Matching Items (50)
Filtering by
- Genre: Doctoral Dissertation
Description
Immunotherapy has been revitalized with the advent of immune checkpoint blockade
treatments, and neo-antigens are the targets of immune system in cancer patients who
respond to the treatments. The cancer vaccine field is focused on using neo-antigens from
unique point mutations of genomic sequence in the cancer patient for making
personalized cancer vaccines. However, we choose a different path to find frameshift
neo-antigens at the mRNA level and develop broadly effective cancer vaccines based on
frameshift antigens.
In this dissertation, I have summarized and characterized all the potential frameshift
antigens from microsatellite regions in human, dog and mouse. A list of frameshift
antigens was validated by PCR in tumor samples and the mutation rate was calculated for
one candidate – SEC62. I develop a method to screen the antibody response against
frameshift antigens in human and dog cancer patients by using frameshift peptide arrays.
Frameshift antigens selected by positive antibody response in cancer patients or by MHC
predictions show protection in different mouse tumor models. A dog version of the
cancer vaccine based on frameshift antigens was developed and tested in a small safety
trial. The results demonstrate that the vaccine is safe and it can induce strong B and T cell
immune responses. Further, I built the human exon junction frameshift database which
includes all possible frameshift antigens from mis-splicing events in exon junctions, and I
develop a method to find potential frameshift antigens from large cancer
immunosignature dataset with these databases. In addition, I test the idea of ‘early cancer
diagnosis, early treatment’ in a transgenic mouse cancer model. The results show that
ii
early treatment gives significantly better protection than late treatment and the correct
time point for treatment is crucial to give the best clinical benefit. A model for early
treatment is developed with these results.
Frameshift neo-antigens from microsatellite regions and mis-splicing events are
abundant at mRNA level and they are better antigens than neo-antigens from point
mutations in the genomic sequences of cancer patients in terms of high immunogenicity,
low probability to cause autoimmune diseases and low cost to develop a broadly effective
vaccine. This dissertation demonstrates the feasibility of using frameshift antigens for
cancer vaccine development.
treatments, and neo-antigens are the targets of immune system in cancer patients who
respond to the treatments. The cancer vaccine field is focused on using neo-antigens from
unique point mutations of genomic sequence in the cancer patient for making
personalized cancer vaccines. However, we choose a different path to find frameshift
neo-antigens at the mRNA level and develop broadly effective cancer vaccines based on
frameshift antigens.
In this dissertation, I have summarized and characterized all the potential frameshift
antigens from microsatellite regions in human, dog and mouse. A list of frameshift
antigens was validated by PCR in tumor samples and the mutation rate was calculated for
one candidate – SEC62. I develop a method to screen the antibody response against
frameshift antigens in human and dog cancer patients by using frameshift peptide arrays.
Frameshift antigens selected by positive antibody response in cancer patients or by MHC
predictions show protection in different mouse tumor models. A dog version of the
cancer vaccine based on frameshift antigens was developed and tested in a small safety
trial. The results demonstrate that the vaccine is safe and it can induce strong B and T cell
immune responses. Further, I built the human exon junction frameshift database which
includes all possible frameshift antigens from mis-splicing events in exon junctions, and I
develop a method to find potential frameshift antigens from large cancer
immunosignature dataset with these databases. In addition, I test the idea of ‘early cancer
diagnosis, early treatment’ in a transgenic mouse cancer model. The results show that
ii
early treatment gives significantly better protection than late treatment and the correct
time point for treatment is crucial to give the best clinical benefit. A model for early
treatment is developed with these results.
Frameshift neo-antigens from microsatellite regions and mis-splicing events are
abundant at mRNA level and they are better antigens than neo-antigens from point
mutations in the genomic sequences of cancer patients in terms of high immunogenicity,
low probability to cause autoimmune diseases and low cost to develop a broadly effective
vaccine. This dissertation demonstrates the feasibility of using frameshift antigens for
cancer vaccine development.
ContributorsZhang, Jian (Author) / Johnston, Stephen Albert (Thesis advisor) / Chang, Yung (Committee member) / Stafford, Phillip (Committee member) / Chen, Qiang (Committee member) / Arizona State University (Publisher)
Created2018
Description
Alzheimer’s disease (AD) is a progressive neurodegenerative disease that affects 5.4 million Americans. AD leads to memory loss, changes in behavior, and death. The key hallmarks of the disease are amyloid plaques and tau tangles, consisting of amyloid-β oligomers and hyperphosphorylated tau, respectively.
