A thorough discussion about personal genomics - Personalized Perspectives

A thorough discussion about personal genomics — what it means for the average consumer, the health care system, and the research community often raises more questions than it answers. While the public discourse on genetic privacy can be traced back to the days of the Human Genome Project, only recently has a new era been ushered in thanks to the steady decrease in the cost of DNA sequencing with promises of a tailor-made approach to medical treatment and new discoveries from rich genetic data sets. Depending on whom you ask, personal genetic information should either be protected at all costs as personal property or is merely information fit to published online for the whole world to see and contains nothing more revealing about health than, say, the knowledge that someone smokes.

That there is such concern over whether genetic information is more vulnerable to attack or misuse than traditional personal health care records may be an unintended consequence of the hype that touted personal genomics as a means to discover all there is to know about a person. "We've done it to ourselves. The way we were selling this idea of genomic data providing much better insight into who you are, and your future, than all other types of data it was very effective and we really meant it," says Misha Angrist, an assistant professor at Duke University's Institute for Genome Sciences and Policy. "However, until we find all that dark inherited matter that we haven't identified to date, most of our genomic signals are not nearly as disclosing as knowing your health risks because you're a smoker. But you can imagine that if one wanted to be a bit worried about the health care system, having a whole community saying that we're going to [be] developing the preeminent disclosing data source, people who were likely to get scared were going to get scared."

During the first few months of 2011 alone, advocacy groups like the Forum for Genetic Equity, concerned citizens, and a handful of state representatives began efforts to protect personal genetic information. In January, a group of Massachusetts state senators introduced the Massachusetts Genetic Bill of Rights in an attempt to make up for perceived shortcomings of the federal US Genetic Information Nondiscrimination Act of 2008. "This is a new era in medicine and we need to make sure that [there are] some sort of safeguards. We thought it would be important to deal with this quickly, rather than at some future time after perhaps people had already lost some of their rights," says Massachusetts Senator Harriette Chandler, who is a lead sponsor of the bill. "There obviously are issues; the insurance industry is not going to like this because they feel that they want to know any genetic information that the individual has, but what we're trying to say is that basically genetic information is your property, like any other property you have, and you have a right to privacy with respect to genetic material."

In March, representatives in Vermont and California introduced similar bills in an attempt to declare genetic information the exclusive property of the individual, among other protections. These bills face many hearings and debate sessions before having a chance of being enacted into law, but the movement is expected to spread across the country.

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Direct-to-consumer whole-genome now in India - Personalized Genomics to your doorstep

Avesthagen launches commercial Whole Genome Scanning Bringing Personalized Genomics to your doorstep.


Avesthagen will use Affymetrix technology to decipher the association between single nucleotide polymorphisms (SNPs)/ mutation and predisposition to the disease. The DNA chip used by Avesthagen for whole genome scanning features more than 1.8 million markers of genetic variation that include SNPs as well as probes for copy number variation (CNV).


A whole genome scan of an individual would provide information to understand his/her own genetic make-up that would lead to an increased awareness about the predisposition to a disease(s). The diseases, which are offered by Avesthagen, include major types of cancer, cardiovascular diseases, diabetes, schizophrenia, Alzheimer’s, asthma, anemia, arthritis and others. The technology platform at Avesthagen is able to interrogate the genetic markers (SNPs and CNVs) across an individual’s genome to decipher the association of the markers to the diseases.


By employing a streamlined sample collection and delivery system, Indian customers will now have access to personalized genomics services, which until now were only available in the developed markets. Avesthagen will leverage its expertise in genomics technology and state-of-the-art high throughput facilities for carrying out genomic analysis. The facility can process 200 samples per month.


The whole genome scan will be carried out on DNA extracted from saliva / buccal swab provided by the individual. The collection kit for saliva can be ordered by writing a mail to info@avesthagen.com. The results of the analyses will be available to the individual through an on-line secure web portal. The entire process is completed in 15 days after receiving the sample at Avesthagen.


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Next generation sequencing establishes genetic link between two rare diseases

This one is not so recent article, nevertheless very interesting and path breaking,

Scientists have successfully used "next generation sequencing" to identify mutations that may cause a rare and mysterious genetic disorder. The research, published by Cell Press on July 29th in the American Journal of Human Genetics, demonstrates that sequencing an affected individual's entire "exome"; that is, all of the genes that carry instructions for producing proteins, can reveal critical genes that when mutant, cause inherited disorders.

