DNA Diagnostics

							Using DNA Diagnostic Testing to Identify Family Diseases
DNA diagnostics is the field of medical testing and studies that allows you to determine a disease diagnosis or susceptibility to a condition for a patient or their family members. A DNA diagnostic test could provide valuable information to those with conditions such as cancer, diabetes and asthma, or at risk for these diseases.

Using years of research, your family medical history, and DNA diagnostic tests, your doctor may be able to determine if you are at risk to develop a certain disease, or need to take preventative measures. DNA diagnostic testing is a growing industry with promising possibilities. As science and medical research progresses, doctors and scientists are looking for answers to new questions.

The Future of DNA Diagnostic Testing
Your DNA may be able to determine if you will develop a disease later in life or have a recurrence of cancer. Although tests may be expensive, it is possible that in the future DNA diagnostic testing could significantly lower health care costs by allowing patients to take preventative measures or avoid costly unnecessary medical treatment, such as chemotherapy.

The American Cancer Institute estimates that national costs for treating cancer run upwards of $126 billion per year. DNA diagnostic testing could allow those with a high risk for developing a disease to understand risks they face. These tests could also provide insight to measures they can take to prevent onset of a disease, as well as tailor a course of treatment to a patient’s unique genetic makeup.

DNA Diagnostic Testing Centers
Because of increasing reliability, DNA diagnostic tests are being used not only at research specific institutes, but in medical and clinical labs as well. Your doctor may suggest that you participate in chromosome studies, direct DNA studies, or even biochemical genetic testing. Although some consider DNA diagnostic testing to be controversial due to ethical and privacy issues, the results and uses for the results are increasingly promising.

DNA Diagnostic Testing For Cancer
A simple DNA test may help determine whether or not you are susceptible to certain types of cancer. Certain combinations of known risk genes may indicate a much greater likelihood of developing cancer, or experiencing a recurrence of a certain type of cancer. For example, in 2008, researchers at the Swedish medical university Karolinska Institutet identified five relatively common gene variants that indicate susceptibility for developing prostate cancer. A test will likely be widely available in the next few years for young men to indicate higher-than-average risk for developing prostate cancer.

Direct Testing at DNA Diagnostic Center
If you have a family history of a disease or show symptoms of a certain genetic disorder, your doctor may suggest testing for family DNA traits. A DNA test may indicate a predisposition or susceptibility to having or passing on certain diseases, including:
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cystic fibrosis Huntington’s disease sickle cell anemia Tay-Sachs disease.

Challenges of DNA Diagnostic Testing
Like prescription drugs, DNA diagnostic tests may be evaluated by the FDA (U.S. Food and Drug Administration) because they are considered medical devices, which require approval by this agency. The results of a test may convince patients to not undergo chemotherapy treatment, or otherwise alter their course of medical care.

DNA diagnostic testing is also expensive, and may not be covered or reimbursable by health insurance policies. Profit margins for such tests are huge, and the market for DNA diagnostic testing is rapidly growing. Critics of DNA diagnostic testing complain that the tests are expensive and time consuming. Source- http://www.genetics-health.com/articles/dna-diagnostic-testing/index.php

Neurogenetics DNA Diagnostic Laboratory
The Neurogenetics DNA Diagnostic Lab tests for over 25 neurodegenerative disorders, and we expand our services every year, both in volume and diseases tested. In most cases, we are the only U.S. lab conducting testing for the rarer disorders. This exclusivity makes us a valuable resource to the medical community around the country and the world. Some of our test protocols have been developed directly from the Massachusetts General Hospital research laboratories actively working in these areas. We maintain a close working affiliation with these laboratories, which continually keeps our technology and interpretation up to date. The Neurogenetics DNA Diagnostic Lab is specifically for cases in which patients have been screened by a neurologist or other medical professional and have, or may have a rare neurogenetic disorder. Patients should not contact us directly. Certifications and affiliations for the Neurogenetics DNA Diagnostic Lab include:
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CLIA certification: Our lab meets all standards set by the U.S. government through the Clinical Laboratory Improvement Amendments (CLIA) program. CLIA Laboratory Certificate of Accreditation resources for researchers: Geneticists from this and affiliated labs at Mass General offer consultations for laboratory test protocol development and activation for other Partners and Mass

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General research labs. We also give referrals to other labs that are looking for atypical cases of the disorders they study.
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Harvard Medical School teaching affiliation: Our lab is a teaching site for the Harvard Molecular Genetics, Clinical Genetics and Molecular Genetic Pathology fellowship programs.

Diagnostic Testing Since our founding in 1994, we have completed more than 25,000 tests while acting as a local, regional, national and international service to referring physicians and reference labs. In order to screen negative cases that are important for further research study, we also support ongoing translational research in Norrie disease, NCL diseases, dystonia disorders and amyotrophic lateral sclerosis (ALS) disorders. Source - http://massgeneral.org/neurology/research/resourcelab.aspx?id=43#

Molecular Diagnostics Markets
The technologies that constitute molecular diagnostics--like first-generation amplification, DNA probes, fluorescent in situ hybridization (FISH), second-generation biochips and microfluidics, nextgeneration signal detection, biosensors, and molecular labels--are influencing the discovery of therapeutic molecules, the screening and diagnosis of patients, and the optimization of drug therapy. In the past few years, this rapidly evolving field has seen several fascinating developments. This Publications report describes the specific market segment of the in vitro diagnostics market known as molecular diagnostics and includes all of the generally accepted clinical analytical activities in use today. It examines the prevalent clinical-measurement devices, as well as their reagents and supplies as utilized in hospitals, clinics, large reference laboratories and doctor’s offices. Diagnostic tests marketed primarily as over-the-counter are generally not included in this report, although there is inevitably some overlap. The main objectives of this analysis are: 1) identifying viable technology drivers through a comprehensive look at platform technologies for molecular diagnostics, including probe-based nucleic acid assays, microarrays and sequencing; 2) obtaining a complete understanding of the chief molecular diagnostics tests--i.e., predictive, screening, prognostic, monitoring, pharmacogenomic and theranostic--from their basic principles to their applications; 3) discovering feasible market opportunities by identifying high-growth applications in different clinical diagnostic areas and by focusing on expanding markets, such as communicable diseases, cardiology and oncology; and 4) focusing on global industry development through an indepth analysis of the major world markets for molecular diagnostics, including growth forecasts. Source - http://www.prminds.com/pressrelease.php?id=29619

