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Description
Induced pluripotent stem cells (iPSCs) are an intriguing approach for neurological disease modeling, because neural lineage-specific cell types that retain the donors' complex genetics can be established in vitro. The statistical power of these iPSC-based models, however, is dependent on accurate diagnoses of the somatic cell donors; unfortunately, many neurodegenerative

Induced pluripotent stem cells (iPSCs) are an intriguing approach for neurological disease modeling, because neural lineage-specific cell types that retain the donors' complex genetics can be established in vitro. The statistical power of these iPSC-based models, however, is dependent on accurate diagnoses of the somatic cell donors; unfortunately, many neurodegenerative diseases are commonly misdiagnosed in live human subjects. Postmortem histopathological examination of a donor's brain, combined with premortem clinical criteria, is often the most robust approach to correctly classify an individual as a disease-specific case or unaffected control. We describe the establishment of primary dermal fibroblasts cells lines from 28 autopsy donors. These fibroblasts were used to examine the proliferative effects of establishment protocol, tissue amount, biopsy site, and donor age. As proof-of-principle, iPSCs were generated from fibroblasts from a 75-year-old male, whole body donor, defined as an unaffected neurological control by both clinical and histopathological criteria. To our knowledge, this is the first study describing autopsy donor-derived somatic cells being used for iPSC generation and subsequent neural differentiation. This unique approach also enables us to compare iPSC-derived cell cultures to endogenous tissues from the same donor. We utilized RNA sequencing (RNA-Seq) to evaluate the transcriptional progression of in vitro-differentiated neural cells (over a timecourse of 0, 35, 70, 105 and 140 days), and compared this with donor-identical temporal lobe tissue. We observed in vitro progression towards the reference brain tissue, supported by (i) a significant increasing monotonic correlation between the days of our timecourse and the number of actively transcribed protein-coding genes and long intergenic non-coding RNAs (lincRNAs) (P < 0.05), consistent with the transcriptional complexity of the brain, (ii) an increase in CpG methylation after neural differentiation that resembled the epigenomic signature of the endogenous tissue, and (iii) a significant decreasing monotonic correlation between the days of our timecourse and the percent of in vitro to brain-tissue differences (P < 0.05) for tissue-specific protein-coding genes and all putative lincRNAs. These studies support the utility of autopsy donors' somatic cells for iPSC-based neurological disease models, and provide evidence that in vitro neural differentiation can result in physiologically progression.
ContributorsHjelm, Brooke E (Author) / Craig, David W. (Thesis advisor) / Wilson-Rawls, Norma J. (Thesis advisor) / Huentelman, Matthew J. (Committee member) / Mason, Hugh S. (Committee member) / Kusumi, Kenro (Committee member) / Arizona State University (Publisher)
Created2013
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Description
Rapid advancements in genomic technologies have increased our understanding of rare human disease. Generation of multiple types of biological data including genetic variation from genome or exome, expression from transcriptome, methylation patterns from epigenome, protein complexity from proteome and metabolite information from metabolome is feasible. "Omics" tools provide comprehensive view

