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Posts from the ‘Genetic condition’ Category

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!

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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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:

Towards a World without Genetic Diseases

I always dream about it. I really believe that in the next decades, we’re going to find a cure or at least a proper treatment for all the important genetic conditions/diseases. Until then, people struggling with these disorders have to learn how to handle their problem. First, here is a beautiful example:

Now, let’s see how we can get closer to that dream-world. I know it’s not going to be a patient-based post, but please forgive me this time. Here are 3 major improvements around muscular dystrophies, the first two articles present new diagnostic possibilities, while the third one is about the therapy:

A new genetic test targeting the most common types of muscular dystrophy–those caused by mutations in the dystrophin gene–is far quicker with greater accuracy and sensitivity than existing tests. It can be used to confirm clinical diagnoses, to test female family members who may be carriers, and to perform prenatal testing.

The average human gene consists of 3000 bases, but sizes vary greatly, with the largest known human gene being dystrophin at 2.4 million bases… Now researchers at Emory university has developed a microarray based test to check for mutations in this gene… Mutations in the dystrophin such as point mutations in a sequence of DNA can result in mistakes in gene expression and non-functional proteins that causes Duchenne muscular dystrophy (DMD).

Antisense-mediated exon skipping is currently one of the most promising therapeutic approaches for Duchenne muscular dystrophy (DMD). Using antisense oligonucleotides (AONs) targeting specific exons the DMD reading frame is restored and partially functional dystrophins are produced.

What is also crucial regarding genetic conditions? To avoid the diagnostic delay (so to diagnose the disorders in time):

The Sun Center of Excellence for Visual Genomics has been working towards using visual data exploration as a means to shed light on the causes of genetics disease.

Recently they developed 4D visualization virtual real atlas of the human body and other organism, with time being the fourth dimension. 4D enables you to virtually view the changes occurring in diseased state or genetically affected individuals and can be used for surgical studies.

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Source: Christoph W. Sensen (via)

Japanese investigators from the RIKEN Research Institute are reporting that they created fluorescent DNA probes that can attach to a specific DNA gene sequence, and detect single nucleotide alterations. The development of such PRODAN-conjugated DNA probes can pave the way for a diagnostic modality to identify single nucleotide polymorphisms (SNPs) responsible for a wide variety of genetic disorders.

And an other interesting essay on an important question: Why a genetic defect present at birth manifests in disease only in later life?

Many innovational diagnostic/therapeutic possibilities. Anyway, I’ve been thinking for a while about a Diagnosaurus-like software for physicians to let them diagnose genetic conditions easier and faster. What do you think? Are you interested in collaborate?

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Related articles:

Pseudomonas infections and cystic fibrosis

Pseudomonas infection causes serious problems in people with cystic fibrosis. Check out MicrobiologyBytes for more!

Face to face: Gaucher Disease

Some months ago, I wrote about Pompe disease, a rare, but important genetic disorder. I wanted to build awareness on the diagnostic delay, the cause of many misdiagnoses. Now, here is an other outstanding project about Gaucher disease. First, an excerpt from the Wikipedia article:

Gaucher’s disease is the most common of the lysosomal storage diseases. Symptoms may include enlarged spleen and liver, liver malfunction, skeletal disorders and bone lesions…

A journal-blog called Face to face, My journey for the Gaucher Initiative says:

Through this journal I will be documenting my journey to meet the faces behind the Gaucher Initiative, a humanitarian program that provides Gaucher patients in developing countries with the enzyme replacement therapy, Cerezyme, free of charge. I have the rare opportunity to meet with patients and their families to see how the Gaucher Initiative has and continues to affect their lives.

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Inspirational stories! Check it out for more!

Giving Babies A Chance to Survive

I got a letter from Natalie Maniscalco who is working at The Jeffrey Modell Foundation. She asked me to post this message about the Foundation and the importance of avoiding diagnostic delay:

Mission

The Jeffrey Modell Foundation (JMF) was established by Vicki and Fred Modell in memory of their son, Jeffrey, who died at the age of 15 of a Primary Immunodeficiency (PI). The Foundation is dedicated to early and precise diagnosis, meaningful treatments and ultimately cures for Primary Immunodeficiencies.

What you need to know:

PI is a genetic defect in a child’s immune system. It’s more common than you think, it’s chronic, and if untreated, it can be deadly.

It affects as many as 1 million children and young adults – more common than childhood leukemia and lymphoma combined.