DNA Diagnostic Center
Advances in a DNA diagnostic center allow a new method of DNA fingerprinting. It comes from a single drop of a mother’s blood. This new method of testing can show a mother-to-be if her unborn child has an inherited condition such as cystic fibrosis. Best yet, the blood sample eliminates the need for risky amniocenteses in which the uterine wall is punctured for retrieval of umbilical fluid. Because a pregnant woman’s blood has her own DNA plus that of her unborn child, doctors can search for markers of a host of genetic disorders developing in her fetus. Cystic fibrosis comes from a recessive gene which can come from the mother and her father. So far, no test has worked perfectly however a new technique called digital polymerase chain reaction, or dPCR, is narrowing the likelihood of cystic fibrosis in the unborn by allowing doctors to count the number of copies of the recessive gene in the blood sample of the pregnant woman. Scientists are excited about this new test because it is the most accurate predictor yet of disease in an unborn child. More testing needs to be done before dPCR can be widely administered. The dPCR is expected to draw controversy among right-to-life supporters. Though the incidence of miscarriage is expected to go down with this new, safer way of testing without breaching the uterus, some fear more women will abort their defective fetuses. Pro-life advocates argue children born with Down ’s syndrome have a better prognosis today and should not be terminated from the womb once a pre-birth diagnosis is made. Ultimately the dPCR screening test will be yet another tool of information so that expectant parents can make choices involving their families in a knowledgeable way. It’s one advance in the rapidly changing world of a DNA diagnostic center and its services. Source - http://dnatestingcenters.net/dna-diagnostic-center-a-breakthrough.html

Fluorescence energy transfer detection as a homogeneous DNA diagnostic  method
A homogeneous DNA diagnostic assay based on template-directed primer extension detected by fluorescence resonance energy transfer, named template-directed dye-terminator incorporation (TDI) assay, has been developed for mutation detection and high throughput genome analysis. Here, we report the successful application of the TDI assay to detect mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene, the human leukocyte antigen H (HLA-H) gene, and the receptor tyrosin kinase (RET) protooncogene that are associated with cystic fibrosis, hemochromatosis, and multiple endocrine neoplasia, type 2, respectively. Starting with total human

DNA, the samples are amplified by the PCR followed by enzymatic degradation of excess primers and deoxyribonucleoside triphosphates before the primer extension reaction is performed. All these standardized steps are performed in the same tube, and the fluorescence changes are monitored in real time, making it a useful clinical DNA diagnostic method. Source - http://www.pnas.org/content/94/20/10756.abstract

A survey of DNA diagnostic laboratories regarding DNA banking
This article reports the findings of a survey of 148 academically based and commercial DNA diagnostic labs regarding DNA banking (defined as the storage of individual DNA samples in some form with identifiers for later retrieval). The population surveyed consisted of all laboratories listed with HELIX, a national directory of DNA diagnostic labs that includes a fairly comprehensive listing of clinical service labs as well as a large number of research labs. The survey was concerned primarily with the legal and ethical issues that the long-term storage of DNA may raise. The survey inquired into the respondents' policies and procedures concerning (1) the extent of DNA banking and of interest in developing DNA banking in academia and industry and (2) the degree to which DNA banks had developed written internal policies and/or a written depositor's agreement (a signed document defining the rights and obligations of the person from whom the sample was taken and the bank) designed to anticipate or prevent some of the ethical and legal problems that can arise from the long-term retention of DNA. Our research suggests that (1) the activity of DNA banking is growing, particularly in the academic setting, and (2) most academically based DNA banks lack written internal policies, written depositor's agreements, or other relevant documentation regarding important aspects of this activity. Source - http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1801090/

A DNA diagnostic biosensor: development, characterisation and performance
The aim of this work is to develop a sensor for specific DNA sequences, using non-complex synthetic single-stranded oligonucleotides as a model system. A capacitance-based sensor for the direct detection of DNA sequences is described. Hybridisation of analyte DNA with immobilised DNA on the silicon surface induces charge effects, altering the dielectric properties of the biolayer, and can be detected by the associated change in the measured capacitance. DNA has been immobilised on a silicon electrode either by passive adsorption or covalent coupling via 4aminobutyldimethylmethoxysilane (4-ABDMMS). The work presented here introduces a colourimetric immunodetection technique for the evaluation of the immobilisation process and describes the electrical characterisation and performance of three silicon-based sequence-specific

DNA sensors. These sensors consisted of a standard electrolyte-insulator-semiconductor (EIS) structure with covalently bound probe DNA, a mechanically degraded structure with passively adsorbed probe DNA and a mechanically degraded structure with covalently bound probe DNA. The last device had an improved signal to noise ratio and was, therefore, used to construct a standard curve, revealing a detection limit of 100 pmol DNA. On addition of analyte DNA, there was a decrease in measured capacitance. This response was fast, specific and required no addition of mediators to enhance or amplify the signal. This device can be optimised for the detection of complex sequences. Source - http://www.sciencedirect.com/

