Whole genome sequencing
Whole genome sequencing (also known as full genome sequencing, complete genome sequencing, or entire genome sequencing) is a laboratory process that determines the complete DNA sequence of an organism's genome at a single time. This entails sequencing all of an organism's chromosomal DNA as well as DNA contained in the mitochondria and, for plants, in the chloroplast.
Whole genome sequencing should not be confused with DNA profiling, which only determines the likelihood that genetic material came from a particular individual or group, and does not contain additional information on genetic relationships, origin or susceptibility to specific diseases. Also unlike full genome sequencing, SNP genotyping covers less than 0.1% of the genome. Almost all truly complete genomes are of microbes; the term "full genome" is thus sometimes used loosely to mean "greater than 95%". The remainder of this article focuses on nearly complete human genomes.
High-throughput genome sequencing technologies have largely been used as a research tool and are currently being introduced in the clinics. In the future of personalized medicine, whole genome sequence data will be an important tool to guide therapeutic intervention. The tool of gene sequencing at SNP level is also used to pinpoint functional variants from association studies and improve the knowledge available to researchers interested in evolutionary biology, and hence may lay the foundation for predicting disease susceptibility and drug response.
- 1 A brief history of whole genome sequencing
- 2 Cells used for sequencing
- 3 Mutation frequencies in cancers
- 4 Early techniques
- 5 Current techniques
- 6 Commercialization
- 7 Disruption to DNA array market
- 8 Sequencing versus analysis
- 9 Diagnostic use and societal impact
- 10 Ethical concerns
- 11 People with public genome sequences
- 12 See also
- 13 References
- 14 External links
A brief history of whole genome sequencing
The shift from manual DNA sequencing methods such as Maxam-Gilbert sequencing and Sanger sequencing in the 1970s and 1980s to more rapid, automated sequencing methods in the 1990s played a crucial role in giving scientists the ability to sequence whole genomes. Haemophilus influenzae, a commensal bacterium which resides in the human respiratory tract was the first organism to have its entire genome sequenced (Figure 2.1). The entire genome of this bacterium was published in 1995. The genomes of H. influenzae, other Bacteria, and some Archaea were the first to be sequenced - largely due to their small genome size. H. influenzae has a genome of 1,830,140 base pairs of DNA. In contrast, eukaryotes, both unicellular and multicellular such as Amoeba dubia and humans (Homo sapiens) respectively, have much larger genomes (see C-value paradox). Amoeba dubia has a genome of 700 billion nucleotide pairs spread across thousands of chromosomes. Humans contain fewer nucleotide pairs (about 3.2 billion in each germ cell - note the exact size of the human genome is still being revised) than A. dubia however their genome size far outweighs the genome size of individual bacteria.
The first bacterial and archaeal genomes, including that of H. influenzae, were sequenced by Shotgun sequencing. In 1996, the first eukaryotic genome - that of the yeast Saccharomyces cerevisiae was sequenced. S. cerevisiae, a model organism in biology has a genome of only around 12 million nucleotide pairs. S. cerevisiae was the first unicellular eukaryote to have its whole genome sequenced. The first multicellular eukaryote, and animal, to have its whole genome sequenced was the nematode worm: Caenorhabditis elegans in 1998 (Figure 2.2). Eukaryotic genomes are sequenced by several methods including Shotgun sequencing of short DNA fragments and sequencing of larger DNA clones from DNA libraries (see library (biology)) such as Bacterial artificial chromosomes (BACs) and Yeast artificial chromosomes (YACs).
In 1999, the entire DNA sequence of human chromosome 22, the shortest human autosome, was published. By the year 2000, the second animal and second invertebrate (yet first insect) genome was sequenced - that of the fruit fly Drosophila melanogaster (Figure 2.3) - a popular choice of model organism in experimental research. The first plant genome - that of the model organism Arabidopsis thaliana - was also fully sequenced by 2000 (Figure 2.4). By 2001, a draft of the entire human genome sequence was published. The genome of the laboratory mouse Mus musculus was completed in 2002 (Figure 2.5).
