Personal genomics
Encyclopedia
Personal genomics is the branch of genomics
concerned with the sequencing
and analysis
of the genome of an individual. The genotyping stage employs different techniques, including single-nucleotide polymorphism (SNP) analysis chips (typically 0.02% of the genome), or partial or full genome sequencing
. Once the genotypes are known, the individual's genotype can be compared with the published literature to determine likelihood of trait expression and disease risk.
Automated sequencers have increased the speed and reduced the cost of sequencing, making it possible to offer genetic testing to consumers.
is the use of the information produced by personal genomics techniques when deciding what medical treatments are appropriate for a particular individual.
An example of the use of predictive medicine is pharmacogenomics
, in which genetic information can be used to select the most appropriate drug to prescribe to a patient. The drug should be chosen to maximize the probability of obtaining the desired result in the patient and minimize the probability that the patient will experience side effects. Genetic information may allow physicians to tailor therapy to a given patient, in order to increase drug efficacy and minimize side effects. There are only a few examples in which this information is currently useful in clinical practice.
Disease risk may be calculated based on genetic markers and genome-wide association studies, though most common medical conditions are multifactorial and the actual risk to the individual depends on both genetic and environmental components.
The National Human Genome Research Institute, part of the U.S. National Institutes of Health
, has set a target to be able to sequence a human-sized genome for US$100,000 by 2009 and US$1,000 by 2014.
There are 6 billion base pairs in the diploid human genome. Statistical analysis reveals that a coverage of approximately ten times is required to get coverage of both alleles in 90% human genome from 25 base-pair reads with shotgun sequencing. This means a total of 60 billion base pairs that must be sequenced. An Applied Biosystems
SOLiD, Illumina
or Helicos sequencing machine can sequence 2 to 10 billion base pairs in each $8,000 to $18,000 run. The purchase cost, personnel costs and data processing costs must also be taken into account. Sequencing a human genome cost approximately $300,000 in 2008.
In 2009, Complete Genomics of Mountain View
announced that it would provide full genome sequencing
for $5,000, from June 2009. This will only be available to institutions, not individuals.
Approximately 1 million babies are born in Canada each year; to sequence all of their genomes would cost approximately $1 billion per year, or just 1% of Canada’s total healthcare budget. Given the ethical concerns about presymptomatic genetic testing of minors, it is likely that personal genomics will first be applied to adults who can provide consent to undergo such testing.
In June 2009, Illumina
announced the launch of its own Personal Full Genome Sequencing
Service at a depth of 30X for $48,000 per genome. Only one year later, in 2010, they cut the price 60% to $19,500. Prices are expected to drop further over the next few years through economies of scale and increased competition.
Knome
's whole genome sequencing approach aims, instead, to read every site in the whole euchromatic portion of a person's genome (roughly 3 billion sites). While significantly more expensive than SNP chip-based genotyping
, this approach yields significantly more data, identifying both novel (never-before-seen) and known sequence variants, some of which may be particularly relevant in efforts to understand personal health, as well as ancestry.
analysis characterizes the differences and similarities between whole genomes. It may be applied to both genomes from individuals from different species or individuals from the same species, generally at lower cost than sequencing from scratch.
is discriminating on the basis of information obtained from an individual’s genome. Genetic non-discrimination laws have been enacted in some US states and, at the federal level, by the Genetic Information Nondiscrimination Act
(GINA). The GINA legislation prevents discrimination by health insurers and employers, but does not apply to life insurance or long-term care insurance.
that are so rare that no conclusions may be drawn about their impact, creating uncertainty in the analysis of individual genomes, particularly in the context of clinical care. Czech medical geneticist Eva Machácková writes: "In some cases it is difficult to distinguish if the detected sequence variant is a causal mutation or a neutral (polymorphic) variation without any effect on phenotype. The interpretation of rare sequence variants of unknown significance detected in disease-causing genes becomes an increasingly important problem."
Genomics
Genomics is a discipline in genetics concerning the study of the genomes of organisms. The field includes intensive efforts to determine the entire DNA sequence of organisms and fine-scale genetic mapping efforts. The field also includes studies of intragenomic phenomena such as heterosis,...
concerned with the sequencing
DNA sequencing
DNA sequencing includes several methods and technologies that are used for determining the order of the nucleotide bases—adenine, guanine, cytosine, and thymine—in a molecule of DNA....
and analysis
Bioinformatics
Bioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...
of the genome of an individual. The genotyping stage employs different techniques, including single-nucleotide polymorphism (SNP) analysis chips (typically 0.02% of the genome), or partial or full genome sequencing
Full genome sequencing
Full genome sequencing , also known as whole 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...
. Once the genotypes are known, the individual's genotype can be compared with the published literature to determine likelihood of trait expression and disease risk.