A Homogeneous-Ligase-Mediated DNA Diagnostic  Test
Single-nucleotide variations are the most widely distributed genetic markers in the human genome. A subset of these variations, the substitution mutations, are responsible for most genetic disorders. As single nucleotide polymorphism (SNP) markers are being developed for molecular diagnosis of genetic disorders and large-scale population studies for genetic analysis of complex traits, a simple, sensitive, and specific test for single nucleotide changes is highly desirable. In this report we describe the development of a homogeneous DNA detection method that requires no further manipulations after the initial reaction is set up. This assay, named dye-labeled oligonucleotide ligation (DOL), combines the PCR and the oligonucleotide ligation reaction in a two-stage thermal cycling sequence with fluorescence resonance energy transfer (FRET) detection monitored in real time. Because FRET occurs only when the donor and acceptor dyes are in close proximity, one can infer the genotype or mutational status of a DNA sample by monitoring the specific ligation of dye-labeled oligonucleotide probes. We have successfully applied the DOL assay to genotype 10 SNPs or mutations. By designing the PCR primers and ligation probes in a consistent manner, multiple assays can be done under the same thermal cycling conditions. The standardized design and execution of the DOL assay means that it can be automated for high-throughput genotyping in large-scale population studies. Source - http://genome.cshlp.org/content/8/5/549.abstract

ALTERNATIVE METHODS FOR DNA DIAGNOSTIC TESTING OF HORSES

Several service genotyping laboratories are now offering DNA diagnostic tests for genetic defects such as Hyperkalemic Periodic Paralysis (HYPP) and Lethal White Foal Syndrome (LWFS) as well as for coat colour/patterns such are Chestnut Colour Coat (CCC) and Tobiano (Tob). These tests are based on the detection of polymorphic variants of the genes causing these conditions, following their PCR amplification and restriction enzyme digestion. We report the successful development of an alternative testing procedure for these conditions. We have devised DNA tests based on a technology called Allele Specific Fluorescently Labeled PCR (ASFL PCR) in which the PCR products amplified from the submitted hair samples are separated and analysed on a 3700 DNA Analyser (Applied

Biosystems). Briefly, all DNA diagnostic tests represent four individual gene-specific multiplex reactions that detect a single nucleotide polymorphism distinguishing wild type and mutant alleles using a different fluorescent dye. Each test also includes internal PCR controls and DNA derived from horses that are known homozygotes for the mutant and wild type alleles, and are heterozygous carriers of these alleles. Our results demonstrate that the assays we have developed for HYPP, LWFS, CCC and Tob are highly sensitive and detect all polymorphisms without any spurious interpretation. The ASFL PCR-based approach is an accurate and robust replacement of the restriction enzyme digestion-based polymorphism detection systems. The ASFL PCR system reported here is not hampered by problems associated with partial digestion, gel separation and intensity of staining, and also lends itself to a high throughput capillary genotyping platform. Source - http://www.intl-pag.org/11/abstracts/P2c_P123_XI.html

DNA diagnostic method based on fluorescence resonance energy transfer
A new method for DNA diagnostics based on template-directed primer extension and detection by fluorescence resonance energy transfer is described. In this method, amplified genomic DNA fragments containing polymorphic sites are incubated with a 5'-fluoresceinlabeled primer (designed to hybridize to the DNA template adjacent to the polymorphic site) in the presence of allelic dye-labeled dideoxyribonucleoside triphosphates and a modified Taq DNA polymerase (Klentaq1-FY). The dye- labeled primer is extended one base by the dyeterminator specific for the allele present on the template. At the end of the genotyping reaction, the fluorescence intensities of the two dyes in the reaction mixture are analyzed directly without separation or purification. This homogeneous DNA diagnostic method, which we call the template-directed dye-terminator incorporation assay, is shown to be highly sensitive and specific and is suitable for automated genotyping of large numbers of samples.
Source - http://nar.oxfordjournals.org/cgi/content/abstract/25/2/347

Tools for DNA Diagnostics
Potential for U.S. Economic Benefit. Deoxyribonucleic acid (DNA) attained celebrity status among molecules in the 1950s when scientists first uncovered its now famous double helix structure. In the following decades, scientists began to show how the molecular basis of life flows from DNA. Since 1990, the National Institutes of Health and the Department of Energy have been funding a major effort—called the Human Genome Project (HGP)—to map out the thousands of individual genes strung along the 46 chromosomes in human cells and to sequence each gene. Each gene is made of four kinds of building blocks, called nucleotides, that link into linear sequences hundreds or thousands of nucleotides long. In the end, researchers hope to have mapped and sequenced the entire human genome, which is about 3 billion nucleotides long. Scientists and physicians expect that the HGP will prove to be a fountain of insights to now poorly understood biological phenomena and diseases and to new treatments for genetically based ailments. Industry—the biotechnology sector and users of biotechnology’s wares—expects that it will become both the impetus and basis of new multibillion dollar markets stemming from DNA-based diagnostic tests. According to industry projections for 1997, the DNA-based portion of the in-vitro (outside of the body) diagnostics industry is expected to reach into the vicinity of $500 million of a total estimated market of well over $18 billion, up from a $58 million portion of an estimated $5 billion market in 1992.