Currently, thousands of genomes have been sequenced.
Cells used for sequencing
Almost any biological sample containing a full copy of the DNA—even a very small amount of DNA or ancient DNA—can provide the genetic material necessary for full genome sequencing. Such samples may include saliva, epithelial cells, bone marrow, hair (as long as the hair contains a hair follicle), seeds, plant leaves, or anything else that has DNA-containing cells.
The genome sequence of a single cell selected from a mixed population of cells can be determined using techniques of single cell genome sequencing. This has important advantages in environmental microbiology in cases where a single cell of a particular microorganism species can be isolated from a mixed population by microscopy on the basis of its morphological or other distinguishing characteristics. In such cases the normally necessary steps of isolation and growth of the organism in culture may be omitted, thus allowing the sequencing of a much greater spectrum of organism genomes.
Single cell genome sequencing is being tested as a method of preimplantation genetic diagnosis, wherein a cell from the embryo created by in vitro fertilization is taken and analyzed before embryo transfer into the uterus. After implantation, cell-free fetal DNA can be taken by simple venipuncture from the mother and used for whole genome sequencing of the fetus.
Mutation frequencies in cancers
Whole genome sequencing has established the mutation frequency for whole human genomes. The mutation frequency in the whole genome between generations for humans (parent to child) is about 70 new mutations per generation. An even lower level of variation was found comparing whole genome sequencing in blood cells for a pair of monozygotic (identical twins) 100 year old centenarians. Only 8 somatic differences were found, though somatic variation occurring in less than 20% of blood cells would be undetected.
In the specifically protein coding regions of the human genome, it is estimated that there are about 0.35 mutations that would change the protein sequence between parent/child generations (less than one mutated protein per generation).
Cancers, however, have much higher mutation frequencies. The particular frequency depends on tissue type, whether there is a mis-match DNA repair deficiency, and exposure to DNA damaging agents such as UV-irradiation or components of tobacco smoke. Tuna and Amos have summarized the mutation frequencies per megabase (Mb), as shown in the table (along with the indicated frequencies of mutations per genome).
The high mutation frequencies in cancers reflect the genome instability characteristic of cancers.
|Cell type||Mutation frequency/Mb||Mutation frequency per diploid genome|
|Acute lymphocytic leukemia||0.3||1,800|
|Chronic lymphocytic leukemia||<1||<6,000|
|Microsatellite stable (MSS) colon cancer||2.8||16,800|
|Microsatellite instable (MSI) colon cancer (mismatch repair deficient)||47||282,000|
|Small cell lung cancer||7.4||44,400|
|Non-small cell lung cancer (smokers)||10.5||63,000|
|Non-small cell lung cancer (never-smokers)||0.6||3,600|
|Lung adenocarcinoma (smokers)||9.8||58,500|
|Lung adenocarcinoma (never-smokers)||1.7||10,200|
|Chronic UV-irradiation induced melanoma||111||666,000|
|Non-UV-induced melanoma of hairless skin of extremities||3-14||18,000-84,000|
|Non-UV-induced melanoma of hair-bearing skin||5-55||30,000-330,000|
Sequencing of nearly an entire human genome was first accomplished in 2000 partly through the use of shotgun sequencing technology. While full genome shotgun sequencing for small (4000–7000 base pair) genomes was already in use in 1979, broader application benefited from pairwise end sequencing, known colloquially as double-barrel shotgun sequencing. As sequencing projects began to take on longer and more complicated genomes, multiple groups began to realize that useful information could be obtained by sequencing both ends of a fragment of DNA. Although sequencing both ends of the same fragment and keeping track of the paired data was more cumbersome than sequencing a single end of two distinct fragments, the knowledge that the two sequences were oriented in opposite directions and were about the length of a fragment apart from each other was valuable in reconstructing the sequence of the original target fragment.
