Next generation sequencing in clinical medicine: Challenges and lessons for pathology and biomedical informatics.

The Human Genome Project (HGP) provided the initial draft of mankind's DNA sequence in 2001. The HGP was produced by 23 collaborating laboratories using Sanger sequencing of mapped regions as well as shotgun sequencing techniques in a process that occupied 13 years at a cost of ~$3 billion. Today, Next Generation Sequencing (NGS) techniques represent the next phase in the evolution of DNA sequencing technology at dramatically reduced cost compared to traditional Sanger sequencing. A single laboratory today can sequence the entire human genome in a few days for a few thousand dollars in reagents and staff time. Routine whole exome or even whole genome sequencing of clinical patients is well within the realm of affordability for many academic institutions across the country. This paper reviews current sequencing technology methods and upcoming advancements in sequencing technology as well as challenges associated with data generation, data manipulation and data storage. Implementation of routine NGS data in cancer genomics is discussed along with potential pitfalls in the interpretation of the NGS data. The overarching importance of bioinformatics in the clinical implementation of NGS is emphasized.[7] We also review the issue of physician education which also is an important consideration for the successful implementation of NGS in the clinical workplace. NGS technologies represent a golden opportunity for the next generation of pathologists to be at the leading edge of the personalized medicine approaches coming our way. Often under-emphasized issues of data access and control as well as potential ethical implications of whole genome NGS sequencing are also discussed. Despite some challenges, it's hard not to be optimistic about the future of personalized genome sequencing and its potential impact on patient care and the advancement of knowledge of human biology and disease in the near future.

Integrating research and education at research-extensive universities with research-intensive communities.

Although the Boyer Commission (1998) lamented the lack of research opportunities for all undergraduates at research-extensive universities, it did not provide a feasible solution consistent with the mandate for faculty to maintain sustainable physiology research programs. The costs associated with one-on-one mentoring, and the lack of a sufficient number of faculty members to give intensive attention to undergraduate researchers, make one-on-one mentoring impractical. We therefore developed and implemented the "research-intensive community" model with the aim of aligning diverse goals of participants while simultaneously optimizing research productivity. The fundamental organizational unit is a team consisting of one graduate student and three undergraduates from different majors, supervised by a faculty member. Undergraduate workshops, Graduate Leadership Forums, and computer-mediated communication provide an infrastructure to optimize programmatic efficiency and sustain a multilevel, interdisciplinary community of scholars dedicated to research. While the model radically increases the number of undergraduates that can be supported by a single faculty member, the inherent resilience and scalability of the resulting complex adaptive system enables a research-intensive community program to evolve and grow.

Mechanics of the left ventricular myocardial interstitium: effects of acute and chronic myocardial edema.

Myocardial interstitial edema forms as a result of several disease states and clinical interventions. Acute myocardial interstitial edema is associated with compromised systolic and diastolic cardiac function and increased stiffness of the left ventricular chamber. Formation of chronic myocardial interstitial edema results in deposition of interstitial collagen, which causes interstitial fibrosis. To assess the effect of myocardial interstitial edema on the mechanical properties of the left ventricle and the myocardial interstitium, we induced acute and chronic interstitial edema in dogs. Acute myocardial edema was generated by coronary sinus pressure elevation, while chronic myocardial edema was generated by chronic pulmonary artery banding. The pressure-volume relationships of the left ventricular myocardial interstitium and left ventricular chamber for control animals were compared with acutely and chronically edematous animals. Collagen content of nonedematous and chronically edematous animals was also compared. Generating acute myocardial interstitial edema resulted in decreased left ventricular chamber compliance compared with nonedematous animals. With chronic edema, the primary form of collagen changed from type I to III. Left ventricular chamber compliance in animals made chronically edematous was significantly higher than nonedematous animals. The change in primary collagen type secondary to chronic left ventricular myocardial interstitial edema provides direct evidence for structural remodeling. The resulting functional adaptation allows the chronically edematous heart to maintain left ventricular chamber compliance when challenged with acute edema, thus preserving cardiac function over a wide range of interstitial fluid pressures.