By 2005, DNA probes are expected to account for $6 billion, or 15 percent, of a $40 billion in-vitro diagnostics market. At the moment, the United States enjoys a lead position in this ever more global industry. That’s where the ATP’s focus on Tools for DNA Diagnostics comes in. According to representatives in the pharmaceutical, biotechnology, and analytical instrumentation industries, reaping the full potential of the HGP will require the development of new methods, instruments, and data-handling protocols. More specifically, DNA analyses and sequence interpretation will have to speed up by a factor of 10 and costs will have to fall to one-tenth to one-hundredth of the present price tag, which is in the range of $100 or more per test. Meeting these goals will help U.S. companies maintain their advantageous position in the coming years of the biotechnology revolution. The industries and technical arenas that stand to benefit from the program include healthcare, forensics, biological and biomedical research, environmental monitoring and bioremediation, toxicology, bioengineering, drug design, animal husbandry, agriculture, and quality control in the food industry. Technology Challenge. The initial goal of the ATP Tools for DNA Diagnostics focused program is to develop cost-effective methods for sequencing, interpreting, and storing DNA sequences for diagnostic applications ranging from healthcare to agriculture to environmental monitoring. Moreover, these methods need to be highly automated, miniaturized whenever possible, easy to use, and inexpensive as well as able to determine and analyze DNA sequences accurately and rapidly. A working system meeting these criteria might begin with the injection of a sample into a cassette, which then would be positioned automatically into an instrument that performs the sequencing and stores the results. These results then could be displayed immediately on a computer screen and transferred to a patient’s records. By the end of the multiyear program, industry should have the technical tools and know-how in hand with which they can design, engineer, and produce commercial products like this one. Industry Commitment. About 20 companies, which range in size from large established pharmaceutical firms to small start-up companies as well as non-profit research organizations, submitted the "white papers" from which DNA diagnostics emerged as an area that the biotechnology industry perceives to be badly in need of development. These papers made it clear that the program will require expertise in biological sample preparation, molecular biology, microfabrication, surface chemistry, instrumentation development and engineering, molecular detection technologies, information and data handling, and other areas. No single company can claim that it has all of those strengths, but a collection of companies, working toward common goals, can. Significance of ATP Funds. A glimpse of what this focused program in Tools for DNA Diagnostics might mean comes from a current ATP project. The project involves the Genosensor Consortium, a group of companies that combines expertise in instrumentation, microelectronics, chemical synthesis of DNA, and diagnostic test development. Without ATP funding, the risk would have been too high for the smaller consortium members to even consider pursuing the goals of the project. Larger members, whose stockholders may not be patient enough to wait for long-term payoff, also would likely have put the project on hold. The ATP focused program on Tools for DNA Diagnostics can leverage existing government investments in DNA research to achieve the aim of low-cost DNA diagnostic technologies on a much larger scale. It can help U.S. industry to maintain its global leadership in the biotechnology industry. The HGP goes part of the way by supporting the research that produces the maps and sequences. But it does not support technology development for diagnostics, which ultimately must be more user friendly and automated than state-of-the-art instruments for basic research in the laboratory setting. At the moment, companies that are well positioned to develop DNA diagnostic tools are often hesitant to push forward without additional government support because any of a number of competing analytical methodologies could turn out to be the most suitable for DNA diagnostics. Betting on one technology, which is all that most companies could hope to do, is too much of a gamble. The ATP Tools for DNA Diagnostics focused program both reduces and dilutes that risk. The payoff could be the technology base for a new multibillion dollar industrial base in the United States that will keep the country on top in biotechnology and widen its scope of industrial applications.

Source - http://www.atp.nist.gov/focus/tfdd.htm

DNA Diagnostic Assay for Chlamydia Using Nanoparticle
There is a continued interest in the development of new on-chip protocols for the determination of the causes of infectious disease. In this paper, we demonstrate the use of surface-enhanced resonance Raman scattering (SERRS) for detecting the clinically relevant nucleic acid sequences of Chlamydia trachomatis in a bead-based lab-on-a-chip format, incorporating a solid-phase sample clean-up on-chip. The assay uses streptavidinated polymer microspheres to capture a biotinylated PCR product of the oligonucleotide sequence, which was subsequently hybridized against a complementary rhodamine-labeled, Raman active probe. Central to the assay is an in-channel integrated microfilter, which was used to retain the microspheres, enabling the bound target to be separated from the rest of the sample as part of a solid-phase clean-up (thereby removing any contributions from the background). After washing, the bound Rhodamine labeled detection probe was released thermally from the microspheres by heating and was subsequently mixed on-chip with a stream of silver nanoparticles. The signal was detected downstream using a Raman spectrometer to collect the SERRS response. The assay offers several advantages over traditional laboratory methods, including: the speed of the assay on-chip, the potential for sample clean-up; and the low volume of sample required. Source - http://pubs.acs.org/doi/abs/10.1021/ac061769i

DNA diagnostic methods in detection of herpes simplex and varicella-zoster infection
To compare Tzanck smears, viral cultures, and DNA diagnostic methods using the polymerase chain reaction (PCR) in detection of herpes simplex virus (HSV) or varicella zoster virus (VZV) infection in clinically suspected cases the authors conducted a 12-month trial comparing PCR with viral cultures and Tzanck smears in patients with clinically suspected HSV or VZV infection. Both ambulatory and hospitalized patients were recruited from a tertiary referral center and the Miami (Fla) Veterans Affairs Medical Center. Convenience samples of patients were clinically suspected to have HSV (n = 48) or VZV (n = 35). To be included in the final analysis patients needed to have a positive Tzanck smear, viral culture, or PCR result. Patients who were clinically suspected to have HSV but had VZV by viral culture or PCR were analyzed in the VZV group. Similarly, patients who were clinically suspected to have VZV, but had HSV by viral culture or PCR were analysed in the HSV group. Seventy-seven patients were available for final analysis: HSV (n = 30), VZV (n = 32), and 15 control cases who did not have evidence of viral infection. For HSV, PCR detected HSV DNA sequences in 73% of stained smears and 83% of unstained smears. For VZV infection, VZV DNA sequences were detected in 88% of stained smears and 97% of unstained smears. Viral DNA sequences were not detected in the 15 control cases. Viral cultures were positive in 83% and 44% of HSV and VZV cases,

