Dec 10, 2009

Structural variation in the human genome.

Nat Rev Genet. 2006 Feb;7(2):85-97.

Feuk L, Carson AR, Scherer SW.

The Centre for Applied Genomics and Program in Genetics and Genomic Biology, The Hospital for Sick Children, Department of Molecular and Medical Genetics, University of Toronto, Ontario, Canada.

The first wave of information from the analysis of the human genome revealed SNPs to be the main source of genetic and phenotypic human variation. However, the advent of genome-scanning technologies has now uncovered an unexpectedly large extent of what we term ’structural variation’ in the human genome. This comprises microscopic and, more commonly, submicroscopic variants, which include deletions, duplications and large-scale copy-number variants – collectively termed copy-number variants or copy-number polymorphisms – as well as insertions, inversions and translocations. Rapidly accumulating evidence indicates that structural variants can comprise millions of nucleotides of heterogeneity within every genome, and are likely to make an important contribution to human diversity and disease susceptibility

Dec 7, 2009

Overweight and Obesity

Obesity definition is very straightforward. Obesity is simply defined as being overweight. It signifies that excessive amounts of fat are collected in your body, which leads to the overmuch body weight. An individual’s weight must be in balance with his or her height, which entails within the body mass index (BMI). The ideal BMI goes between 18.5 to 24.9. So, in clinical terms Body mass index of 30 and above is defined as obesity.Obesity has bad effects on the general health and lifestyle of a person. People who are obese become very inactive as they realize it hard to take part in great number of everyday activities. They cannot move easily, they are all the time exhausted and they are put in risk of becoming sick with diverse kinds of illnesses ranging from cardiovascular, cancer, diabetes, and lots of others.

What are the causes of obesity. As already stated that most common reasons for obesity can be inactive lifestyle, high intake of calories and even scientific reasons (like psychiatric, medical and genetic causes). As mentioned above, a inert and unmoving lifestyle is the first on the list of causes of obesity. An individual finds it troublesome to exercise or go in for some sport, which step by step has negative influence on his weight making him obese.Genetics or heredity is another cause of obesity. It has been found out that the gene for Obesity has been circulated from generation to generation. Thus, the children whose parents are obese show a tendency to be obese.

People who are afflicted with genetic factors for obesity have many problems with losing weight in the long term. What is more, obesity may appear because of some psychological problems. It signifies that people show a tendency of overeating themselves when they are hopeless, upset, enraged, even weary with something that, consequently, leads to obesity. As well, several diseases and conditions like Cushing’s syndrome, Hypothyroidism, Depression, and certain neurological problems cause gluttony which successively causes storing of too much fat in the body.
But, the most general reason why people overeat is that they lack time to eat healthy food as they are overcharged with many responsibilities. Wild schedules have given to the use of fast and processed food, which, on one hand, don’t have enough vitamins and minerals and, on the other, has a high amount of calories.

So, how may a person eliminate obesity? Obese people think that they will be fat till the end of their life and that they will never slim down. Of course this is nonsense, and there is a solution. You may easily cure obesity on condition that provided that you are well organized, have a strong will, and on condition that you comply with the regulations that you must follow before you decide to begin with a diet. It is most important to recognize the problem and then go to your doctor who will will best advise what to do considering your obesity issue.

Fortunately, there are great numbers of weight loss plans today, which show outstanding results. Or you may even select some other methods that fit your needs, among which some may be very extreme like obesity surgical process or ingestion of anti-obesity drugs. Very recently, genetic analysis is proving to have some very good efefcts on weight loss plans. For more information www.genebright.com

Nov 30, 2009

Un esame del sangue per diagnosticare le malattie mentali

Di AipsiMed , Dom, 12/10/2008 - 08:47


Un esame del sangue potrebbe presto essere utilizzato per diagnosticare e valutare la gravità di alcune malattie mentali, tra cui il Disturbo Bipolare. Prove di laboratorio in grado di rilevare le malattie mentali sono state a lungo considerate il "Santo Graal" della psichiatria.L'obiettivo di un nuovo studio è stato quello di identificare i geni o i biomarcatori che potrebbero essere utilizzati per monitorare la gravità dei sintomi della mania o depressione in pazienti con diagnosi di Disturbo Bipolare.L’idea di realizzare test genetici per la malattia mentale hanno portato a molte controversie, e secondo Art Caplan, direttore del Centro di Bioetica presso l'Università della Pennsylvania, un test genetico sullo stato mentale porterebbe ad intensificare il dibattito.Il Dr Carlos Pato, presidente del Dipartimento di Psichiatria presso la University of Southern California School of Medicine di Los Angeles, pensa che un test per la malattia mentale non dovrebbe essere considerato diversamente da quelli utilizzati per altre condizioni mediche, come il diabete o il rischio di malattie cardiache."Dobbiamo guardare al di là dello stigma che accompagna la malattia mentale, perché la cosa più importante è avere una diagnosi molto chiara per ottenere il miglior trattamento per il paziente", ha detto Pato.Il nuovo studio, progettato per valutare la gravità della malattia da un team di ricercatori guidati da Alexander Niculescu dell’ Indiana University School of Medicine di Indianapolis, pubblicato dalla rivista Molecular Psychiatry avrebbe consentito di identificare 10 geni utili per la previsione dei disturbi dell’umore.Anche se questo metodo non è perfetto, sostiene lo stesso Niculescu, il tasso di accuratezza è equiparabile ad altri esami clinici, come ad esempio alcuni metodi di screening dei tumori.Molto lavoro resta ancora da fare per confermare questi risultati ma, sempre secondo Niculescu, i test potrebbero essere disponibili sul mercato in appena cinque anni.ReferenceIdentifying blood biomarkers for mood disorders using convergent functional genomics.Le-Niculescu H, Kurian SM, Yehyawi N, Dike C, Patel SD, Edenberg HJ, Tsuang MT, Salomon DR, Nurnberger JI Jr, Niculescu AB.Mol Psychiatry. 2008 Feb 26;Candidate genes, pathways and mechanisms for bipolar (manic-depressive) and related disorders: an expanded convergent functional genomics approach.Ogden CA, Rich ME, Schork NJ, Paulus MP, Geyer MA, Lohr JB, Kuczenski R, Niculescu AB.Laboratory of Neurophenomics, University of California, San Diego, CA, USAMol Psychiatry. 2004 Nov;9(11):1007-29.Evaluating the validity of blood-based membrane potential changes for the identification of bipolar disorder IThiruvengadam AP, Chandrasekaran K.University of Maryland School of Medicine, Baltimore, MD, USA.J Affect Disord. 2007 Jun;100(1-3):75-82. Epub 2006 Nov 17 (Fonte: Brainlab)

