CombiMatrix Molecular Diagnostics Launches Microarray Test for Detection of Autism Spectrum Disorder

CombiMatrix  has completed the clinical validation of the  BAC array CGH based clinical microarray tests. ATScan is designed to detect known genomic copy-number variations  associated with Autism Spectrum Disorder and this test is now available to physicians and consumers.

microarray-based Clinical diagnostic tests

 Pathwork Diagnostics, and the Virginia Commonwealth University School of Medicine has initiated an investigational study Genomics-Based diagnostic Test to determine a tumor’s origin so that tissue-specific management can begin.

The test uses microarrays from Affymetrix

More news on Pathworks website 

Affymetrix expands into personalized medicine The next big thing

Affymetrix expands into personalized medicine! Why because The next big thing in health care? is You the individual

personalized medicine is the place step every one wants to be. Roche recently went after Nimblegen for a small foothold in this developing ssicne field, Now its the turn of Affymetrix the leader in microarray DNA chips.

The company is trying to get ahead of the market curve by partnering with drug companies that are making precisely targeted medicines, tailored for patients who have specific gene variations

the company opened the Affymetrix Clinical Services Laboratory to analyze the genes in blood and saliva samples for pharmaceutical companies, diagnostic laboratory businesses and hospitals

Microarray to detect mutations in largest Human Gene

The average human gene consists of 3000 bases, but sizes vary greatly, with the largest known human gene being dystrophin at 2.4 million bases. Residing at Chromosome 4 it has long been of interest to the medical community because its the gene responsible for huntington’s disease, polycystic kidney disease, a form of muscular dystrophy and a variety of other inherited disorders. Chromosome 2 is noteworthy for being the second largest human chromosome, trailing only chromosome 1 in size. It is also home to the gene with the longest known, protein-coding sequence – a 280,000 base pair gene that codes for a muscle protein, called titin, which is 33,000 amino acids long.

Now reseacrhers at Emory university has developed a microarray based test to chek for mutations in this gene. The current test do not detect all types of mutation that affects 1 in 3500 males according to the university wesbite.

Mutations in the dystrophin such as point mutations in a sequence of DNA can result in mistakes in gene  expression and nonfunctional proteins that causes Duchenne muscular dystrophy (DMD).

A detailed presentation of the advantages of the test is available at the Emory Genetics Testing website. The test offeredon the Nimblegen CGH array platform gains more prominance as the company is now being acquired by Roche who has plans to dominate the clinical microarray market with its products in genetics testing space

The emory university Genetics testing lab offers numerous other genetic tests

12 DNA tests that Could Change Your Life-selected by Forbes

The complete list is published at forbes website

  • Breast Cancer
  • Adult-Onset Diabetes
  • Obesity
  • Drug Metabolism
  • Crohn’s Disease
  • Prostate Cancer
  • Duchenne Muscular Dystrophy
  • Rett Syndrome
  • Macular Degeneration
  • Alzheimer’s Disease
  • Heart Attack

Gene Testing:

Related Blogs

eyeondna , gensherpa , OmicsOmics

Microarray based DRUG DISCOVERY and CLINICAL DIAGNOSIS and biosensor designed to identify viruses

 Prof. David Dandy of Colorado State University chemical and biological engineering has proven that called microarray assays can be used for biomedical disease and drug screening assays could rapidly increase drug discovery,

Although not ready for hospital or office use, microarrays represent a novel miniaturized multi-spot diagnostic format that has huge potential for patient diagnosis if found reliable and approved.

Smaller is often better, according to a new scientific study that appears this week in the Proceedings of the National Academy of Sciences by Professor David Dandy, Dr. David Dandyhead of the Department of Chemical and Biological Engineering at Colorado State. Dandy co-wrote the paper with David Grainger, a former chemistry professor at Colorado State who now is chair of the Department of Pharmaceutics & Pharmaceutical Chemistry at the University of Utah.

The study was funded by a multi-year, $2.5 million grant from the National Institutes of Health.

“This work is extremely useful from an industrial perspective,” said Michael Lochhead, chief scientist at Accelr8 Technology Corp., a Denver-based developer of innovative materials and instrumentation for advanced applications in medical instrumentation, basic research, drug discovery, and bio-detection.

