AppId is over the quota
Article Opinions: 1 postsHigh-throughput DNA sequencing technologies are leading to a revolution in how clinicians diagnose and treat cancer. The molecular profiles of individual tumors are beginning to be used in the design of chemotherapeutic programs optimized for the treatment of individual patients. The real revolution, however, is coming with the emerging capability to inexpensively and accurately sequence the entire genome of cancers, allowing for the identification of specific mutations responsible for the disease in individual patients.
There is only one downside. Those sequencing technologies provide massive amounts of data that are not easily processed and translated by scientists. That's why Georgia Tech has created a new data analysis algorithm that quickly transforms complex RNA sequence data into usable content for biologists and clinicians. The RNA-Seq analysis pipeline (R-SAP) was developed by School of Biology Professor John McDonald and Ph.D. Bioinformatics candidate Vinay Mittal. Details of the pipeline are published in the journal Nucleic Acids Research.
"A major bottleneck in the realization of the dream of personalized medicine is no longer technological. It's computational," said McDonald, director of Georgia Tech's newly created Integrated Cancer Research Center. "R-SAP follows a hierarchical decision-making procedure to accurately characterize various classes of gene transcripts in cancer samples."
There are at least 23,000 pieces of RNA in the human genome that encode the sequence of proteins. Millions of other pieces help regulate the production of proteins. R-SAP is able to quickly determine every gene's level of RNA expression and provide information about splice variants, biomarkers and chimeric RNAs. Biologists and clinicians will be able to more readily use this data to compare the RNA profiles or "transcriptomes" of normal cells with those of individual cancers and thereby be in a better position to develop optimized personal therapies.
Personalized approaches to cancer medicine are already in widespread use for a few "cancer biomarkers" including variants of the BRAC 1 gene that can be used to identify women with a high risk of developing breast and ovarian cancer.
"Our goal was to design a pipeline that is easily installable with parallel processing capabilities," said Mittal. "R-SAP can make 100 million reads in just 90 minutes. Running the program simultaneously on multiple CPUs can further decrease that time."
R-SAP is open source software, freely accessible at the McDonald Lab website*.
"This is another example of Georgia Tech's ability to merge computer technology with science to create an essential feature of next-generation bioinformatics tools," said McDonald. "We hope that R-SAP will be a useful and user-friendly instrument for scientists and clinicians in the field of cancer biology."
Additional References Citations Article adapted by Medical News Today from original press release. Click 'references' tab above for source.
Visit our cancer / oncology section for the latest news on this subject. *http://www.mcdonaldlab.biology.gatech.edu/r-sap.htm
Georgia Institute of Technology Please use one of the following formats to cite this article in your essay, paper or report:
MLA
Georgia Institute of Technology. "Computational Algorithm Developed To Assist In Cancer Treatments." Medical News Today. MediLexicon, Intl., 15 Feb. 2012. Web.
16 Feb. 2012.
Georgia Institute of Technology. (2012, February 15). "Computational Algorithm Developed To Assist In Cancer Treatments." Medical News Today. Retrieved from
http://www.medicalnewstoday.com/releases/241626.php.
Please note: If no author information is provided, the source is cited instead.
Rate this article:
(Hover over the stars then click to rate) Patient / Public:
or Health Professional:
Visitor Opinions In Chronological Order (1)Molecular Cancer Medicine is Still Waiting for its First Killer "App"posted by Gregory D. Pawelski on 15 Feb 2012 at 1:39 pm
One of the high-paying glamorous jobs of the new millenium was bioinformatics. Some statisticians have said that we're going to cure diseases in the near time frame. Those same statisticians reacted that we didn't know how to handle one gene (and they still don't), never mind 23,000 genes or the millions of other pieces that help regulate the production of proteins.
In molecular cancer medicine, as it involves drug selection, things are not nearly so clear cut as they appear. Biological technology seems so elegant and beautiful, but a beautiful biological technology is no different than a beautiful computer technology, it's not worth much without some very good applications ("apps"), and personalized molecular medicine is still waiting for its first killer app.
