Personal genomics

Part of a series on Genetic genealogy
Concepts
Population genetics Haplogroup/ Haplotype Most recent common ancestor Human mitochondrial DNA haplogroups Human Y-chromosome DNA haplogroups Genomics
Other
Y-chromosome haplogroups by populations Genealogical DNA test Personal genomics Genographic Project

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.

Use of personal genomics in predictive medicine

Predictive medicine 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.^{[citation needed]}

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.^{[citation needed]}

Cost of sequencing an individual’s genome

Typical cost of sequencing a human-sized genome, on a logarithmic scale. Note the drastic trend faster than Moore's law beginning in January 2008 as post-Sanger sequencing came online at sequencing centers.

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, 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.^{[citation needed]}

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.

Timeline of personal genomes sequenced

Year	Cost	Personal genomes sequenced	Company	Source
2003	$3,000,000,000	1	Various
2009	$48,000	100	Illumina
2010	$19,500	1000+	Illumina
2011	$19,500 to $4,000	?	Illumina

Comparative genomics

Comparative genomics 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.^{[citation needed]}

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.com charges $1100 to carry out genotyping of approximately 1 million SNPs and provides risk estimates for 47 diseases as well as ancestry analyses.

• Existence Genetics provides genetic testing services through healthcare providers and health and wellness organizations, with prices starting at $299. This company provides testing for over 1,200 common and rare diseases and traits, including heart disease, cancer, autoimmune diseases, obesity, nutrigenomics, pharmacogenomics, fitness & athletic performance, preventable sudden cardiac death, and malignant hyperthermia. Existence Genetics provides fitness & athletic performance genetic testing services for Equinox Fitness.

• Navigenics, 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. Affymetrix Genome-Wide Human SNP Array 6.0 , which genotypes 900,000 SNPs.

• Pathway Genomics analyzes over 100 genetic markers to identify genetic risk for common health conditions such as melanoma, prostate cancer and rheumatoid arthritis.

• 23andMe sells mail order kits for SNP genotyping. 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.

• SNPedia 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.

• Knome 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.

• Illumina, Oxford Nanopore Technologies, Sequenom, Pacific Biosciences, Complete Genomics and 454 Life Sciences are commercializing full genome sequencing but do not provide genetic analysis or counselling.

Ethical issues

Genetic discrimination 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,^{[citation needed]} 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.

Other issues

Full sequencing of the genome can identify polymorphisms 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 genomics
• Full Genome Sequencing
• Bioinformatics
• Genomics
• Systems biology
• Transcriptomics
• Omics
• Population groups in biomedicine
• Genomic counseling

References

36. Sweet K and Michaelis R. "The Busy Physician's Guide to Genetics, Genomics and Personalized Medicine". SpringerLink Scientific Press. May, 2011.

External links

• Personalgenome.org
• Personalgenome.net
• Genomics.org
• DNATest.org
• Personal Genomics Blog
• SNPedia
• BioResolve Complaints
• Personal Genomics Institute (PGI)
• National Geographic Genographic Project