Rapid advancements in genomic technologies have increased our understanding of rare human disease. Generation of multiple types of biological data including genetic variation from genome or exome, expression from transcriptome, methylation patterns from epigenome, protein complexity from proteome and metabolite information from metabolome is feasible. "Omics" tools provide comprehensive view into biological mechanisms that impact disease trait and risk. In spite of available data types and ability to collect them simultaneously from patients, researchers still rely on their independent analysis. Combining information from multiple biological data can reduce missing information, increase confidence in single data findings, and provide a more complete view of genotype-phenotype correlations. Although rare disease genetics has been greatly improved by exome sequencing, a substantial portion of clinical patients remain undiagnosed. Multiple frameworks for integrative analysis of genomic and transcriptomic data are presented with focus on identifying functional genetic variations in patients with undiagnosed, rare childhood conditions. Direct quantitation of X inactivation ratio was developed from genomic and transcriptomic data using allele specific expression and segregation analysis to determine magnitude and inheritance mode of X inactivation. This approach was applied in two families revealing non-random X inactivation in female patients. Expression based analysis of X inactivation showed high correlation with standard clinical assay. These findings improved understanding of molecular mechanisms underlying X-linked disorders. In addition multivariate outlier analysis of gene and exon level data from RNA-seq using Mahalanobis distance, and its integration of distance scores with genomic data found genotype-phenotype correlations in variant prioritization process in 25 families. Mahalanobis distance scores revealed variants with large transcriptional impact in patients. In this dataset, frameshift variants were more likely result in outlier expression signatures than other types of functional variants. Integration of outlier estimates with genetic variants corroborated previously identified, presumed causal variants and highlighted new candidate in previously un-diagnosed case. Integrative genomic approaches in easily attainable tissue will facilitate the search for biomarkers that impact disease trait, uncover pharmacogenomics targets, provide novel insight into molecular underpinnings of un-characterized conditions, and help improve analytical approaches that use large datasets.
ContributorsSzelinger, Szabolcs (Author) / Craig, David W. (Thesis advisor) / Kusumi, Kenro (Thesis advisor) / Narayan, Vinodh (Committee member) / Rosenberg, Michael S. (Committee member) / Huentelman, Matthew J (Committee member) / Arizona State University (Publisher)
Created2015
Description
In 2014, the Centers for Medicare and Medicaid Services (CMS), which oversees the federal Clinical Laboratories Improvement Amendments (CLIA) program, issued guidance that the CLIA requirements apply when researchers seek to return individual-level research findings to study participants or their physician (Centers for Medicare & Medicaid Services, 2014). The present

In 2014, the Centers for Medicare and Medicaid Services (CMS), which oversees the federal Clinical Laboratories Improvement Amendments (CLIA) program, issued guidance that the CLIA requirements apply when researchers seek to return individual-level research findings to study participants or their physician (Centers for Medicare & Medicaid Services, 2014). The present study explores the stance of U.S. Institutional Review Boards (IRBs) toward the applicability of and compliance with the CLIA regulations when studies plan to return individual research results (RIRR). I performed a document content analysis of 73 IRB policies and supporting documents from 30 United States (U.S.) institutions funded for biomedical research by the National Institutes of Health in 2017. Documents analyzed included policies, procedures, guidance, protocol and consent templates, and miscellaneous documents (such as IRB presentations) found to address the RIRR to study participants. I used qualitative content and document analysis to identify themes across institutions related to the CLIA regulations and the RIRR. Basic descriptive statistics were used to represent the data quantitatively. The study found that 96.67% (n=29) of institutions had documents that addressed the RIRR to participants. The majority of the institutions had at least one document that referenced the CLIA regulations when discussing the practice of disclosing participant-specific results [76.67% (n=23)]. The majority of institutions [56.67% (n=17)] indicated that they require compliance with the CLIA regulations for returning individual study findings to participants, while 13.33% (n=4) recommended compliance. The intent of two (6.67%) institutions was vague or unclear, while seven (26.67%) institutions were silent on the topic altogether. Of the 23 institutions that referenced “CLIA” in their documents, 52.17% only mentioned CLIA in a one or two-sentence blurb, providing very little guidance to investigators. The study results provide evidence that the majority of U.S. biomedical institutions require or recommend compliance with CLIA stipulations when investigators intend to return individual research results to study participants. However, the data indicates there is heterogeneity and variation in the quality of the guidance provided.
ContributorsBuchholtz, Stephanie (Author) / Robert, Jason S. (Thesis advisor) / Ellison, Karin D. (Committee member) / Carpten, John D. (Committee member) / Craig, David W. (Committee member) / Marchant, Gary E. (Committee member) / Arizona State University (Publisher)
Created2021