Perrault syndrome is a recessive disorder that is associated with hearing loss in both boys and girls, and failure of ovarian function in girls. Some individuals with Perrault syndrome also have neurological symptoms. Prior to the current study, no genes for Perrault syndrome had been identified.

A research group led by Mary-Claire King, PhD, from the University of Washington in Seattle studied the genetics of Perrault syndrome in a small family, originally of Irish and Italian ancestry, that included two sisters with well-characterized Perrault syndrome.

"Because the family is small and not consanguineous (both parents descended from a common ancestor), standard genetic mapping techniques would not have been informative in identifying the responsible gene," explains Dr. King. "Instead, we attempted to identify the gene responsible for Perrault syndrome in this family through the use of whole exome sequencing." The exome can be thought of as a kind of genetic blueprint for the synthesis of proteins.

After sequencing the entire exome of one of the sisters, the researchers identified a single gene (HSD17B4) that exhibited two rare functional variants. This gene encodes D-bifunctional protein (DBP), a multifunctional enzyme involved in lipid metabolism. Underscoring the genetic diversity of the disease, the researchers went on to show that six other families with Perrault syndrome had normal HSD17B4.

"Other mutations in HSD17B4 are known to cause a very severe congenital syndrome called DBP deficiency that is generally fatal within the first two years of life," says Dr. King. "No girls with DBP deficiency have been reported to survive past puberty, so ovarian abnormalities have not previously been known to be associated with this illness. The few reported long term survivors of DBP deficiency exhibit hearing loss and neurological dysfunction."

Taken together, the findings indicate that Perrault syndrome and DBP deficiency share some clinical symptoms and that very mild cases of DBP deficiency may be under-diagnosed. "Our research also demonstrates that whole exome sequencing can reveal critical genes in small nonconsanguinous families," concludes Dr. King.

The unknown future rolls toward us 23andMe, The story continues

The tables turn, it's 23andMe's turn to send a letter to FDA... Continuing the story Reading Between Lines slapped with cease and desist letters.

Direct-to-consumer genomics firm 23andMe has sent a letter to the heads of the US Food and Drug Administration and National Institutes of Health asking for a collaborative effort to develop guidelines for genetic testing.

The firm posted the letter that it sent to FDA Commissioner Margaret Hamburg and NIH Director Francis Collins on its blog, The Spittoon, last night.

23andMe is one of several companies to be targeted recently by FDA, which sent letters to several firms saying that it believes the firms are selling unapproved diagnostic devices. The other firms that received letters were Knome, 23andMe, Decode Genetics, Navigenics, and Illumina, the last of which was cited for providing the tools that are used to provide genetic information to certain of the DTC genomics' customers.

In the letter sent to FDA and NIH, 23andMe noted that there have been reports of inconsistencies in the results provided by DTC genetic test providers. Specifically, it pointed to a paper published in October 2009 in the journal Nature, in which the authors cited inconsistencies in the results provided by 23andMe and Navigenics.

Though Nature did not publish a joint response from 23andMe and Navigenics to that paper, the firms made it publicly available. In that response, they took exception to some of the methods used, but they also said they agreed with most of the recommendations made by the authors, who were from the J. Craig Venter Institute and the Scripps Translational Science Institute.

"We believe that it is important to emphasize that different genetic testing companies can report inconsistent results even when based on tests with proven analytical validity," 23andMe wrote this week in its letter to FDA and NIH. It added that such inconsistent results may be confusing to physicians and consumers alike.

The firm asked FDA and NIH for help in developing broadly applicable standards and guidelines for providing genetic test results and risk estimates. For example, the firm said such a collaborative effort could develop guidelines for acceptable analytical validity; standards for the positive and negative predictive value of tests; and best practices for companies that could lead to results being readily compared across companies.

"We note that any framework developed for genetic testing companies must consider the multiple high throughput technologies on the horizon, including genome, exome and transcriptome sequencing," it said in the letter. "For this reason, the set of ideas we present above does not include having an organization define a specific set of markers as an acceptable genetic test."

