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Posts from the ‘Gene’ Category

A Google-Powered Gene Sequence Web Search Engine

Yesterday, David Rothman shared an interesting application with me. Query Gene is a Google-powered search engine with which you can combine text and gene sequence fragment web searches. What can you do if you have a sequence and you’d like to know whether this sequence has ever been associated with genetic diseases?

Query Gene is a web-based program that searches for information about genetic sequences on the web. It is distinctive because it is not limited to a single database, but instead captures genetic information on the entire Internet using Google. Query Gene works by taking a gene sequence in combination with other search terms, finds similar sequences using NCBI’s MegaBlast, retrieves the descriptions of those matching genes from NCBI’s Entrez Nucleotide database, and performs a series of Google searches using the combination of your original search terms and each gene description.

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In their example, they inserted a nucleotide sequence and a search term (genetic disease associated with). This application identified the sequence as human hemoglobin beta and listed search results like sickle cell disease.

Isn’t it fantastic?

23andMe: The Re-Review

A week ago, I wrote a review about the three major companies focusing on personalized genetics. That time, I couldn’t include all the required information in the section of 23andMe. Now, here is the re-review:

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Website:

  • Design: Great! Clear structure, big buttons, nice colors. That’s how it should look like because all the functions are easily accessible.

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  • Informativeness: I must say, nearly perfect. Own pages for experts and laypeople as well. Sections for the scientific and the medical communities. Tutorials, descriptions, explanations about the basic concepts of genetics and their service. Like David P. Hamilton noted that more information about genetic counseling would be needed.

Service:

  • Cost: Price per kit is $999 plus shipping.
  • Target: Breast Cancer, Crohn’s Disease, Heart Attack, Multiple Sclerosis, Obesity, Prostate Cancer, Restless Legs Syndrome, Diabetes Type 1 and 2, Venous Thromboembolism, Bitter Taste Perception, Earwax Type, Lactose Intolerance and Muscle Fiber and Sports. Read about the genetic associations here.
  • Media Coverage: BBGM, My Biotech Life and VentureBeat.

Just one more note about direct-to-consumer genetic testing:

Some argue it is too early to make personalized genetic information directly available to consumers, contending that the level of public understanding has not matured to the point that most people are able to understand their results, and that genetic associations discovered to-date have little actual significance.

23andMe believes people have the right to access their personal genetic information. Genetic information is a fundamental element of a person’s body, identity and individuality. As such, the rights that people enjoy with regard to financial, medical and other forms of personal information should apply to genetic information as well.

I’ve always been optimistic, but I don’t think the public is ready right now. Can you really tell the patient about his/her susceptibility to medical conditions? I’ve been working with COPD-related SNPs and there are plenty of SNPs that indicate a higher risk for COPD, there are others that indicate lower risk, and there are many more that we know nothing about. The only thing I can tell my patient is that based on the SNPs I analyzed, he/she has a risk regarding that specific condition, but that’s all. Forget about universal susceptibility rates! Is this information worth $999?

One example is the risk for obesity. They analyze a SNP of the gene FTO (rs3751812 – Nature article requires subscription). Maybe the reason is my lack of expertise, but can we tell the patient anything about the risk for obesity by analyzing one gene’s one SNP? Or do they make only one SNP public for business reasons? The answer of 23andMe would be most welcome!

I understand that they had to launch the service, but we’ll need years of research to make it really useful. Anyway, it’s very important to promote the work of the first personalized genetic companies including 23andMe as I believe, they hold the key to the future of medicine. What do yout think?

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.

Mendel’s Garden #17: Blog Carnival of Genetics

This time, it’s the honor of Scienceroll to host Mendel’s Garden, the blog carnival totally devoted to all the fields of genetics. I thought I couldn’t find enough articles as most of the bloggers were on their vacation. But I have to share 30(!) blogposts with you and as I would like to make it easier to go through all the submissions, I also present some funny videos on genetics. Enjoy and welcome in Mendel’s Garden!

Let’s listen to music while reading the articles! Mendel-rap?

Plants/animals:

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Evolution:

DNA/Research:

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Human genetics:

I tried to interpret these genetic news and opinions like that, but there are other solutions as well. Which one would you prefer? Maybe this one?

Our September host is going to be Balancing Life. Send your submissions via the official blogcarnival form. Thanks for watching!