Nov 28, 2009

Genetica: test del Dna per scoprire l'infedeltà. Laboratorio invece del detective

Roma, 20 nov. (Adnkronos Salute) - Il tradimento coniugale si dimostra nel laboratorio d'analisi. Accade in Messico dove alcuni centri di diagnosi puntano alla conquista di un nuovo mercato, quello dell'infedeltà, proponendo test del Dna ad hoc per dimostrare scientificamente l'esistenza di un'amante. Il coniuge che ha un sospetto, infatti, si rivolge direttamente ai laboratori portando un indumento intimo, un lenzuolo, un bicchiere o persino un chewing-gum masticato per cercare tracce di saliva, sperma, peli o capelli dell'altro.

Con specifici test del Dna, consentiti nel Paese sudamericano anche senza l'autorizzazione dell'interessato, si può poi determinare se le tracce trovate appartengono al cliente o a qualcun altro. Queste analisi, pronte in circa una settimana, posso costare dai 200 ai 500 dollari (dai 135 euro ai 335 euro circa).

Questo nuovo business, appena avviato, in Messico ha avuto un successo immediato. "La richiesta di 'test d'infedeltà' - spiega Jorge Guillen, che dirige uno dei laboratori che propone queste analisi - è in continuo aumento. Mi è capitato di avere 50 richieste in una sola giornata. Ma è una cosa nuova per molti e ci sono molti fraintendimenti: molti clienti vengono da noi perché credono che l'infedeltà sia scritta nei geni".

Nov 26, 2009

Progressi negli strumenti di analisi genetica e medicina personalizzata

Un sofisticato algoritmo computazionale, applicato ad un vasto insieme di marcatori genetici, è riuscito a raggiungere una maggiore accuratezza, rispetto ai metodi convenzionali, nell’individuare il rischio di diabete tipo 1. Un team di ricercatori, guidati dal Dr.Hakonarson, direttore del Center for Applied Genomics presso il Children’s Hospital di Philadelphia, afferma che la loro tecnica applicata ad alcune malattie multigeniche, tra cui il diabete, consente di ottenere miglioramenti nella prospettiva di personalizzare la medicina sulla base del profilo genetico di ciascun individuo. Gli studi di associazione sull’intero genoma (GWAS), nei quali vengono impiegati strumenti automatici che esaminano l’intero genoma umano alla ricerca di varianti genetiche, potrebbero permettere ai medici di predire accuratamente il rischio di ogni individuo relativo ad una specifica malattia e, quindi, guidarli nelle strategie di prevenzione e trattamento.

13 Novembre 2009

Nov 24, 2009

IBM promette la genetica personalizzata

Per ora è solo una simulazione al supercomputer. Ma i nanotubi, altro campo di eccellenza di BigBlue, potrebbero garantire cure più efficaci: non appena passeranno dalla teoria alla pratica



Roma - Da quando, all'inizio del nuovo millennio, il tanto chiacchierato Human Genome Project ha portato all'identificazione dei circa 25mila geni di cui è composto il codice ereditario di ogni singolo essere umano, la scienza biomolecolare ancora manca di un approccio pratico adeguato alle mirabolanti promesse della "medicina personalizzata" su base genetica. Stando a quanto sostiene IBM, però, uno dei problemi fondamentali di questa particolare branca della ricerca starebbe per essere risolto grazie all'impiego di apposite nanostrutture in grado di veicolare (con opportuni meccanismi di "stop-and-go" bio-elettronico) i filamenti di DNA da analizzare.


La fase di sequenziamento del DNA, utile a identificare i singoli geni del paziente per valutare eventuali predisposizioni a patologie o a condizioni metaboliche particolari, è col tempo diventata una pratica abbastanza comune ma ancora ferma ai laboratori che hanno i fondi sufficienti a permettersi la strumentazione adeguata. Anche in questo caso, a ogni modo, la procedura di sequenziamento dei geni non va esattamente alla velocità della luce, e anche per i kit attualmente disponibili come prodotti commerciali occorre aspettare qualche settimana per conoscere i risultati.


"Sono stati fatti alcuni tentativi per sequenziare il DNA molto più velocemente di quanto fatto con il primo genoma umano", dice il ricercatore di computational biology Gustavo Stolovitzky in forze a IBM, e il meglio chi si è ottenuto finora è stato "usare complicati preparati di sample" in cui il DNA viene tagliuzzato, amplificato, analizzato attraverso la trascrittasi inversa e ottiche sofisticate il cui impiego richiede parecchio lavoro: per giungere a risultati comunque insufficienti in prospettiva di una medicina personalizzata.



L'approccio seguito dal dottor Stolovitzky e colleghi prevede invece l'utilizzo di strutture nanotubiche bucherellate, con fori delle dimensioni di tre miliardesimi di metro attraverso cui far passare il filamento di DNA da analizzare. Un'idea che gli scienziati carezzano da tempo, quella di usare la nanotecnologia per mimare il funzionamento delle proteine "sequenziatrici" presenti nelle cellule vive, che però risolta la questione del "passaggio" del DNA all'interno di un nano-cunicolo obbligato continua a presentare il problema della velocità eccessiva di tale passaggio.