Informatics and computer technology can do much to improve patients care. However, while this bottom-up approach generates data that may be much more quantitative, we will still have to show that it can have an impact from the top-down.
The top-down approach in systems biology focuses on addressing questions that need to be answered and optimizing the path to their solution. In other words, top-down research (i.e. functional profiling) has important implications for understanding human disease.
| post followup | alert a moderator |
Add Your Opinion
Please note that we publish your name, but we do not publish your email address. It is only used to let you know when your message is published. We do not use it for any other purpose. Please see our privacy policy for more information.
If you write about specific medications or operations, please do not name health care professionals by name.
All opinions are moderated before being included (to stop spam)
Your Name:* E-mail Address:* Title For Opinion:* Opinion:* This is to help prevent SPAM submissions. Please enter the words exactly as they appear, including capital letters and punctuation.** Fields marked with a * need to be filled in before you hit the submit button.
Contact Our News Editors
For any corrections of factual information, or to contact the editors please use our feedback form.
Please send any medical news or health news press releases to:
back to top
home
popular news by year
all written articles
health videos
contact us
your news:
news category list
personalize homepage
weekly newsletters
daily news alerts
company:
about us
advertising
news licensing
article submission
more:
accessibility
help / faq
links
free website feeds
free tools & content
Privacy Policy | Terms and ConditionsMediLexicon International Ltd
Bexhill-on-Sea, United Kingdom
MediLexicon International Ltd © 2004-2012 All rights reserved.
Cancer / OncologyWhat is Cancer?
Cancer is a class of diseases characterized by out-of-control cell growth. There are over 100 different types of cancer, and each is classified by the type of cell that is initially affected. Read more...Most Popular Articles 1 Month 3 Months 6 Months 1US Cancer Screening Below National Targets2Tumors Continue Growing Even When Cells Get Old3Breast Cancer Survival - Why Avastin And Sutent Don't Help4Cancer Screening Rates Low Among Ethnic Groups, USA5Malignant Melanoma Recurrence - How To Avoid It After Targeted Treatment67% Of Americans Have Oral HPV7Statins May Work Against Certain Breast Cancers8Cancer Patients' Health Benefits From Physical Activity 1US Cancer Screening Below National Targets2Tumors Continue Growing Even When Cells Get Old3Roche's Avastin Receives EU Approval For Ovarian Cancer4Breast Cancer Survival - Why Avastin And Sutent Don't Help5Cancer Deaths - Enormous Drop Over Last 20 Years, USA6Cancer Screening Rates Low Among Ethnic Groups, USA7Coffee Emerges As Protective Against Cancer And Other Diseases8Breast Cancer Survival In Younger Breast Cancer Patients Improves With Bone Drug9Malignant Melanoma Recurrence - How To Avoid It After Targeted Treatment10Cancer Vaccine