The critical importance of this work is illustrated by the fact that, to date, a single microarray-based test has been approved by the FDA for clinical use.

According to Roche, the manufacturer of this diagnostic microarray, “This test analyzes a patient’s Cytochrome P450 2D6 and 2C19 genotypes from genomic DNA extracted from a blood sample. Test results will allow physicians to consider unique genetic information from patients in selecting medications and doses of medications for a wide variety of common conditions such as cardiac diseases, pain and cancer.”

 

 

‘Personalized Medicine’ Goal of Human Genetics Initiative

Oregon Health & Science University effort, launched 25-April 2007 during National DNA Day, will meld genetics and clinical care

OHSU today is launching the Human Genetics Initiative (HGI), an effort that brings together the university’s vast array of genetics research resources and brainpower, and applies them in a health care setting. It will allow the university to seek new ways of understanding the role of genetics in common disorders like obesity, hypertension, osteoporosis and diabetes.

The goal of HGI is to accelerate the translation of scientific knowledge to patient care by recruiting new geneticists, building a campuswide bank of advanced technology, developing new educational programs for the next generation of health care providers, and, eventually, establishing a novel delivery model for genetics health care.

Theranostics-Genetics Testing for Clinical Diagnostics for Personalized Medicine

Theranostics is the term used to describe the proposed process of diagnostic therapy for individual patients – to test them for possible reaction to taking a new medication and to tailor a treatment for them based on the test results or in plain english Personalized Medicine.

Personalized medicine is the use of detailed information about a patient’s genotype or level of gene expression and a patient’s clinical data in order to select a medication, therapy or preventative measure that is particularly suited to that patient at the time of administration

The test results are used to tailor treatment, usually with a drug that targets a particular gene or protein.

Seen the movie Gattaca it shows glipses of the what to come.

This method is looked as the possible end result of new advances made in Pharmacogenomics, Drug Discovery using Genetics, Molecular Biology and Microarray chips technology

The technology is set to grow by leaps as new companies are introducing new microarray chip which are getting cheaper day by day

Already there are microarraychips approved by FDA for clinical diagnostics

Defra funds team to build microarray biochip to detect disease outbreaks

A single test for more than 600 deadly viruses is being developed by a group of Defra-funded scientists, offering the possibility of spotting a disease outbreak in hours rather than days.

The microarray, which is being led by the Central Science Laboratory near York, with £1.5m funding from Defra, will detect viruses that affect humans, animals, plants, fish and bees including avian influenza, rabies and foot and mouth.

Animal and plant researchers will be able to use the same test to identify many viruses, saving time and resources in the event of an outbreak It will also help to quickly identify when a virus has jumped from one species to another and when new strains of existing disease emerge in the future.

its not so much of junk DNA- University of Oxford Scientists discoveres Cancer cure with it

 Junk DNA is not junk after all

Recently, scientists at the University of Oxford have discovered that ‘junk’ genetic material can switch off cancer tumours, preventing them from growing.

By using RNA to switch off a gene involved in controlling cell division, Oxford University scientists may have found a role for RNA in developing new cancer therapies. RNA is the mirror image of DNA, and is used to pass on instructions to the cell to build the proteins that run every body function.

The Human Genome Project found that human DNA carries approximately 34,000 genes that produce proteins. The remaining majority of the genome constituted what was considered to be junk DNA as it had no obvious function. However, this is set to change.

‘‘There has been a quiet revolution taking place in biology in past few years,’’ said Dr Alexandre Akoulitchev, a Senior Research Fellow at Oxford. ‘‘Scientists have begun to see ‘junk’ DNA as having an important function. The variety of RNA types produced from this so called ‘junk’ is staggering and the functional implications are huge.”

Akoulitchev studied the RNA that regulates a gene called DHFR. This gene produces an enzyme that controls the production of molecules called tetrahydrofolate and thymine that cells need to divide rapidly.