L'applicazione di un voltaggio alle due estremità di un chip contenente i nanotubi di cui sopra farebbe insomma scorrere il DNA da un'estremità all'altra senza problemi, ma troppo velocemente per poter misurare i nucleotidi e sequenziare il corredo genetico del paziente. Nelle simulazioni al supercomputer Blue Gene di IBM tale problema è stato risolto con il design di un chip composto da uno stack di strati di silicio, ognuno dei quali capace di condurre un particolare tipo di voltaggio all'interno dei nanopori.


I singoli voltaggi sarebbero poi in grado di intrappolare i gruppi fosfato presenti nei quattro tipi di nucleotidi esistenti, bloccando il velocissimo scorrere del filamento di materiale genetico e facendo letteralmente avanzare la procedure di sequencing un nucleotide alla volta per non lasciarsene scappare nessuno. Stabilito che il sistema funziona a livello di principio, sostiene IBM, per trasformare in realtà di tutti i giorni la medicina personalizzata a base genetica e le diagnosi veloci delle infezioni ora non resterebbe che trovare il modo di "leggere" i voltaggi corrispondenti ai singoli nucleotidi e convertirli in informazioni digitali manipolabili al computer.


Alfonso Maruccia

Nov 20, 2009

Using Microsatellites and SNPs as Tools in Medical Genetic Diagnostics and Research

Out of the hat of medical research

Of many interesting stories for us to blog about this week -- so many that they'll be spilling over into next week -- here's one that seems to represent a more sensible approach to disease than the relentless focus on genetics that we so commonly see. It's about a new effort by pharmaceutical companies to invest in vaccine development. The AP story says

Malaria. Tuberculosis. Alzheimer's disease. AIDS. Pandemic flu. Genital herpes. Urinary tract infections. Grass allergies. Traveler's diarrhea. You name it, the pharmaceutical industry is working on a vaccine to prevent it.

Another story of what seems to be money well-spent appears on the BBC website. Researchers have developed a new-fangled lab-on-a-chip that will allow easier, faster and cheaper diagnosis of dozens of diseases.
The device relies on an array of antibody molecules that are designed to latch on to the protein-based molecular markers of disease in blood.
The antibodies are chemically connected to molecules that emit light of a specific colour when illuminated - but only when they have bound to the disease markers.

Some of the vaccines in the pipeline won't pan out, but some surely will, and we can imagine the lab-on-a-chip device being useful in many settings, including medically underserved areas, so we find these stories rather heartening. The money being invested is private, not taxpayer money, but not long ago a lot of pharmaceutical money was being bet on personalized genomics, and so on, which our regular readers will recognize as efforts we wouldn't have put our money on. So, it's good to see that following the money takes us in a different direction these days -- industry sees a lot more promise in preventing and treating infectious disease than in fixing genes. Indeed, a lot more disease seems to be infectious than the age of genetics led us to believe.

The Fall of deCode Genetics
It's interesting to juxtapose these two stories with this story from the Wednesday New York Times that reports on the demise of a company established to "exploit the promise of the human genome", that is, to profit from what it could learn about genetic disease from the genealogies of Iceland. Predicated on the idea that common genetic variants would be found to explain most complex disease, deCode Genetics set out to find those variants in Iceland and then develop drugs to target them. But, it turns out that complex disease is too complex for that. Again, regular readers won't be surprised if we find it hard to suppress a little "told you so".

Now, here we want to be careful about the concepts -- and it's related to central issues in The Mermaid's Tale. Life is lived, day to day, on the molecular level. Infection is essentially attack from without, and the immune system tries to recognize molecular signatures of the invading soldiers, to latch onto them and destroy them. Vaccines traditionally help the immune system do that, by exposing it to harmless mimics of the real thing (dead viruses, so to speak).

There are countless infectious diseases, affecting of most body systems, and more and more complex 'chronic' diseases that were thought to be 'environmental' or 'genetic' in the traditional senses, seem to be turning out to have infectious or inflammatory components. Thus, enhanced abilities to make vaccines could have farther-reaching implications than has been thought.

The immune system is 'genetic' of course, and its functions are fairly close to genes in many ways. But there may be other and perhaps even surprising ways this subject can bring us back to genetics. We'll deal with them in a post in the near future....

Nov 8, 2009

Complete Genomics and ISB Team Up for Huge Whole Genome Study

The era of genetic studies based on whole genome sequencing is definitely upon us. According to a recent press release, Complete Genomics will provide the Institute for Systems Biology with 100 (nearly) whole genome sequences to researchHuntington’s disease – a degenerative brain condition which affects nearly 1 in 10,000 people in the US.
This will be the largest genetic association study of its kind ever. While the genetic causes for Huntington’s are well understood, the study will focus on the unknown “disease modifiers” – genes that cause the variation in severity in patients. If successful, the ISB study will also boost Complete Genomics’ reputation for sequencing.There are many ways to associate genes with diseases.

Companies like 23andMe regularly use SNPs (single nucleotide polymorphisms) to identify individuals with high risks for certain conditions. The ISB study, however, will examine nearly all of the genome – looking at SNPs, and sequences of DNA that cannot be analyzed with today’s SNP technology. As whole genome sequencing becomes cheaper (CG is at $20k and dropping) more and more research institutes will be able to follow in ISB’s footsteps and find important discoveries in the less well known stretches of your DNA.

That’s going to lead to a better understanding of the associations between illness and genetics and ultimately provide you with improved healthcare.Of course, the study isn’t remarkable simply for using whole genome sequences, it’s the number of those genomes that’s impressive. 100 genomes (probably around $20k each) is a substantial research investment. ISB is taking advantage of the patient pool size by looking at volunteers with severe forms of Huntington’s, members that exhibit a family history of the disease, unaffected family members, and control groups.

