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Posts from the ‘Genetic testing’ Category

Number of Genomes Sequenced

I remember when Hsien-Hsien Lei tried to list all the people who had their genomes sequenced. Here is a more comprehensive list from SNPedia. Now the FuturePundit blog shared some interesting projections about the number of people who would have their genomes sequenced in the future:

  • 2001-2009: A Human Genome
  • 2010: 1,000 Genomes – Learning the Ropes
  • 2011: 50,000 Genomes – Clinical Flirtation
  • 2012: 250,000 Genomes – Clinical Early Adoption
  • 2013: 1 Million Genomes – Consumer Awareness
  • 2014: 5 Million Genomes – Consumer Reality
  • 2015-2020: 25 Million Genomes And Beyond – A Brave New World

The cost of sequencing is still decreasing, but the cost of data analysis and whether it can affect medical decision-making are different questions. Even if many of us thought we would be quite ahead as of now, there is still a long way to go.

Community Data in Genetics

23andMe is a direct-to-consumer genetic company that also launched the 23andWe project in which they tried to use the data they obtain from patients in studies. Now the results are published in PLoS Genetics.

Despite the recent rapid growth in genome-wide data, much of human variation remains entirely unexplained. A significant challenge in the pursuit of the genetic basis for variation in common human traits is the efficient, coordinated collection of genotype and phenotype data. We have developed a novel research framework that facilitates the parallel study of a wide assortment of traits within a single cohort.

The approach takes advantage of the interactivity of the Web both to gather data and to present genetic information to research participants, while taking care to correct for the population structure inherent to this study design.

Here we report initial results from a participant-driven study of 22 traits. Replications of associations (in the genes OCA2, HERC2, SLC45A2, SLC24A4, IRF4, TYR, TYRP1, ASIP, and MC1R) for hair color, eye color, and freckling validate the Web-based, self-reporting paradigm. The identification of novel associations for hair morphology (rs17646946, near TCHH; rs7349332, near WNT10A; and rs1556547, near OFCC1), freckling (rs2153271, in BNC2), the ability to smell the methanethiol produced after eating asparagus (rs4481887, near OR2M7), and photic sneeze reflex (rs10427255, near ZEB2, and rs11856995, near NR2F2) illustrates the power of the approach.

Although it’s a great example for how the online data can be used for scientific purposes, it does raise some questions about patient privacy.

GINAhelp.org

Have you ever had problems with understanding what GINA, the Genetic Information Nondiscrimination Act, is really about? Anyway, this is a U.S. federal legislation that protects Americans from discrimination on the basis of genetic information. According to Spittoon:

The Genetic Alliance, the Genetics and Public Policy Center at the Johns Hopkins University, and the National Coalition for Health Professional Education in Genetics have created an online resource to help people better understand the protections GINA provides.  This information is available in English and Spanish at www.GINAhelp.org.

You can find out more about genetic information, GINA and health insurance; also GINA and employment.

Personalized Genetics: FDA, DTC and GINA

Here are some interesting news and announcements to keep you absolutely up-to-date regarding the improvements of personalized medicine.

There are a number of reasons why DTC genetic testing may soon find itself subject to increased federal regulatory oversight. However, 23andMe’s widely publicized data error should not be one of those reasons. In fact, the sample swap, while unfortunately timed, actually presents a compelling argument in favor of the direct-to-consumer model for genetic testing.

A personalized medicine study from the Coriell Institute for Medical Research suggests that patients who undergo genetic testing are more likely to change their personal habits, writes Emily Singer at the Technology Review Editors’ blog.

Stanford University School of Medicine today said that it will offer a new course that gives medical and graduate students an option to study their personal genotype data. The university said that it believes it is the first medical school to offer students such a course. However, the University of Pennsylvania School of Medicine offered its fourth-year medical students a similar course in personalized medicine this past year.

Esther Dyson about Genomics

Esther Dyson answers questions about the direct-to-consumer genome market at the recent New York City Quantified Self Show&Tell meetup:

Personalized Genomics News: From Virtuality to the Streets

  • DNA As Crystal Ball: Buyer Beware (Newsweek): A genome-wide association study identified a new gene variant associated with Alzheimer’s disease but it turned out clinically it’s not useful.

“Adding these genes to traditional risk factors, such as age and sex, does nothing to aid prediction” of whether someone will develop Alzheimer’s, she told me. “Knowing your genetic status will not help. We may still be in the Stone Age when it comes to gene-based prediction.”

The United States House of Representatives Committee on Energy and Commerce today launched an investigation into direct-to-consumer (DTC) genetic testing, sending letters to three prominent DTC companies: 23andMe, Pathway Genomics and Navigenics.

  • 23andme: A detailed review of the data the blogger just received from 23andMe.

The family said they received no medical counseling here and are making their own conclusions.  One comment made is that the parents stated they will probably be using more pharmaceuticals, interesting.

A patient analyzes her own 23andMe data:

23andMe swapped samples!

What we were all afraid of finally happened. 23andMe admitted that it swapped some samples in the lab. Even if these things happen in labs, it should really not happen in such a sensitive area. We, bloggers and geneticians, have been writing about how hard it is for patients to analyze and interprete their direct-to-consumer genetic results properly and how hard it is for this market to remain attractive despite all the criticisms. And now they swap samples. Daniel MacArthur at Genetic Future has a nice review about all the related articles and news.

For example, a mother posted her recent story on the 23andMe community:

Still upset I checked family inheritance and noticed my daughter shared with me, and then I checked my son’s. He was not a match for any of us. I checked his haplogroup’s and they were different from ours. I started screaming. A month before my son was born two local hospitals had baby switches. I panicked and I checked over and over. My kid’s were sitting at the computer because we all wanted to see the results. My son laughed but he looked upset. I called my sister in tears.

Here is the full 23andMe announcement:

We recently determined that a number of new 23andMe customer samples were incorrectly processed by our contracted lab. We want to clarify what happened with the sample errors, how it happened and what we’re doing to prevent it from happening again. Providing each and every one of our customers with accurate data is 23andMe’s number one priority, and we fully realize the gravity of this incident.

Up to 96 customers may have received and viewed data that was not their own. Upon learning of the mix-ups, we immediately identified all customers potentially affected, notified them of the problem and removed the data from their accounts. The lab is now concurrently conducting an investigation and re-processing the samples of the affected customers and their accurate results will be posted early next week. We expect the investigation will be complete over the next several days and we will provide further details when we have them.

We are currently putting additional procedures in place that will add an extra layer of safeguards to help assure that similar incidents do not occur in the future. We are deliberating on a process that would include removing manual steps at the lab, completely automating the sample analyses, and implementing further checks of the data before it gets loaded into customer accounts. Please be assured that our testing laboratory’s processes comply with strict professional, regulatory, and corporate quality assurance standards for ensuring that all laboratory test results are accurate. The laboratory will adopt corrective action as warranted based on the findings of the investigation.

The science behind 23andMe’s personal genetics service remains proven and sound. We recognize that this is a very serious issue and your trust is of the utmost importance. We hope that this helps clarify what has happened and what we are doing to prevent these problems in the future. Please contact me at khomenko@23andme.com if you have any further questions. We appreciate your comments and feedback.

I cannot wait to hear what you have to say, Steve!

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