Spit and know your future

Personal genomics makes individualised healthcare possible; but experts remain wary

 
By Dinsa Sachan
Last Updated: Thursday 17 September 2015 | 10:08:27 AM

SOUMYA Swaminathan’s 16-year-old son, Sudarshan, loves sports, and is training to be a footballer. Two years ago, he was confused which sport to train in. “He would come home and say he wants to play cricket. Next week it would be football,” says Swaminathan. Then she heard about the sports DNA test offered by Super Religare Laboratories (SRL). The Mumbai-based firm had just launched the test, which would examine DNA from your saliva sample for variants of a gene linked with sporting prowess. It turned out that Sudarshan had a genetic predilection for power sports. “So we decided to focus on football and basketball,” she adds.

Gene testing is no longer restricted to paternity testing and DNA fingerprinting for criminal cases. It has varied avenues from giving details about what diseases you are likely to contract to which sports are suited for you. Experts say the personal genomics is the future of science. All you have to do is give saliva or blood sample and within days a comprehensive feedback on your health, which includes what diseases you are more or less likely to develop over your lifetime, is handed over to you.

“Personalised medicine means different things to different people. Some see it as targeted genomics where changes in specific genes predict responses to specific therapies,” says John Tomaszewski, president, American Society for Clinical Pathology. Others might see it as cellular engineering where one’s own cells are removed, re-engineered to treat a specific disease, and then re-infused into the patient, he adds. Both of these strategies are in limited use today, but hold hope for individualised healthcare.

Beginning and future

The seeds of personalised genomics were first sown in 1990 when the Human Genome Project (HGP) was conceived by a team of scientists in the US. The project, which lasted 13 years, identified and mapped the entire human genome—approximately 30,000 genes.

The Personal Genome Project (PGP), pioneered by George Church, one of HGP’s founders, is the next step. HGP mapped the genome of an anonymous person, while the PGP, when completed, will have genetic information of several individuals as well as their phenotypic information. Through this researchers can study the connections between gene functions and physical traits. The project is in process gathering genotypical information for 100,000 participants.

Rush to capitalise on science

Besides the research-based projects like PGP, the more visible side of the personal genomics industry are commercial enterprises like 23andme, Navigenics and Knome that offer different genetic tests to people. Companies like the California-based 23andme, which was floated in 2006, take a saliva sample of the customer and predict susceptibility to 199 genomic conditions including cancer and diabetes. It also has a research division, 23andWe, which published its first paper in June 2011 pinpointing genetic origins of the Parkinson’s disease.

23andme, along with ventures like Navigenics, belongs to the directto-consumer bracket that rely on SNP (single nucleotide polymorphism) genotyping. SNPs are particular point-locations in human DNA showing errors. Some SNP’s influence traits like physical appearance and susceptibility to diseases.

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23andme sequences only a portion of one’s genome. Other players like Knome and Illumina, whose technology is used by a number of projects, offer whole genome sequencing services, which list every minute detail of your genetic fingerprint. Knome’s DNA analytics service is priced at US $4,998. When it was launched, 23andme charged US $999 for its sequencing service. The cost was slashed to US $399 two years later. Now, the company offers a package for USÔÇê$99, which includes a year’s mandatory subscription for USÔÇê$9 per month in which participants are informed about any new updates from their single saliva sample.

“The price to sequence bases has fallen a million times from when HGP started with three billion ,” says Richard Resnick, CEO of GenomeQuest, a genome sequence management company. He adds that the cost will drop to as low as US $1,000 till next year.

Where India stands

Although companies like 23andme have not yet arrived in India, the country has been making strides in the field of personal genomics. Institute of Genomics and Integrative Biology (IGIB) in New Delhi mapped the first human genome in 2009. “Though India started slow in the field we are catching up,” says Rajesh Gokhale, Director, IGIB.