This is the first large sequence study that CG will attempt with their newly expanded facilities. It also puts them squarely on the path to achieving their goal of sequencing 10,000 genomes by the end of 2010. By expanding the range of DNA analysis to outside the standard set of SNPs, CG and other whole genome sequence companies are allowing geneticists to really examine the exome (protein coding sections) and regulatory portions of DNA. As CG, Illumina, and others make whole genome sequencing more affordable, these associated scientific advantages will become even more desirable. That’s going to mean big business growth in the next few years. Hopefully it will also mean big successes in medicine as well.

November 5th, 2009 by Aaron Saenz


Nov 5, 2009

Health care and personalized genetics

How does a simple petri dish of DNA constitute the identity of a complex human being—from the way she laughs to her love of Cocoa Krispies? It turns out that the question of how biology determines identity interests not only the philosophically-inclined, but those in the drug and healthcare industry as well.
In a recent study published in Molecular Systems Biology, a computational biology team at Columbia explored the very questions that drive the current research on personalized care: How does a cell take a genotype and translate it into a phenotype? More specifically, how do genes determine our responses to medicine?

“The idea behind personalized care is that each of us is very different - we look different, we behave different, we have clearly different disease susceptibilities. All these things are genetically determined. Genetics also determines our responses to drugs,” Dr. Dana Pe’er, head of that computational biology research team, explained. Like many gadget lovers today, patients are clamoring for one-pill-fits-all cures. Tylenol, for instance, claims to relieve four different types of aches, fever, cold, cramps and arthritis. But with standardization comes the possibility of unpleasant side effects, such as, in the case of Tylenol, liver damage.
Medicines tailored to individuals would reduce the possibility of such side effects. But wouldn’t personalized care be much more expensive than the generic options we have now? “It would be cheaper!” Pe’er exclaims. “It would do away with the trial and error. A cancer patient has to pay $100,000 for chemotherapy. Won’t it be nice to tell them, ‘This won’t work for you because of your genes?’ Instead of getting it right on the third try, you can get it right on the first try.
”She also points out that avoiding all the adverse effects saves “tons of money and pain,” and that the “right meds put you back in the workforce in one day instead of three.”

A genotype scan currently costs a hefty $399, but patients only need it once in a lifetime. So what’s stopping personalized care from becoming an everyday reality? Part of the reason is that the science hasn’t yet come that far. According to Pe’er, the technology developed to investigate the connection between genotype and phenotype in terms of drug-responses is only a few years old, and the task it faces is gargantuan.
Pe’er analogizes: “Imagine there’s this huge cave, maze-like, with lots of passageways and everything’s pitch dark. Trying to do research on humans is like searching in this cave without even knowing what you’re looking for.”
To improve the search for the human genes that are related to drug resistance, Pe’er and her team focused on an easier subject: yeast, the common “workhorse” that scientists use to develop technology to apply to humans. By manipulating and testing 104 strains of yeast, they improved old search methods that traditionally relied on genetics by creating a new method that also harnesses gene expression (RNA), which indicates which genes are actively used. Their RNA-utilizing algorithm accurately predicted strain resistance for 87 of the 94 drugs tested, effectively narrowing down the number of genes related to drug resistance.

The main opponents of personalized care are not health insurers. For them, Pe’er believes, profits will rise with the reduction of the trial-and-error process which forces insurers to pay up with every treatment. Instead, pharmaceutical companies are the real antagonists: in order to maximize profit, they want standardized drugs to serve the whole population and not just a section of it. Recent pressure from the FDA—which has threatened to take drugs with adverse side effects off the shelves—has lead to heavy investment in a new field that combines pharmaceutical research and genetics: pharmocogenics. Pharmeceutical companies like Eli Lilly, who’ve been involved in legal disputes for marketing unapproved drugs, are now increasingly involved in studies on patient responses due to genetic variation.

But even if all pharmaceuticals participate to produce personalized medicine on a large scale, the truth is that we are not yet ready for personalized care. Patients and doctors are not adequately trained to interpret genotypes and translate them into appropriate treatments.
Specialized knowledge needs to be transferred from genetic-researchers to everyday medical practitioners. As Joel Burrill points out in an interview with Wired Science, unless medical schools adapt their training programs, there will be a shortage of DNA interpreters. Web sites like 23andme.com do a good job of explaining what the data means, but a large-scale implementation of personalized care would require more than Web sites.
Perhaps just as importantly, the legal infrastructure to protect the privacy of genetic information isn’t sufficiently established. It would be a veritable disaster if health insurers or workplaces got a hold of their clients’ or employees’ genetic predispositions to illnesses.Despite these obstacles, Pe’er believes that personalized care will be a reality within our lifetimes. Things are moving, even if slowly, in the right direction.

By Sarah Ngu

Oct 30, 2009

Learning of Risk of Alzheimer’s Seems to Do No Harm

A genetic test that can find an increased risk of Alzheimer’s diseasedoes no psychological harm to people who take it, even if they test positive for a risky gene, a new study finds.

The results challenge views long held by the medical establishment, which has discouraged people from being tested, arguing that the test is not definitive, that it may needlessly frighten people into thinking a terrible disease is hanging over them and that testing is pointless anyway because there is no way to cure or prevent the dementiacaused by Alzheimer’s.

Follow the lonk and read the full article.

Oct 28, 2009

As genetic medicine races ahead, docs are left behind

Genetic tests that can help predict and refine a patient's response to drug therapy may be the first big thing in personalized medicine. But the vast majority of physicians don't know how to use them, a new survey finds.