Genetic Testing: BlogMix and a funny video

I’ve been totally busy because of my summer practice at the department of pediatrics. I’ve seen many cases when genetic tests are needed (a strange haemophilia-related case, hereditary spherocytosis, etc.). I thought I should be your aggregator for today, so I tried to collect the most interesting posts on genetic testing, and I also present a new genetic blog. Then after reading all of these, don’t miss the funny video about a parody of a public service announcement on genetic testing.

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Source

Medicine 2.0 means that you can read valuable comments and opinions which are unlikely to be published in a scientific paper. Hsien-Hsien Lei greatly answers common questions about genetic testing.

Steven Murphy, the Gene Sherpa always informs us about new techniques and procedures that make it easier to diagnose (genetic) conditions and to predict risks for diseases. This time, in his article No More Skin Biopsies?, he says, it does demonstrate how ubiquitous genetic soon will be in the office.

Blaine Bettinger, our favourite genetic genealogist, describes the pros and cons of autosomal genetic testing. He says, no autosomal test, now or in the future, will ever be able to completely define a person or a person’s heritage. The solution could be the easy and fast whole genome sequencing. We hope it’s going to be reality soon.

After writing my Awesome Genetic Announcements post, Cicada from bioephemera.com asked me to express my opinion about how we can handle untreatable disorders (such as early-onset Alzheimers, or bipolar disorder) and whether one’s genetic risks could lead to being uninsured and unemployed.

  1. We don’t have to handle those. In a personalized genetic practice, an easy solution could be that the patient chooses from a list that what kind of diseases, conditions, genes they want to know about.
  2. For answering the second question, I just have to show you the winner of the post of the week award: Medical Ethics 2.0 from The Personal Genome. This post will really answer everything regarding medical ethics and insurance problems.

As I’ve promised, here is a new blog on the sky of the genetic blogosphere, Cancer Genetics. Ramūnas Janavičius, a clinical genetics resident doctor from Vilnius University, Lithuania, who is interested in human cancer genetics. He thinks that we help his work, but the truth is that he does a great service for us and the readers for writing about cancer genetics (an awesome topic!). Follow his blog in the future!

At last, let’s have some fun (actually it’s not as funny as you think):

Next time, I’m going to write about my conception on what a personalized genetic practice is like.

Related links:

Genetic Breakthroughs for Today

Three announcements that could have a big impact on genetic testing:

Scientists have developed a new technique to identify genes that increase the chance of women developing breast cancer. They hope it will lead to a single blood test which would reveal a woman’s risk of getting the disease.

Scientists found two genes responsible for breast cancer two years ago. But now new research led by Cancer Research UK’s Cambridge Research Institute, published in the Nature journal, has found five more.

The Swedish National Board of Health and Welfare has approved the highly-controversial procedure for three families whose children risk dying unless they receive a transplant of healthy stem cells from a sibling with a tissue match.

But for the first time authorities will allow the embryos to be screened to find a tissue match for a sick sibling, in a process called human leukocyte antigen testing (HLA).

Prize4Life — an X-PRIZE-style competition intended to stimulate innovation and produce tangible results in ALS (Amyotrophic Lateral Sclerosis) research — recently awarded its first prizes: Five researchers each received $15,000 to develop a biomarker for tracking the progression of ALS, a fatal disease.

Such a biomarker would enable scientists to test for ALS before the visible onset of symptoms, similar to markers in the blood of AIDS patients.

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Hsien at Eye on DNA and Steven at The genes Sherpa will probably post their comments on these findings.

My posts on the same subjects from before:

Genetic Wikis

I hope that David Rothman will like this little list of genetic wikis. The first three wikis are from Wetpaint, where you can create your own wiki. I’ve learnt about it at Medical 2.0.

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Wikimedia projects:

And some others from different subjects:

And at last, have you ever heard about the Gene Wiki? According to a document found at The Synaptic Leap:

The Gene Wiki is a genomics community-based, collaborative, workflow first envisioned by Marc A. Marti-Renom, head of the structural Genomics Unit at the Prince Felipe Research Center in Valencia Spain. The aim of the Gene Wiki is to tap into the collective intelligence of the science community to:

  • More thoroughly aggregate distributed genomics knowledge,
  • to help prioritize research projects for genomic-driven drug development, and
  • to mobilize distributed scientific resources based on the prioritization of a knowledgeable community.

