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Posts from the ‘Genetic screening’ Category

What you have to know about personalized genetics

Genes load the gun. Lifestyle pulls the trigger.

By Dr. Elliot Joslin

I’ve written at least a hundred times about personalized medicine so it’s the perfect time to come up with a short description of what individualized medicine is about. In this new world of medicine, you get a treatment that is not only based on the epidemiological data of your population, but your own genetic background. But let’s start with a more appropriate definition:

Personalized medicine is use of information and data from a patient’s genotype, level of gene expression and/or other clinical information to stratify disease, select a medication, provide a therapy, or initiate a preventative measure that is particularly suited to that patient at the time of administration. Personalized medicine makes it possible to give: “the appropriate drug, at the appropriate dose, to the appropriate patient, at the appropriate time”. The benefits of this approach are in its accuracy, efficacy, safety and speed.

All right, here is an even shorter one.

…turning genetic variations associated with population-level risks of disease into medically advice useful for a single person sitting in an exam room.

We can also watch it on video:

Who are the key players?

23andMe: Single Nucleotide Polymorphism and genealogy analysis for 1000$. Check out my review or the demo account I created.

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Knome: Whole-genome sequencing for 350,000$. Check out my review.

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Navigenics: Will launch the service in days. My review is here.
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Helix Health: A New York company founded by our gene sherpa, Steve Murphy, who answered my questions some months ago. Helix Health focuses on the family history of the patient and their genetic background as well. Genetic counselors discuss the disease-specific risks with the patients.

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DecodeMe: It analyzes over one million variants in our genomes; calculates genetic risk for 23 diseases and finds our ancestors for $985.

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Who and what do stand behind the whole concept?

Archon X PRIZE for Genomics: The $10 million X PRIZE for Genomics prize purse will be awarded to the first Team that can build a device and use it to sequence 100 human genomes within 10 days or less, with an accuracy of no more than one error in every 100,000 bases sequenced, with sequences accurately covering at least 98% of the genome, and at a recurring cost of no more than $10,000 per genome.

The aim is the 1000$ genome.

Craig Venter’s genome that was published in September, 2007.

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Who and what should you follow to know everything about personalized medicine?

Personalized Genetics: Back in Business

It’s been a long time I haven’t written about the hypest field of medicine. So from now, I’ll get back to posting 2-4 times a week about individualized medicine. If you know nothing about it, check out my page dedicated to the subject.

Similarly, such technology will lead to individual genetic screening for disease risk using chipe that interact with the tiny bits f DNA we shed every time we touch something. Companies commercializing this approach also already exist and have products.

While reading these two blogposts, listen to the presentation of Kathy Giacomini (University of California): How Drugs May Be Tailored to Your Genetic Makeup

  • UK controversy over 23AndMe (Genetic Future): The Human Genetics Commission (and the Gene Sherpa) have already condemned 23andMe as a dangerous waste of money and called for regulations to control their marketing.
  • Don’t forget to check out the online tutorials and on-site training of OpenHelix. They focus on genetics and some tools devoted to genomics.

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Global Awakening in Genetic Counseling

I’ve recently come across this article at Nature Precedings written by Janice Edwards, Jacquie Greenberg and Margaret Sahhar. Check out these excerpts:

According to the National Society of Genetic Counselors in the USA “ To offer an optimum genetic service in a country it has been estimated that approximately 2 genetic counsellors per 1 million of the population would be the minimum number required.” Yet, the number of trained genetic counselors is estimated at less than 3000 worldwide.

Wow, we would need even more! Genetic counselors should play an important role in those genetic companies.

As global awakening in genetics continues, the Transnational Alliance for Genetic Counseling will promote transnational collaborations in genetic counselor education and research, stimulating international understanding of the role of genetics on human lives.

I wish I could promote more efficiently projects like this one.

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Here is an other great example from Scientificblogging.com. The Clinical Genetics column is maintained by Prof. Camillo Di Cicco (University of Rome/Medicine) and you can find dozens of well-structured and valuable articles about genetic conditions there. I’ll definitely follow the RSS of his page.