Oct 25, 2009

Smart Genetics Shuts Its Doors

Direct-to-consumer genetic testing company, Smart Genetics, has gone out of business.
The two-year-old company sold HIV Mirror and Alzheimer’s Mirror, DNA tests for HIV progression to AIDS and Alzheimer’s risk respectively.I first wrote about HIVmirror in June 2007. Aimed at HIV+ individuals, the test analyzes the CCR5 Delta32 and CCR2-64I genetic variants previously shown to slow the progression of HIV infection to AIDS.
Alzheimer’s Mirror examined the APOE gene.CEO and co-founder Julian Awad first received funding for the company while at the Wharton School of Business. He was later profiled by CBS News for Alzheimer’s Mirror and found that his own personal lifetime risk of Alzheimer’s disease is about 9 to 10 percent compared to 15% for the general population.
Ironically, he was also mentioned in a Wharton article from 2007 – Can Anyone Make Sense — or Money — Out of Personal DNA Testing?
Apparently not.

by Dr. Hsien-Hsien Lei

Oct 23, 2009

Jumping On Genetic Testing: The War of the SNPs

How many SNPs does it take to provide a definitive disease risk profile? Quite a few, apparently, as companies continue to pile them higher and deeper into genetic tests. Firms have bet that these tests will be widely adopted by physicians and the public to predict everything from risk of lung cancer among smokers, to prostate cancer, to Alzheimer’s disease, to baldness.

All told, about three dozen companies claim that they can provide genetic testing that predicts an individual’s risk of developing almost everything. “There is a bit of a wild wild west going on in terms of some of the DNA testing that’s out there,” said Francis S. Collins, M.D., Ph.D., the newly appointed NIH head, in an interview with CBS News in September 2008 with regard to a new offering from Smart Genetics purporting to predict susceptibility to Alzheimer’s disease (AD).

“Some of it is done by reputable companies, but there are some that are even unscrupulous who will offer you tests or DNA variations that, frankly, you’re not sure what they mean at all.” Smart Genetics stopped offering its controversial Alzheimer’s Mirror genetic test just eight months after introducing it, and the company subsequently shut its doors.

(Genetic Engineering & Biotechnology News)

Oct 13, 2009

CyGene Launches New Website for Direct-to-Consumer Genetic Test Marketing

CORAL SPRINGS, Fla., Aug. 26, 2009 (GLOBE NEWSWIRE) -- CyGene Laboratories Inc. (Pink Sheets:CYGE) today announced that it has launched a new website, www.cygenedirect.com, where consumers can get information and order predictive genetic tests geared to inform consumers about specific options to help improve health, while maintaining anonymity.  The consumer-friendly website features easy online ordering of the company's products. The site also includes comprehensive personal assessment information and details about potential benefits of the products, as well as detailed consumer information about genetics and genetic testing. The site also features links to the company's blog and its social media sites.  "People have a unique opportunity with CyGene to start learning about their personal genetics and how their genes may impact their lives. Generally, this will be their first brush with this exciting new field of science and our new website can help them find out how genetic testing works, which kits are best for them, and how they can be used to improve overall quality of life and athletic performance," said Martin Munzer, president and CEO of CyGene. "And our new site makes it easier than ever for people to get the information and products they're looking for with guaranteed anonymity."  The new creative direction of CyGeneDirect.com comes by way of Infinity Arts. "Our objective for CyGeneDirect.com was to re-invigorate the consumer website to be more compelling; easy to understand, navigate and relate to, while strategically improving visibility on the internet via search engines and online social mediums," said Michael Leahy, CEO for Infinity Arts.  About CyGene Laboratories Inc.  CyGene Laboratories Inc., based in Coral Springs, Fla., is a biotechnology company focused on introducing genetic predisposition and diagnostic testing into the general population. With five patents issued, CyGene's scientific expertise is in DNA analysis and diagnostic technologies. Incorporated in 1995, CyGene has been developing technology and introducing products that address the growing demand for genetic knowledge implementation and utilization. CyGene currently markets eight DNA predictive genetic test panels in accordance with its patent pending business model, sold direct to consumers and through physicians and other healthcare practitioners. CyGene's process offers customers access to the most updated science, guaranteeing their anonymity and keeping consumers on the cutting edge of genetic discoveries at the lowest possible price. The method also allows customers who have purchased a previous genetic test panel a low cost upgrade to their genetic report as new genetic discoveries become available.  For more information about CyGene Laboratories and its products, visit the Company's website at www.CyGeneDirect.com.

Oct 10, 2009

Genetic Testing in France

By Tamar G. McLachlan


Well we visited The Geneticist Today; a Professor Labrune, at the Hospital Beclere (somewhere on the outskirts of Paris). Actually, it is in the direction of Versailles and my husband commented on how exciting it is to be in a place where we could hop over to Versailles after a doctor's visit. The fact that I was a.) freezing b.) nauseous c.) trying not to pass out from the bus ride kept me from agreeing enthusiastically.


We secured this appointment in the complex yet sincere way that the French do everything. After many emails and several intense consults with friends and family, I was convinced (not to mention a bit panicked) that it was essential that I be tested for a variety of genetic diseases (including the Jewish ones). Apparently, even though neither my husband nor I have any history of genetic diseases of any sort in our families, this testing is common in the USA and so we were advised to pursue it.


In my normal pre-pregnancy state I tend a TAD towards the anxious side. In my pregnant state with hormones running rampant I am pretty close to hysteria much of the time. I searched the internet, examined pregnancy books and grilled friends and family doctors at home about the dangers of genetic illnesses. Visions of deformed babies and childhood deaths haunted me. Meanwhile, my Parisian GYN looked at me blankly when I mentioned that I must be tested for a variety of diseases, a.s.a.p. She had no idea what I was asking.


True to French form, after my doc greeted my anxieties with a look of curiosity and confusion, she set off on a search through the hospital to find the answers to my questions. After a forty-five minute tour of the hospital, consulting with a variety of physicians, she returned to her office (where I was not-so-patiently waiting) to tell me that this hospital does not in fact perform such screening (what?! This is common practice in the USA!)


In fact, since it is a specialized concern, she would refer me to a genetics specialist who would give me an individual consult.


