Personal genomics

Personal genomics is a branch of genomics where individual genomes are genotyped and analyzed using bioinformatics tools. It is also related to traditional population genetics. The genotyping stage can have many different experimental approaches. However, the cheapest approach is using SNP(Single Nucleotide Polymorphism) chips that are commericially available. The other major approach is carrying out the full genome sequencing. Once the genotypes are known, there are many bioinformatics analysis tools that can compare individual genomes and find disease association of the genes and loci. The most important aspect of personal genomics is that it leads to the personal medicine where patients can take genotype specific drugs for medical treatments.

The personal genomics is not a single individual's vision or invention. Many researchers for decades anticipated this biological branch will eventually arrive with minimum cost of genotyping. Due to the advent of cheap and fast sequencers, full genome personal genomics is becoming a reality.

Genomics used to mean academic research on consensus genomes which have been assembled from many different individuals of a particular species. The personal genomics changes this into customized bioinformatic discovery on individuals.

Use of Personal Genomics in Personalized Medicine
Personalized 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 personalized medicine is in selecting which drug to prescribe to a patient. The drug should be chosen to maximize the probability of obtaining the desired result in the patient and minimizing the probability that the patient will experience side effects.

The probabilities of obtaining the desired result and of experiencing side effects are both dependent on information that can be obtained by analysis of the patient’s genome.

Genomics is itself a rapidly developing field. As new techniques are developed in genomics it is likely that some of them will be applied in personal genomics and personalized medicine.

Cost of Sequencing an Individual’s Genome
There is currently great interest in personal genomics. This is being fuelled by the rapid drop in the cost of sequencing a human genome. This drop in cost is due to the continual development of new, faster, cheaper DNA sequencing technologies such as single-molecule real-time sequencing.

The National Human Genome Research Institute, part of the U.S. National Institute 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 is a widespread belief that within 10 years the cost of sequencing a human genome will fall to $1,000.

There are 6 billion base pairs in the diploid human genome. Lander-Waterman analysis reveals that a coverage of approximately ten times is required to assemble a human genome from 25 base-pair reads with shotgun sequencing. This means a total of 60 billion base pairs that must be sequenced. A Solexa/Illumina sequencing machine can sequence 1.5 billion base pairs in each $8,000 run. The purchase cost, personnel costs and data processing costs must also be taken into account. Sequencing a human genome therefore costs approximately $1 million in 2008.

A cost of $1 million per individual is still too high for governments to introduce programs into health services to sequence the genomes of all individuals in a country. However, when the cost of sequencing a human genome falls below $1,000 this may become viable. For example, 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.

Comparative Genomics
Comparative genomics analysis is concerned with characterising 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. In personal genomics and personalized medicine, we are concerned with comparing the genomes of different humans. It is likely that many of the techniques which are developed in comparative genomic analysis will be useful in personal genomics and personalized medicine.

SNPs (Single Nucleotide Polymorphisms) have proven to be an effective technique for characterizing the differences between two genomes from the same species. It is likely that SNP genotyping will play an important role in personalized medicine.

A SNP is a single base pair mutation at a particular position in a genome.

It may consist of a substitution (replacing one base pair by another), an insertion of a single base pair or deletion of a single base pair. Figure 2 shows three examples of SNPs.

SNPs are not the best way to describe all differences one can find between two human genomes. For example, one genome may contain a long repeated subsequence that is not present in the other, or one genome may contain a region which repeats a subsequence a different number of times in one genome than the other.

Personalized Medicine Services Already Available
Three companies which offer personalized medicine services already exist. They are likely to be the first of many.

“23andMe” sells mail order kits for SNP genotyping. The $1,000 kit contains everything a patient needs to take their own saliva sample. The patient then mails the sample to 23andMe who carry out microarray analysis on it. This provides genotype information for about 600,000 SNPs. This information is used to estimate the genetic risk of the patient for many diseases.

“DecodeMe.com” offers a similar service to “23andMe.” “DecodeMe.com” charges $985 to carry out an analysis of approximately 1 million SNPs and estimate the risk of 29 diseases.

A third company, Navigenics, has stated that they will offer similar SNP genotyping services later in 2008.

Ethical Issues
While personalized medicine will certainly be a great asset to healthcare, it opens up several ethical issues which will need to be thought about carefully. No doubt there will be a huge amount of debate concerning the ethics of personalised medicine in the coming years.

Genetic discrimination is discriminating on the grounds of information obtained from an individual’s genome. In the U.S. nearly every state has already enacted genetic non-discrimination laws.

The likelihood of an individual developing breast cancer is affected by which alleles they have of particular genes. Screening can reveal breast cancer in the early stages, allowing it to be successfully treated. 50% of breast cancers occur in the 12% of the population who are at greatest risk. This poses a very difficult question for health services: Is it ethical to deny somebody free screening for a disease if they are genetically at low risk of developing that disease?