respectively. The Tzanck smear was positive in 60% and 75% of HSV and VZV cases, respectively. The authors conclude that PCR is a reliable method for detecting HSV and VZV DNA sequences from single stained and unstained Tzanck smears. It is clearly superior to viral culture in identifying VZV infection and is equivalent to conventional culture techniques in identifying cases of HSV. AS/D.J. Morris\To compare Tzanck smears, viral cultures, and DNA diagnostic methods using the polymerase chain reaction (PCR) in detection of herpes simplex virus (HSV) or varicella-zoster virus (VZV) infection in clinically suspected cases the authors conducted a 12-month trial comparing PCR with viral cultures and Tzanck smears in patients with clinically suspected HSV or VZV infection. Both ambulatory and hospitalized patients were recruited from a tertiary referral center and the Miami (Fla) Veterans Affairs Medical Center. Convenience samples of patients were clinically suspected to have HSV (n = 48) or VZV (n = 35). To be included in the final analysis patients needed to have a positive Tzanck smear, viral culture, or PCR result. Patients who were clinically suspected to have HSV but had VZV by viral culture or PCR were analyzed in the VZV group. Similarly, patients who were clinically suspected to have VZV, but had HSV by viral culture or PCR were analysed in the HSV group. Seventy-seven patients were available for final analysis: HSV (n = 30), VZV (n = 32), and 15 control cases who did not have evidence of viral infection. For HSV, PCR detected HSV DNA sequences in 73% of stained smears and 83% of unstained smears. For VZV infection, VZV DNA sequences were detected in 88% of stained smears and 97% of unstained smears. Viral DNA sequences were not detected in the 15 control cases. Viral cultures were positive in 83% and 44% of HSV and VZV cases, respectively. The Tzanck smear was positive in 60% and 75% of HSV and VZV cases, respectively. The authors conclude that PCR is a reliable method for detecting HSV and VZV DNA sequences from single stained and unstained Tzanck smears. It is clearly superior to viral culture in identifying VZV infection and is equivalent to conventional culture techniques in identifying cases of HSV. Source - http://www.cababstractsplus.org/abstracts/Abstract.aspx?AcNo=19932000619

Report on DNA-based diagnostic test and equipment market in the US from Research and Markets
DNA-based diagnostics are established in laboratory medicine with many of the top tests run for infectious disease. The U.S. market for DNA-based infectious disease tests is today a $1.1 billion industry. Nucleic acid testing (NAT) is used to screen blood supplies; DNA-based tests are rapidly emerging as an oncology standard as well; and newer tests are more slowly developing as a way to treat other non-infectious diseases such as chronic diseases and diseases of aging. However, they still operate largely outside of core medical practice today which is the doctor's office and hospital lab. Evidence that DNA-based testing can

appreciably improve the quality of healthcare is still murky, but policymakers and scientific researchers believe that DNA-based diagnostics (also called genomics-based molecular diagnostics) will change the way medicine is practiced in the coming decades. This Fuji-Keizai USA report examines the key players and issues in commercializing DNAbased diagnostics in the United States. It covers the market for testing products for infectious diseases, human cancers and pharmacogenomics, and the instrumentation needed to perform the tests. It analyzes U.S. market structure and size by major product segments. It covers distribution structure; development trends and technology advances; regulations and policies for genetic privacy, insurance coverage and DNA counseling; and a future market outlook through 2012 - including market drivers and obstacles. The report contains profiles of 15 companies including U.S.-based public and private companies: Abbott Molecular Diagnostics, Celera, Genomic Health, Myriad Genetics, GenProbe and Life Technologies (formerly Applied Biosystems). For key players such as Siemens Healthcare, BioMérieux and Qiagen, whose core business operates in non-U.S. regions, we cover their U.S.-oriented activities and product portfolios. Others covered: Novartis V&D, Becton Dickinson, Interleukin Genetics, Hologic/Third Wave Technologies, and Decode. Most of the market-leading companies cater to the traditional medical channel and regulatory path, although companies having great success with largely unregulated laboratory-developed tests also factor into this report. Newer companies selling personal genomic scans directly to consumers are growing in number but are not the primary focus here, although they are covered briefly in the section C ( 27 companies). Key Topics Covered: Section A: Market Condition
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Market Overview Market Trends, 2008-2010 Market Share by Product Segment of Surveyed Companies Distribution Structure New Product Development Trends Technology Character in DNA Diagnostic Product Development Future of Market Issues and Strategy for the DNA-Based Diagnostic and Test Business

Section B: Company Case Studies (15 Companies)
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Company In-Brief Revenue by Business Segment (DNA-based Diagnostics and Tests, Drugs, Medical Equipment, etc.) Product Revenue Forecasts, 2007-2009 Most Important Product for Sales and Marketing Spending - and Key Reason for Spending on Product Distribution Policy R&D Activity Technology Trends New Product Development Activity Profitability Business Policies

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Market Trends (Roadmap): Future DNA Diagnostic and Test Market Outlook

Section C: Additional Companies in DNA-based Diagnostics, by Market Segment Common Research Item
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Location/Contact Information URL Private or Public Revenue Current Product Developing Product & Application Technology, R&D and Commercialization Strategic Alliance and Partner

Source - http://www.news-medical.net/news/20090827/Report-on-DNA-based-diagnostic-test-andequipment-market-in-the-US-from-Research-and-Markets.aspx

Is there a DNA test for FSHD?
Yes. There is a DNA test for FSHD. It is highly reliable for most cases . The test detects the 4q35 DNA deletion described in the Genetics section of this website. Although several factors may occasionally complicate the test, confirmation of the 4q35 deletion is 98% reliable as a presumptive diagnosis of FSHD. The test requires no more than a small amount of blood that one’s physician sends to a testing laboratory. The laboratory extracts sufficient DNA for the test from the cells present in the blood. The FSH Society can provide information regarding the test and laboratories that currently offer it. It does not, however, endorse any test or laboratory. An individual should consult his or her physician and the laboratories about the DNA diagnostic test. Currently, there is no DNA test available for those relatively few cases where there is no linkage between FSHD and chromosome 4. What causes FSHD? The cause of FSHD is not yet precisely known. Scientists do have some pieces of the puzzle and more knowledge is being gained each year. The most important discovery to date is that FSHD is usually associated with a small DNA deletion on chromosome 4. How is the FSHD DNA test performed? DNA is analyzed using a method called Southern blotting. DNA, which is a very long molecule, is cut into small, measurable fragments. The size of the DNA fragments in the region of chromosome 4 that is important for the diagnosis of FSHD is measured. Individuals who have FSHD almost always have a DNA fragment that is unusually small, due to the deletion on chromosome 4.