The first published description of the use of paired ends was in 1990 as part of the sequencing of the human HPRT locus, although the use of paired ends was limited to closing gaps after the application of a traditional shotgun sequencing approach. The first theoretical description of a pure pairwise end sequencing strategy, assuming fragments of constant length, was in 1991. In 1995 Roach et al. introduced the innovation of using fragments of varying sizes, and demonstrated that a pure pairwise end-sequencing strategy would be possible on large targets. The strategy was subsequently adopted by The Institute for Genomic Research (TIGR) to sequence the entire genome of the bacterium Haemophilus influenzae in 1995, and then by Celera Genomics to sequence the entire fruit fly genome in 2000, and subsequently the entire human genome. Applied Biosystems, now called Life Technologies, manufactured the automated capillary sequencers utilized by both Celera Genomics and The Human Genome Project.
While capillary sequencing was the first approach to successfully sequence a nearly full human genome, it is still too expensive and takes too long for commercial purposes. Because of this, since 2005 capillary sequencing has been progressively displaced by newer technologies such as pyrosequencing, SMRT sequencing, and nanopore technology; all of these new technologies nevertheless continue to employ the basic shotgun strategy, namely, parallelization and template generation via genome fragmentation.
Because the sequence data that is produced can be quite large (for example, there are approximately six billion base pairs in each human diploid genome), genomic data is stored electronically and requires a large amount of computing power and storage capacity. Full genome sequencing would have been nearly impossible before the advent of the microprocessor, computers, and the Information Age.
One possible way to accomplish the cost-effective high-throughput sequencing necessary to accomplish full genome sequencing is by using nanopore technology, which is a patented technology held by Harvard University and Oxford Nanopore Technologies and licensed to biotechnology companies. To facilitate their full genome sequencing initiatives, Illumina licensed nanopore sequencing technology from Oxford Nanopore Technologies and Sequenom licensed the technology from Harvard University.
Another possible way to accomplish cost-effective high-throughput sequencing is by utilizing fluorophore technology. Pacific Biosciences is currently using this approach in their SMRT (single molecule real time) DNA sequencing technology.
Pyrosequencing is a method of DNA sequencing based on the sequencing by synthesis principle. The technique was developed by Pål Nyrén and his student Mostafa Ronaghi at the Royal Institute of Technology in Stockholm in 1996, and is currently being used by 454 Life Sciences as a basis for a full genome sequencing platform.
A number of public and private companies are competing to develop a full genome sequencing platform that is commercially robust for both research and clinical use, including Illumina, Knome, Sequenom, 454 Life Sciences, Pacific Biosciences, Complete Genomics, Helicos Biosciences, GE Global Research (General Electric), Affymetrix, IBM, Intelligent Bio-Systems, Life Technologies and Oxford Nanopore Technologies. These companies are heavily financed and backed by venture capitalists, hedge funds, and investment banks.
In October 2006, the X Prize Foundation, working in collaboration with the J. Craig Venter Science Foundation, established the Archon X Prize for Genomics, intending to award US$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 1,000,000 bases sequenced, with sequences accurately covering at least 98% of the genome, and at a recurring cost of no more than $1,000 per genome". An error rate of 1 in 1,000,000 bases, out of a total of approximately six billion bases in the human diploid genome, would mean about 6,000 errors per genome. The error rates required for widespread clinical use, such as predictive medicine is currently set by over 1,400 clinical single gene sequencing tests (for example, errors in BRCA1 gene for breast cancer risk analysis). As of August 2013[update], the Archon X Prize for Genomics has been cancelled.
In March 2009, it was announced that Complete Genomics has signed a deal with the Broad Institute to sequence cancer patients' genomes and will be sequencing five full genomes to start. In April 2009, Complete Genomics announced that it plans to sequence 1,000 full genomes between June 2009 and the end of the year and that they plan to be able to sequence one million full genomes per year by 2013.