“Switching off the DHFR gene could help prevent ordinary cells from developing into cancerous tumour cells, by slowing down their replication. In fact, one of the first anti-cancer drugs, Methotrexate, acts by binding and inhibiting the enzyme produced by this gene. Targeting the gene itself would cut the enzyme out of the picture altogether. Understanding how we can use RNA to switch off or inhibit DHFR and other genes may have important therapeutic implications for developing new anti-cancer treatments.”

This research was funded by The Wellcome Trust and the Medical Research Council.

Original paper: Repression of the human dihydrofolate reductase gene by a non-coding interfering transcript was published in Nature on 22nd January 2006.

Microarray based Bio Detection Technologies

DNA microarray detection of antimicrobial resistance genes in diverse bacteria

Study published at http://cat.inist.fr/?aModele=afficheN&cpsidt=17459830
High throughput genotyping is essential for studying the spread of multiple antimicrobial resistance. A test oligonucleotide microarray designed to detect 94 antimicrobial resistance genes was constructed and successfully used to identify antimicrobial resistance genes in control strains. The microarray was then used to assay 51 distantly related bacteria, including Gram-negative and Gram-positive isolates, resulting in the identification of 61 different antimicrobial resistance genes in these bacteria. These results were consistent with their known gene content and resistance phenotypes. Microarray results were confirmed by polymerase chain reaction and Southern blot analysis. These results demonstrate that this approach could be used to construct a microarray to detect all sequenced antimicrobial resistance genes in nearly all bacteria.

Genetically Guided Treatment For Cancer

Two critical characteristics of breast cancer that are important to treatment can be identified by measuring gene expression in the tumor, a research team led by scientists at The University of Texas M. D. Anderson Cancer Center reports in Lancet Oncology online.

Researchers developed and validated a new genomic microarray test that identifies whether a tumor’s growth is fueled by the female hormone estrogen and the role of a growth factor receptor known as HER-2 that makes a tumor vulnerable to a specific drug.

“This is one important step towards personalized diagnosis and treatment planning based on an integrated genomic test of an individual tumor,” said senior author W. Fraser Symmans, M.D., associate professor in the M. D. Anderson Department of Pathology.

The Lancet Oncology paper results are the latest in an effort by the research team to develop a single test to quickly and efficiently determine the characteristics and vulnerabilities of a patient’s breast cancer and ultimately to guide treatment.

About 70 percent of breast cancers are estrogen-receptor positive and another 15 to 25 percent are human epidermal growth factor receptor-2 (HER-2) positive. Each receptor status requires different types of treatment.

“This moves us closer to developing an integrated single genomic test that could estimate the risk of cancer relapse after surgery, determine the ER and HER2 receptor status, and also gauge the sensitivity of the tumor to hormone therapy and chemotherapy,” says Lajos Pusztai, M.D., Ph.D., associate professor in the M. D. Anderson Department of Breast Medical Oncology, and team leader with Symmans.

Last fall, the group published a study showing that a genomic microarray test can also predict a patient’s response to chemotherapy. They also presented a paper in December showing that another genomic index predicts how an ER-positive patient will respond to hormonal therapy.

The study was funded by the National Cancer Institute, the Breast Cancer Research Foundation and the Goodwin Foundation.

Co-authors with Symmans and Pusztai are: first author Yun Gong, M.D., and Nour Sneige, M.D., of the M. D. Anderson Department of Pathology; Kai Yan, Keith Anderson, and Kenneth Hess, of the M. D. Anderson Department of Biostatistics; Feng Lin, M.D., Vicente Valero, M.D., Daniel Booser, M.D., Jaime Mejia, M.D., and Gabriel Hortobagyi, M.D., of the M. D. Anderson Department of Breast Medical Oncology; Christos Sotiriou, M.D., Ph.D., Institut Jules Bordet, Brussels, Belgium; Fabrice Andre, M.D., of Institut Gustave Roussy, Villejuif, France; Frankie Holmes, M.D., John Pippen Jr., M.D., and Svetislava Vukelja, M.D., of U.S. Oncology-Texas Oncology; Henry Gomez, M.D., of the Instituto Nacional de Enfermedades Neoplasicas, Lima, Peru; and Luis Barajas, M.D., Departmento de Ginecologia Oncologica, Instituto Mexicano del Seguro Social, Guadalajara, Mexico.