Here is a video of Marti-Remon talking about making genomic data open and available for everyone (at Google TechTalks April 07, 2006):

Further reading:

Personalized Genetics/Genomics: Blogterview with Steven Murphy, MD

I’ve recently decided to deepen my knowledge on the field of personalized genetics/genomics as it has an exceptional future in the realm of medicine (and business). And who is the right person to answer my geek questions? Of course, Steven Murphy, MD, the blogger of the Gene Sherpa. He is the Clinical Genetics Fellow at Yale University and is also the founder of a Personalized Medicine practice.

  • We’ve heard a lot about personalized medicine, but please tell us more about personalized genetics.

Sure. There are some fundamental differences here. When I think about personalized genetics (Which is different than personalized genomics) I think about modifier genes involved in single gene disorders such as Cystic Fibrosis. A few months ago, I diagnosed a 70 year old woman with CF. She had been treated as if she had emphysema, had never smoked, and no Alpha 1 Antitrypsin deficiency. Something didn’t sit right with me. We had her get sweat tested and sequenced. Guess what? Compound heterozygote with one Delta 508 mutation. How could this happen? Modifier genes. There is a nice review of modifier genes in CF several months back in the New England Journal of Medicine. That is personalized genetics in my opinion…

Should we treat you aggresively or not? This woman clearly did ok without Creon (pancreatic enzymes), aggressve pulmonary toilet, or inhaled antibiotics. Now with the newborn screen we detect so many more patients with Cystic Fibrosis. Who should we treat? How should we treat? Personalized Genetics is like personalized medicine for those with single gene disorders. I remind you that “No gene is an Island” so we need to take it in context of the rest.

  • Personalized genetics or genomics? Is there any important difference?

Personalized Genomics is a totaly different animal. Here we deal with what everyone affectionately calls the “Personal Genome”. This is the dream of everyone gets a genome sequenced at birth, we assess risk, create prevention plans, identify idosyncratic drug reactions prior to medication therapy. The fear is obvious…”When is GATACA coming?” I think that we need to put protections in place to prevent discrimination from more than just employers and insurers. What about that University you want to get in to? In addition there are several problems with whole genome screening aside from its multimillion dollar pricetag (which is dropping quickly). That is the problem in medicine known as the incidentaloma.

Quite often when ordering a CT scan, or chest xray, or what ever radiologic test we find tumors/cysts/masses in a completely asymptomatic patient. Does this mean we identify a cancer or other life threatening thing before it can cause damage? Sometimes, but more often than not we end up spending thousands of dollars evaluating something that turns out to be nothing. Just an incidental finding in an otherwise asymptomatic patient. An article entitled The incidentalome: a threat to genomic medicine.” was published in JAMA in July of 2006. Mathemeticians modeled sequencing the whole genome. As they get up to sequencing 10.000 people they find that the fraction of the population with a false positive result skyrockets up to 60%. What does this mean? Well, we have to carefully select who we test. Or better yet we need an immense database of “Normal Variants”. At a minimum we will need 1000s of “sequence specialists” or “computer sequence analysis programs” to evaluate and decide if the “work up” is indicated or not. Personal Genomics is very complex, even more than personalized medicine.

  • What about the big companies focusing on personalized genomics/genetics?

We have key players including Illumina, 454 who has now been eaten by Roche, Affymetrix, Ventner, I could go on and on. The newest one to watch for is from the brainchild of 454 Jonathan Rothberg. He is launching a company called RainDance technologies. RainDance is already collaborating with Bayer Pharmaceuticals on high-throughput screening assays, noting the vastly superior statistics and reagent costs. What this means is a whole new means to sequence. If you add that into the nanopore sequencing mix at Harvard, then you have a robust field for development. I am sure I have missed a few, but these seem to be the key and future players to me.

As for personalized genetics, I know that the old stalwards like Genzyme, Genentech, BioMarin are all playing a role in defining the right infusion/pill for the right person with the right monogenic disease. Also you cannot forget about TGen who is building a presonalized medicine medical school in Arizona. My gosh I could just ramble about all of these things, but I will spare you all the details.

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  • As bioinformatics plays an important role in this rising field of medicine, how can web (especially web 2.0 ) help personalized genetics?

Web 2.0 and 3.0 can be best harnessed by networks of researchers sharing findings in open source forum. We need to give up the “Prize” for publication. Instead we need to nurture inter-institutional collaboration. In fact I would say we should prize how many universities were involved in every study. The web infrastructure can allow all of these things. In fact imagine coming up with a question in EST and shipping it to Mumbai for analysis during EST night-time. This is already happening in business. True, research takes more than overnight, but what if we were just talking about design. We could literally be working 24/7 to solve problems!

