Highlight HEALTH

Welcome to the 32nd edition of Gene Genie, a blog carnival devoted to genes and genetic conditions. This edition includes some excellent articles on genes and gene-related diseases, genetics, genomics and personalized genetics.

logo credit: Ricardo @ My Biotech Life

Google Health launched publicly this week and to recognize the event, the last section of the carnival is devoted to articles specifically about the service. Google, financial backer of 23andMe, also funds the Personal Genome Project, which plans to unlock the secrets of common diseases by decoding the DNA of 100,000 people in the world’s biggest gene sequencing project [1]. With the vast number of genetic data points collected for each genome sequenced, a digital system for the movement and storage of personal health information is critical for the widespread use of individualized healthcare. Google’s entrance into the online personal health records market may thus help to accelerate the era of personalized medicine.

With these thoughts in mind, let’s get to this month’s edition of the Genie.

Genes and gene-related diseases

Dr Shock MD PhD

Rates of depression and other psychiatric disorders are higher in people who have two copies of a genetic variant of the serotonin transporter gene as a function of exposure to increasing levels of stressful life events. A recent study examined the biological reactivity to stress in people with two copies of the allele [3]. Dr. Shock asks How Can Genes and Stress Cause Depression?.

Genetics & Health

Researchers in Canada recently tested the hypothesis that DNA methylation plays a role in alterations in gene expression in the suicide brain [4]. Elaine Warburton describes Suicide - Genetic Changes in Brain as a Result of Childhood Abuse.

Think Gene

Schwann cells insulate nerves in the peripheral nervous system and can dedifferentiate with injury to accelerate healing. A recent study demonstrates that c-Jun is an important regulator of this plasticity [5]. Josh Hill reports that c-Jun is Turning Back the Clock for Schwann Cells.

Eye on DNA

Hsien-Hsien considers the possibility of 23andMe showing personalized ads for personalized medicine, and hopes that the Parkinson’s Institute and Clinical Center will have compliant study participants when 23andMe Collaborates on Study of Parkinson’s Disease Genetics.

Retail Genomics

Simon Lin also writes about the collaboration between 23andMe and the Parkinson’s Institute. 23andme is Shaking up Clinical Research, and Simon’s happy to see the combination of consumer genomics and clinical trials.

The Skeptical Alchemist

Mice laking the glucose transporter gene Glut2 fail to control their food intake, suggesting a role for glucose sensing in the brain. Steppen Wolf reviews a study in humans showing that individuals with a genetic variant of the same glucose transporter, GLUT2, have a higher daily intake of sugar [6]. Now there’s Finally an Excuse for My Sweet Tooth!.

The Spittoon

A recent genome-wide association study in Asians found an association between a SNP of the gene PSCA and an increased risk of diffuse-type gastric cancer [7]. Erin Cline reviews the study in SNPWatch: Researchers Find SNP Associated with Diffuse-type Gastric Cancer.

Genetics

Nimravid’s Weblog

The foundation of comparative genomics is that genes that are shared between closely related species have similar function and cause similar phenotypes when deleted from the genome. Nimravid reviews a systematic examination of this hypothesis [8]. Are You a Human or a Mouse?

Greg Laden’s Blog

A method for increasing the power of genetic studies in canines is to sample dogs of the same breed but from different geographic areas. A recent study assessed the genetic variation among dogs of the same breed collected from different geographic regions [9]. Greg Laden reviews the study and describes genetic variation, disease-connected alleles and dogs in his article Evolutionary Genetics of Canine Population Structure.

Adaptive Complexity

A review of genome-wide association studies highlights the knowledge gained and challenges that remain as researchers work to identify sequence variation and disease predisposition [10]. Adaptive Complexity covers The First Report Card for Genome Wide Association Studies.

PredictER Blog

Jere Odell writes about a genetic counselor’s response to a Nature article reporting the genomic DNA sequence of James D. Watson [11]. Dr Watson’s Genetic Counselor: Witty or Insulting?

Sciencebase

David Bradley discusses Genetic Manipulation and asks, “Do the GM pros outweigh the cons?”

Genomics

Genomicron

T Ryan Gregory explores the multiple meanings of the term genome, clarifying “what is a genome?” and “Whose Genome was sequenced?”

Gene Sherpas: Personalized Medicine and You

Timing is everything. Steve Murphy highlights two major impacts on the future of Genomic Medicine last week when he writes about Timing, GINA is Law and the Future of Genomic Medicine.

Giovanna Di Sauro

A recent study used transgenesis to evaluate the function of sequences obtained from an extinct species in transgenic mice [12]. Giovanna Di Sauro tells us about Jurassic Park in the real world with her article Tasmanian Park: Extinct Mammalian DNA Back to Life.

Next Generation Sequencing

The NGS blog reports that the Genome Reference Consortium Launched. The consortium’s goal is to correct the small number of regions in the reference that are misrepresented, to close as many gaps as possible and to produce alternative assemblies of structurally variant loci.

Personalized Genetics

Scienceroll

Berci Meskó discusses the recent improvements of individualized medicine in his article Personalized Genetics: Privacy and the Virtual Gene.