Contact: Scott Merville
University of Texas M. D. Anderson Cancer Center

NYIT Professor Discovers Next Generation of DNA and RNA Microarrays brings hopes of personalized medicine

A novel invention developed by a scientist from New York Institute of Technology (NYIT) could revolutionize biological and clinical research and may lead to treatments for cancer, AIDS, Alzheimer’s, diabetes, and genetic and infectious diseases.

The invention allows the immobilisation of intact. double-stranded, multi-stranded or alternative DNA or RNA and has the potential to revolutionise biological and clinical research by allowing scientists to duplicate the cell environment and experiment with human, bacterial and viral genes.

Since the discovery of DNA, biologists have worked to unlock the secrets of the human cell.

Scientist Dr. Claude E. Gagna, Ph.D., an associate professor at NYIT’s School of Health Professions, Behavioral and Life Sciences, discovered how to immobilize intact double-stranded (ds-), multi-stranded or alternative DNA and RNA on one microarray. This immobilization allows scientists to duplicate the environment of a cell, and study, examine and experiment with human, bacterial and viral genes. This invention provides the methodology to analyze more than 150,000 non-denatured genes.

The “Gagna/NYIT Multi-Stranded and Alternative DNA, RNA and Plasmid Microarray,” has been patented (#6,936,461) in the United States and is pending in Europe and Asia. Gagna’s discovery will help scientists understand how transitions in DNA structure regulate gene expression (B-DNA to Z-DNA), and how DNA-protein, and DNA-drug interactions regulate genes. The breakthrough can aid in genetic screening, clinical diagnosis, forensics, DNA synthesis-sequencing and biodefense.

“This patent represents a leap forward from conventional DNA microarrays that use hybridisation,” said Dr Gagna, associate professor of the New York Institute of Technology.

This will help pharmaceutical companies produce new classes of drugs that target genes, with fewer side effects,” Dr Gagna continued.

“It will lower the cost and increase the speed of drug discovery, saving millions of dollars.”

Since the invention of the DNA microarray in 1991, the technology has become one of the most powerful research tools for drug discovery research allowing scientist to perform thousands of experiments with incredible accuracy and speed. According to MarketResearch.com sales of DNA microarrays are expected to be higher than $5.3bn (€ bn) by 2009.

The technology hinges around a novel surface that increases the adherence of DNA to the microarray so that any type of nucleic acid can be anchored, unlike conventional arrays that allow only single-stranded DNA to be immobilised.

Additionally, Gagna has developed a novel surface that increases the adherence of the DNA to the microarray so that any type of nucleic acid can be anchored. Unlike conventional microarrays, which immobilize single-stranded DNA, scientists will now be able to “secure intact, non-denatured, unaltered ds-DNA, triplex-, quadruplex-, or pentaplex DNA onto the microarray,” says Gagna. “With this technology, one day we will have tailor-made molecular medicine for patients.”

“With this technology, one day we will have tailor-made molecular medicine for patients,” said Dr Gagna.

and sure the news site are buzzing with the discovery

read more about the research and the original article details at

Dr Gagna, associate professor of the New York Institute of Technology. and also at www.nyit.edu/dnamicroarrays


Microarray test to anlyse the role of estrogen in breast cancer

Two critical characteristics of breast cancer that are important to treatment can be identified by measuring gene expression in the tumor, a research team led by scientists at The University of Texas M. D. Anderson Cancer Center reports in Lancet Oncology online.

Researchers developed and validated a new genomic microarray test that identifies whether a tumor’s growth is fueled by the female hormone estrogen and the role of a growth factor receptor known as HER-2 that makes a tumor vulnerable to a specific drug. The status of these factors is now determined by pathology tests.

About 70 percent of breast cancers are estrogen-receptor positive and another 15 to 25 percent are human epidermal growth factor receptor-2 (HER-2) positive. Each receptor status requires different types of treatment.