Significantly Reduces Tumor Size 1US Cancer Screening Below National Targets2Tumors Continue Growing Even When Cells Get Old3Roche's Avastin Receives EU Approval For Ovarian Cancer4Breast Cancer Survival - Why Avastin And Sutent Don't Help5Cancer Deaths - Enormous Drop Over Last 20 Years, USA6Cancer Screening Rates Low Among Ethnic Groups, USA7Coffee Emerges As Protective Against Cancer And Other Diseases8Breast Cancer Survival In Younger Breast Cancer Patients Improves With Bone Drug9Malignant Melanoma Recurrence - How To Avoid It After Targeted Treatment10Cancer Vaccine Significantly Reduces Tumor Size Follow Our Cancer News On Twitter
Get the latest news for this category delivered straight to your Twitter account. Simply visit our Cancer / Oncology Twitter account and select the 'follow' option.Conditions Information-- select from list --Abscess (Dental)AchalasiaAchilles TendinitisAcid RefluxAcneAcoustic Neuroma (Vestibular Schwannoma)AcromegalyActinomicosisAcute Lymphoblastic LeukemiaAcute Myeloid LeukemiaAddictionAddison’s Disease (Primary Adrenal Insufficiency)ADHDAgoraphobiaAir Embolism (Gas Embolism)Alcohol PoisoningAlcoholic Liver DiseaseAlcoholismAlopecia AreataAltitude Sickness (Acute Mountain Sickness)Alzheimer's DiseaseAMD / Macular DegenerationAmenorrheaAmnesiaAmniocentesisAnagen EffluviumAnal CancerAnal FissureAnal Itching (Itchy Bottom)AnaphylaxisAndrogen Insensitivity Syndrome (AIS)AnemiaAnemia (Vitamin Deficiency)AneurysmAngerAnginaAngioedemaAnorexia & BulimiaAntiphospholipid Syndrome (Hughes Syndrome)AnxietyAphasiaAppendicitisArrhythmiaArthritisAsperger SyndromeAsthmaAstigmatismAtaxiaAtrial FibrillationAtrophic Vaginitis (Vaginal Atrophy)AutismAvian InfluenzaBack PainBacterial VaginosisBaker's Cyst (Popliteal Cyst)BalanitisBartholin's CystBed Sores (Pressure Ulcers)Bell's PalsyBinge Eating DisorderBipolar DisorderBird FluBladder cancerBladder StonesBlepharitisBody Dysmorphic DisorderBody Odor (B.O.)Boils, furuncles, carbunclesBone CancerBorderline Personality Disorder (BPD)BotulismBrain Abscess (Cerebral Abscess)Breast CancerBreast Cancer (Male)Breast LumpsBronchiectasis (Bronchiectasia)BronchitisBursitisCancerCandidiasisCarbon Monoxide PoisoningCarpal Tunnel SyndromeCartilage DamageCataractsCatatonic SchizophreniaCelluliteCellulitisCerebral PalsyCerebrovascular DiseaseCervical SpondylosisCharcot-Marie-Tooth DiseaseChickenpoxChild AbuseChildhood SchizophreniaChlamydiaCholecystitis (Gallbladder Inflammation)CholeraCholestasis Of Pregnancy (Obstetric Cholestasis)CholesterolChronic Fatigue Syndrome (CFS)Chronic Fatigue Syndrome (CFS)Chronic Kidney FailureChronic Rhinosinusitis (CRS)CirrhosisCJDClaustrophobiaClostridium Difficile (C. Difficile)Clubfoot (Talipes Equinovarus)Cluster HeadacheCold SoresColicColon CancerColorectal CancerComa (Comatose)Common ColdComplex Regional Pain Syndrome (CRPS)ConcussionCongenital Heart Disease (Congenital Heart Defect)Conjunctivitis (allergic)Conjunctivitis (infective)ConstipationCOPD & EmphysemaCorns / CallusesCoronary Heart Disease (Coronary Artery Disease)Costello SyndromeCoughCrabs (Pubic Lice)CraniosynostosisCreutzfeldt-Jakob