Automated sequencers have increased the speed and reduced the cost of sequencing, making it possible to offer genetic testing to consumers.
Use of personal genomics in predictive medicine
Predictive medicinePredictive medicine
Predictive medicine is a rapidly emerging field of medicine that entails predicting disease and instituting preventive measures in order to either prevent the disease altogether or significantly decrease its impact upon the patient...
is the use of the information produced by personal genomics techniques when deciding what medical treatments are appropriate for a particular individual.
An example of the use of predictive medicine is pharmacogenomics
Pharmacogenomics
Pharmacogenomics is the branch of pharmacology which deals with the influence of genetic variation on drug response in patients by correlating gene expression or single-nucleotide polymorphisms with a drug's efficacy or toxicity...
, in which genetic information can be used to select the most appropriate drug to prescribe to a patient. The drug should be chosen to maximize the probability of obtaining the desired result in the patient and minimize the probability that the patient will experience side effects. Genetic information may allow physicians to tailor therapy to a given patient, in order to increase drug efficacy and minimize side effects. There are only a few examples in which this information is currently useful in clinical practice.
Disease risk may be calculated based on genetic markers and genome-wide association studies, though most common medical conditions are multifactorial and the actual risk to the individual depends on both genetic and environmental components.
Cost of sequencing an individual’s genome
The cost of sequencing a human genome is dropping rapidly, due to the continual development of new, faster, cheaper DNA sequencing technologies such as "next generation DNA sequencing".The National Human Genome Research Institute, part of the U.S. National Institutes of Health
National Institutes of Health
The National Institutes of Health are an agency of the United States Department of Health and Human Services and are the primary agency of the United States government responsible for biomedical and health-related research. Its science and engineering counterpart is the National Science Foundation...
, has set a target to be able to sequence a human-sized genome for US$100,000 by 2009 and US$1,000 by 2014.
There are 6 billion base pairs in the diploid human genome. Statistical analysis reveals that a coverage of approximately ten times is required to get coverage of both alleles in 90% human genome from 25 base-pair reads with shotgun sequencing. This means a total of 60 billion base pairs that must be sequenced. An Applied Biosystems
Applied Biosystems
Applied Biosystems, Inc. started as GeneCo , was the name of a pioneer biotechnology company founded in 1981 in Foster City, California, in the San Francisco Bay Area...
SOLiD, Illumina
Illumina (company)
Illumina, Inc. is a company incorporated in April 1998 that develops, manufactures and markets integrated systems for the analysis of genetic variation and biological function. Using its technologies, the company provides a line of products and services that serve the sequencing, genotyping and...
or Helicos sequencing machine can sequence 2 to 10 billion base pairs in each $8,000 to $18,000 run. The purchase cost, personnel costs and data processing costs must also be taken into account. Sequencing a human genome cost approximately $300,000 in 2008.
In 2009, Complete Genomics of Mountain View
Mountain View
-Canada:*Mountain View County, Alberta, a municipal district*Mountain View, Alberta, a hamlet in Cardston County*Mountain View, Ontario, a community in Prince Edward County*Mountain View No...
announced that it would provide full genome sequencing
Full genome sequencing
Full genome sequencing , also known as whole 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...
for $5,000, from June 2009. This will only be available to institutions, not individuals.
Approximately 1 million babies are born in Canada each year; to sequence all of their genomes would cost approximately $1 billion per year, or just 1% of Canada’s total healthcare budget. Given the ethical concerns about presymptomatic genetic testing of minors, it is likely that personal genomics will first be applied to adults who can provide consent to undergo such testing.
In June 2009, Illumina
Illumina (company)
Illumina, Inc. is a company incorporated in April 1998 that develops, manufactures and markets integrated systems for the analysis of genetic variation and biological function. Using its technologies, the company provides a line of products and services that serve the sequencing, genotyping and...
announced the launch of its own Personal Full Genome Sequencing
Full genome sequencing
Full genome sequencing , also known as whole 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...
Service at a depth of 30X for $48,000 per genome. Only one year later, in 2010, they cut the price 60% to $19,500. Prices are expected to drop further over the next few years through economies of scale and increased competition.
Knome
Knome
Knome is an American personal genomics company that sells human whole genome and exome analysis and sequencing services to researchers and consumers...
's whole genome sequencing approach aims, instead, to read every site in the whole euchromatic portion of a person's genome (roughly 3 billion sites). While significantly more expensive than SNP chip-based genotyping
Genotyping
Genotyping is the process of determining differences in the genetic make-up of an individual by examining the individual's DNA sequence using biological assays and comparing it to another individual's sequence or a reference sequence. It reveals the alleles an individual has inherited from their...
, this approach yields significantly more data, identifying both novel (never-before-seen) and known sequence variants, some of which may be particularly relevant in efforts to understand personal health, as well as ancestry.