Frustrated that I couldn't just have the blood test done and over with then and there (I abhor blood tests), I grudgingly took the information and waited for my appointment. This was one of my many lessons in the French health system, which is related to the French culture in general. The French, as a whole, feel entitled to good care. They feel it is their right and their privilege to seek professional advice and help when and where they want it. Because of socialized medicine, there is no hesitancy to refer to specialists. Likewise, there is no hurry to pack many patients into a short time frame, scheduling appointments 15 minutes apart as in the USA.


In two months, I have visited my GYN four times and only once has it been for an actual exam. The others were all consults or opportunities for me to address concerns and get information. Two of these consults included my husband. When I call my doctor, I actually reach her directly on the phone. If I have anything other than a brief question, she schedules an appointment to talk in person. Sometimes these appointments last up to an hour. My private insurance (since I don't qualify for social security) covers 90% of all my care.


Therefore the entire mentality is different. French people often seek several consultations from several doctors to get different opinions. They are not restricted by primary care referrals and 15 minute sessions. Patients hold onto their own medical records, lab reports and x-rays.


So my husband and I were sent to see Professor Labrune, the Genetics specialist. We had an appointment schedule for 9:30 am and I was so anxious about finding the office and arriving on time that I couldn't sleep the night before. Clay calmly planned out our subway route. The next morning we left before dawn (the sun doesn't rise until 8:30 a.m. --a real downer in the early morning) and shivered our way to the metro. One metro and one extremely nauseating bus ride later, we found ourselves in front of what looked like a warehouse. Armed with only the Professor's name (and no other information), we wandered around the chain link fence, looking for the appropriate entrance. We finally found a sign directing us to Prof Labrune Porte 33. Hesitantly, we entered the "porte', which was actually a delivery entrance. Following a bakery delivery truck in through the door, we found ourselves in a garage, wondering where the heck the doctor's office was. We wandered our way through a door (having asked a confused delivery man where to go), which led to a maze of white hallways. By this time, I was anxious, nauseous and desperately had to use the bathroom, which luckily I found easily. No matter that it was an employee only entrance; this was a desperate situation (besides, I figured "hey I'm a pregnant lady! Back off!"), I could hear my husband asking for directions in the hallway. It turns out that we had come in through the kitchen entrance and were now in the back of the hospital cafeteria. Clearly not where Prof Labrune must be waiting.


We stumbled our way through an ER section, past a row of empty gurneys and up a flight of stairs leading to the information desk. The very friendly woman behind the desk directed us around the corner to pediatrics, where we sat, among an assortment of toddlers and parents, waiting to be seen. My husband beamed at the darling children; I tried to keep from throwing up or passing out.


"Look" I turned to him, "I'm not big on blood tests or hospitals and my French is headed out the window so if you could be the proactive team member here, that would be great. I mean, how the hell do I ask about being a carrier for Taysachs disease in French?"


I was concerned that I would be confronted with a grumpy Professor, who was wondering why we were wasting his time. I was worried that I would have to convince him to authorize the screenings for us (because in the USA, everything is about getting "authorization") and, that I would have to discuss genetics, not my forte… in French, also not my forte.


I couldn't have been more off base. The Professor was a charming, gentle, quiet and patient man who first took our family history. Then he patiently explained the various diseases we were concerned about (in too much detail), their origins (not really necessary) and the percentage of risk. I couldn't believe that we were having this conversation in French! And I actually understood it! Not that I "understood" it. I understood the words. And the context. I was just reveling in my linguistic breakthrough when he pulled out a piece of paper and started to diagram the cell mutation related to one of the diseases. (At this point I had to admit defeat. Not due to language barriers but due to my own science learning disability. Once someone starts talking cells and DNA, I start to lose it). Not wanting to be rude (he was enamored with his description of some particular cell growth), I steered the conversation back to our family trees and what tests would be appropriate for us.


This led to the obligatory piece of any professional consult in France: the paperwork. In order to be tested we must solemnly sign the agreement to show that we fully understood the solemn oath of his professional boundaries (confidentiality, professional courtesy, professional boundaries and a myriad of other issues which seemed to pertain mainly to his limitations as a mortal and not as an agent of God). Then there would be the second set of papers authorizing release of this information to my doctor, which could only be sanctioned with my personal authority. Otherwise, our test results would remain in the secrecy of Professor Labrune. He took this very seriously. An oath of privacy.


After we satisfactorily signed and sanctioned the paperwork, we were led next door to the lab technician to have our blood drawn. Just the thought of this process made me queasy, but my husband, who is quite an experienced blood donor, asserted that this was one of the most professional outfits he had ever seen. Not only were the technician (and her assistant) extremely friendly and caring, they treated us like dear friends, expressing extreme concern over my obvious distaste for the process. Offers of juice, attempts to make jokes, were all lost on me as I did my best to disassociate from the process. They even recommended an anesthetic patch that can be purchased in the pharmacy, to numb the area to be pricked.


I stumbled out of the technician's office (desperate to get away from any sign of B-L-O-O-D) and we returned to the information desk to settle our bill. Having been quoted a fee of $1000 to have this exact procedure (consult and tests) done in Boston, we were shocked to be asked to pay a total of 32.10 euros. I must have heard wrong. She must have meant 300 euros and in my light -headed state I was getting the numbers wrong. Nope. 23 euros for the consult with the Professor and 4 euros for our tests, plus a couple of euros miscellaneous. "You do have insurance that will reimburse you?" she asked me with a concerned look.


I am overwhelmed by the quality of service, professionalism and State of the Art care we have experienced here. I'm sure some of it is luck. But boy have we been lucky.

Oct 9, 2009

Flu H1N1 2009 - Measures in school settings

GENEVA -- WHO is today issuing advice on measures that can be undertaken in schools to reduce the impact of the H1N1 influenza pandemic. Recommendations draw on recent experiences in several countries as well as studies of the health, economic, and social consequences of school closures. These studies were undertaken by members of a WHO informal network for mathematical modelling of the pandemic.