Read the complete article that talkes about the revolutionary test that promises to chage the way cancer is treated

http://www.huliq.com/11047/er-and-her-2-status-of-breast-tumors 

The genetic detective – Pharmacogenomics and personalized medicine

 THe following interesting study was published at  article is from royal society of chemistry website

A selective way to detect genetic variations could help scientists develop personalised medicine.

“[This method] should allow several thousands of single nucleotide variations, at different positions within a person’s genome, to be analysed in parallel.”
– Andreas Marx

Variations in our genetic make-up are responsible for some diseases and are known to be major players in an individual’s predisposition to drug side effects. Convenient and rapid detection of these variations could help doctors to adapt therapies for each patient. This idea has prompted Andreas Marx and colleagues at the University of Konstanz, Germany, to devise a high-throughput technique to detect variations between single nucleotides in genetic sequences. 

Marx’s system uses a microarray of oligonucleotide probes to analyse the DNA. The probes are attached by their 5′ end to a glass surface and treated with an enzyme, a DNA polymerase. The enzyme can add further nucleotides to the unattached ends of the probes. If a probe’s terminal base complements the DNA under investigation, the oligonucleotide chain continues to form; if the base is a mismatch, the chain does not extend further.

A microarray of oligonucleotide probes

Oligonucleotide probes are used to analyse DNA to detect variations between single nucleotides

‘Conventional enzyme-based strategies for detecting single nucleotide variations often lack sufficient selectivity,’ said Marx. The oligonucleotide chain can continue to form even when there is a mismatch. The team was able to increase the selectivity by modifying the terminal nucleotide of the probe with a methoxymethylene group. 

In human DNA, approximately one single nucleotide variation occurs per 1000 bases. This method ‘should allow several thousands of single nucleotide variations, at different positions within a person’s genome, to be analysed in parallel,’ said Marx. ‘This is still a challenging task that none of the present systems is able to achieve reliably.’

Oliver Seitz, an expert in DNA diagnostics at Humboldt University in Berlin, Germany, believes that Marx’s work could have a significant impact in developing diagnostic probes for DNA. ‘The method brings high specificity to the high-throughput format,’ said Seitz. ‘The challenge now is to combine multiplex analysis with specificity and signal amplification in a miniaturised format, to enable point-of-care diagnostics.’

Alison Stoddart

References

Increased single nucleotide discrimination in arrayed primer elongation by 4′C-modified primer probes

J Gaster, G Rangam and A Marx, Chem. Commun., 2007

Indian scientists from CCMB find new genetic mutations- and wins award from UK

UK award for CCMB scientist

The Hindu Business Line:January 22, 2007

Hyderabad: Dr K. Thangaraj, a scientist at the Centre for Cellular and Molecular Biology (CCMB), Hyderabad has received the first Major UK-India Education and Research Initiative (UKIERI) Award.Launched by the UK Prime Minister, Mr Tony Blair, during his last visit to India, the UKIERI award is aimed to promote the innovative research and academic excellence between the two countries.

The award has been given to Dr Thangaraj and his collaborators Dr Mart Mirazon Lahr and Dr Toomas Kivisild of Cambridge University for a four-year collaborative project involving genetic analysis of the various populations in India.

It also involves mutual exchange visits of scientists between CCMB and Cambridge University.

Major Award

This is the first major award given to carry out the research in the field of genomics, out of the six major awards selected from 103 proposals from India and the UK.

The award was presented by Mr Gordon Brown, Chancellor of the Exchequer of Britain, at a function in New Delhi recently, according to a CCMB release.

It carries a research grant of Rs 2.5 crore. The project aims at probing the question: “Was the first `out of Africa’ settlement of Homo sapiens in India?”

Dr Lalji Singh, Director of CCMB, said that the initiative would bring many more international research collaborations in future to the centre.

Indian scientists from CCMB find new genetic mutations

Novel genetic mutations associated with certain neuro-generative disorders, cardio-myopathies and male infertility have been found in Indian population by scientists of the Centre for Cellular and Molecular Biology (CCMB) in studies conducted in collaboration with other medical institutions.

The mutations have been found in mitochondrial DNA which is inherited from the mother, unlike the chromosomal DNA, inherited from both the parents. Mitochondrion plays an important role in cellular energy metabolism. In the past decade, genetic variations in mitochondrial DNA have been linked with various disorders, particularly neurological.