Rho-associated, coiled-coil-containing protein kinase (ROCK) is an enzyme that plays important roles in neuronal cells including mediating actin organization and dendritic spine morphogenesis. The ROCK inhibitor Fasudil has been shown to increase learning and working memory in aged rats, but another ROCK inhibitor, Y27632, was shown to impair learning and memory. I am interested in exploring how these, and other ROCK inhibitors, may be acting mechanistically to result in very different outcomes in treated animals.
Preliminary research on thirteen different ROCK inhibitors provides evidence that while Fasudil and a novel ROCK inhibitor, T343, decrease tau phosphorylation in vitro, Y27632 increases tau phosphorylation at a low dose and decreases at a high dose. Meanwhile, novel ROCK inhibitor T299 increases tau phosphorylation at a high dosage.
Further, an in vivo study using triple transgenic AD mice provides evidence that Fasudil improves reference memory and fear memory in both transgenic and wild-type mice, while Y27632 impairs reference memory in transgenic mice. Fasudil also decreases tau phosphorylation and Aβ in vivo, while Y27632 significantly increases the p-tau to total tau ratio.
Rho-associated, coiled-coil-containing protein kinase (ROCK) is an enzyme that plays important roles in neuronal cells including mediating actin organization and dendritic spine morphogenesis. The ROCK inhibitor Fasudil has been shown to increase learning and working memory in aged rats, but another ROCK inhibitor, Y27632, was shown to impair learning and memory. I am interested in exploring how these, and other ROCK inhibitors, may be acting mechanistically to result in very different outcomes in treated animals.
Preliminary research on thirteen different ROCK inhibitors provides evidence that while Fasudil and a novel ROCK inhibitor, T343, decrease tau phosphorylation in vitro, Y27632 increases tau phosphorylation at a low dose and decreases at a high dose. Meanwhile, novel ROCK inhibitor T299 increases tau phosphorylation at a high dosage.
Further, an in vivo study using triple transgenic AD mice provides evidence that Fasudil improves reference memory and fear memory in both transgenic and wild-type mice, while Y27632 impairs reference memory in transgenic mice. Fasudil also decreases tau phosphorylation and Aβ in vivo, while Y27632 significantly increases the p-tau to total tau ratio.
ContributorsTurk, Mari (Author) / Huentelman, Matt (Thesis advisor) / Kusumi, Kenro (Thesis advisor) / Jensen, Kendall (Committee member) / Stabenfeldt, Sarah (Committee member) / Arizona State University (Publisher)
Created2017
Description
Satellite cells are adult muscle stem cells that activate, proliferate, and differentiate into myofibers upon muscle damage. Satellite cells can be cultured and manipulated in vitro, and thus represent an accessible model for studying skeletal muscle biology, and a potential source of autologous stem cells for regenerative medicine. This work summarizes efforts to further understanding of satellite cell biology, using novel model organisms, bioengineering, and molecular and cellular approaches. Lizards are evolutionarily the closest vertebrates to humans that regenerate entire appendages. An analysis of lizard myoprogenitor cell transcriptome determined they were most transcriptionally similar to mammalian satellite cells. Further examination showed that among genes with the highest level of expression in lizard satellite cells were an increased number of regulators of chondrogenesis. In micromass culture, lizard satellite cells formed nodules that expressed chondrogenic regulatory genes, thus demonstrating increased musculoskeletal plasticity. However, to exploit satellite cells for therapeutics, development of an ex vivo culture is necessary. This work investigates whether substrates composed of extracellular matrix (ECM) proteins, as either coatings or hydrogels, can support expansion of this population whilst maintaining their myogenic potency. Stiffer substrates are necessary for in vitro proliferation and differentiation of satellite cells, while the ECM composition was not significantly important. Additionally, satellite cells on hydrogels entered a quiescent state that could be reversed when the cells were subsequently cultured on Matrigel. Proliferation and gene expression data further indicated that C2C12 cells are not a good proxy for satellite cells. To further understand how different signaling pathways control satellite cell behavior, an investigation of the Notch inhibitor protein Numb was carried out. Numb deficient satellite cells fail to activate, proliferate and participate in muscle repair. Examination of Numb isoform expression in satellite cells and embryonic tissues revealed that while developing limb bud, neural tube, and heart express the long and short isoforms of NUMB, satellite cells predominantly express the short isoforms. A preliminary immunoprecipitation- proteomics experiment suggested that the roles of NUMB in satellite cells are related to cell cycle modulation, cytoskeleton dynamics, and regulation of transcription factors necessary for satellite cell function.