PredictER Blog

How would personalized genetic information change the perceptions of risk and behaviors of people making retirement plans? Jere Odell ponders Retirement and Risk: Betting on Your Genes?

Think Gene

Personalized genetic services test for SNPs, DNA sequence variations that occur when a single nucleotide — A, T, C or G — in the genome is changed, producing different alleles. Most services test between 500,000 and 1,000,000 SNPs, yet interpret less that 100 traits. Kevin Fischer demonstrates how to get more information about your genome. Tell me Everything: How To Use SNPedia for 23andMe and deCODEme.

The Genetic Genealogist

How reproducible are the results of genome scanning services? Blaine Bettinger evaluates the Accuracy of Large-Scale Genome Scanning Services. He follows the article up by assessing the Reproducibility of SNP Testing.

DNA Direct Talk

After speaking about competition in the lab testing space at the Executive War College on Laboratory and Pathology Management, Trisha Brown reports that It’s Not Just the Test, It’s the Service.

Genetic Future

Daniel reflects on a panel discussion on direct-to-consumer genetic testing of 23andMe, deCODEme and Navigenics at Cold Spring Harbor.

Genome Alberta Education

In an on-going blog series that serves as a ‘consumer guide to personal genotyping’, Mike Spear describes Genomics at Quinpool, recounting some comments and questions from the Youth Forum on Personal Genomics where students and a panel of experts looked at his personal genome test report and SNP file.

Google Health

business | bytes | genes | molecules

Deepak Singh gives the service a quick synopsis in his article Your Personal Health: Google Health is Live.

TechCrunch

Techcrunch gives Google Health A Quick Hands-On Look.

ReadWriteWeb

Richard MacManus reviews the limitations of Google Health in his article Google Health Launches - Cautious, Non-Innovative Entry into Health 2.0.

e-patients.net

As Google Releases Google Health, John Grohol expresses concern that an individual’s Google Health record may be an ideal way for other companies to market to them based on their specific health concerns.

Pimm - Partial immortalization

Attila Csordas gives us some background of Google Health’s product manager, asking that we Meet Dr. Google Health: Roni Zeiger, right from Stanford!

Scienceroll

Berci Meskó hopes he will never get pharma ads or spams from doctors based on his health profile when he announces Google Health: The First Steps.

Conclusion

That concludes the 32nd edition of Gene Genie. My thanks to everyone who submitted an article. You can find more information about the carnival as well as the hosting schedule and past editions at the Gene Genie Website. The next edition will be hosted at Neurophilosophy on June 8th.

References

1. Google Backs Harvard Scientist’s 100,000-Genome Quest (Update2). Bloomberg.com 2008 Feb 29.
2. Pearson H. Genetics: what is a gene? Nature. 2006 May 25;441(7092):398-401.
   View abstract
3. Gotlib et al. HPA axis reactivity: a mechanism underlying the associations among 5-HTTLPR, stress, and depression. Biol Psychiatry. 2008 May 1;63(9):847-51. Epub 2007 Nov 19.
   View abstract
4. McGowan et al. Promoter-wide hypermethylation of the ribosomal RNA gene promoter in the suicide brain. PLoS ONE. 2008 May 7;3(5):e2085.
   View abstract
5. Parkinson et al. c-Jun is a negative regulator of myelination. J Cell Biol. 2008 May 19;181(4):625-37.
   View abstract
6. Eny et al. Genetic variant in the glucose transporter type 2 is associated with higher intakes of sugars in two distinct populations. Physiol Genomics. 2008 May 13;33(3):355-60. Epub 2008 Mar 18.
   View abstract
7. The Study Group of Millennium Genome Project for Cancer. Genetic variation in PSCA is associated with susceptibility to diffuse-type gastric cancer. Nat Genet. 2008 May 18. [Epub ahead of print]
   View abstract
8. Liao and Zhang. Null mutations in human and mouse orthologs frequently result in different phenotypes. Proc Natl Acad Sci U S A. 2008 May 13;105(19):6987-92. Epub 2008 May 5.
   View abstract
9. Quignon et al. Canine population structure: assessment and impact of intra-breed stratification on SNP-based association studies. PLoS ONE. 2007 Dec 19;2(12):e1324.
   View abstract
10. McCarthy et al. Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Nat Rev Genet. 2008 May;9(5):356-69.
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11. Roche MI. A case of genetic counselling for Dr Watson. Nature. 2008 May 15;453(7193):281.
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12. Pask et al. Resurrection of DNA Function In Vivo from an Extinct Genome. PLoS ONE. 2008 May 21;3(5):e2240.
    View abstract

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As 2007 comes to a close, I would like to thank you for your readership. Just over one year ago, I launched two websites, Highlight HEALTH and the Highlight HEALTH Web Directory. Here at Highlight HEALTH, my goal was to write about biomedical research I found interesting and to make it easier for people to understand research findings, empowering them to have more productive discussions with their physicians and to make informed decisions about healthcare. The Highlight HEALTH Web Directory is my endeavor to catalog and make available health-related websites I find to be informative and useful. More recently, I’ve also started writing about Web 2.0 in Health, Fitness and Medicine, and plan to publish a series of review articles on a number of health-focused social networks.