In June 2009, Illumina announced that they were launching their own Personal Full Genome Sequencing Service at a depth of 30× for $48,000 per genome. Jay Flatley, Illumina's President and CEO, stated that "during the next five years, perhaps markedly sooner," the price point for full genome sequencing will fall from $48,000 to under $1,000.
In August 2009, the founder of Helicos Biosciences, Stephen Quake, stated that using the company's Single Molecule Sequencer he sequenced his own full genome for less than $50,000. He stated that he expects the cost to decrease to the $1,000 range within the next two to three years.
In August 2009, Pacific Biosciences secured an additional $68 million in new financing, bringing their total capitalization to $188 million. Pacific Biosciences said they are going to use this additional investment in order to prepare for the upcoming launch of their full genome sequencing service in 2010. Complete Genomics followed by securing another $45 million in a fourth round venture funding during the same month. Complete Genomics has also made the claim that it will sequence 10,000 full genomes by the end of 2010.
In October 2009, IBM announced that they were also in the heated race to provide full genome sequencing for under $1,000, with their ultimate goal being able to provide their service for US$100 per genome. IBM's full genome sequencing technology, which uses nanopores, is known as the "DNA Transistor".
In November 2009, Complete Genomics published a peer-reviewed paper in Science demonstrating its ability to sequence a complete human genome for $1,700. If true, this would mean the cost of full genome sequencing has come down exponentially within just a single year from around $100,000 to $50,000 and now to $1,700. This consumables cost was clearly detailed in the Science paper. However, Complete Genomics has previously released statements that it was unable to follow through on. For example, the company stated it would officially launch and release its service during the "summer of 2009", provide a "$5,000" full genome sequencing service by the "summer of 2009", and "sequence 1,000 genomes between June 2009 and the end of 2009" – all of which, as of November 2009, have not yet occurred. Complete Genomics launched its R&D human genome sequencing service in October 2008 and its commercial service in May 2010. The company sequenced 50 genomes in 2009. Since then, it has significantly increased the throughput of its genome sequencing factory and was able to sequence and analyze 300 genomes in Q3 2010.
Also in November 2009, Complete Genomics announced that it was beginning a large-scale human genome sequencing study of Huntington's disease (up to 100 genomes) with the Institute for Systems Biology.
In March 2010, Researchers from the Medical College of Wisconsin announced the first successful use of Genome Wide sequencing to change the treatment of a patient. This story was later retold in a Pulitzer prize winning article  and touted as a significant accomplishment in the journal Nature and by the director of the NIH in presentations at congress.
In June 2010, Illumina lowered the cost of its individual sequencing service to $19,500 from $48,000.
In May 2011, Illumina lowered its Full Genome Sequencing service to $5,000 per human genome, or $4,000 if ordering 50 or more. Helicos Biosciences, Pacific Biosciences, Complete Genomics, Illumina, Sequenom, ION Torrent Systems, Halcyon Molecular, NABsys, IBM, and GE Global appear to all be going head to head in the race to commercialize full genome sequencing.
In January 2012, Life Technologies introduced a sequencer claimed to decode a human genome in one day for $1,000 although these claims have yet to be validated by customers on commercial devices. A UK firm spun out from Oxford University has come up with a DNA sequencing machine (the MinION) the size of a USB memory stick which costs $900 and can sequence smaller genomes (but not full human genomes in the first version). (While Oxford Nanopore stated in February that they would target having a sequencer in commercial early access by the end of 2012, this did not occur.)
In November 2012, Gene by Gene, Ltd started offering whole genome sequencing at an introductory price of $5,495 (with a minimum requirement of 3 samples per order). Currently the price is $6,995 and the minimum requirement has been removed. However, more recent verification on the price for whole genome sequencing, as posted on the Web site of "Gene by Gene" (2015-09-07) shows that instead of decreasing, the price has significantly increased, to 9,995.00 USD for a basic whole genome sequence without analysis, or 10,395.00 USD for a whole genome sequence with alignment and variant calling.