Senior scientist of CCMB Kumaraswamy Thangaraj, who led the research teams, told  that they had begun studying the molecular basis of mitochondrial disorders in the population a couple of years ago. They focussed on neuro-muscular diseases, cardiomyopathy, male infertility and recurrent pregnancy loss and analysed hundreds of samples in each category.

The studies showed new genetic variations associated with neuro-generative disorders like MELAS (Mitochondrial encephalopathy lactic acidosis stroke-like episodes) and Leigh, cardiomyopathies and male infertility. Dr. Thangaraj said most of the mutations found in the Western were not found here. “Since Indians have a unique origin, the genetic variations will be different,” he added. CCMB scientists are analysing samples to identify specific sets of mutations associated with mitochondrial disorders for early diagnosis. Regarding genetic causes for male infertility, he said the problem of low sperm motility was looked into to understand the involvement of mitochondrial DNA. C11994T mutation in ND4 gene of mitochondria was found to be associated with low motility, he added

 

 

Microarray for clinical diagnostics in hand-foot-and-mouth disease

The following study was published in journal of clinical microbiology,

Combining Multiplex Reverse Transcription-PCR and a Diagnostic Microarray To Detect and Differentiate Enterovirus 71 and Coxsackievirus A16

Tsan-Chi Chen,1,2 Guang-Wu Chen,3 Chao Agnes Hsiung,4 Jyh-Yuan Yang,5 Shin-Ru Shih,6 Yiu-Kay Lai,2 and Jyh-Lyh Juang1* Division of Molecular and Genomic Medicine, National Health Research Institutes, Miaoli, Taiwan,1 Department of Life Science and Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan,2 Department of Computer Science and Information Engineering, Chang Gung University, Taoyuan, Taiwan,3 Biostatistics and Bioinformatics, National Health Research Institutes, Miaoli, Taiwan,4 Center for Disease Control, Department of Health, Taipei, Taiwan,5 Department of Medical Biotechnology and Laboratory Science, Chang Gung University, Taoyuan, Taiwan6

Received 18 November 2005/ Returned for modification 16 January 2006/ Accepted 7 April 2006

Cluster A enteroviruses, including enterovirus 71 (EV71) and coxsackievirus A16 (CA16), are known to cause hand-foot-and-mouth disease (HFMD). Despite the close genetic relationship between these two viruses, EV71 is generally known to be a more perpetuating pathogen involved in severe clinical manifestations and deaths. While the serotyping of enteroviruses is mostly done by conventional immunological methods, many clinical isolates remain unclassifiable due to the limited number of antibodies against enterovirus surface proteins. Array-based assays are able to detect several serotypes with high accuracy. We combined an enterovirus microarray with multiplex reverse transcription-PCR to try to develop a method of sensitively and accurately detecting and differentiating EV71 and CA16. In an effort to design serotype-specific probes for detection of the virus, we first did an elaborate bioinformatic analysis of the sequence database derived from different enterovirus serotypes. We then constructed a microarray using 60-mer degenerate oligonucleotide probes covalently bound to array slides. Using this enterovirus microarray to study 144 clinical specimens from patients infected with HFMD or suspected to have HFMD, we found that it had a diagnostic accuracy of 92.0% for EV71 and 95.8% for CA16. Diagnostic accuracy for other enteroviruses (non-EV71 or -CA16) was 92.0%. All specimens were analyzed in parallel by real-time PCR and subsequently confirmed by neutralization tests. This highly sensitive array-based assay may become a useful alternative in clinical diagnostics of EV71 and CA16.


* Corresponding author. Mailing address: Division of Molecular and Genomic Medicine, National Health Research Institutes, 35 Keyan Road, Zhunan, Miaoli 350, Taiwan. Phone: 886-37-246-166, ext. 35308. Fax: 886-37-586-459. E-mail: juang@nhri.org.tw.


