Mandatory HIV Testing Issues in State Newborn Screening Programs

The newborn screening model is fairly straightforward. Typically, before the infant is discharged from the hospital (around 24 to 36 hours of age), heel stick blood is placed on special filter paper, dried, and mailed to the state health department for testing. Medical and laboratory research has led to the discovery that other diseases could also be screened in newborns using these dried blood specimens. Currently, all states and the District of Columbia test all newborns for at least PKU and congenital hypothyroidism. There are generally five criteria to satisfy before a disease is considered appropriate for newborn screening: 1. The disease must be well defined and serious enough to justify mass screening; 2. There must be an accurate testing method available; 3. The cost of the test must be reasonable; 4. There must be available treatment for the disorder; and 5. There must be adequate medical management facilities to refer infants for confirmatory diagnosis and treatment. Although newborn screening is often classified as genetic screening, these criteria do not require that the screened disorder have a genetic origin. In fact, congenital hypothyroidism, which is part of every newborn screening program in this country, is usually not a genetic disease

Mandatory HIV Testing Issues in State Newborn Screening Programs

The newborn screening model is fairly straightforward. Typically, before the infant is discharged from the hospital (around 24 to 36 hours of age), heel stick blood is placed on special filter paper, dried, and mailed to the state health department for testing. Medical and laboratory research has led to the discovery that other diseases could also be screened in newborns using these dried blood specimens. Currently, all states and the District of Columbia test all newborns for at least PKU and congenital hypothyroidism. There are generally five criteria to satisfy before a disease is considered appropriate for newborn screening: 1. The disease must be well defined and serious enough to justify mass screening; 2. There must be an accurate testing method available; 3. The cost of the test must be reasonable; 4. There must be available treatment for the disorder; and 5. There must be adequate medical management facilities to refer infants for confirmatory diagnosis and treatment. Although newborn screening is often classified as genetic screening, these criteria do not require that the screened disorder have a genetic origin. In fact, congenital hypothyroidism, which is part of every newborn screening program in this country, is usually not a genetic disease

Advances in the Stille reaction and new methods for continuous flow Pd-catalyzed C-N bond forming reactions

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 2010.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Vita. Cataloged from student-submitted PDF version of thesis.Includes bibliographical references.Chapter 1: A highly active catalyst system based upon a biaryl monophosphine ligand, XPhos, for the palladium-catalyzed Stille reaction has been developed. This method allows for the coupling of aryl chlorides with a range of tributylarylstannanes to produce the corresponding biaryl compounds in good to excellent yields (61-98%) in short reaction times (4 h). Palladium(II) acetate [Pd(OAc)2] and XPhos in a 1:1.1 ratio were milled into a fine powder that was used as pre-catalyst for these reactions. Chapter 2: A catalyst system for the Stille cross-coupling reactions of aryl mesylates and tosylates is reported. Using the combination of Pd(OAc)2, XPhos, and CsF in t-BuOH an array of aryl and heteroaryl sulfonates were successfully employed in these reactions. Morever, heteroarylstannanes, such as furyl, thienyl, and N-methylpyrrolyl, which are often prone to decomposition, were efficiently coupled under these conditions. Ortho-substitution on the stannane coupling partner was well tolerated; however, the presence of ortho substituents on the aryl sulfonates greatly reduced the efficiency of these reactions. Chapter 3: A continuous-flow, multistep Heck synthesis was made possible by integrating microreactors, liquid-liquid extraction, and microfluidic distillation. The microfluidic distillation enabled solvent exchange from CH2Cl2 in the first reaction step to N,N-dimethylformamide (DMF) in the final reaction step. Chapter 4: A method to mitigate clogging of microsystems during Pd-catalyzed C-N bond-forming reactions under continuous flow conditions was developed. Bridging of particles across the channel and deposition of materials on the walls of the microreactor were both found to be causes that led to clogging and techniques to minimize their effects using sonication were developed. This system allows Pd-catalyzed amination reactions for the formation of a diaryl amines to proceed for extended periods of time without significant pressure increase in the reactor. Chapter 5: A highly efficient method for the Pd-catalyzed coupling of aryl chloride and anilines has been developed. Catalysts based on allyl palladium chloride dimer and BrettPhos, using biphasic reaction conditions of toluene and water with KOH as a base, provided excellent yields for these reactions. The use of a packed bed reactor allowed for these reactions to be run in a continuous flow manner.by John R. Naber.Ph.D

Stille Cross-Coupling Reactions of Aryl Mesylates and Tosylates Using a Biarylphosphine Based Catalyst System