My dream is just that. The spirit of innovation, collaboration, and revolution all moving to solve the greatest code ever devised…DNA

I’m very thankful to Steven Murphy for the kind answers! Follow his blog for the most interesting news and explanations of personalized genetics.

Gene Genie #7 is up at the Gene Sherpa!

One of the best editions ever has been posted at the Gene Sherpa. The topic is (surprising, right?) personalized genetics. Steve Murphy covered the subject with interesting descriptions and collected about a dozen of submissions.

Still we must never forget the roots of genetics. I am all too aware of the struggle people with metabolic diseases go through every day. We hear about this at Fight Pompe I am not surprised by the struggle to keep up with costs of this horrible disease.

Thank you, Steve for hosting!

Next time, we’re going to Eye on DNA!

Visit the official website of the carnival at genegenie.wordpress.com and let us know if you plan to host an edition!

Here are all the issues of Gene genie:

Gene Genie: a Famous Blog Carnival’s Sixth Issue

467px-dna_repair.jpgYou may realized that our favourite blog carnival, Gene Genie has been mentioned in the last issue of Cell. So as it became a famous blog carnival with the goal of covering the whole genome before 2082, in the sixth issue, I’m going to mention at least a dozen of posts, articles focusing on genes and gene-related diseases. If you happen to remember the time when I hosted Grand rounds, the weekly blog carnival of the best of the medical blogosphere, you’ll not be astonished by these weird videos of genetics. So let’s get ready to the genes…

My Biotech Life presents a gene called Tbx1 whose inactivation leads to DiGeorge syndrome, a rare congenital disease. He also describes Tbx2/3 transcription factors and their role in embryonic development.

The SciencetificBlogging Team has an article on the genetic aspects of autism. Researchers (University of Iowa) have showed that if a mutation occurs in sperm cells of a father (who doesn’t have autism), it can be passed on to his children.

DNA Direct Talk raised some concerns about the gene discovery for heart disease risk, and made an informative list of facts about Mucolipidosis type IV, a neurodegenerative disorder.

Ok, there are thousands of genes, but what we know about non-coding DNA? Larry Moran at Sandwalk tells us everything of the subject and if you’re there, it’s worth taking a look at the comments. Larry also wrote a well-referenced post on human genes for the pyruvate dehydrogenase complex.

The Afarensis Blog examines this question regarding the Intelligent Design – evolution debate as “when some bit of DNA, thought to be non-coding, looks like it has a function, ID proponents are quick to trumpet this as evidence against evolution”.

If you want to know more about sex chromosomes from an evolutionary point of view, don’t miss Evolgen’s interesting article. Let’s take a break now with a Mendel-rap:

We should continue with clinical genetics and a little bit of fun. Hsien-Hsien Lei has made an interview with Dr. Keith Batchelder, the leader of Genomic Healthcare Strategies, a company focusing on personalized medicine and the intersection of personal genetic information with healthcare.

An amazing case is described by Chris Depelteau at Cool MRI Stuff about the resolution of Chiari malformation after repair. The body is so awesome, isn’t it?

I’m amazed when scientists, physicians present an important issue to the public in a readable and totally understandable style. The genetic genealogist did exactly that by answering some so called “frequently asked questions” about GINA, the Genetic Information Non-Discrimination Act that has recently passed the House of Representatives.

MC at Neurophilosophy introduces a program called Gene2Music which can transcribe any DNA sequence into music. We should make a podcast of the musics generated by all the genes’ sequences mentioned in Gene Genie…

Sorry for including my submission, but this has become a tradition in Gene Genie, so I’d like to share my thoughts with you on PTC124, a new drug against genetic diseases.

And at last, here is the editor’s choice from Healthbolt.net: Control Your Genetic Destiny! The words of Wade Meredith (Kudos!) should be the message of this issue:

Finding out how your helix is stacked is like getting an advanced copy of the test (your health) before the big exam (the rest of your life). If you already know your weaknesses you can fight them head on, instead of trying to play catch-up once your condition is rapidly deteriorating.

I have to say farewell with an other funny video on the magic of genetics with Gregor Mendel. Thank you for watching!

Here are all the issues of Gene genie:

If you’re thinking about hosting an edition, don’t hesitate to contact me at berci.mesko [at] gmail.com.

Update: for more info, please visit genegenie.wordpress.com!

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