Journal of Clinical Microbiology, June 2006, p. 2212-2219, Vol. 44, No. 6
0095-1137/06/$08.00+0     doi:10.1128/JCM.02393-05
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

Usage of Low-Density Oligonucleotide Microarrays for Prognosis Prediction of Colorectal Cancer Patients

Colorectal cancer (CRC) is one of the most common malignancies. Unfortunately a significant proportion of surgically cured patients in the early stage of the disease develop progression and die from the disease. DNA microarrays technology was used in more than sixty studies focused on colorectal cancer during last five years.

High-density DNA microarrays showed good analytical ability also in colorectal cancer prognosis. However, comparability and reproducibility of studies based on high-density DNA microarrays are notably affected by their technological diversity, and recent findings are not conclusive [4].

This study aimed to find individual up/down-regulated genes associated with progression and metastatic potential of colorectal cancers using low-density oligonucleotide microarrays spotted with genes known to be involved in process of metastasis development. We suppose that focusing on a particular biological pathway may be more useful than genome-wide screening for our purposes.

Molecular characterization of patients at high risk of cancer progression using this more economical and productive expression profiling method may improve our knowledge about cancer progression and dissemination and also assist to oncologists in treatment decision by selecting those patients who will need adjuvant chemotherapy.

Rapid genotyping of methicillin-resistant Staphylococcus aureus (MRSA) using OLigonucleotide microarrays

Published by 

1Institute for Medical Microbiology and Hygiene, Faculty of Medicine ‘Carl Gustav Carus’, Technical University of Dresden, Dresden and 2Clondiag Chip Technologies GmbH, Jena, Germany
ABSTRACT
This study evaluated a DNA oligonucleotide array that recognised 38 different Staphylococcus aureus targets, including all relevant resistance determinants and some toxins and species-specific controls. A new method for labelling sample DNA, based on a linear multiplex amplification that incorporated biotin-labelled dUTP into the amplicon, was established, and allowed detection of hybridisation of the amplicons to the array with an enzymic precipitation reaction. The whole assay was validated by hybridisations with a panel of reference strains and cloned specific PCR products of all targets. To
evaluate performance under routine conditions, the assay was used to test 100 methicillin-resistant S. aureus (MRSA) isolates collected from a university hospital in Saxony, Germany. The results showed a high correlation with conventional susceptibility data. The ermA and ermC macrolide resistance genes were found in 40% and 32% of the isolates, respectively. The most prevalent aminoglycoside resistance gene was aphA3 (57% of the isolates), followed by aacA–aphD (29%) and aadD (29%); tet genes, mupR
and dfrA were rare. There were no isolates with van genes or genes involved in resistance to quinupristin–dalfopristin. Enterotoxins were detected in 27% of the isolates. Genes encoding Panton– Valentine leukocidin, toxic shock syndrome toxin and exfoliative toxins were not found. The DNA array facilitated rapid and reliable detection of resistance determinants and toxins under conditions used in a routine laboratory and has the potential to be used for array-based high-throughput screening.

complete article at http://www.clondiag.com/pub/CMI-2005_Genotyping%20of%20MRSA.pdf

Similar studies are also published at

http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1393086

Microarray for Clinical Diagnostics- For detecting sepsis

http://www.biologynews.net/archives/2006/12/19/gene_chip_technology_shows_potential_for_identifying_lifethreatening_blood_infection.html

Right now there’s no rapid way to diagnose sepsis, a fast-moving blood infection that is a leading cause of death in hospital intensive care units. The illness unleashes a powerful inflammatory response that can quickly overwhelm the body, causing organ failure and death, often within days.

New research now suggests that doctors one day could quickly distinguish sepsis from widespread non-infectious inflammation based on genetic profiles of patients’ blood. Testing this method in mice, researchers at Washington University School of Medicine in St. Louis found the profiles could accurately discriminate between the two conditions 94 percent of the time. The molecular profiles measure differences in patterns of gene expression that are unique to sepsis vs. non-infectious inflammation.

The researchers used microarrays, also called gene chips, to analyze patterns of gene expression in the mice. The same technology is already used by doctors to diagnose breast cancer and predict a patient’s response to various chemotherapy drugs, but this is the first time researchers have attempted to use gene chips to distinguish sepsis from non-infectious inflammation.

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