A catalyst system for the Stille cross-coupling reactions of aryl mesylates and tosylates is reported. Using the combination of Pd(OAc)[subscript 2], XPhos, and CsF in t-BuOH an array of aryl and heteroaryl sulfonates were successfully employed in these reactions. Morever, heteroarylstannanes, such as furyl, thienyl, and N-methylpyrrolyl, which are often prone to decomposition, were efficiently coupled under these conditions. Ortho-substitution on the stannane coupling partner was well tolerated; however, the presence of ortho substituents on the aryl sulfonates greatly reduced the efficiency of these reactions.National Institutes of Health (U.S.) (Grant GM-46059)Merck & Co.Boehringer Ingelheim Pharmaceutical

An informatics model for tissue banks – Lessons learned from the Cooperative Prostate Cancer Tissue Resource

BACKGROUND: Advances in molecular biology and growing requirements from biomarker validation studies have generated a need for tissue banks to provide quality-controlled tissue samples with standardized clinical annotation. The NCI Cooperative Prostate Cancer Tissue Resource (CPCTR) is a distributed tissue bank that comprises four academic centers and provides thousands of clinically annotated prostate cancer specimens to researchers. Here we describe the CPCTR information management system architecture, common data element (CDE) development, query interfaces, data curation, and quality control. METHODS: Data managers review the medical records to collect and continuously update information for the 145 clinical, pathological and inventorial CDEs that the Resource maintains for each case. An Access-based data entry tool provides de-identification and a standard communication mechanism between each group and a central CPCTR database. Standardized automated quality control audits have been implemented. Centrally, an Oracle database has web interfaces allowing multiple user-types, including the general public, to mine de-identified information from all of the sites with three levels of specificity and granularity as well as to request tissues through a formal letter of intent. RESULTS: Since July 2003, CPCTR has offered over 6,000 cases (38,000 blocks) of highly characterized prostate cancer biospecimens, including several tissue microarrays (TMA). The Resource developed a website with interfaces for the general public as well as researchers and internal members. These user groups have utilized the web-tools for public query of summary data on the cases that were available, to prepare requests, and to receive tissues. As of December 2005, the Resource received over 130 tissue requests, of which 45 have been reviewed, approved and filled. Additionally, the Resource implemented the TMA Data Exchange Specification in its TMA program and created a computer program for calculating PSA recurrence. CONCLUSION: Building a biorepository infrastructure that meets today's research needs involves time and input of many individuals from diverse disciplines. The CPCTR can provide large volumes of carefully annotated prostate tissue for research initiatives such as Specialized Programs of Research Excellence (SPOREs) and for biomarker validation studies and its experience can help development of collaborative, large scale, virtual tissue banks in other organ systems

Application of a risk-management framework for integration of stromal tumor-infiltrating lymphocytes in clinical trials

Stromal tumor-infiltrating lymphocytes (sTILs) are a potential predictive biomarker for immunotherapy response in metastatic triple-negative breast cancer (TNBC). To incorporate sTILs into clinical trials and diagnostics, reliable assessment is essential. In this review, we propose a new concept, namely the implementation of a risk-management framework that enables the use of sTILs as a stratification factor in clinical trials. We present the design of a biomarker risk-mitigation workflow that can be applied to any biomarker incorporation in clinical trials. We demonstrate the implementation of this concept using sTILs as an integral biomarker in a single-center phase II immunotherapy trial for metastatic TNBC (TONIC trial, NCT02499367), using this workflow to mitigate risks of suboptimal inclusion of sTILs in this specific trial. In this review, we demonstrate that a web-based scoring platform can mitigate potential risk factors when including sTILs in clinical trials, and we argue that this framework can be applied for any future biomarker-driven clinical trial setting

Pitfalls in assessing stromal tumor infiltrating lymphocytes (sTILs) in breast cancer

Abstract: Stromal tumor-infiltrating lymphocytes (sTILs) are important prognostic and predictive biomarkers in triple-negative (TNBC) and HER2-positive breast cancer. Incorporating sTILs into clinical practice necessitates reproducible assessment. Previously developed standardized scoring guidelines have been widely embraced by the clinical and research communities. We evaluated sources of variability in sTIL assessment by pathologists in three previous sTIL ring studies. We identify common challenges and evaluate impact of discrepancies on outcome estimates in early TNBC using a newly-developed prognostic tool. Discordant sTIL assessment is driven by heterogeneity in lymphocyte distribution. Additional factors include: technical slide-related issues; scoring outside the tumor boundary; tumors with minimal assessable stroma; including lymphocytes associated with other structures; and including other inflammatory cells. Small variations in sTIL assessment modestly alter risk estimation in early TNBC but have the potential to affect treatment selection if cutpoints are employed. Scoring and averaging multiple areas, as well as use of reference images, improve consistency of sTIL evaluation. Moreover, to assist in avoiding the pitfalls identified in this analysis, we developed an educational resource available at www.tilsinbreastcancer.org/pitfalls