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Welcome to The Visible Embryo, a comprehensive educational resource on human development from conception to birth.

The Visible Embryo provides visual references for changes in fetal development throughout pregnancy and can be navigated via fetal development or maternal changes.

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Pregnancy Timeline by SemestersFemale Reproductive SystemFertilizationThe Appearance of SomitesFirst TrimesterSecond TrimesterThird TrimesterFetal liver is producing blood cellsHead may position into pelvisBrain convolutions beginFull TermWhite fat begins to be madeWhite fat begins to be madeHead may position into pelvisImmune system beginningImmune system beginningPeriod of rapid brain growthBrain convolutions beginLungs begin to produce surfactantSensory brain waves begin to activateSensory brain waves begin to activateInner Ear Bones HardenBone marrow starts making blood cellsBone marrow starts making blood cellsBrown fat surrounds lymphatic systemFetal sexual organs visibleFinger and toe prints appearFinger and toe prints appearHeartbeat can be detectedHeartbeat can be detectedBasic Brain Structure in PlaceThe Appearance of SomitesFirst Detectable Brain WavesA Four Chambered HeartBeginning Cerebral HemispheresEnd of Embryonic PeriodEnd of Embryonic PeriodFirst Thin Layer of Skin AppearsThird TrimesterDevelopmental Timeline
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February 7, 2012--------News Archive Return to: News Alerts

PyroMaker, online DNA sequencer

WHO Child Growth Charts

What Is Your BMI?

       

New Virtual Tool to Diagnose Genetic Mutations

Detecting mutations for diagnosis and treatment of cancer can be complex with results difficult, if not impossible, to interpret. Now, free software can help identify complex genetic mutations

DNA sequencing to detect genetic mutations can aid in the diagnosis and selection of treatment for cancer. However, two current methods of testing DNA samples, Sanger sequencing and pyrosequencing, occasionally produce complex results that can be difficult or impossible to interpret.

Scientists at the Johns Hopkins University School of Medicine have developed a free software program, Pyromaker, that can more accurately identify such complex genetic mutations.

The technology is described in the Journal of Molecular Diagnostics.

Pyromaker is a web-based application that produces simulated pyrograms based on user input including the percentage of tumor and normal cells, the wild-type sequence, the dispensation order, and any number of mutant sequences. Pyromaker calculates the relative mutant and wild-type allele percentages and then uses these to generate the expected signal at each point in the dispensation sequence. The final result is a virtual trace of the expected pyrogram.

The researchers validated Pyromaker against actual pyrograms containing common mutations in the KRAS gene, which plays an important role in the pathogenesis of a variety of tumors. The actual pyrograms and virtual pyrograms were quantitatively identical for all mutations tested.

They then demonstrated that all codon 12 and 13 single and complex mutations generate unique pyrograms. However, some complex mutations were indistinguishable from single base mutations, indicating that complex mutations may be underreported.

Working with two complex pyrograms that were difficult to interpret initially, the researchers identified five approaches to resolve them: Sanger sequencing alone, hypothesis testing with Pyromaker, Pyromaker iterative mutation re-creation, melting curve analysis, and TA cloning with Sanger sequencing.

Senior author James R. Eshleman, MD, PhD, Professor of Pathology and Oncology, Associate Director, Molecular Diagnostics Laboratory, Johns Hopkins University School of Medicine, explains, "User-directed hypothesis testing allows for generating virtual traces that can be compared to the actual data to clarify ambiguous results from pyrosequencing and the Sanger method. Alternatively, Pyromaker can quickly and efficiently test the possibilities that can explain a complicated polysequencing result." Both strategies were able to successfully identify the complex mutations.

TA cloning and sequencing also provided unequivocal interpretation, but this method is labor intensive, risks plasmid contamination of the laboratory, may delay reporting, and is not routinely used in most clinical diagnostic laboratories.

"Although pyrosequencing and Sanger sequencing are both powerful tools to resolve most mutations, for certain complex cases, neither of them alone is enough to provide a definitive interpretation," notes Dr. Eshleman. "Additional methods, such as Pyromaker analysis or TA cloning and sequencing, allow one to definitively diagnose the variant allele. Pyromaker is available free online and can be accessed from any computer with internet access. Iterative Pyromaker analysis is the least expensive and fastest method to resolve these cases."

Pyromaker has been made freely available at http://pyromaker.pathology.jhmi.edu.

The article is "A Virtual Pyrogram Generator to Resolve Complex Pyrosequencing Results," by G. Chen, M.T. Olson, A. O'Neill, A. Norris-Kirby, K. Beierl, S. Harada, M. Debeljak, K. Rivera-Roman, S. Finley, A. Stafford, C.D. Gocke, M-T. Lin, and J. R. Eshleman (doi: 10.1016/j.jmoldx.2011.12.001). The Journal of Molecular Diagnostics, Volume 14, Issue 2 (March 2012) published by Elsevier.

Original article: http://www.eurekalert.org/pub_releases/2012-02/ehs-nvt020312.php