And we shouldn’t forget about some open notebook projects. Stew at Flags and Lollipops asked a question:

Is there a super-semantic-web-enabled phenotype database out there*? I want to ask a question like ‘give a list of monogenic disorders whose locus has been confirmed by at least two labs, broken down by type of causative mutation type’ and get an answer.

So, I really believe we’re moving forward. Let me know please if you happen to know more similar methods to promote genetic conditions and the science of genetics.

Newborn Screening for “Bubble Boy Disease”: Interview

On the 1st of January, the state of Wisconsin made a major step in the field of newborn screening. The collaboration of Wisconsin State Laboratory of Hygiene, Children’s Hospital of Wisconsin and the Jeffrey Modell Foundation resulted in screening newborns for Severe Combined Immune Deficiency (SCID). According to the Wikipedia article this is:

…a genetic disorder in which both B and T cells of the adaptive immune system are crippled, due to a defect in one of several possible genes. SCID is a severe form of heritable immunodeficiency. It is also known as the “bubble boy” disease because its victims are extremely vulnerable to infectious diseases.

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I’ve already presented The Jeffrey Modell Foundation (headquarters in New York) to you in June. Now, to know more about this medical breakthrough, Dr. Jack Routes from the Children’s Hospital of Wisconsin answered some of my questions:

  • How common is the so-called “Bubble Boy Disease” in the US and in your hospital?

There is no good data on the actual incidence of the disease in the US. It is estimated that at least 1:100,000 newborns have SCID. Our newborn screening program will better ascertain the true incidence of SCID in Wisconsin.

  • Is a blood sample taken from a newborn enough for the screening process?

All newborn screening tests are performed from blood spotted on a newborn screening card—the newborn gets a heel stick and blood is put on a special filter paper on the newborn screening card. A small punch is taken from the filter paper and the SCID screening test is performed.

  • Please tell us some more details of the screening of SCID! How sensitive and predictive is the test?

Please see the article ( J Allergy Clin Immunol. 2005 Feb;115(2):391-8.) for a discussion of the assay. These are the only published data to date. The assay is a real time, quantitative PCR that measures the number of T cell receptor excision circles (TRECs) in the punch from a newborn screening card. TRECs are a surrogate marker for functional, naïve T cells, which will be reduced in most, but not all causes of SCID. Our group has improved the TREC assay (false positive rate is <0.01%) over the results reported in the JACI paper. There is no data on sensitivity and positive predictive value of the test—-this issue will be addressed by the WI SCID screening program.

  • Do you plan to add new medical conditions to the newborn screening program?

Wisconsin constantly evaluates other genetic diseases to add for newborn screening. The WI Newborn Screening Umbrella Committee addresses this issue and I am not a member of this committee and do not know if other tests are being considered in the near future.

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(Source)

I’m thankful to Dr. John Routes for the answers. This is a great example of how to construct a successful newborn screening program. Just to show you the difference, in Hungary, they screen newborns for only 4 (while they screen for 47 in Wisconsin) genetic conditions (galactosaemia, congenital hypothyreosis, biotinidase deficiency and phenylketonuria)

Gene Genie #19: Geneticalization

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Many thanks to Ricardo Vidal for the logo!

Gene Genie is the blog carnival of genes and gene-related diseases. Our plan is to cover the whole genome before 2082 (it means 14-15 genes every two weeks). But we also accept articles on the news of genomics and personalized genetics. Let’s get ready to the geneticalization:

DNA:


Hsien-Hsien Lei at Eye on DNA tells us that New Line Genetics and SellMyDNA.com Offer $5,000 for Your DNA. Would you sell it?

Nature’s Nascent has a short report about the amazing story of Hugh Rienhoff, his daughter and her DNA.

Misha Angrist at Genomeboy comments the same story in the Don’t try this at home, kids post.

Genes:

Steve Murphy, our Gene Sherpa, expresses his opinion on a new gene in sudden cardiac death.

Ramūnas Janavičius at Cancer-Genetics examines the single nucleotides polymorphisms of the gene SMAD7 which is important in scleroderma as well.

Larry Moran, our favourite professor and author of Sandwalk, has a post about diversity and the major histocompatibility (MHC) loci.

Elaine Warburton at Genetics and Health targets the FOXP2 gene which is believed to play a role in speech and language and wishes Happy Birthday to BRCA2!