Experience to date has demonstrated the role of schools in amplifying transmission of the pandemic virus, both within schools and into the wider community. While outbreaks in schools are clearly an important dimension of the current pandemic, no single measure can stop or limit transmission in schools, which provide multiple opportunities for spread of the virus.

WHO recommends the use of a range of measures that can be adapted to the local epidemiological situation, available resources, and the social role played by many schools. National and local authorities are in the best position to make decisions about these measures and how they should be adapted and implemented.

WHO continues to recommend that students, teachers, and other staff who feel unwell should stay home. Plans should be in place, and space made available, to isolate students and staff who become ill while at school.

Schools should promote hand hygiene and respiratory etiquette and be stocked with appropriate supplies. Proper cleaning and ventilation and measures to reduce crowding are also advised.

School closures and class suspensions

Decisions about if and when schools should be closed during the pandemic are complex and highly context-specific. WHO cannot provide specific recommendations for or against school closure that are applicable to all settings. However, some general guidance comes from recent experience in several countries in both the northern and southern hemispheres, mathematical modelling, and experience during seasonal epidemics of influenza.

School closure can operate as a proactive measure, aimed at reducing transmission in the school and spread into the wider community. School closure can also be a reactive measure, when schools close or classes are suspended because high levels of absenteeism among students and staff make it impractical to continue classes.

The main health benefit of proactive school closure comes from slowing down the spread of an outbreak within a given area and thus flattening the peak of infections. This benefit becomes especially important when the number of people requiring medical care at the peak of the pandemic threatens to saturate or overwhelm health care capacity. By slowing the speed of spread, school closure can also buy some time as countries intensify preparedness measures or build up supplies of vaccines, antiviral drugs, and other interventions.

The timing of school closure is critically important. Modelling studies suggest that school closure has its greatest benefits when schools are closed very early in an outbreak, ideally before 1% of the population falls ill. Under ideal conditions, school closure can reduce the demand for health care by an estimated 30–50% at the peak of the pandemic. However, if schools close too late in the course of a community-wide outbreak, the resulting reduction in transmission is likely to be very limited.

Policies for school closure need to include measures that limit contact among students when not in school. If students congregate in a setting other than a school, they will continue to spread the virus, and the benefits of school closure will be greatly reduced, if not negated.

Economic and social costs

When making decisions, health officials and school authorities need to be aware of economic and social costs that can be disproportionately high when viewed against these potential benefits.

The main economic cost arises from absenteeism of working parents or guardians who have to stay home to take care of their children. Studies estimate that school closures can lead to the absence of 16% of the workforce, in addition to normal levels of absenteeism and absenteeism due to illness. Such estimates will, however, vary considerably across countries depending on several factors, including the structure of the workforce.

Paradoxically, while school closure can reduce the peak demand on health care systems, it can also disrupt the provision of essential health care, as many doctors and nurses are parents of school-age children.

Decisions also need to consider social welfare issues. Children’s health and well-being can be compromised if highly beneficial school-based social programmes, such as the provision of meals, are interrupted or if young children are left at home without supervision.

Oct 7, 2009

Genetic testing for breast or ovarian cancer risk may be greatly underutilized

Although a test for gene mutations known to significantly increase the risk of hereditary breast or ovarian cancer has been available for more than a decade, a new study finds that few women with family histories of these cancers are even discussing genetic testing with their physicians or other health care providers.

In a report in theJournal of General Internal Medicine, which has been released online, investigators from the Massachusetts General Hospital (MGH) Institute of Health Policy and Dana-Farber Cancer Institute note that their findings illustrate the challenges of bringing genetic information into real-world clinical practice. "Testing for BRCA1 and 2 mutations has been around a long time and should be a good indicator of whether genetic testing is making its way into regular medical practice," says Douglas Levy, PhD, of the MGH Institute for Health Policy, the study's lead author. "When a well-established genetic test is not being incorporated into clinical practice when appropriate, we are a long way from meeting the promise of personalized, genetically-tailored medical care.

"Most women's lifetime risk of breast cancer is about 13 percent, and the risk for ovarian cancer is less than 2 percent. But women with mutations in the BRCA1 or BRCA2 genes may be 3 to 7 times more likely to develop breast cancer and 9 to 30 times more likely to develop ovarian cancer than women with unaltered forms of the genes. Several organizations have issued clinical guidelines designating who should be screened for BRCA1/2 mutations, and while there have been discrepancies among the guidelines, all of them include a history of breast or ovarian cancer in close relatives among the criteria indicating elevated risk. The authors note that most U.S. health insurers cover at least part of the cost of BRCA1/2 testing for at-risk women.

Sep 22, 2009

Flu symptoms self-assessment: Do you have seasonal or swine flu (H1N1)?

Influenza is a viral infection that attacks your respiratory system, including your nose, throat, bronchial tubes and lungs.

If you're generally healthy and you catch influenza — commonly called the flu — you're likely to feel rotten for a few days, but you probably won't develop complications or need hospital care. If you have a weakened immune system or chronic illness, though, influenza can be fatal.

For those at high risk of influenza, the first line of defense is an annual flu shot. This year, in addition to a regular flu shot, you may need a different flu shot for protection against novel H1N1 swine flu, a new type of influenza identified earlier this year. The first doses of swine flu vaccine will be available later this fall, after seasonal flu immunization begins.

Initially, the flu may seem like a common cold with a runny nose, sneezing and sore throat. But colds usually develop slowly, whereas the flu tends to come on suddenly. And although a cold can be a nuisance, you usually feel much worse with the flu.