A series of publications in 2012 showed the utility of SMRT sequencing from Pacific Biosciences in generating full genome sequences with de novo assembly. Some of these papers reported automated pipelines that could be used for generating these whole-genome assemblies. Other papers demonstrated how PacBio sequence data could be used to upgrade draft genomes to complete genomes.
Disruption to DNA array market
Full genome sequencing provides information on a genome that is orders of magnitude larger than that provided by the previous leader in genotyping technology, DNA arrays. For humans, DNA arrays currently provide genotypic information on up to one million genetic variants, while full genome sequencing will provide information on all six billion bases in the human genome, or 3,000 times more data. Because of this, full genome sequencing is considered a disruptive innovation to the DNA array markets as the accuracy of both range from 99.98% to 99.999% (in non-repetitive DNA regions) and their consumables cost of $5000 per 6 billion base pairs is competitive (for some applications) with DNA arrays ($500 per 1 million basepairs). Agilent, another established DNA array manufacturer, is working on targeted (selective region) genome sequencing technologies. It is thought that Affymetrix, the pioneer of array technology in the 1990s, has fallen behind due to significant corporate and stock turbulence and is currently not working on any known full genome sequencing approach. It is unknown what will happen to the DNA array market once full genome sequencing becomes commercially widespread, especially as companies and laboratories providing this disruptive technology start to realize economies of scale. It is postulated, however, that this new technology may significantly diminish the total market size for arrays and any other sequencing technology once it becomes commonplace for individuals and newborns to have their full genomes sequenced.
Sequencing versus analysis
In principle, full genome sequencing can provide raw data on all six billion nucleotides in an individual's DNA. However, it does not provide an analysis of what that information means or how it might be utilized in various clinical applications, such as in medicine to help prevent disease. As of 2010 the companies that are working on providing full genome sequencing provide clinical CLIA certified data (Illumina) and analytical services for the interpretation of the full genome data (Knome), with only one institution offering sequencing and analysis in a clinical setting. Nevertheless there is plenty of room for researchers or companies to improve such analyses and make it useful to physicians and patients.
Diagnostic use and societal impact
Inexpensive, time-efficient full genome sequencing will be a major accomplishment not only for the field of genomics, but for the entire human civilization because, for the first time, individuals will be able to have their entire genome sequenced. Utilizing this information, it is speculated that health care professionals, such as physicians and genetic counselors, will eventually be able to use genomic information to predict what diseases a person may get in the future and attempt to either minimize the impact of that disease or avoid it altogether through the implementation of personalized, preventive medicine. Full genome sequencing will allow health care professionals to analyze the entire human genome of an individual and therefore detect all disease-related genetic variants, regardless of the genetic variant's prevalence or frequency. This will enable the rapidly emerging medical fields of predictive medicine and personalized medicine and will mark a significant leap forward for the clinical genetic revolution. Full genome sequencing is clearly of great importance for research into the basis of genetic disease and has shown significant benefit to a subset of individuals with rare disease in the clinical setting. Illumina's CEO, Jay Flatley, stated in February 2009 that "A complete DNA read-out for every newborn will be technically feasible and affordable in less than five years, promising a revolution in healthcare" and that "by 2019 it will have become routine to map infants' genes when they are born". This potential use of genome sequencing is highly controversial, as it runs counter to established ethical norms for predictive genetic testing of asymptomatic minors that have been well established in the fields of medical genetics and genetic counseling. The traditional guidelines for genetic testing have been developed over the course of several decades since it first became possible to test for genetic markers associated with disease, prior to the advent of cost-effective, comprehensive genetic screening. It is established that norms, such as in the sciences and the field of genetics, are subject to change and evolve over time. It is unknown whether traditional norms practiced in medical genetics today will be altered by new technological advancements such as full genome sequencing.
