Clinical Sequencing Exploratory Research Consortium: Accelerating Evidence-Based Practice of Genomic Medicine

Despite rapid technical progress and demonstrable effectiveness for some types of diagnosis and therapy, much remains to be learned about clinical genome and exome sequencing (CGES) and its role within the practice of medicine. The Clinical Sequencing Exploratory Research (CSER) consortium includes 18 extramural research projects, one National Human Genome Research Institute (NHGRI) intramural project, and a coordinating center funded by the NHGRI and National Cancer Institute. The consortium is exploring analytic and clinical validity and utility, as well as the ethical, legal, and social implications of sequencing via multidisciplinary approaches; it has thus far recruited 5,577 participants across a spectrum of symptomatic and healthy children and adults by utilizing both germline and cancer sequencing. The CSER consortium is analyzing data and creating publically available procedures and tools related to participant preferences and consent, variant classification, disclosure and management of primary and secondary findings, health outcomes, and integration with electronic health records. Future research directions will refine measures of clinical utility of CGES in both germline and somatic testing, evaluate the use of CGES for screening in healthy individuals, explore the penetrance of pathogenic variants through extensive phenotyping, reduce discordances in public databases of genes and variants, examine social and ethnic disparities in the provision of genomics services, explore regulatory issues, and estimate the value and downstream costs of sequencing. The CSER consortium has established a shared community of research sites by using diverse approaches to pursue the evidence-based development of best practices in genomic medicine

Addressing a clinical challenge: guidelines for the diagnosis and treatment of leishmaniasis

Abstract Leishmaniasis is a chronic intracellular parasitic infection that travelers, immigrants, deployed military personnel, and refugees from endemic global areas acquire from the bite of infected sand flies and carry with them, including to non-endemic countries where leishmaniasis may be an unfamiliar illness to medical providers. This commentary discusses the first clinical practice guidelines produced by the Infectious Diseases Society of America and American Society of Tropical Medicine and Hygiene for the diagnosis and management of leishmaniasis, targeted for clinicians in North America

Shiga Toxin-Producing Escherichia coli-Associated Kidney Failure in a 40-Year-Old Patient and Late Diagnosis by Novel Bacteriologic and Toxin Detection Methods

Infection with Shiga toxin-producing Escherichia coli (STEC) is the most common cause of kidney failure in children. High morbidity is also associated with infections in the elderly. We describe STEC-associated kidney failure in a 40-year-old patient, including the methods used to identify STEC a month after disease onset

The Immunology of a Healing Response in Cutaneous Leishmaniasis Treated with Localized Heat or Systemic Antimonial Therapy.

BACKGROUND:The effectiveness of systemic antimonial (sodium stibogluconate, Pentostam, SSG) treatment versus local heat therapy (Thermomed) for cutaneous leishmaniasis was studied previously and showed similar healing rates. We hypothesized that different curative immune responses might develop with systemic and local treatment modalities. METHODS:We studied the peripheral blood immune cells in a cohort of 54 cutaneous Leishmania major subjects treated with SSG or TM. Multiparameter flow cytometry, lymphoproliferative assays and cytokine production were analyzed in order to investigate the differences in the immune responses of subjects before, on and after treatment. RESULTS:Healing cutaneous leishmaniasis lead to a significant decline in circulating T cells and NKT-like cells, accompanied by an expansion in NK cells, regardless of treatment modality. Functional changes involved decreased antigen specific CD4+ T cell proliferation (hyporesponsiveness) seen with CD8+ T cell depletion. Moreover, the healing (or healed) state was characterized by fewer circulating regulatory T cells, reduced IFN-γ production and an overall contraction in polyfunctional CD4+ T cells. CONCLUSION:Healing from cutaneous Leishmaniasis is a dynamic process that alters circulating lymphocyte populations and subsets of T, NK and NKT-like cells. Immunology of healing, through local or systemic treatments, culminated in similar changes in frequency, quality, and antigen specific responsiveness with immunomodulation possibly via a CD8+ T cell dependent mechanism. Understanding the evolving immunologic changes during healing of human leishmaniasis informs protective immune mechanisms

Identification of responding populations by CFDA-SE labeling and flow cytometry analysis.

<p>Identification of proliferating lymphocytes based on expression of (<b>A</b>) CD4 and CD8 or (<b>B</b>) CD25. Circles represent SSG subjects and triangles represent TM subjects. Black and grey are for PRE and POST respectively. Bars represent medians.</p

Identification of activated and regulatory T cell populations by flow cytometry.

<p><b>(A)</b> Freshly isolated cells were stained for CD3, CD4, CD8 and CD25 for identification of activated T cells. Data obtained from 31 subjects (circles for SSG subjects and triangles for TM subjects) for which pre-treatment (black) and post-treatment (grey) cells were available. Bars represent medians. <b>(B)</b> Identification of Treg cells from thawed PBMC. Aggregate data from 20 donors for CD4⁺CD25^high Foxp3⁺. P values derived using the Wilcoxon matched pairs test.</p

Lymphoproliferative response and cytokine production.

<p>(<b>A</b>) Whole PBMC or CD8⁺T cell-depleted PBMC (CD8 depl PBMC) from 18 subjects (circles) and 16 subjects (triangles) treated respectively with SSG and TM at pre-treatment (black) and post-treatment (grey) stages were stimulated with SLA for 6 days followed by an 8 hour pulse with [³H]-thymidine. Lymphocyte stimulation index (LSI) was determined as fold-increase in mean cpm from triplicate wells over unstimulated wells. An LSI ≥ 5 (dotted line) is considered a positive response. (<b>B</b>) <i>L</i>. <i>major</i> antigen responses in whole PBMC stratified by treatment arm. (<b>C-E</b>) Cytokine production following stimulation with SLA. (<b>C</b>) IFN-γ, (<b>D</b>) TNF-α and (E) IL-10 production by total PBMC or CD8⁺ cell-depleted PBMC was quantified from supernatants sampled on day 6 of the lymphoproliferation assays. Bars represent medians. <i>P</i> values were derived using the Wilcoxon matched pairs test.</p

Demographic characteristics and outcome presented by treatment arm.

<p>* Mann-Whitney</p><p>** Fisher exact</p><p>***Vassarstats</p><p>Demographic characteristics and outcome presented by treatment arm.</p