23andMe-Led Team Offers Program to Enroll Parkinson's Patients

The personal genetics service firm 23andMe, the Michael J. Fox Foundation for Parkinson's Research, and the Parkinson's Institute and Clinical Center announced yesterday that they are enrolling 10,000 people to be part of a new Parkinson's disease community. The effort is aimed at establishing the resources necessary for future genome-wide association studies and other research initiatives.

In an effort to entice individuals with Parkinson's disease to participate, 23andMe is slashing the price of its service from $399 to $25 for a limited time for up to 10,000 individuals with Parkinson's disease who sign up through the Parkinson's Institute or the Michael J. Fox Foundation. Google co-founder Sergey Brin, who is married to 23andMe co-founder Ann Wojcicki, will ante up an undisclosed amount of cash to subsidize the genotyping costs.

To be eligible, individuals must have physician-diagnosed Parkinson's disease and agree to provide saliva samples and fill out online surveys about their condition. Members of the Parkinson's community will also have access to the complete 23andMe Personal Genome Service. Current 23andMe customers who do not have the disease can participate as healthy controls in the project by voluntarily filling out the company's Parkinson's disease survey.

The latest research project is distinct from a collaboration between the same organizations announced last spring, Rachel Cohen, manager of communications at 23andMe. Cohen said that effort was specifically aimed at developing web-based diagnostic tools for Parkinson's disease, whereas the latest project is aimed at making sure they have individuals with Parkinson's disease on board for research efforts.

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Complete Genomics Service Targets $1000 Genome by 2009

Complete Genomics emerged from stealth mode today brandishing an audacious service model for wholesale next-generation sequencing, with its first human genome already assembled and the CEO’s pledge to reach the magical “$1000 genome” price point as early as spring 2009.

Based in Mountain View, Calif., Complete Genomics has raised $46 million in three rounds of financing since its incorporation in 2006. Unlike its commercial next-gen sequencing rivals – Roche/454, Illumina, Applied Biosystems (ABI) and Helicos – Complete Genomics will not be selling individual instruments, but rather offer a service aimed initially at big pharma and major genome institutes.

“Our mission is to be the global leader in complete human genome sequencing,” chairman, president and CEO Clifford Reid in a briefing last week. “We are setting out to completely change the economics of genome sequencing so that we can do diagnostic quality human genome sequencing at a medically affordable price. Essentially, [we’ll] transition this genome sequencing world from a scientific and academic endeavor into a pharmaceutical and medical endeavor.”

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Johns Hopkins Center Launches Genetic Rights Educational Effort

Previous blogging on the topic of GINA GINA Aftermath - Consumers Still Wary of Genetic Tests and in the series of blogs closing following the personal genomics industry scene. Now here is some thing very interesting and very vital that is about education the common man about GINA. Johns Hopkins University’s Genetics and Public Policy Center has launched an educational effort aimed at informing the public of how their genetic data can and cannot be used under the recently enacted Genetic Information Nondiscrimination Act.

As part of its so-called “Project GINA,” the GPPC plans “to disseminate information” about the legislation to healthcare stakeholders and the general public, GPPC Law and Policy Director Susannah Baruch told last week. As part of its plan, the GPPC will launch a web site describing and explaining the federal law that bars health insurers and employers from discriminating based on genetic data. The website, slated to launch in September, will outline what protections are provided under the law, contain a FAQ page, and will provide updates describing how federal and state regulators are implementing the law.

Until the launch of the site, however, GPPC is providing information on GINA under the “What’s Happening” heading on its homepage.

Ahead of the website’s launch, GPPC has made preliminary efforts to educate the public and stakeholders about the law through peer-reviewed publications, webinars, and fact sheets. GPPC recently hosted a series of webinars with the Bureau of National Affairs and has disseminated informational fact sheets describing GINA’s provisions.

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GINA Aftermath - Consumers Still Wary of Genetic Tests

Previously blogging on GINA Dawn of the GATTACA era! now Industry Survey Shows: The surveyors found that only five percent of consumers said that they were “very likely” to take a disease-specific genetic test in the next few years, and 15 percent said they would be “likely” to take one.

A total of 35 percent said that they would not submit to genetic tests, with 14 percent citing concerns about privacy, 5 percent saying they would not want to know about the results of their tests, and 16 percent saying both reasons would compel them to avoid genetic tests.