Currently available newborn screening for childhood diseases allows detection of rare disorders that can be prevented or better treated by early detection and intervention. Specific genetic tests are also available to determine an etiology when a child's symptoms appear to have a genetic basis. Full genome sequencing, in addition has the potential to reveal a large amount of information (such as carrier status for autosomal recessive disorders, genetic risk factors for complex adult-onset diseases, and other predictive medical and non-medical information) that is currently not completely understood, may not be clinically useful to the child during childhood, and may not necessarily be wanted by the individual upon reaching adulthood. In addition to predicting disease risk in childhood, genetic testing may have other benefits (such as discovery of non-paternity) but may also have potential downsides (genetic discrimination, loss of anonymity, and psychological impacts). Many publications regarding ethical guidelines for predictive genetic testing of asymptomatic minors may therefore have more to do with protecting minors and preserving the individual's privacy and autonomy to know or not to know their genetic information, than with the technology that makes the tests themselves possible.
Due to recent cost reductions (see above) whole genome sequencing has become a realistic application in DNA diagnostics. In 2013, the 3Gb-TEST consortium obtained funding from the European Union to prepare the health care system for these innovations in DNA diagnostics. Quality assessment schemes, Health technology assessment and guidelines have to be in place. The 3Gb-TEST consortium has identified the analysis and interpretation of sequence data as the most complicated step in the diagnostic process. At the Consortium meeting in Athens in September 2014, the Consortium coined the word genotranslation for this crucial step. This step leads to a so-called genoreport. Guidelines are needed to determine the required content of these reports.
The majority of ethicists insist that the privacy of individuals undergoing genetic testing must be protected under all circumstances. Data obtained from whole genome sequencing can not only reveal much information about the individual who is the source of DNA, but it can also reveal much probabilistic information about the DNA sequence of close genetic relatives. Furthermore, the data obtained from whole genome sequencing can also reveal much useful predictive information about the relatives present and future health risks. This raises important questions about what obligations, if any, are owed to the family members of the individuals who are undergoing genetic testing. In the Western/European society, tested individuals are usually encouraged to share important information on the genetic diagnosis with their close relatives since the importance of the genetic diagnosis for offspring and other close relatives is usually one of the reasons for seeking a genetic testing in the first place. Nevertheless, Sijmons et al. (2011) also mention that a major ethical dilemma can develop when the patients refuse to share information on a diagnosis that is made for serious genetic disorder that is highly preventable and where there is a high risk to relatives carrying the same disease mutation. Under such circumstances, the clinician may suspect that the relatives would rather know of the diagnosis and hence the clinician can face a conflict of interest with respect to patient-doctor confidentiality.
Another major privacy concern is the scientific need to put information on patient's genotypes and phenotypes into the public scientific databases such as the locus specific databases. Although only anonymous patient data are submitted to the locus specific databases, patients might still be identifiable by their relatives in the case of finding a rare disease or a rare missense mutation.
People with public genome sequences
The first nearly complete human genomes sequenced were J. Craig Venter's (American at 7.5-fold average coverage) in 2007, followed by James Watson's (American at 7.4-fold), a Han Chinese (YH at 36-fold), a Yoruban from Nigeria (at 30-fold), a female leukemia patient (at 33 and 14-fold coverage for tumor and normal tissues), and Seong-Jin Kim (Korean at 29-fold). The first two persons with their full genome sequenced, James Watson and Craig Venter, two American scientists of European ancestry, were found to be genetically more closely related to and having more alleles in common with Korean scientist, Seong-Jin Kim (1,824,482 and 1,736,340, respectively) than with each other (1,715,851). Steve Jobs was among the first 20 people to have their whole genome sequenced, reportedly for the cost of $100,000. As of June 2012[update], there are 69 nearly complete human genomes publicly available.(reference - page not found) Commercialization of full genome sequencing is in an early stage and growing rapidly.
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What does this imply for the existence of human races? Basically, that people with similar genetic features can be found in distant places, and that each local population contains a vast array of genotypes. Among the first genomes completely typed were those of James Watson and Craig Venter, two U.S. geneticists of European origin; they share more alleles with Seong-Jin Kim, a Korean scientist (1,824,482 and 1,736,340, respectively) than with each other (1,715,851).
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