Common signs and symptoms of the flu include:

  • Fever over 101 F (38 C) in adults, and often as high as 103 to 105 F (39.5 C to 40.5 C) in children
  • Chills and sweats
  • Headache
  • Dry cough
  • Muscular aches and pains, especially in your back, arms and legs
  • Fatigue and weakness
  • Nasal congestion
  • Loss of appetite
  • Diarrhea and vomiting in children

When to see a doctor
If you have flu symptoms and are at risk of complications, see your doctor right away. Taking antiviral drugs within the first 48 hours after you first notice symptoms may reduce the length of your illness by a day or two and may help prevent more serious problems. Seek immediate medical care if you have signs and symptoms of pneumonia. These include a severe cough that brings up phlegm, a high fever and a sharp pain when you breathe deeply. If you have bacterial pneumonia, you'll need treatment with antibiotics.

Flu viruses travel through the air in droplets when someone with the infection coughs, sneezes or talks. You can inhale the droplets directly, or you can pick up the germs from an object, such as a telephone or computer keyboard, and then transfer them to your eyes, nose or mouth.

The flu is caused by three types (strains) of viruses — influenza A, B and C. Type A can be responsible for the deadly influenza pandemics (worldwide epidemics) that strike every 10 to 40 years. Type B can lead to smaller, more localized outbreaks. And either types A or B can cause the flu that circulates almost every winter. Type C has never been connected with a large epidemic.

Type C is a fairly stable virus, but types A and B are constantly changing, with new strains appearing regularly. Once you've had the flu, you develop antibodies to the strain that caused it, but those antibodies won't protect you from new strains. That's why doctors recommend getting a flu shot every year.

You're at increased risk of influenza or its complications if you:

  • Are an infant or young child
  • Are over age 50
  • Are a resident of a nursing home or other long term care facility
  • Have a chronic disorder, such as diabetes or heart, kidney or lung disease
  • Have a weakened immune system, such as from medications or HIV infection
  • Will be pregnant during flu season
  • Work in a health care facility where you're more likely to be exposed to the flu virus
  • Are in regular, close contact with infants or young children

Children on long-term aspirin therapy also may be at greater risk.

The flu vaccine is safe for children 6 months and older. If your child isn't at risk of the flu but lives with someone who is, you still may want to have your child vaccinated. That way, your child is less likely to infect others. The more people immunized, the less likely it is that the flu will spread through a community.

Sep 11, 2009

Get Your Entire Genome From Complete Genomics For $5000

It’s getting progressively cheaper to sequence your entire genome. Earlier in June, Illuminaannounced it would provide sequencing for close to $50k, half of their original price. Not to be outdone, Complete Genomics just released on Monday that it had gathered $45 million dollars in funding. The Silicon Valley based company is planning to use that money to further develop their streamline sequencing operations so that they can offer a complete genome for just $5000 by next year. CG’s goal is to finish 10,000 sequences by years end 2010. Even though that’s later than we had hoped, it’s still a whole lot of DNA and at the cheapest price for a whole genome seen so far. The question is, can they really pull it off?

We’ve been looking for a company, any company really, to break the $1000 price mark for a complete genome sequencing sometime in the next few years. That’s about the point where retail sales of the service will explode. With their exponentially decreasing price tag, Complete Genomics might be on that path. However, we know of at least one company that is trying to reach that goal by the end of this year. Stay tuned for that story in the next few weeks.

If you’ve never heard of Complete Genomics, read our first and second story to catch up. Basically they use a common form of short read sequencing and throw in a ton of computer power to sequence a human genome. Interest in personal genomics is escalating as genetic links to diseases are discovered. 23andMe already offers some testing for such diseases and is hoping to gather samples for further clinical trials. By providing the entire genome for perusal on the cheap, CG could make it economically feasible to expand that research into many more illnesses. Already, we’ve shown you how some facilities are erroneously promising to predict a child’s aptitudebased on genetic sampling. Perhaps with the cheap sequencing CG could provide, scientific research will match pace with the growing demand for such testing.

Daniel MacArthur of Genetic Future was able to pry CG head Cliff Reid to provide some details in how they hope to achieve their goals. First, Reid disclosed that the test won’t be offered directly to consumers, but rather through retail providers such as Knome and 23andMe. That means the price you or I will see could be considerably higher than $5k. Whatever the retail price, Reid promises 120 billion base pairs sequenced, 98% of the genome, with just one error in 10,000. That’s considerably better stats than what CG offered in February (92% of genome, about one error in 1,000).

Between now and year’s end 2009, Complete Genomics will focus on its dozens of customers currently in the line up. These include the Broad Institute out of MIT and Harvard which announced it was purchasing at least 5 genomes from CG in March. The Broad Institute reportedly paid $20k for each of their genomes which might be taken as the current baseline price for CG customers. If so, that’s a factor of four that the company has to make up between now and next year.

But scaling is no problem for genome sequencing. Remember that it took 15 years to sequence the first human genome, but the next 6 were done in 24 months. Now we’re talking about doing thousands a year. That’s just nuts and one of the amazing parts about sequencing that I love. Exponential growth is sexy science. And it’s supposed to be one of CG’s strengths. They just finished their first genome in the summer of 2008, and are now on schedule to finish 100 by the end of 2009. Current estimates of finishing 1000 by mid 2010, and 9000 more by the end of that year fit within the exponential growth curve. As MacArthur points out, most of these sequencing services will likely be purchased by researchers in genomic and cancer studies. So the demand is also there.

How can CG scale so quickly? By remaining inflexible but efficient. Their process doesn’t rely on making huge improvements in sequencing technology. Or finding a new sequencing technique. It comes down to streamlining the process. Stick to one task, human genome sequencing, miniaturize whenever possible, fewer reagents means lower costs, and build build build. You can bet a huge portion of that $45 million is going to expanding their facilities in Mountain View.

Who provides the cheap genomes is probably less important than the change it will create. While scientific research will undoubtedly benefit first, the public at large will likely become a dominant consumer. Genetic information is on the journey to becoming one of the most important sets of data someone can know about themselves, with insights into disease, aptitudes, and longevity. Give us the chance for cheap access to that info and you’ll never run out of customers. Just a little while longer, it’s bound to happen.