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Posts from the ‘Genetic screening’ Category

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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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:

PediDraw: A web-based tool for drawing a pedigree in genetic counseling

I’ve recently come across a great article on a new and useful webtool (hardcore genetics 2.0). An excerpt of the BioMed Central article:

Drawing a pedigree is a prerequisite in genetic counseling. Currently, most pedigrees are drawn by hand or by drawing software.

We developed an online pedigree drawing tool, PediDraw, which enables users to generate pedigrees after inputting the family information step-by-step on web. It outputs a pedigree or table to present a family history to the counselors.

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Today, I took a look at it. I created this diagram in about one minute (click to enlarge):

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For a clinical geneticist, it’s an incredibly useful, free webtool. We need such improvements to make genetic counseling more appropriate.

I’m thankful to Min He, one of the authors for the kind help!

Awesome Genetic Announcements

467px-dna_repair.jpgI’ve always had a dream: I enter a centre of genomics where I get my DNA sequenced in one week for cc. 1000$ then my geneticists tell me what kind of diseases I will definitely acquire through my life and what kind of diseases I have elevated risk for. Then I can change lifestyle, diet, I can do more exercises or repair some genes (gene therapy) so I could be much more optimistic about my future.

After reading some recent announcements and publications, it seems that my dream is getting closer and closer to reality. A Nature article, Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls have studied seven common familial diseases by genome-wide association analysis in 16,179 individual:

  • Bipolar disorder
  • Coronary artery disease
  • Crohn’s disease
  • Hypertension
  • Rheumatoid arthritis
  • Type 1 diabetes
  • Type 2 diabetes

A simple but important observation is that GWA analysis provides a highly effective approach for exploring the genetic underpinnings of common familial diseases. Our yield of novel, highly significant association findings is comparable to, or exceeds, the number of those hitherto-generated by candidate gene or positional cloning efforts.

According to a Telegraph article:

Together the seven diseases affect more than 20 million people across the UK, with coronary heart disease alone claiming the lives of 105,000 people every year, making it the country’s biggest killer. The study has identified, for the first time, some of the genes that trigger these diseases…

New preventive strategies and new treatments depend on a detailed understanding of the genetic, behavioural and environmental factors that conspire to cause disease.

Though, the Economic and Social Research Council’s Genomics Policy and Research Forum urges wider debate on genes discovery announcement:

The Economic and Social Research Council’s (ESRC) Genomics Policy and Research Forum1, based at the University of Edinburgh, is calling for wider debate about the implications of the recent genes discovery announcement.2

The Forum agrees that the study demonstrates the great potential for large-scale genomic research to improve our understanding of health and disease, but feels it is important not to view the results in isolation.

What about the future? Forget that genomics centre. Just use your Personal DNA Analyzer and find those “bad” genes.

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Tell us your opinion! Are you afraid of improved genetic testing?

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.

Genetics has a new profession

I’ve recently found an interesting site, the geneticcounselor.net that tries to describe this great profession via news, links and articles.

Genetic counselors are health professionals who are trained to help families understand genetic disorders and to provide information and support to those families. They may also serve as patient advocates by referring individuals or families to local services that can be of assistance. To help understand the genetic counselors mission, let’s have a quick look at how genetic counselors relate to those not yet born

The best way to inform the public about genetics and prenatal testing is to talk to them directly.

A video on prenatal testing:

Direct-to-consumer (DTC) Commercial and Counseling Session:

Further reading:

Update: Don’t miss Steve Murphy’s reaction about National Society of Genetic Counselors.

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