disease (CJD)CristoporidiosisCrohn's DiseaseCroupCryptorchidism (Undescended Testicle)Cushing's SyndromeCystic FibrosisCystitisCystsCytomegalovirus (CMV)DandruffDeep Vein ThrombosisDehydrationDementiaDengue Fever?DepressionDetached RetinaDHTDiabetesDiabetes InsipidusDiabetic RetinopathyDiarrheaDiphtheriaDiscoid Eczema (Nummular Dermatitis)Disorganized Schizophrenia (Hebephrenia)DiverticulitisDouble Vision (Diplopia)Down SyndromeDry Eye SyndromeDry Mouth (Xerostomia)Dupuytren’s ContractureDysenteryDyslexiaDysphagiaDyspraxiaDystoniaE.coliEctopic PregnancyEctropionEczemaEdemaEmbolismEmphysemaEncephalitisEndocarditisEndometriosisEnuresis - BedwettingEpidermolysis BullosaEpiglottitisEpilepsyEpiphora (Watering Eye)Erectile DysfunctionEsophageal CancerEsophagitisEuthanasia (Assisted Suicide)Exophthalmos (Bulging Eyes)Eye Melanoma (Ocular Melanoma)Febrile Seizures (Convulsions)Female Genital MutilationFeverFibroidsFibromyalgiaFlat Feet (Fallen Arches)FlatulenceFood AllergyFracture (Broken Bones)FrostbiteFrozen ShoulderGallstonesGanglion CystGangreneGastroenteritis / Food PoisoningGenital WartsGERDGiardiasisGilbert SyndromeGingivitisGlandular FeverGlaucomaGlomerulonephritisGlue EarGluten Intolerance / Celiac DiseaseGoiter (Goitre)GonorrheaGoutGraves’ DiseaseGuillain-Barré SyndromeGum Disease (Gingivitis)Hair Loss / BaldnessHalitosis (Bad Breath)HangoverHay FeverHead LiceHeadachesHeart AttackHeart Block (AV Bundle/Bundle Branch Block)Heart DiseaseHeart FailureHeartburnHeat Rash (Prickly Heat)Heel PainHemochromatosisHemophiliaHemroids / HemorrhoidsHepatitisHerniaHerpesHiccupsHiccups (Hiccoughs)High Blood PressureHirsutism (Excessive Hairiness)HIV / AIDSHivesHormone Replacement Therapy (HRT)Huntington's DiseaseHydrocephalus (Water On The Brain)Hyperhidrosis (Excessive Sweating)HypertensionHyperthyroidismHypertrophic CardiomyopathyHypertrophic CardiomyopathyHypochondriaHypoglycemiaHypotensionHypothermiaHypothyroidismHysterectomyImpacted Wisdom TeethImpetigoIncontinence (bowel)Incontinence (urinary)IndigestionInfant JaundiceInfertilityInfluenza / FluIngrown ToenailInsomniaIrregular Periods (Oligomenorrhea)Irritable Bowel Syndrome (IBS)Irritable Hip (Acute Transient Synovitis)Japanese EncephalitisJaundice (icterus)Jet LagKawasaki DiseaseKetosisKidney CancerKidney Infection (Pyelonephritis)Kidney StonesLactose IntoleranceLaryngeal Cancer (Cancer Of The Larynx)LaryngitisLazy EyeLeg CrampsLegionnaires' DiseaseLeukemiaLichen PlanusListeria Infection (Listeriosis)Liver CancerLung CancerLupusLyme DiseaseLymphedemaLymphomaMal De Debarquement Syndrome (MdDS)MalariaMalnutritionMarfan SyndromeMastitisMeaslesMeniere's diseaseMeningitisMenopauseMental HealthMesotheliomaMetatarsalgia (Stone Bruise)MigraineMolesMolluscum ContagiosumMorning Sickness (Nausea Gravidarum)Morton's NeuromaMotion Sickness (Travel Sickness)Motor Neuron DiseaseMouth CancerMRSAMultiple MyelomaMultiple SclerosisMumpsMunchausen SyndromeMunchausen Syndrome By ProxyMuscular Dystrophy (MD)Myasthenia Gravis (Goldflam Disease)Nail Fungal InfectionNarcissistic Personality DisorderNarcolepsyNasal PolypsNDM-1Necrotizing