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Posts from the ‘Genetic testing’ Category

DNA Dilemma on Newsweek

Mary Carmichael at Newsweek had a great series of articles focusing on direct-to-consumer genetic testing. An excerpt:

I’ve been following DTC genetics since 2007, when wide scanning first became available to the public. Since then, a number of writers have gotten wide-scale genetic tests and expounded on the results. Indeed, I sometimes wonder if I’m the last science reporter on earth with virgin genes. (Technical virgin: My doctor gave me a cystic fibrosis carrier test when I was pregnant.) Initially, I put off getting a full-genome scan because I wasn’t sure how useful such a test would be. I had no particular reason to take one, save curiosity. I wouldn’t expect to find anything serious and potentially life-altering like the Huntington’s disease gene in my results, because my family medical history is thankfully rather boring. The data most likely to be medically relevant to me would concern the genetics of common diseases, and at the time, many comprehensive and well-designed studies of those were still getting underway. I decided to wait a few years and see how research progressed. But here I am, three years later, still unsure.

Health 2.0 News: Centrifuge for Labor and Behind Healthcare.gov

At the moment the sensitivity and specificity of a lot of genetic tests for complex, polygenic disorders (for which we haven’t yet identified all the genetic variants that increase risk) are unlikely to match those of standard diagnostic or screening tests.  What’s likely is that the predictive capacity of these tests will improve as more variants are identified, and/or if additional non-genetic information is included in the test.

  • Statistical analysis is a collaboratively edited question and answer site for people who love stats. It’s 100% free, no registration required.

National Society of Genetic Counselors: Interview with Elizabeth Kearney

Elizabeth Kearney, the President of the National Society of Genetic Counselors in the US, gave me an interview this weekend, and commented on how direct-to-consumer (DTC) genomic companies should provide their customers with genetic counseling, which is a crucial part in the whole process.

As President of NSGC, Liz Kearney is responsible for leading the association and serving as the chief spokesperson. Liz is committed to promoting the many benefits genetic counselors bring to other healthcare professionals and patients.  Liz received her genetic counseling degree from the University of Michigan in 1996 and practiced in a variety of settings, including prenatal diagnosis centers, a general genetics department, and a diagnostic laboratory.  She also earned an MBA from Northwestern University in 2006, and in 2007.

1) Recent news have been focusing on regulations around DTC genomic companies such as 23andMe, Pathway Genomics or Navigenics. How do you think DTC genomics should be regulated?

The NSGC would support regulation that requires the involvement of a qualified healthcare provider in ordering, interpreting, and delivering genetic information. In the mean time, the NSGC strongly recommends that consumers talk to a genetic counselor prior to having genetic testing to discuss what questions or concerns they have. A genetic counselor has specialized training in both medical genetics and counseling and will review a person’s family and medical history in light of the person’s specific questions to determine if there is appropriate testing available.

2) We, genetic bloggers, have been writing a lot about the potential problems with these genetic tests and the harm they can cause to laypeople. Is genetic counseling the solution for this?

Seeking genetic counseling prior to genetic testing is an excellent way to protect against potential harm to consumers who do not have much knowledge or experience with genetics. Sometimes tests will provide helpful information and sometimes the information is either not helpful or even alarming.

For example, if you have concerns about a history of diabetes, a genetic counselor would review the family history in detail before ordering any genetic testing. It may be that the family history is sufficient to raise concerns about your chances to develop diabetes, and then the genetic counselor would recommend you talk to your primary care doctor about regular diabetes screening. Additional genetic testing may only confirm what is already known (through reporting an increased chance) or falsely reassure you (through reporting a lower chance) because the genetic factors tested are not the ones causing diabetes in your family.

On the other hand, genetic tests can reveal powerful information. For example, a 30 year-old male with shortness of breath saw his doctor, who performed an ultrasound detecting a thickening of the heart muscle (hypertrophic cardiomyopathy). This thickening can be an inherited and treatable condition. The cardiologist worked with a genetic counselor to order the appropriate genetic testing, and the genetic counselor explained the positive results which allowed identification of other relatives at-risk to allow surveillance and earlier treatment. The testing may have helped save or prolong the lives of the individual and/or his relatives, but the doctor and patient needed the help of the genetic counselor to identify the right test for him and explain the results.

3) How can I contact a genetic counselor after ordering DTC genetic tests? As I can order such tests online, could I also contact genetic counselors the same way? What about patient privacy?

Patients who have DTC genetic testing can absolutely contact a genetic counselor to review the results afterward. You can find a genetic counselor by visiting www.nsgc.org, and clicking on the “Find a Counselor” link on the left-hand side of the homepage. The drawback of waiting to contact a genetic counselor until after ordering testing is that you may pay for genetic testing that is not helpful in answering your specific questions or may reveal alarming information that you weren’t expecting to receive.

Recent legislation, the Genetic Information Nondiscrimination Act (GINA), protects people from discrimination by their employer or insurer based on genetic information in the absence of manifestation of disease. Therefore, consumers can be comfortable sharing genetic test results with a genetic counselor or other healthcare provider if it is in the context of their medical care.

4) Genetic counseling is the most important part of the whole DTC genomics process. Do you think DTC genomic companies do their best to provide their customers with the possibility of speaking with a genetic counselor?

Each company is different, but consumers should look for companies that employ genetic counselors and strongly encourage or require speaking with a genetic counselor prior to genetic testing.

Personalized Genomics: DTC Companies are in Huge Trouble

Today’s US Congress Committee on Energy and Commerce hearing into the direct-to-consumer genetic testing industry was a vicious affair. Representatives from testing companies 23andMe, Navigenics and Pathway faced a barrage of questions about the accuracy and utility of their tests, made all the worse by the fact that many of the Committee’s members seemed unable to distinguish between the more responsible companies in the field and the scammers and bottom-feeders.

Therefore, while advertising beef, the genetics community only seems to be delivering tofu. The complexity of genetic diseases has been far greater than anticipated, and the public’s interest in learning about genetic predispositions is unexpectedly low. So, will genetics ever impact primary care? It already has and will continue to do so, but it is likely to continue in an evolutionary rather than revolutionary manner. Primary health care providers who keep current by reading the medical literature and attending professional meetings will not be left in the dust. And, in time, the benefits of genetic technology will benefit our patients.

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:

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