This past month, I started the Highlight HEALTH Network, an aggregation of content from both sites to allow readers to keep up with the latest articles on Highlight HEALTH and the newest additions to the Highlight HEALTH Web Directory, all from a single source.

Here are the most popular articles for 2007 (top 20 based on the number of page views/number of days posted):

1. The Highlight HEALTH Network RSS Dashboard Widget
2. Smoking Cessation Timeline: What Happens When You Quit
3. Dichloroacetate Not Ready for Therapeutic Use
4. The Highlight HEALTH Network
5. New Common Cold Virus Variant Deadly
6. Common Therapy for Prostate Cancer May Promote Metastasis
7. Overweight Kids and TV: An Advertising Epidemic
8. Saline Nasal Irrigation More Effective than Spray for Chronic Sinus Symptoms
9. Pediatric Grand Rounds 2.8
10. The Genetics of Panic Disorder
11. Smoking Duration vs. Intensity and the Impact on Lung Cancer Risk
12. Social Networks and Health - The Research and the Reviews
13. Quercetin
14. American Obesity Rate Levels Off
15. Biodegradable Polymers for Drug and Gene Delivery
16. Individual Genetics, Coffee Consumption, BRCA1 and Breast Cancer
17. The Flu, Your Health and the Importance of Vaccination
18. SCHIP Funding and Fiscal Irresponsibility
19. DNA Amplification by Polymerase Chain Reaction (PCR)
20. Sinus Congestion

Thank you and Best of Health in the coming year!

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What does the diagnosis of hereditary diseases, the detection and diagnosis of infectious diseases, personalized DNA sequencing, DNA cloning, genetic functional analysis, genetic fingerprinting and DNA-based phylogeny have in common?

The all employ a widely used molecular technique called polymerase chain reaction or PCR.

The idea was conceived by Kary Mullis in the early 1980s and was first described, albeit briefly, in an article investigating the mutation that causes sickle cell anemia [1]. The details of the method and its uses were discussed in greater detail over the next two years [2-3]. PCR revolutionized molecular genetics by allowing rapid duplication and analysis of DNA.

The PCR method

PCR is used to amplify a specific region of DNA in order to produce a large number of nearly identical copies. The method uses a heatstable DNA replication enzyme called a DNA polymerase, the four deoxynucleotide building blocks of DNA and two small single-stranded DNA segments called primers, which flank the “target” region of DNA to be amplified and are complementary to each strand (meaning the matching strand to which its bases pair).

There are 3 basic steps in PCR that are carried out at different temperatures to create conditions optimal for:

1. DNA denaturation (meaning to separate the double-stranded DNA into single strands).
2. Primer binding or hybridization to each of the single strands of DNA at either the beginning or the end of the target sequence, depending upon the single-strand of DNA. Hybridization combines complementary, single-stranded DNA into a single molecule. This process is called annealing.
3. DNA polymerase elongation. The enzyme attaches to the primer-single-stranded DNA duplex and synthesizes the complementary strand of DNA, using the existing single-strand as a template.

Newly synthesized DNA strands can serve as additional template for complementary strand synthesis. PCR rapidly amplifies DNA; because both strands are copied, there is an exponential increase in the number of copies. Assuming there is only a single copy of the target gene before cycling starts:

After 35 cycles of PCR, there will be over 68 billion copies! In reality, PCR starts with many copies of the target gene, so the end result is typically higher. Each cycle only takes a few minutes. Factoring in the time to change temperatures, the entire process can be done in several hours.

More recently, a new method of PCR quantification called real-time PCR or quantitative real-time PCR (qRT-PCR) was developed [4]. qRT-PCR enables the detection and quantification of a specific DNA sequence using a fluorescent reporter (either a dye or a modified DNA oligonucleotide probe), which increases in direct proportion to the amount of DNA amplified in a reaction.

It’s easier to understand how PCR works with pictures. Visit DNA Interactive to view an animation of PCR. DNA Interactive is an award-winning educational web site created in 2003 to celebrate the 50th anniversary of the discovery of the DNA double helix structure.

The advent of PCR and recombinant DNA technologies have enabled numerous applications in basic and clinical research. PCR is often regarded as one of the most important scientific advances in molecular biology. Indeed, Kary Mullis holds the only Nobel Prize ever awarded to a scientist in the biotechnology industry. He received the Nobel Prize for Chemistry in 1993.

References

1. Saiki et al. Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science. 1985 Dec 20;230(4732):1350-4.
   View abstract
2. Mullis et al. Specific enzymatic amplification of DNA in vitro: the polymerase chain reaction. Cold Spring Harb Symp Quant Biol. 1986;51 Pt 1:263-73.
   View abstract
3. Mullis and Faloona. Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction. Methods Enzymol. 1987;155:335-50.
   View abstract
4. Higuchi et al. Kinetic PCR analysis: real-time monitoring of DNA amplification reactions. Biotechnology (N Y). 1993 Sep;11(9):1026-30.
   View abstract

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