FasciitisNeurofibromatosisNeuromyelitis Optica (Devic's Disease)NeuropathyNicotine Dependence (Dangers Of Smoking)Noonan SyndromeNorovirus InfectionObesityObsessive Compulsive DisorderObsessive Compulsive Disorder (OCD)Obstructive Sleep Apnea (OSA)Occupational AsthmaOpioid-Induced Constipation (OIC)Oral Thrush (Babies)Oral Thrush (Oral Candidiasis)OsteoarthritisOsteochondritis DissecansOsteomyelitis (Bone Infection)OsteopathyOsteoporosisOtitis Externa (Swimmer's Ear)Ovarian CancerOvarian CystPaget's Disease (Of Bone)PainPainful Intercourse (Dyspareunia)Pancreatic CancerPancreatitis (acute)Pancreatitis (chronic)Panic AttacksParanoid SchizophreniaParasitesParkinson's DiseasePelvic Inflammatory DiseasePeptic UlcersPericarditisPeriod PainsPeripheral Artery Disease (PAD)Personality DisordersPilesPimplesPinworms (Threadworms)PleurisyPneumococcal DiseasePneumoniaPolioPost Traumatic Stress Disorder (PTSD)Postherpetic NeuralgiaPostpartum DepressionPrader-Willi SyndromePremature EjaculationPrimary Sclerosing CholangitisProgeriaProstate CancerPsoriasisPsoriasisPulmonary Edema (Oedema)Pulmonary EmbolismQ FeverRabiesRadiation Sickness (Radiation Poisoning)Ramsay Hunt SyndromeRaynaud's DiseaseRectocele (Proctocele)Repetitive Strain Injury (RSI)Restless Legs SyndromeRheumatic FeverRheumatoid ArthritisRhinitis, Non-AllergicRicketsRingwormRosaceaRubellaRuptured SpleenSalivary Gland CancerSalmonellaSARSScabiesScarlet Fever (Scarlatina)Schistosomiasis (Bilharzia)Schizoaffective DisorderSchizophreniaSciaticaSclerodermaScoliosisScurvySeasonal Affective DisorderSexual Addiction (Nymphomania)ShinglesShort Stature (Dwarfism)SinusitisSjogren's SyndromeSkin Cancer / MelanomaSlapped Cheek SyndromeSocial Anxiety DisorderSpina BifidaSpinal Muscular AtrophySquint (Strabismus)StammeringStrep Throat / Sore ThroatStressStress IncontinenceStrokeStye (Hordeolum)Subarachnoid HemorrhageSuicidal ThoughtsSwine FluSyphilisTachycardia (Fast Heart Beat)Tapeworms (Cestodes)Teeth Grinding (Bruxism)Tendinitis (Tendonitis)Testicular CancerTesticular TorsionTetanusThyroid CancerThyroid NodulesTinnitusTiredness / FatigueTobacco Smoke ToxinsTonsillitisTourette SyndromeToxic Shock Syndrome (TSS)Transient Ischemic Attacktransient ischemic attackTraumatic Brain Injury (TBI)Trigeminal NeuralgiaTriple X SyndromeTuberculosisTurner SyndromeTyphoidUlcerative ColitisUmbilical HerniaUrinary Tract Infection (UTI)UveitisVaculitis (Angiitis)Vaginal CancerVaginismusVaginitisValley Fever (Coccidioidomycosis)VaricoceleVaricose Eczema (Stasis Dermatitis)Varicose VeinsVentricular FibrillationVertigoVesicoureteral Reflux (VUR)Vitamin B12 DeficiencyVocal Cord Paresis (Paralysis)Von Willebrand DiseaseVulvar Cancer (Vulval Cancer)VulvodyniaWartsWater On The Knee (Knee Effusion)Water Retention (Fluid Retention)Wegener's GranulomatosisWernicke-Korsakoff SyndromeWest Nile Virus (WNV)Wheat AllergyWhipple's DiseaseWilliams SyndromeWilms’ Tumor (Nephroblastoma)Wolff-Parkinson-White SyndromeYellow FeverYipsZollinger-Ellison Syndrome
View list of all 'What Is...' articles »
Posts
0 comments: on "Computational Algorithm Developed To Assist In Cancer Treatments"
Post a Comment