DNA methylation analysis by digital bisulfite genomic sequencing and digital MethyLight

Alterations in cytosine-5 DNA methylation are frequently observed in most types of human cancer. Although assays utilizing PCR amplification of bisulfite-converted DNA are widely employed to analyze these DNA methylation alterations, they are generally limited in throughput capacity, detection sensitivity, and or resolution. Digital PCR, in which a DNA sample is analyzed in distributive fashion over multiple reaction chambers, allows for enumeration of discrete template DNA molecules, as well as sequestration of non-specific primer annealing templates into negative chambers, thereby increasing the signal-to-noise ratio in positive chambers. Here, we have applied digital PCR technology to bisulfite-converted DNA for single-molecule high-resolution DNA methylation analysis and for increased sensitivity DNA methylation detection. We developed digital bisulfite genomic DNA sequencing to efficiently determine single-basepair DNA methylation patterns on single-molecule DNA templates without an interim cloning step. We also developed digital MethyLight, which surpasses traditional MethyLight in detection sensitivity and quantitative accuracy for low quantities of DNA. Using digital MethyLight, we identified single-molecule, cancer-specific DNA hypermethylation events in the CpG islands of RUNX3, CLDN5 and FOXE1 present in plasma samples from breast cancer patients

Intermediate Scales in SUSY SO(10), b-\tau unification and Hot Dark Matter Neutrinos

Considerations of massive neutrinos, baryogenesis as well as fermion mass textures in the grand unified theory framework provide strong motivations for supersymmetric(SUSY) SO(10) as the theory beyond the standard model. If one wants to simultaneously solve the strong CP problem via the Peccei-Quinn mechanism, the most natural way to implement it within the framework of the SUSY SO(10) model is to have an intermediate scale ($v_{BL}$) (corresponding to B-L symmetry breaking) around the invisible axion scale of about 10$^{11}$ - 10$^{12}$ GeV. Such a scale is also desirable if $\nu_{\tau}$ is to constitute the hot dark matter (HDM) of the universe. In this paper, we discuss examples of superstring inspired SUSY SO(10) models with intermediate scales that are consistent with the low energy precision measurements of the standard model gauge couplings. The hypothesis of $b-\tau$ unification which is a successful prediction of many grand unified theories is then required of these models and the resulting prediction of $b$-quark mass is used as a measure of viability of these schemes. Detailed analysis of a model with a $v_{BL}\simeq 10^{11}$ GeV, which satisfies both the requirements of invisible axion and $\nu_{\tau}$ as HDM is presented and shown to lead to $m_b\simeq 4.9$ GeV in the one-loop approximation.Comment: Latex file; 20 pages; Four figures available on reques

Prediction of Glioblastoma Multiform Response to Bevacizumab Treatment Using Multi-Parametric MRI

Glioblastoma multiform (GBM) is a highly malignant brain tumor. Bevacizumab is a recent therapy for stopping tumor growth and even shrinking tumor through inhibition of vascular development (angiogenesis). This paper presents a non-invasive approach based on image analysis of multi-parametric magnetic resonance images (MRI) to predict response of GBM to this treatment. The resulting prediction system has potential to be used by physicians to optimize treatment plans of the GBM patients. The proposed method applies signal decomposition and histogram analysis methods to extract statistical features from Gd-enhanced regions of tumor that quantify its microstructural characteristics. MRI studies of 12 patients at multiple time points before and up to four months after treatment are used in this work. Changes in the Gd-enhancement as well as necrosis and edema after treatment are used to evaluate the response. Leave-one-out cross validation method is applied to evaluate prediction quality of the models. Predictive models developed in this work have large regression coefficients (maximum R2 = 0.95) indicating their capability to predict response to therapy

Effects of 126 dimensional Higgs scalar on Bottom-Tau unification and quasi-infrared fixed point

In the presence of ${\bf 126 + \bar{126}}$ Higgs multiplets in a SO(10) theory, the fermion masses get contributions from an induced vacuum expectation value (VEV) of a $SU(2)_L$ doublet residing in ${\bf 126}$ which differentiates between quarks and leptons by a relative sign leading to a significant correction to the prediction of the mass ratio of the bottom quark and the tau lepton for ranges of the mass of this extra doublet. We perform a two-loop renormalization group analysis of the minimal version of the one-step supersymmetric SO(10) model to display this and re-calculate the corrections to the top quark mass in the presence of such an induced VEV. We show that these effects make the infra-red fixed point scenario consistent with experimental results.Comment: revised version with same conclusions. To appear in Phys. Rev.

Comparison of ADC metrics and their association with outcome for patients with newly diagnosed glioblastoma being treated with radiation therapy, temozolomide, erlotinib and bevacizumab

To evaluate metrics that describe changes in apparent diffusion coefficient (ADC) and to examine their association with clinical outcome for patients with newly diagnosed GBM who were participating in a Phase II clinical trial of treatment with radiation (RT), temozolomide, erlatonib and bevacizumab. Thirty six patients were imaged after surgery but prior to therapy and at regular follow-up time points. The following ADC metrics were evaluated: (1) histogram percentiles within the T2-hyperintense lesion (T2L) at serial follow-ups; (2) parameters obtained by fitting a two-mixture normal distribution to the histogram within the contrast-enhancing lesion (CEL) at baseline; (3) parameters obtained using both traditional and graded functional diffusion maps within the CEL and T2L. Cox Proportional Hazards models were employed to assess the association of the ADC parameters with overall survival (OS) and progression-free survival (PFS). A lower ADC percentile value within the T2L at early follow-up time points was associated with worse outcome. Of particular interest is that, even when adjusting for clinical prognostic factors, the ADC(10%) within the T2L at 2 months was strongly associated with OS (p < 0.001) and PFS (p < 0.007). fDM metrics showed an association with OS and PFS within the CEL when considered by univariate analysis, but not in the T2L. Our study emphasizes the value of ADC metrics obtained from the T2L at the post-RT time point as non-invasive biomarkers for assessing residual tumor in patients with newly diagnosed GBM being treated with combination therapy that includes the anti-angiogenic agent bevacizumab

The reverse side of the victory: flare up of symptoms after discontinuation of sunitinib or sorafenib in renal cell cancer patients. A report of three cases.

Contains fulltext : 81207.pdf (publisher's version ) (Closed access

Absolute quantitative detection of ABL tyrosine kinase domain point mutations in chronic myeloid leukemia using a novel nanofluidic platform and mutation-specific PCR.

No abstract availabl