On the commercial side, only SRL has set its shop in the country. It takes a cheek swab and tests it for variations within the gene (ACTN3) associated with athletic performance in numerous studies. SRL tests children for two variants of the gene. According to B R Das, research and development chief at SRL, individual having the R variant of the gene have a possibility of excelling in sports that require short, powerful bursts of energy. The other variant, X, may be more useful in endurance sports like cricket. The test has been taken by 3,000 people across India. It costs Rs 2,000.

Binay Panda, head of Ganit Labs, Institute of Bioinformatics and Biotechnology in Bengaluru, believes India should develop its genomic potential in the direction which can benefit population at large. He sees a potential in medicine. His lab is trying to pin down the genetic causes of cancer. “This can help us devise specific diagnostic and prognostic techniques that would detect cancer at an early stage,” he adds.

In doubt

But experts remain critical about the disease assessments made by companies. “As far as sequencing some parts of genome and making predictions is concerned, we do know a fair amount about specific diseases and mutations associated with them,” says Kevin Rosenblatt, director, Center for Clinical Proteomics at The University of Texas Medical School at Houston. But when we consider the whole genome and the vast number of mutations that each of us carries in our DNA, science is not that well developed, he adds.

Gil Atzmon, assistant professor of genetics and medicine, Albert Einstein College of Medicine in the US, says, “Risk is not necessarily illness, and the probability of getting a disease is dependent on many factors, especially when epigenetics—response of gen ome to stress, diet, toxins and much more—is introduced to the equation.” He adds that two people can have the same genetic blueprint but are vulnerable to different diseases based on the environment they interact with. Andras Pellionisz, head of HolGenTech Inc, which makes genome analysing software, believes analysing genomes presents various challenges which current technology is not adequately prepared to meet. “The biggest challenge is interpretation. Genome is a changing repository of information because mutations and actual sequence alterations happen throughout life.”

Indian researchers are also wary of such endeavors. “The test by SRL measures one factor of energy metabolism. Will you become a sportsperson or not depends on other factors like environment also,” says Gokhale. Panda dubs the tests as “recreational genomics”.

Ethical and legal issues

When genomics companies were sprouting, the debate revolved aro und ethical issues and these still continue to haunt it. Critics question the repercussions of telling people what diseases they are vulnerable to. There are also concerns that health insurance companies might exploit the information and not insure one based on the probability of having a specific disease. Though US has a law— The Genetic Information Nondiscrimination Act—that protects US citizens from “genetic discrimination” no other country has such a legislation.

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  • Dinsa Sachan' article

    Dinsa Sachan' article encapsulates the emerging Industrialization of Genomics so tightly that only a little clarification is required for readers in India (who stand out in viewership of the Google Tech Talk YouTube http://www.youtube.com/watch?v=WJMFuc75V_w "Is IT ready for the Dreaded DNA Data Deluge".

    Dinsa quotes me: ÔÇ£The biggest challenge is interpretation. Genome is a changing repository of information because mutations and actual sequence alterations happen throughout life.ÔÇØ IT experts, familiar to "information" as defined by mathematician Shannon know that the A,C,T,G four bases technically constitute a "2-bit massively parallel data-flow device". However, biological definition of "information" is not yet defined (if two pictures composed of identical number of pixels, one showing your mother living far away, the other showing a stranger, which picture contains more "information" for you?). This is where Crick went wrong with his "Central Dogma of Molecular Biology", pontificating over half a Century ago, that proteins "never" recourse to DNA altering its "sequence information". Today we know that "sequence information" constantly changes not only in the technical sense of mutations e.g. when you fly to visit your mother, due to radiation through flight or smoking just a few cigarettes and a letter becomes knocked out - but the accessible sequence information changes even more massively through epigenomic effects, rendering long sequences unreadable due to e.g. methylation and chromatin modulation. Philosophycally, this constant change translates to "The Genome is NOT your Destiny" - and business-wise that HolGenTech, Inc. turns Industrialization of Genomics into a "repeat customer mode". - Dr. Pellionisz

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