PZ Myers at Pharyngula says mutations in the CFTR gene cause Cystic Fibrosis.

Alan Cann at MicrobiologyBytes reports that a variation in two key genes can predict the course of progression to AIDS.

Razib Kahn at Gene Expression has a reference-full article about the Neandertals’ red hair.

Genome Sequencing and Genetic Research:

Strange facts about DNA, genes, genetics and the human genome.

Philippe Campeau at OMMBID Blog shares some articles about neurotransmitter diseases with us.

Ramunas again with Knome | The First Whole-Genome Sequencing Co.

David Hamilton at VentureBeat presents gene-expression diagnostics.

T. Ryan Gregory at Genomicron asks a strange question: Are you a cat genome person or a dog genome person?

The Biotech Weblog had an interesting post about a FISH-based test identifing genetic abnormalities in plasma cell malignancies.

Nautilus talks about an important issue, Opportunities for women in early genetics.

The study of the week award goes to the PredictER blog: Genetic Research: Watson or Spears?

Personalized Genetics:

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Deepak Singh at business|bytes|genes|molecules presents a cautionary note about Your personal health.

Rahul Shetty at Constructive Medicine examines the exact definition of Personal Health Records.

has a fantastic imaginary story.

Elaine Warburton at Genetics and Health raised some concerns: Personalized Medicine leaves public confused.

And on Scienceroll, I continued my series about the best posts of personalized genetics in this weekend’s summary part one and part two.

Let’s finish this edition with an other idiot video, the guy’s name is Gene Gene, the dancing machine (I’m sorry for the bad humour…):

The 20th, jubilee issue of Gene Genie will be hosted by BiteSize Bio on November 18th. Don’t forget to submit your articles via the official page.

And also check out the Gene Genie official blog! If you’d like to host an edition, don’t hesitate to contact me at berci.mesko [at] gmail.com.

The Best Description of Personalized Medicine

An excerpt from an article at Wired Science with the best description of personalized medicine ever (in red):

After talking about the tricky task of turning genetic variations associated with population-level risks of disease into medically advice useful for a single person sitting in an exam room, the panel was asked whether they’d recommend gene testing for everyone.

“For healthy patients with no family risks for anything, I wouldn’t advise tests for anything,” Lawrence Brody from the NHGRI said. Rosen voiced his own agreement, and Jeffrey Gulcher of DeCode Genetics nodded.

…personalized medicine would be a wonderful thing, but it’s a long ways off. In the meantime, doctors have a tough time with probabilities and the limitations of predictive values. And direct-to-consumer genetic tests are a crock.

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It’s an important and hard question. If we shouldn’t test healthy patients, then why they test for cystic fibrosis in almost all the newborns regardless of ethnicity in the US?

Related links:

Web 2.0 and clinical genetics: in practice

Ramūnas Janavičius at cancer-genetics.com sent me some exceptional links to resources of clinical genetics. Why is it important? Once I wrote that:

Look, we can’t expect physicians (from any kind of medical specialties) to know everything about all the cc. 4000 genetic conditions. But we can help them how to find relevant information and quickly understandable material on genetic conditions.

Last week, I got a chance to see how our geneticists work at the department of pediatrics. I admire their work, but in special cases, they had to search for syndromes in books! I mean they had to go through it page by page. I always dream about a software (a Diagnosaurus-like gadget) with which we could make it easier for physicians to diagnose a genetic condition. You just enter the symptoms and you get a useful list for differential diagnosis. OMIM (Online Mendelian Inheritance in Man) doesn’t work like that.

So using web 2.0’s features, we can get closer and closer to this dream. The Clinical Genetics Blog uses del.icio.us to tag many resources to make it easier to search for genetic conditions:

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There is also an image collection at Flickr.com.

And the link of the week award goes to the Handbook of Genetic Counseling:

This book is designed as an introduction to the discipline and practice of genetic counseling. The text provides an introduction to genetic counseling as a clinical practice and includes sample counseling outlines and letters for students of genetic counseling. Additional outline and letter examples are highly encouraged.

It is just awesome! If we could merge this collection with the tags and the images into a Diagnosaurus-like software, we could create the best database of clinical genetics. What is your opinion?

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