Data Access and Interactive Visualization of Whole Genome Sequence of Sickle Cell Patients within the St. Jude Cloud

With the increase in availability of high depth whole genome sequencing (WGS) data of individuals with sickle cell disease (SCD), easy access to the raw sequencing data remains an issue due to technical and regulatory challenges. A compliant system that can provide facile data access would accelerate scientific discovery of genetic variants associated with clinical phenotypes. Cloud storage and computing provide an ultimate solution to this data access, which we have shown through the St. Jude Cloud (https://stjude.cloud) where over 5000 whole genome sequences for pediatric cancer patients are being shared in collaboration with DNANexus and Microsoft. Here we expand the St. Jude Cloud to sickle cell disease data through the Sickle Genome Project (SGP) Data Portal (https://pecan.stjude.org/permalink/sgp) to allow instantaneous raw data access (following data access committee approval), as well as visualization of genotype calls at individual level in a novel genome. The SGP WGS data was generated from 871 patients from St. Jude Children's Research Hospital (St. Jude) through the Sickle Cell Clinical Research and Intervention Program (SCCRIP, Pediatr Blood Cancer. 2018 May 24: e27228) and from Baylor College of Medicine (BCM). All study participants provided informed consent for genomic study and data sharing on IRB-approved research protocols.The SGP data portal will have multi-tiered access. All users will have access to a general heat map view which shows anonymized patient ...
Source: Blood - Category: Hematology Authors: Tags: 113. Hemoglobinopathies, Excluding Thalassemia-Basic and Translational Science: Sickle Cell Disease-Genomic, Gene Regulation, and Pain Mechanisms Source Type: research

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This study was supported by the Swiss National Science Foundation No. 31-124861 to GS. Conflict of Interest Statement The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. Supplementary Material The Supplementary Material for this article can be found online at: https://www.frontiersin.org/articles/10.3389/fphar.2019.00414/full#supplementary-material References Chava, K. R., Tauseef, M., Sharma, T., and Mehta, D. (2012). Cyclic AMP response element-binding protein prevents endothelial permeability...
Source: Frontiers in Pharmacology - Category: Drugs & Pharmacology Source Type: research
Clarification pertains to opioid prescribing for cancer patients, cancer survivors, sickle cell disease
Source: The Doctors Lounge - Oncology - Category: Cancer & Oncology Tags: Oncology, Pharmacy, Anesthesiology & amp; Pain, Institutional, Source Type: news
In this study, we used HUT as the means to provide an all-encompassing assessment of cardiac and/or peripheral autonomic function in normal controls, SCD subjects and non-SCD subjects with chronic anemia. We hypothesized that by identifying different categories of HUT response among these subjects, we would be able to isolate the autonomic phenotypes that might place SCD subjects at increased risk for microvascular occlusion and VOC. We then employed the causal modeling approach, which utilizes signal analysis and system identification techniques, to probe and disentangle the functional mechanisms involved in the cardiovas...
Source: Frontiers in Physiology - Category: Physiology Source Type: research
Some insurers had cited the CDC’s previous opioid guidelines and refused to pay for prescriptions for patients with cancer or sickle cell anemia, or other chronic pain conditions.
Source: WebMD Health - Category: Consumer Health News Source Type: news
TUESDAY, April 9, 2019 -- People with severe pain from cancer or sickle cell anemia should not be denied coverage for opioid painkillers, a new clarification on federal guidelines states. In the wake of the national opioid epidemic, various medical...
Source: Drugs.com - Daily MedNews - Category: General Medicine Source Type: news
Backgroundβ-globin gene transfer has the potential for substantial clinical benefit in patients with sickle cell disease (SCD). LentiGlobin Drug Product (DP) contains autologous CD34+ hematopoietic stem cells (HSCs) transduced with the BB305 lentiviral vector (LVV), encoding β-globin with an anti-sickling substitution (T87Q). The safety and efficacy of LentiGlobin gene therapy is being evaluated in the ongoing Phase 1 HGB-206 study (NCT02140554). Results in the initial 7 patients treated with LentiGlobin DP from steady state bone marrow harvested (BMH) HSCs using original DP manufacturing process (Group A) demons...
Source: Blood - Category: Hematology Authors: Tags: 801. Gene Therapy and Transfer: Gene Therapy for Blood Cell Disorders Source Type: research
Although sickle cell disease (SCD) is a monogenic disorder, the severity and specific organ dysfunction and failure are strongly influenced by genetic modifiers. Rapid identification of all modifiers in patients and well-phenotyped cohorts will better define the impact of relevant variants on clinical status, inform disease biology, and identify new therapeutic strategies. We created the Sickle Genome Project (SGP), a whole genome sequencing (WGS) strategy, to define genomic variation and modifiers of SCD. We performed WGS on 871 African American SCD patients from St. Jude Children's Research Hospital who participated in t...
Source: Blood - Category: Hematology Authors: Tags: 113. Hemoglobinopathies, Excluding Thalassemia-Basic and Translational Science: Poster III Source Type: research
ConclusionHospitalization rates are rising among most age-groups of adults with SCD. The reasons for this finding are unclear but the rising rates may reflect the fragmentation of care for SCD in adults as well as age-related increases in pain-related comorbidities and SCD complications as SCD patients live longer. However, there has been no associated increase in-hospital SCD mortality, supporting extant data which suggest that the rate of opioid-related deaths in SCD is low, and the use of opioids for pain control may be considered relatively safe in the SCD population.DisclosuresNo relevant conflicts of interest to declare.
Source: Blood - Category: Hematology Authors: Tags: 901. Health Services Research-Non-Malignant Conditions: Sickle Cell Disease Source Type: research
Sickle cell disease is a genetic blood disorder with significant morbidity and mortality. This disease is characterized by vaso-occlusive pain crisis and end-organ damage, ultimately contributing to poor quality of life and reduced life expectancy. While many advances have been made in the management of sickle cell disease, there remains room for improvement in the delivery of care for these patients.The Lifespan Academic Medical Center is the largest health care organization in the state of Rhode Island. In January of 2018, a large cohort of patients was referred to Lifespan's Cancer Institute for treatment of sickle cell...
Source: Blood - Category: Hematology Authors: Tags: 114. Hemoglobinopathies, Excluding Thalassemia-Clinical Source Type: research
This study was approved by the IRB at UHCMC. Within a 24-hour period, RBC adhesion to LN was quantitated by microscopy after passage of unprocessed whole blood through a LN-coated microfluidic adhesion assay, the SCD biochip [1]. Samples were analyzed for hemoglobin (Hb) phenotype by high-performance liquid chromatography (HPLC) in the clinical lab. Correlative clinical data, including, baseline lab values, and medical history, were obtained from the patients' medical records and used to characterize our results. Data from people with multiple samples were used as median values.Results:Blood samples from 19 unselected pati...
Source: Blood - Category: Hematology Authors: Tags: 114. Hemoglobinopathies, Excluding Thalassemia-Clinical: Poster II Source Type: research
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