to particular chromosomes. The production of raw sequence data is only the beginning of its detailed bioinformatical analysis.[118] Yet new methods for sequencing and correcting sequencing errors were developed.[119]

Sometimes, the raw reads produced by the sequencer are correct and precise only in a fraction of their length. Using the entire read may introduce artifacts in the downstream analyses like genome assembly, snp calling, or gene expression estimation. Two classes of trimming programs have been introduced, based on the window-based or the running-sum classes of algorithms.[120] This is a partial list of the trimming algorithms currently available, specifying the algorithm class they belong to:

Human genetics have been included within the field of bioethics since the early 1970s[127] and the growth in the use of DNA sequencing (particularly high-throughput sequencing) has introduced a number of ethical issues. One key issue is the ownership of an individual's DNA and the data produced when that DNA is sequenced.[128] Regarding the DNA molecule itself, the leading legal case on this topic, Moore v. Regents of the University of California (1990) ruled that individuals have no property rights to discarded cells or any profits made using these cells (for instance, as a patented cell line). However, individuals have a right to informed consent regarding removal and use of cells. Regarding the data produced through DNA sequencing, Moore gives the individual no rights to the information derived from their DNA.[128]

As DNA sequencing becomes more widespread, the storage, security and sharing of genomic data has also become more important.[128][129] For instance, one concern is that insurers may use an individual's genomic data to modify their quote, depending on the perceived future health of the individual based on their DNA.[129][130] In May 2008, the Genetic Information Nondiscrimination Act (GINA) was signed in the United States, prohibiting discrimination on the basis of genetic information with respect to health insurance and employment.[131][132] In 2012, the US Presidential Commission for the Study of Bioethical Issues reported that existing privacy legislation for DNA sequencing data such as GINA and the Health Insurance Portability and Accountability Act were insufficient, noting that whole-genome sequencing data was particularly sensitive, as it could be used to identify not only the individual from which the data was created, but also their relatives.[133][134]

Ethical issues have also been raised by the increasing use of genetic variation screening, both in newborns, and in adults by companies such as 23andMe.[135][136] It has been asserted that screening for genetic variations can be harmful, increasing anxiety in individuals who have been found to have an increased risk of disease.[137] For example, in one case noted in Time, doctors screening an ill baby for genetic variants chose not to inform the parents of an unrelated variant linked to dementia due to the harm it would cause to the parents.[138] However, a 2011 study in The New England Journal of Medicine has shown that individuals undergoing disease risk profiling did not show increased levels of anxiety.[137]

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DNA sequencing - Wikipedia, the free encyclopedia