Browsing by Author "Schroeder, Andrew"

Now showing 1 - 2 of 2
  • Thumbnail Image
    Item
    A multimodal and integrated approach to interrogate human kidney biopsies with rigor and reproducibility: guidelines from the Kidney Precision Medicine Project
    (American Physiological Society, 2021) El-Achkar, Tarek M.; Eadon, Michael T.; Menon, Rajasree; Lake, Blue B.; Sigdel, Tara K.; Alexandrov, Theodore; Parikh, Samir; Zhang, Guanshi; Dobi, Dejan; Dunn, Kenneth W.; Otto, Edgar A.; Anderton, Christopher R.; Carson, Jonas M.; Luo, Jinghui; Park, Chris; Hamidi, Habib; Zhou, Jian; Hoover, Paul; Schroeder, Andrew; Joanes, Marianinha; Azeloglu, Evren U.; Sealfon, Rachel; Winfree, Seth; Steck, Becky; He, Yongqun; D’Agati, Vivette; Iyengar, Ravi; Troyanskaya, Olga G.; Barisoni, Laura; Gaut, Joseph; Zhang, Kun; Laszik, Zoltan; Rovin, Brad H.; Dagher, Pierre C.; Sharma, Kumar; Sarwal, Minnie M.; Hodgin, Jeffrey B.; Alpers, Charles E.; Kretzler, Matthias; Jain, Sanjay; Medicine, School of Medicine
    Comprehensive and spatially mapped molecular atlases of organs at a cellular level are a critical resource to gain insights into pathogenic mechanisms and personalized therapies for diseases. The Kidney Precision Medicine Project (KPMP) is an endeavor to generate three-dimensional (3-D) molecular atlases of healthy and diseased kidney biopsies by using multiple state-of-the-art omics and imaging technologies across several institutions. Obtaining rigorous and reproducible results from disparate methods and at different sites to interrogate biomolecules at a single-cell level or in 3-D space is a significant challenge that can be a futile exercise if not well controlled. We describe a “follow the tissue” pipeline for generating a reliable and authentic single-cell/region 3-D molecular atlas of human adult kidney. Our approach emphasizes quality assurance, quality control, validation, and harmonization across different omics and imaging technologies from sample procurement, processing, storage, shipping to data generation, analysis, and sharing. We established benchmarks for quality control, rigor, reproducibility, and feasibility across multiple technologies through a pilot experiment using common source tissue that was processed and analyzed at different institutions and different technologies. A peer review system was established to critically review quality control measures and the reproducibility of data generated by each technology before their being approved to interrogate clinical biopsy specimens. The process established economizes the use of valuable biopsy tissue for multiomics and imaging analysis with stringent quality control to ensure rigor and reproducibility of results and serves as a model for precision medicine projects across laboratories, institutions and consortia.
  • Thumbnail Image
    Item
    Factors influencing survival among Kenyan children diagnosed with endemic Burkitt lymphom between 2003 and 2011: a historical cohort study
    (Wiley, 2016-09-15) Buckle, Geoffrey; Maranda, Louise; Skiles, Jodi; Ong'echa, John Michael; Foley, Joslyn; Epstein, Mara; Vik, Terry A.; Schroeder, Andrew; Lemberger, Jennifer; Rosmarin, Alan; Remick, Scot C.; Bailey, Jeffrey A.; Vulule, John; Otieno, Juliana A.; Moormann, Ann M.; Pediatrics, School of Medicine
    Discovering how to improve survival and establishing clinical reference points for children diagnosed with endemic Burkitt lymphoma (eBL) in resource-constrained settings has recaptured international attention. Using multivariate analyses, we evaluated 428 children with eBL in Kenya for age, gender, tumor stage, nutritional status, hemoglobin, lactate dehydrogenase (LDH), Epstein-Barr virus (EBV) and Plasmodium falciparum prior to induction of chemotherapy (cyclophosphamide, vincristine, methotrexate, and doxorubicin) to identify predictive and prognostic biomarkers of survival. During this ten year prospective study period, 22% died in-hospital and 78% completed six-courses of chemotherapy. Of those, 16% relapsed or died later; 31% achieved event-free-survival; and 31% were lost to follow-up; the overall one-year survival was 45%. After adjusting for co-variates, low hemoglobin (<8g/dL) and high LDH (>400 mU/ml) were associated with increased risk of death (adjusted Hazard Ratio (aHR)=1.57 [0.97 to 2.41]) and aHR=1.84, [0.91 to 3.69], respectively). Anemic children with malaria were 3.55 times more likely to die [1.10 to 11.44] compared to patients without anemia or malarial infection. EBV load did not differ by tumor stage nor was it associated with survival. System-level factors can also contribute to poor outcomes. Children were more likely to die when inadvertently overdosed by more than 115% of the correct dose of cyclophosphamide (aHR=1.43 [0.84 to 2.43]), or doxorubicin (aHR=1.25, [0.66 to 2.35]), compared to those receiving accurate doses of the respective agent in this setting. This study codifies risk factors associated with poor outcomes for eBL patients in Africa and provides a benchmark by which to assess improvements in survival for new chemotherapeutic approaches.