PI causes the usual childhood illnesses to occur an unusual amount of times.

There are 10 warning signs of the disease, and a simple and inexpensive blood test can identify the disorder in over 95% of the cases.

Once diagnosed, there are several treatment options that can provide a good quality of life and in some cases, even a cure.

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To date, there are 35 Jeffrey Modell Research and Diagnostic Centers in the U.S., Canada, Europe, Middle East, and Asia. Recently they established collaboration with the NIH and Affymetrix to develop a Gene Chip using Microarray technology to do Newborn Screening of Severe Combined Immune Deficiency. The Modells have raised over $40 million for research and education since starting the Foundation in 1987.Focus

  • To affirm its absolute commitments to clinical and basic research in order to better understand and treat Primary Immunodeficiencies.
  • To serve as a national and international source for the dissemination of information and education into the diagnosis and treatment of genetic immunodeficiencies.
  • To serve as a tireless, compassionate advocate on behalf of patients and families to assure their access to excellent and comprehensive care.
  • To promote public awareness of the Primary Immunodeficiency diseases through programs involving our lawmakers as well as lay, scientific, and medical communities.
  • To affirm its commitment to turn pain, despair and suffering of immunodeficient children and adults into comfort and hope.

Further reading:

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:

10 Tips: how to search for genetic conditions

Some months ago, I wrote about Juan Magdaraog who is blogging about his struggle with Pompe disease, a rare, but important genetic condition. He let me know about an essential problem: the diagnostic delay.

The diagnosis often poses a dilemma due to the rarity of the disease, the variable rates of progression and the unspecific phenotypic features… Just take a look at the diagnostic delay diagram, there are from 2 to 4 years between the first symptoms and the diagnosis!

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.

I know that there are hundreds of great resources on the net, but here are my 10 tips, my 10 favourite sites:

1. Online Mendelian Inheritance in Man (17 706 entries)

This database is a catalog of human genes and genetic disorders authored and edited by Dr. Victor A. McKusick and his colleagues at Johns Hopkins and elsewhere, and developed for the World Wide Web by NCBI, the National Center for Biotechnology Information.

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2. Single Gene Disorders and Disability at Centers for Disease Control and Prevention

Single gene disorders (SGDs) are a group of conditions caused by a change (mutation) in one particular gene. There are over 6,000 SGDs and although these disorders are rare individually, when grouped together they account for about 1 in 300 births.

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3. Specific Genetic disorders at National Human Genome Research Institute

Sometimes, physicians are unable to put a name to a genetic condition. When this happens, physicians will say that a child or an adult has an undiagnosed rare or genetic condition. To learn more about how to deal with genetic or rare conditions that have no diagnosis, see this list.

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4. List of genetic disorders at Wikipedia

The following is a list of genetic disorders and their origins. Beside most disorders is a code that indicates the type of fertilization and the chromosome involved.

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5. GeneReviews (392 entries)

GeneReviews are expert-authored, peer-reviewed, current disease descriptions that apply genetic testing to the diagnosis, management, and genetic counseling of patients and families with specific inherited conditions.

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6. Ask the Geneticist

Selected questions and answers are posted within 3 weeks. The confidentiality of all visitors to this site is respected according to the HIPAA Privacy Rule and Georgia and Alabama State law.

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7. National Organization for Rare Disorders

Many libraries, schools, universities, and hospitals subscribe to NORD’s Rare Disease Database for unlimited access to reports on more than 1,150 diseases.

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8. Center for Inherited Disease Research

A centralized facility that provides genotyping and statistical genetics services for investigators seeking to identify genes that contribute to human disease. CIDR concentrates primarily on multifactorial hereditary disease although analysis of single gene disorders can also be accommodated.

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9. Open Directory Project: Genetic Disorders

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10. The best: OrphaNet

ORPHANET aims to improve management and treatment of genetic, auto-immune or infectious rare diseases, rare cancers, or not yet classified rare diseases.

The database contains 2000 diseases in 6 languages written by experts. More than 800 daily updates, 25 collaborate databases, 20,000 connections a day with a total budget of 1.3 million Euros. 20,000 daily users from 150 countries.

Alexa statistics of OrphaNet and Rarediseases.org:

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For many more lists of resources, please see the Disorder Guide or the rarediseases.info page.

Regarding my list, I hope you find at least some of the links useful. And I also hope that physicians could use these resources to know more about rare, genetic conditions and we can forget about the evil diagnostic delay in the near future.

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.

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