Is there an association between the size of the deletion on chromosome 4 and the severity of FSHD in an individual? There does appear to be a relationship between the size of the deletion and the severity and age of onset of FSHD. Large deletions (resulting in very small fragments) appear to be associated with earlier onset and more severe symptoms. Also, large deletions are more likely to be sporadic rather than inherited. Small deletions tend to be associated with later onset and milder symptoms. Is FSHD always associated with a deletion on chromosome 4? No. In about 2% of individuals who have symptoms of FSHD, no deletion is detected on chromosome 4. It is probable that these individuals have a different, unknown gene mutation on the same or another chromosome, which results in similar symptoms. How accurate is DNA testing for FSHD? About 98% of individuals with FSHD can be accurately diagnosed by the DNA test due to the detection of a deletion. In comparison, individuals in the general population without FSHD are extremely unlikely to show a deletion in the same region of chromosome 4. However, within some FSHD families, some individuals may be found who appear to have a deletion, but do not show obvious symptoms of FSHD. This situation is more likely to occur when the deletion is small. How is DNA obtained from an individual who has FSHD? DNA is isolated from white blood cells. A single tube of blood (about a tablespoon) provides enough DNA to perform the test. I have symptoms of FSHD. How can I arrange for a DNA test to confirm FSHD? You can ask your doctor to refer you to your local genetics clinic. There, a detailed family history will be taken. The geneticist will be able to identify those individuals in your family who could most benefit from DNA testing. The geneticist will also be able to arrange for the blood sampling and shipment of the blood to a testing center. The DNA test results are reported to the referring physician (usually a geneticist). Since DNA test results can be difficult to interpret and understand, it is essential to have a skilled professional, such as a geneticist, explain the results of DNA testing. What is meant by sporadic FSHD and inherited FSHD? Sporadic FSHD means a single individual in a family has FSHD, but no one else in the family has symptoms. It also means that the FSHD deletion was identified in the affected individual but not in his/her parents. Once someone is diagnosed with sporadic FSHD, the risk of transmitting FSHD is the same as in the inherited form of FSHD. Inherited FSHD means that the disease is present in multiple members of the family, over two or more generations. I have FSHD. What is the risk that I could have a child with FSHD?

Individuals with FSHD have a 50% chance of having a child with FSHD in each pregnancy. We have been told that our child has sporadic FSHD. Is there any risk FSHD could occur in our next child? Up to 20% of apparently sporadic cases of FSHD arise due to mosaicism for the FSHD deletion in one parent. This means that one parent has a mixture of cells: some with the deletion and some without the deletion. This mixture of cells may or may not be detectable by the DNA test, depending upon the extent of mosaicism in the individual. Therefore, there is a risk of having another child with FSHD, even if there is no detectable deletion in either parent. Is there a prenatal test for FSHD? Yes. Using the same technology of the DNA test described above, prenatal testing is possible. An individual who is interested in a prenatal test for FSHD should consult his or her physician and the genetic testing laboratories. In prenatal diagnosis, fetal cells are obtained primarily by one of two procedures. The earliest procedure is called chorionic villus sampling (CVS). This procedure is performed at about the 10th to 12th week of the pregnancy. The alternative procedure is called amniocentesis. This procedure is performed at about the 15th to 16th week of the pregnancy. Individuals at risk of having a child with FSHD should see a geneticist for counseling as early as possible in the pregnancy, or even before becoming pregnant since it is necessary for their DNA to be tested in order to obtain accurate results. Prenatal diagnosis must be arranged many weeks in advance, through a genetics clinic. Prenatal tests have risks associated with them, and therefore it is important to obtain genetic counseling, and consider all the information about prenatal testing carefully before deciding to proceed. In general, molecular diagnostic laboratories make a special effort to process prenatal DNA samples as rapidly as possible. Is pre-implantation genetic diagnosis (PGD) available for FSHD? Yes. An important aspect to know about PGD is that the statistic mapping techniques are used to infer if the actual deletion that causes FSHD itself is inherited. A study is done on the inheritance pattern of map markers on each allele to ascertain whether the disease-carrying allele has been inherited. There are documented cases where the disease allele is inherited but the deletion of D4Z4 is not inherited due to rearrangement (e.g. the D4Z4 region comes from the other chromosome). With FSHD a prenatal diagnosis usually follows the PGD to be sure the deletion was not passed on.