ContributorsPalade, Joanna (Author) / Wilson-Rawls, Norma (Thesis advisor) / Rawls, Jeffrey (Committee member) / Kusumi, Kenro (Committee member) / Newbern, Jason (Committee member) / Stabenfeldt, Sarah (Committee member) / Arizona State University (Publisher)
Created2020
Description
Necroptosis is a pro-inflammatory mechanism of programmed cell death. It has been implicated in many diseases such as inflammatory diseases, neurodegenerative diseases, cancer and during viral infections. The focus of this research work was to establish the relationship between poxvirus pathogenesis and necroptosis, and the translation implications of necroptosis in oncolytic virotherapy. Vaccinia virus (VACV) is the currently used vaccine for smallpox and it has also been developed as a vaccine vector for several pathogens. E3L is one of the key innate immune evasion genes of VACV and it encodes E3 protein composed of dsRNA binding domain in the C-terminus and Z-NA-binding domain (Z-NA BD) in the N terminus. Both domains are necessary for type 1 interferon resistance and pathogenesis. Recently, it has been shown that in in vitro, the N-terminus of E3 is necessary to inhibit necroptosis occurring through the host-encoded cellular proteins RIP3 and Z-NA-binding protein DAI interaction leading to phosphorylation of MLKL, the key executioner step in the pathway. The research work presented here clearly demonstrates that in a mouse model, the N-terminus of VACV E3 is necessary to inhibit necroptosis during pathogenesis in mice. Another poxvirus belonging to the same family as VACV is monkeypox virus (MPXV) and is an emerging human pathogen. MPXV contains a natural truncation in the N-terminus of its E3 homologue, F3. The results indicate that during MPXV infection in mice, pathogenesis was higher only in DAI knockout mice and not in MLKL knockout mice, suggesting that DAI is possibly activating other proteins not leading to necroptosis. The characterization of VACV as an oncolytic virus was carried out with a focus on future clinical trials. In this study, a pan screening was conducted in various cancer cell lines as many cancers downregulate necroptotic proteins. The results reveal that the N-terminal deletion mutant of VACV selectively replicates in cancer cell lines with a deficient necroptotic pathway and thus, can be used as a potential treatment against specific tumors and evidently, provides abundant scope for future studies.
ContributorsSubramanian, Sambhavi (Author) / Jacobs, Bertram (Thesis advisor) / Newbern, Jason (Thesis advisor) / Blattman, Joseph (Committee member) / Gustin, Kurt (Committee member) / Arizona State University (Publisher)
Created2020
Description
Traumatic injury to the central nervous or musculoskeletal system in traditional amniote models, such as mouse and chicken, is permanent with long-term physiological and functional effects. However, among amniotes, the ability to regrow complex, multi-tissue structures is unique to non-avian reptiles. Structural regeneration is extensively studied in lizards, with most species able to regrow a functional tail. The lizard regenerated tail includes the spinal cord, cartilage, de novo muscle, vasculature, and skin, and unlike mammals, these tissues can be replaced in lizards as adults. These studies focus on the events that occur before and after the tail regrowth phase, identifying conserved mechanisms that enable functional tail regeneration in the green anole lizard, Anolis carolinensis. An examination of coordinated interactions between peripheral nerves, Schwann cells, and skeletal muscle reveal that reformation of the lizard neuromuscular system is dependent upon developmental programs as well as those unique to the adult during late stages of regeneration. On the other hand, transcriptomic analysis of the early injury response identified many immunoregulatory genes that may be essential for inhibiting fibrosis and initiating regenerative programs. Lastly, an anatomical and histological study of regrown alligator tails reveal that regenerative capacity varies between different reptile groups, providing comparative opportunities within amniotes and across vertebrates. In order to identify mechanisms that limit regeneration, these cross-species analyses will be critical. Taken together, these studies serve as a foundation for future experimental work that will reveal the interplay between reparative and regenerative mechanisms in adult amniotes with translational implications for medical therapies.
ContributorsXu, Cindy (Author) / Kusumi, Kenro (Thesis advisor) / Newbern, Jason M (Thesis advisor) / Wilson-Rawls, Jeanne (Committee member) / Fisher, Rebecca E (Committee member) / Arizona State University (Publisher)
Created2020
Description
Flaviviruses (FVs) are among the most medically important arboviruses of the world with the Dengue virus (DENV) accounting for a large percentage of infections observed in tropical and subtropical regions of the world. Globalization, travel, and the expanding range of mosquito vectors, such as Aedes aegypti, have increased the potential of infection rates and illnesses associated with FVs.