Timeline of personal genomes sequenced
| Year | Cost | Personal genomes sequenced | Company | Source |
|---|---|---|---|---|
| 2003 | $3,000,000,000 | 1 | Various | |
| 2009 | $48,000 | 100 | Illumina Illumina (company) Illumina, Inc. is a company incorporated in April 1998 that develops, manufactures and markets integrated systems for the analysis of genetic variation and biological function. Using its technologies, the company provides a line of products and services that serve the sequencing, genotyping and... |
|
| 2010 | $19,500 | 1000+ | Illumina Illumina (company) Illumina, Inc. is a company incorporated in April 1998 that develops, manufactures and markets integrated systems for the analysis of genetic variation and biological function. Using its technologies, the company provides a line of products and services that serve the sequencing, genotyping and... |
|
| 2011 | $19,500 to $4,000 | ? | Illumina Illumina (company) Illumina, Inc. is a company incorporated in April 1998 that develops, manufactures and markets integrated systems for the analysis of genetic variation and biological function. Using its technologies, the company provides a line of products and services that serve the sequencing, genotyping and... |
Comparative genomics
Comparative genomicsComparative genomics
Comparative genomics is the study of the relationship of genome structure and function across different biological species or strains. Comparative genomics is an attempt to take advantage of the information provided by the signatures of selection to understand the function and evolutionary...
analysis characterizes the differences and similarities between whole genomes. It may be applied to both genomes from individuals from different species or individuals from the same species, generally at lower cost than sequencing from scratch.
Services already available
Companies which offer genome-wide personal genomics services have already gone to market and are selling their services direct to the consumer.- deCODEme.comDecode GeneticsdeCODE genetics, Inc. is a biopharmaceutical company based in Reykjavík, Iceland. The company was founded in 1996 to identify human genes associated with common diseases using population studies, and apply the knowledge gained to guide the development of candidate drugs...
charges $1100 to carry out genotyping of approximately 1 million SNPs and provides risk estimates for 47 diseases as well as ancestry analyses.
- Existence GeneticsExistence GeneticsExistence Genetics is a genetic analysis and genetic reporting company that provides the healthcare industry and health & wellness organizations with access to affordable and easy-to-understand information about their client’s genes...
provides genetic testing services through healthcare providers and health and wellness organizations, with prices starting at $350. This company provides testing for over 700 different diseases and traits, including preventable sudden cardiac death, malignant hyperthermia.
- NavigenicsNavigenicsNavigenics, Inc. is a privately held personal genomics company, based in Foster City, California, that uses genetic testing to help people determine their individual risk for dozens of health conditions....
, began offering SNP-based genomic risk assessments as of April 2008. Navigenics is medically focused and emphasizes a clinician's and genetic counselor's role in interpreting results. AffymetrixAffymetrixAffymetrix is a company that manufactures DNA microarrays; it is based in Santa Clara, California, United States. The company was founded by Dr. Stephen Fodor in 1992. It began as a unit in Affymax N.V...
Genome-Wide Human SNP Array 6.0 , which genotypes 900,000 SNPs.
- Pathway GenomicsPathway GenomicsPathway Genomics is a privately held personal genomics company based in San Diego, California. Using DNA genetic testing technologies, the company conducts services to generate personalized reports about an individual’s carrier status, drug response, propensity for the development of certain...
analyzes over 100 genetic markers to identify genetic risk for common health conditions such as melanoma, prostate cancer and rheumatoid arthritis.
- 23andMe23andMe23andMe is a privately held personal genomics and biotechnology company based in Mountain View, California that is developing new methods and technologies that will enable consumers to understand their own genetic information...
sells mail order kits for SNP genotypingSNP genotypingSNP genotyping is the measurement of genetic variations of single nucleotide polymorphisms between members of a species. It is a form of genotyping, which is the measurement of more general genetic variation. SNPs are one of the most common types of genetic variation...
. The $99 kit, with $9.00/month subscription, or $399 without a subscription contains a saliva sample collection container and instructions. The consumer mails the sample to 23andMe for microarray analysis. The information is stored in a user profile and used to estimate the genetic risk of the consumer for 178 diseases and conditions, as well as ancestry analysis. 23andMe utilizes a DNA array manufactured by Illumina.
- SNPediaSNPediaSNPedia is a wiki-based bioinformatics web site that serves as a database of single nucleotide polymorphisms . Each article on a SNP provides a short description, links to scientific articles and personal genomics web sites, as well as microarray information about that SNP...
is a wiki that collects and shares information about the consequences of DNA variations, and through the associated program Promethease, anyone who has obtained DNA data about themselves (from any company) can get a free, independent report containing risk assessments and related information.
- BioresolveBioresolve-External links:* *...
describes a similar service to that of 23andMe; the Ottawa Better Business Bureau gave the company an "F" reliability rating.
