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Posts from the ‘Gene’ Category

Wikipedia: Reliable Sources and Gene Wiki

Wikipedia is a good first place to go to do your research, but should never be the last place to finish with!

We’ve got more than 2 million articles now so our only aim at this stage is to fill up the medical articles with proper references. For those who would like to know more about Wikipedia’s citation policy, check out this: WikiProject Medicine/Reliable sources.

Wikipedia’s medical articles, while not a source of medical advice, are nonetheless an important health information resource. Therefore, it is vital that medical articles be based on reliable published sources. These guidelines supplement the general guidelines at Wikipedia:Reliable sources with specific attention to sources appropriate for medical and health-related articles. The ideal source for such articles would be a general or systematic review in a reputable medical journal, or a widely recognised standard textbook written by experts in a field. It is also useful to reference seminal papers on the subject to document its history and provide context for the experts’ conclusions.

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An other great project is the Gene Wiki presented by

The goal is to create gene stubs for every gene in the human genome. The stubs will have some minimal amount of structured content – links to important databases, GO annotations, PDB structures, etc. It’s our hope/expectation that these stubs will then seed contributions from experts in the field, specifically the “free-text” and unstructured sort of knowledge for which there really isn’t a great resource available.

If you’re interested, check out this link (warning – large page with long load time!) which lists the ~8000 (and counting) pages at Wikipedia that have incorporated structured content from our effort.

If you plan to contribute to this project, take a look at these categories and pages:

Further reading:

Gene Genie #23: Paradise of Genomics

Is it a paradise? You can decide after going through all the submitted articles. It’s my pleasure to host the newest edition of Gene Genie, the blog carnival of clinical genetics and personalized medicine.

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Many thanks to Ricardo Vidal for the logo!

Let’s start with some clinical genetics-related news:

Terra Sigillata talks about the genetics of autism. Don’t forget to check out the comments as well!

Walter Jessen at Highlight Health focuses on the genetics of panic disorder.

I must agree with the opinion of Misha Angrist at Genomeboy: God forbid an Alzheimer’s diagnosis ever bums anyone out.

Elaine Warburton at Genetics and Health shares a new finding with us: Genetic manipulation ‘fixes’ Fragile X syndrome

I’m pretty optimistic as we can see some steps forward in clinical genetics.
We should move on now and focus on the genes!

Ramūnas Janavičius at Cancer-Genetics comes up with a series on breast cancer, the complexity of BRCA genes and COBRA.

Yann Klimentidis features ACTN3 which is an important gene for bodybuiders and powerlifters.

Sandra Porter at Discovering Biology in a Digital World hunts for huntingtin, the gene of Huntington disease.

BabyLab describes p53 & microRNA.

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The next section is dedicated to the scientific and other aspects of human genetics:

Larry Moran at Sandwalk features the human genetic variation “Breakthrough”.

Flags and Lollipops dreams about a super-semantic-web-enabled phenotype database.

On Scienceroll, I provided some more tips on how to search for genetic conditions.

Jason Bobe at The Personal Genome is not too happy about the shortage of physician-geneticists in the United States.

And the friends of Simon Greenhill would use mtDNA to predict population size.

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The last section belongs to my favourite topic, personalized medicine:

Lygeia Ricciardi at Project Healthdesign presents the Best Practices for Employers Offering PHRs.

Hsien-Hsien Lei at Eye on DNA shares the first personal genome results from 23andMe and deCODEme with us.

Corpus Callosum focuses on a really important subject: Genetic Testing for Antidepressant Medication Response.

Steve Murphy, the gene sherpa, says some words about his genetic company, Helix Health.

Deepak Singh at Business|Bytes|Gene|Molecules writes really deep-minded posts these days, the one I chose now is Your Personal Health: A little warning.

Blaine Bettinger at The Genetic Genealogist points out an interesting service, myDNAchoice – Are Your Surfing Habits the Result of Your Genome?

If you are a regular reader of Scienceroll and have seen some of my past editions, you know what is coming next. Yes, the finish with a funny genetics-related video, a rap about chromosomal mutations:

The 24th issue of Gene Genie will be hosted by Biomarker-driven mental health 2.0 on the 20th of January. 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.

Steps Forward in Clinical Genetics

As I promised I’m here again to keep you up-to-date about the wonderful realm of clinical genetics. While there is a shortage of geneticists in the US and in other parts of the world as well, we can see some improvements regarding certain medical conditions. Let’s start with fragile X syndrome.

Fragile X syndrome is the most common cause of mental retardation. As Wikipedia says:

Mutation of the FMR1 gene leads to the transcriptional silencing of the fragile X-mental retardation protein, FMRP. In normal individuals, FMRP binds and facilitates the translation of a number of essential neuronal RNAs. In fragile X patients, however, these RNAs are not translated into proteins.

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Original source: Wikimedia Commons under Free Art License

The researchers of the Picower Institute for Learning and Memory at MIT have reversed symptoms of mental retardation and autism in mice. The FMRP protein binds to the mGR5 receptor on the surface of brain cells. A drug that inhibits the receptor may be useful in treating young Fragile X patients in the future. Check out the great report of Kristina Chew at AutismVox.

Second, FDA approved Kuvan for treatment of phenylketonuria (PKU), an other main cause of mental retardation.

Kuvan works by increasing phenylalanine hydroxylase enzyme activity in PKU patients with some residual PAH enzyme function. This then leads to an increased breakdown (metabolism) of phenylalanine (Phe), resulting in lower levels of Phe in the blood.

And last, but far not least, here is a fantastic article about mutations in breast cancer at Open Medicine. Kelly A Metcalfe and Steven A Narod present a common case and tell us how to help the patients with specific and accurate information or risk. Some weeks ago, Ramunas at Cancer-Genetics shared BOADICEA, a breast and ovarian cancer risk/mutation probability calculation web-application, with us.

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And Hsien-Hsien Lei at Eye on DNA presented Opaldia, a genetic testing company that will offer the Diagenic breast cancer blood test in 2008.

The test detects gene expression patterns in peripheral (circulating) blood and is touted as being able to diagnose asymptomatic breast cancer before it can be detected by manual breast exam or mammograms.

Aren’t these announcements fantastic? Or am I too optimistic?

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!

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