Source - http://www.fshsociety.org/pages/patDiagTest.html

Human DNA-Topoisomerases - Diagnostic and Therapeutic Implications for Cancer

Topoisomerases constitute a family of highly conserved essential enzymes, which exist in all investigated living pro- and eukaryotic cells. They are indispensable for the control of DNA topology. Humans possess 4 types of topoisomerases, i. e. topoisomerase (topo) I, II, III and V. Topo I, a 100-kDa protein, is a member of the type-I enzyme group (type IB). Functionally, it is an ATP-independent DNA single-strand endonuclease and ligase that functions mainly during transcription but also during DNA replication. Topo II belongs to the type-II enzymes and is represented in humans by 2 highly homologous isoforms, (170 kDa) and (180 kDa). Contrary to topo I, the 2 topo II isoforms are ATP-dependent double-strand endonucleases and ligases. Topo I and the -form of topo II are expressed in a proliferationindependent manner, whereas topo II is cell-cycle-regulated. Because of the crucial role of topoisomerases for the maintenance and replication of DNA during proliferation, cells become highly vulnerable when these functions are lost. Consequently, a wide range of drugs with cytostatic effects are topo inhibitors. Topo I inhibitors in clinical use belong to the camptothecin family, e. g. topotecan and irinotecan. Topo II inhibitors are constituents of most chemotherapeutic protocols and form a large heterogeneous group. It includes clinically used compounds such as the podophyllotoxin analogues etoposide and teniposide, the anthracyclines daunorubicin, doxorubicin and idarubicin, the anthracenedione mitoxantrone and amsacrine. Recently, substances with dual specificity that inhibit both topo I and topo II have been found. The clinical relevance of these new compounds remains to be established. Specific inhibitors of topo II have not been described yet. The majority of topo inhibitors interfere with the religation step in the normal action of the enzymes, which leads to a stabilisation of the so-called cleavable complex. This results in DNA single-strand breaks in the case of topo I or double-strand breaks in the case of topo II. DNA single-strand breaks due to topo I inhibition are converted into double-strand breaks in the course of DNA replication. Such topo-mediated DNA strand breaks likely induce repair or apoptosis mechanisms via p53 and/or p21 WAF1/Clip1. As a consequence, while topoisomerases are required for proliferation, proliferation is also essential for efficacious topo inhibition. The cell-cycle-dependent expression of topo IIwas also successfully used for prognostic evaluations of survival in patients with cancer. Source - http://content.karger.com/ProdukteDB/produkte.asp?Doi=27205

Utility Of Circulating DNA As Novel Diagnostics For Human Cancer, Mad Cow Disease And Other Conditions

Chronix Biomedical - developing and applying proprietary techniques to detect and analyze circulating nucleic acid sequences for the diagnosis and management of disease - reported that three recent studies published in peer-reviewed journals have further confirmed the potential diagnostic and prognostic utility of fragments of DNA and RNA that circulate in the blood, known as circulating nucleic acids (CNAs). Data from these studies confirm previous findings showing that CNAs can identify the presence of certain diseases in blood samples months to years before clinical symptoms appear.

"The recent publication of these three studies represents a major milestone in the recognition of CNAs as novel diagnostic tools," said Howard Urnovitz, Ph.D., CEO of Chronix. "Our ability to accurately identify and characterize the presence of significant differences in CNA levels and sequences between healthy and diseased individuals demonstrates how CNAs would be used for diagnosis and disease management in conditions as diverse as bovine spongiform encephalopathy (mad cow disease) and human cancers." In the study appearing in the current online edition of Clinical Chemistry, scientists from Chronix applied ultra-high speed sequencing technology and proprietary data analysis tools to characterize and categorize the CNA markers present in multiple individuals. The resulting databases of CNAs associated with specific disease states can be used to identify persons with undiagnosed disease, and potentially, to track changes in disease status. For example, the study found that one of the presumed healthy volunteers was actually infected with hepatitis B. This study follows publication in January of research from scientists at the University of Calgary, Canada, the University of Göttingen, Germany and Chronix showing the ability of a simple blood test based on circulating DNA sequences to identify the presence of bovine spongiform encephalopathy (BSE) and the related condition chronic wasting disease (CWD) in live animals long before symptoms were evident. This advance is especially significant since BSE can now only be confirmed by examining the brain tissue of dead animals. Following expected confirmation in larger studies, this new approach could revolutionize testing for BSE, making it economically and logistically feasible to screen all cattle in the food chain before BSE symptoms appear. The study was published in the journal Nucleic Acids Research. A third reported study highlights the potential utility of CNAs in the management of cancer. Dr. Urnovitz, and Brian G.M. Durie, M.D., Medical Director and co-founder of the International Myeloma Foundation, identified specific DNA sequences circulating in the blood of a patient with the bone marrow cancer multiple myeloma and tracked variations in these sequences as the patient's myeloma moved in and out of remission. There was also an unexpected finding when CNAs identified the development of a secondary cancer in this patient, before it was clinically apparent. This preliminary study is significant because it shows that CNAs can potentially be used to diagnose, monitor and manage cancer treatment. The abstract reporting this data was published in the journal Blood in connection with the December 2008 meeting of the American Society of Hematology. "This approach opens the door to a new tool that will enable us to follow the progress of cancer treatment and give us an early warning when a myeloma patient is about to come out of remission," said Dr. Durie. "This will allow us to stay ahead of the disease instead of waiting for the patient to get sick before we can act. That capability will represent a major change in the way we treat this cancer." Dr. Urnovitz concluded, "Even in these experiments we found unexpected results undiagnosed hepatitis in one patient and a secondary cancer in another - confirming the utility of CNAs in finding unsuspected disease. With these multiple proof-of-concept experiments now completed, we are embarking on the studies needed to further confirm and commercialize this powerful new approach with important applications in personalized medicine and human health."

Chronix intends to work with a number of industry partners to develop and commercialize its CNA technology for diagnostic and prognostic applications. These emerging markets for novel genetic-based assays have multi-billion dollar potential. Because the Chronix technology can identify early changes in disease status, it also can be used to generate surrogate measures for drug development studies aimed at distinguishing responder and nonresponder patient subgroups. The company has recently initiated discussions with potential pharmaceutical partners. About Chronix Biomedical Chronix Biomedical is pioneering a breakthrough approach to the diagnosis and management of chronic diseases and cancer. It has developed proprietary technology that measures and categorizes circulating nucleic acids, DNA sequences circulating in the blood that are associated with specific changes in disease and health status. Using advanced genome analysis methods, proprietary data tools and disease-specific databases, Chronix has demonstrated the utility of its diagnostic and prognostic approach in mad cow disease and multiple myeloma, and studies in other diseases are underway. The company plans to collaborate with a variety of partners to develop and market its DNA-based assays that have the potential to transform the management of a broad range of cancers and other conditions. Chronix is headquartered in San Jose, California and has research facilities in Germany. Source - http://www.medicalnewstoday.com/articles/141926.php

Quantification of Free Circulating DNA As a Diagnostic Marker in Lung Cancer
From the Departments of Experimental Oncology and Thoracic Surgery, Istituto Nazionale Tumori; Divisions of Thoracic Surgery, Anatomical Pathology, Radiology, and Epidemiology, European Institute of Oncology, Milan; and Applera Italia, Monza, Italy.