- KnomeKnomeKnome is an American personal genomics company that sells human whole genome and exome analysis and sequencing services to researchers and consumers...
provides full genome (98% genome) sequencing services for $4,998 for whole genome sequencing and interpretation for consumers, or $29,500 for whole genome sequencing and analysis for researchers, depending on requirements.
- HelloGene and HelloGenome personal genome information services describe genotyping and full genome sequencing launched by Theragen in Korea. HelloGenome is the first commercial whole genome sequencing service in Asia while HelloGene is the first in Korea. HelloGene uses Affymetrix SNP chips while HelloGenome uses Solexa machines.
- IlluminaIllumina (company)Illumina, Inc. is a company incorporated in April 1998 that develops, manufactures and markets integrated systems for the analysis of genetic variation and biological function. Using its technologies, the company provides a line of products and services that serve the sequencing, genotyping and...
, Oxford Nanopore Technologies, SequenomSequenomSequenom is a manufacturer of DNA massarrays, based in San Diego, California, United States. The MassARRAY platform is used for SNP genotyping, methylation detection and quantitative gene expression analysis. Sequenom also manufactures clinical tests, such as SEQureDx, a noninvasive prenatal test...
, Pacific BiosciencesPacific BiosciencesPacific Biosciences is a biotechnology company founded in 2004 that develops and manufactures systems for gene sequencing and some novel real time biological observation. They describe their platform as single molecule real time sequencing , based on the properties of zero-mode waveguides...
, Complete GenomicsComplete GenomicsComplete Genomics is a life sciences company that has developed and commercialized a DNA sequencing platform for human genome sequencing and analysis. This solution combines the company’s proprietary human genome sequencing technology with its informatics and data management software in an...
and 454 Life Sciences454 Life Sciences454 Life Sciences, is a biotechnology company based in Branford, Connecticut. It is a subsidiary of Roche, and specializes in high-throughput DNA sequencing.-History and Major Achievements:...
are commercializing full genome sequencingFull genome sequencingFull genome sequencing , also known as whole 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...
but do not provide genetic analysis or counselling.
Ethical issues
Genetic discriminationGenetic discrimination
Genetic discrimination occurs when people are treated differently by their employer or insurance company because they have a gene mutation that causes or increases the risk of an inherited disorder. People who undergo genetic testing may be at risk for genetic discrimination.The results of a...
is discriminating on the basis of information obtained from an individual’s genome. Genetic non-discrimination laws have been enacted in some US states and, at the federal level, by the Genetic Information Nondiscrimination Act
Genetic Information Nondiscrimination Act
The Genetic Information Nondiscrimination Act of 2008 , is an Act of Congress in the United States designed to prohibit the improper use of genetic information in health insurance and employment...
(GINA). The GINA legislation prevents discrimination by health insurers and employers, but does not apply to life insurance or long-term care insurance.
Other issues
Full sequencing of the genome can identify polymorphismsPolymorphism (biology)
Polymorphism in biology occurs when two or more clearly different phenotypes exist in the same population of a species — in other words, the occurrence of more than one form or morph...
that are so rare that no conclusions may be drawn about their impact, creating uncertainty in the analysis of individual genomes, particularly in the context of clinical care. Czech medical geneticist Eva Machácková writes: "In some cases it is difficult to distinguish if the detected sequence variant is a causal mutation or a neutral (polymorphic) variation without any effect on phenotype. The interpretation of rare sequence variants of unknown significance detected in disease-causing genes becomes an increasingly important problem."
See also
- Human genome map
- Single-nucleotide polymorphism
- Population genomicsPopulation genomicsPopulation genomics is the large-scale comparison of DNA sequences of populations. Population genomics is a neologism that is associated with population genetics.-References:* *...
- Full Genome SequencingFull genome sequencingFull genome sequencing , also known as whole 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...
- BioinformaticsBioinformaticsBioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...
- GenomicsGenomicsGenomics is a discipline in genetics concerning the study of the genomes of organisms. The field includes intensive efforts to determine the entire DNA sequence of organisms and fine-scale genetic mapping efforts. The field also includes studies of intragenomic phenomena such as heterosis,...
- Systems biologySystems biologySystems biology is a term used to describe a number of trends in bioscience research, and a movement which draws on those trends. Proponents describe systems biology as a biology-based inter-disciplinary study field that focuses on complex interactions in biological systems, claiming that it uses...
- Transcriptomics
- Omics
- Population groups in biomedicine
- Genomic counselingGenomic counselingGenomic counseling is the process by which a person gets informed about his or her genome. In contrast to genetic counseling, which focuses on Mendelian diseases and typically involves person-to-person communication with a medical genetics expert, genomic counseling is not limited to currently...