Although more than 50 percent of those who responded said that they are concerned about getting cancer or heart disease, only 4 percent of those said they had taken a genetic test for a particular disease. Two-thirds of those who did have a genetic test were advised to do so by a doctor.

The respondents had about the same comfort level of sharing genetic information with their spouses or partners as with their doctors, 72 percent and 71 percent respectively.

Only 22 percent of those who responded were comfortable with sharing results from genetic tests with institutions for research purposes, and almost none would give up that information to health insurance companies (3 percent), and even less to employers (2 percent) and prospective employers (1 percent).

From these findings, it is concluded that “makers of these tests might have more success penetrating the market by working through doctors rather than trying to make the case for their products directly to the consumer.”

The company said “The Personalized Medicine and Wellness Survey” is the first of a three-part study on the subject that will be released sometime this summer.

23andMe and The Parkinson’s Institute Announce Initiative to Advance Parkinson’s Disease Research

23andMe, a privately-held personal genetics company, and The Parkinson's Institute and Clinical Center (“Parkinson’s Institute”) today announced a research initiative under which Parkinson’s Institute patients, with financial support from The Michael J. Fox Foundation, will enroll in the 23andMe Personal Genome Service™ to support the development of advanced methods for clinical and epidemiologic research for Parkinson’s disease.

The new research initiative is designed to improve current methods of collecting information for Parkinson’s research by leveraging the internet to dramatically expand the involvement of Parkinson’s patients in clinical research and increase the frequency and quality of patient data collection. Specifically:

• Together, 23andMe and the Parkinson’s Institute will design and validate web-based clinical assessment tools that can be administered to online communities.
• 23andMe will establish a social networking platform to facilitate the development of communities and research projects based on common traits of Parkinson’s disease patients.
• All participating Parkinson’s Institute patients will be enrolled in the 23andMe Personal Genome Service™ and will provide a saliva sample for a comprehensive genome scan generating more than 580,000 data points per patient.
• Parkinson’s Institute patients will provide specific information and insights that will include their individual environmental exposures, family history, disease progression and treatment response.
• Patients’ risk factor and clinical data collected through the newly developed and validated web-based tools will then be merged with their genetic data to conduct research on Parkinson’s disease.
• New surveys will be developed and administered to the growing cohort of patients, generating new risk factor and clinical data for comparison with the existing genetic data.
• Through the deployment of an innovative approach to clinical research information gathering utilizing web-based tools, the initiative will help to expand the involvement of Parkinson’s disease patients in clinical research and increase the frequency and uniformity of patient data collection.

Biomarkers to Open the Door to Personalized Medicine and Represents a Seismic Shift for the Pharma Industry

“For example, the presence of a specific protein in the blood or in any body fluid might indicate a specific infection. Once an association between a biomarker and a disease is clearly established, the one can be used to signal the other, and to a high degree of certainty. As well, changes in the prevalence of a biomarker in the organism can immediately and reliably signpost a patient’s response to treatment”

Some pharmaceutical companies are already advancing their research and harnessing the power of biomarkers, which can:

• Be used to detect the predisposition for disease in a population, screen for its presence, confirm its diagnosis, assess its severity, predict its response to available therapies and measure its clinical course
• Be used as targets to discover new drugs
• Be a decisive factor in determining whether or not to continue research on an entity
• Show early in the development phase whether an entity could lead to side effects that should terminate further research
• Help to make clinical trials more efficient
• Reduce treatment overheads by optimizing dosages and measuring a patient’s response more quickly and accurately

Molecular Connections Private Ltd. Bangalore India has announced the launch of its new Knowledgebase of Clinically Significant Proteins - CliPro.

• Knowledgebase, is a result of manually mining thousands of papers, on proteins present in various human body fluids , with their known concentration values and biomarker information as available in literature
• Platform to analyze protein biomarker- disease associations
• Catalogue of clinically significant proteins in biofluids such as plasma, cerum, CSF, synovial fluid, saliva, urine, peritonial fluid, bal fluid, amniotic fluid, tears
• includes >1000 clinically significant proteins – with ~2000 different disease/pathological correlations
• Biomarkers with disease associations are broadly either diagnostic, prognostic, predictive or efficacy markers

Also read A price tag of around US$1 billion to map human proteome