Purpose: Analysis of circulating DNA in plasma can provide a useful marker for earlier lung cancer detection. This study was designed to assess the sensitivity and specificity of a quantitative molecular assay of circulating DNA to identify patients with lung cancer and monitor their disease. Materials and Methods: The amount of plasma DNA was determined through the use of realtime quantitative polymerase chain reaction (PCR) amplification of the human telomerase reverse transcriptase gene (hTERT) in 100 non–small-cell lung cancer patients and 100 age-, sex-, and smoking-matched controls. Screening performance of the assay was calculated through the receiver operating characteristic (ROC) curve. Odds ratios were calculated using conditional logistic regression analysis. Results: Median concentration of circulating plasma DNA in patients was almost eight times the value detected incontrols (24.3 v 3.1 ng/mL). The area under the ROC curve was 0.94 (95% CI, 0.907 to 0.973). Plasma DNA was a strong risk factor for lung cancer; concentrations in the upper tertile were associated with an 85-fold higher risk than were those in the lowest tertile.

Conclusion: This study shows that higher levels of free circulating DNA can be detected in patients with lung cancer compared with disease-free heavy smokers by a PCR assay, and suggests a new, noninvasive approach for early detection of lung cancer. Levels of plasma DNA could also identify higher-risk individuals for lung cancer screening and chemoprevention trials. Source - http://jco.ascopubs.org/cgi/content/abstract/21/21/3902

Impact of patenting on DNA diagnostic practice
Patents on genes often cover the gene sequence and the link between a disease and mutations in a gene, rather than a technology for the identification of mutations per se. Normally, patents are important for encouraging the development of new diagnostic tools and kits, but there is evidence that they can have severely deleterious effects on the delivery of genetic services. The difference largely depends on the licensing policy of the patent holder. This article describes different ways in which patents are used in this context and how the effects may be mitigated.

The molecular basis for many genetic conditions is being defined by increasingly sophisticated research, and the identification of the germline mutation responsible for an inherited condition is a valuable and accurate diagnostic tool. Such tests are now routinely available for a wide range of conditions, and contribute to the management of families at risk of genetic disorders. Genetic tests may be used to: * confirm a diagnosis of a genetic condition (eg Duchenne muscular dystrophy in a patient with a clinical diagnosis of the disease) * identify individuals at increased risk of certain conditions (eg familial cancer susceptibility) * identify individuals predicted to develop a lateonset disorder (eg Huntington's disease) * diagnose a genetic condition in utero (prenatal test). The identification of the genes in which mutations cause genetic disease is rarely the work of a single laboratory, and the molecular techniques used are rarely unique. In this article, how patenting issues may impact upon the availability of such tests within the NHS will be discussed, using three different examples of tests for very different genetic conditions, all with important healthcare implications. Three models for the impact of gene patenting in the delivery of genetic services The open model: no one knows, but (nearly) everybody pays Cystic fibrosis (CF) is a severe autosomal recessive disorder that affects the epithelia of the respiratory tract, exocrine pancreas, intestine, male genital tract, hepatobiliary system and

exocrine sweat glands, resulting in complex multisystem disease. Pulmonary disease is the major cause of morbidity and mortality in CF.1 It is caused by biallelic mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. The identification of this gene in 1989 was a prime example of 'reverse genetics' or positional cloning.2 A large international collaboration had led to the localisation of the faulty gene to chromosome 7, but it took several years for laboratories to explore the region of this chromosome to identify and clone the CFTR gene. Once the gene was identified (with the benefit of this prior knowledge) and its sequence was known, it became possible to test patients for mutations in this gene. More than 1,000 different alterations in this gene have now been described. This information has been collated onto a public database initiated by the Cystic Fibrosis Genetic Analysis Consortium and hosted by a group in Toronto.3 There are common mutations in this gene, however, specifically the deltaF508 (F508del) mutation which accounts for about 70% of those detected in the Caucasian population. A further handful of mutations account for an additional 0.5-5% each, and others are rare, so that in most cases it is sufficient to screen for a limited set of mutations to identify the causal one(s) in a Caucasian patient. Diagnostic laboratories and companies have taken advantage of this and developed kits for the simplified identification of the most common mutations. The difference between these kits resides in the source technology (which is often the proprietary right of the manufacturers) and not in the sequence interrogated for the mutation. There are guidelines which specify a set of 25 mutations (a mutation panel) that should be included for good practice.4 The CFTR gene was patented by the Hospital for Sick Children, Toronto, and the University of Michigan. The patentees granted free access to gene sequences for diagnostic testing using commonly available technologies for mutation analysis, but they have collected royalties on genebased commercial test kits and from companies that offer commercial testing. As a result of this broad license, competition between different kit manufacturers has gradually improved the sensitivities of their assays. In the meantime, CFTR testing has become widely available at a reasonable cost. Such a licensing policy is therefore acceptable and practical. By using the commercial kits, the diagnostic laboratories indirectly pay royalties to the patentees yet still retain the possibility of offering testing using 'home brew' methods, on which no royalties have been requested, at least not in the public sector. It seems that the genetic or medical community has no major objections to this model. What is not publicly known is how much the cost of the kits actually represents royalty fees. It would be interesting to get an idea of the 'value' of a gene or mutation in intellectual property terms.
Source - http://findarticles.com/p/articles/mi_7505/is_200802/ai_n32261194/