The DENV and the Zika (ZIKV) FVs frequently co-circulate and generally cause mild self-liming febrile illnesses. However, a secondary infection with a heterologous DENV serotype may lead to life threatening dengue hemorrhagic fever (DHF) and dengue shock syndrome (DSS). DHF/DSS have been linked to antibody dependent enhancement of infection (ADE), a phenomenon that occurs when antibodies (Abs) formed against an initial infection with one serotype of DENV cross-reacts but does not neutralize a heterologous DENV serotype in a secondary infection. Furthermore, Abs raised against the ZIKV have been observed to cross-react with the DENV and vice versa, which can potentially cause ADE and lead to severe DENV disease. The ZIKV can be transmitted vertically and has been linked to devastating congenital defects such as microcephaly in newborns. FDA approved treatments do not exist for DENV and ZIKV illnesses. Thus, there is a need for safe and effective treatments for these co-circulating viruses. Here, a tetravalent bispecific antibody (bsAb) targeting the ZIKV and all four serotypes of the DENV was expressed in the Nicotiana benthamiana (N. benthamiana) plant. Functional assays of the DENV/ZIKV bsAb demonstrated binding, neutralization, and a significant reduction in ADE activity against both the DENV and the ZIKV.
A single chain variable fragment (scFv) and a diabody based on an antibody directed against the immune checkpoint inhibitor PD-L1, were also expressed in N. benthamiana leaves. The smaller sizes of the scFv and diabody confers them with the ability to penetrate deeper tissues making them beneficial in diagnostics, imaging, and possibly cancer therapy. The past few decades has seen long strives in recombinant protein production in plants with significant improvements in production, safety, and efficacy. These characteristics make plants an attractive platform for the production of recombinant proteins, biologics, and therapeutics.
The DENV and the Zika (ZIKV) FVs frequently co-circulate and generally cause mild self-liming febrile illnesses. However, a secondary infection with a heterologous DENV serotype may lead to life threatening dengue hemorrhagic fever (DHF) and dengue shock syndrome (DSS). DHF/DSS have been linked to antibody dependent enhancement of infection (ADE), a phenomenon that occurs when antibodies (Abs) formed against an initial infection with one serotype of DENV cross-reacts but does not neutralize a heterologous DENV serotype in a secondary infection. Furthermore, Abs raised against the ZIKV have been observed to cross-react with the DENV and vice versa, which can potentially cause ADE and lead to severe DENV disease. The ZIKV can be transmitted vertically and has been linked to devastating congenital defects such as microcephaly in newborns. FDA approved treatments do not exist for DENV and ZIKV illnesses. Thus, there is a need for safe and effective treatments for these co-circulating viruses. Here, a tetravalent bispecific antibody (bsAb) targeting the ZIKV and all four serotypes of the DENV was expressed in the Nicotiana benthamiana (N. benthamiana) plant. Functional assays of the DENV/ZIKV bsAb demonstrated binding, neutralization, and a significant reduction in ADE activity against both the DENV and the ZIKV.
A single chain variable fragment (scFv) and a diabody based on an antibody directed against the immune checkpoint inhibitor PD-L1, were also expressed in N. benthamiana leaves. The smaller sizes of the scFv and diabody confers them with the ability to penetrate deeper tissues making them beneficial in diagnostics, imaging, and possibly cancer therapy. The past few decades has seen long strives in recombinant protein production in plants with significant improvements in production, safety, and efficacy. These characteristics make plants an attractive platform for the production of recombinant proteins, biologics, and therapeutics.
ContributorsEsqueda, Adrian (Author) / Chen, Qiang (Thesis advisor) / Arntzen, Charles (Committee member) / Lake, Douglas (Committee member) / Mason, Hugh (Committee member) / Arizona State University (Publisher)
Created2019
Description
Vitellogenin (Vg) is an ancient and highly conserved multifunctional protein. It is primarily known for its role in egg-yolk formation but also serves functions pertaining to immunity, longevity, nutrient storage, and oxidative stress relief. In the honey bee (Apis mellifera), Vg has evolved still further to include important social functions that are critical to the maintenance and proliferation of colonies. Here, Vg is used to synthesize royal jelly, a glandular secretion produced by a subset of the worker caste that is fed to the queen and young larvae and which is essential for caste development and social immunity. Moreover, Vg in the worker caste sets the pace of their behavioral development as they transition between different tasks throughout their life. In this dissertation, I make several new discoveries about Vg functionality. First, I uncover a colony-level immune pathway in bees that uses royal jelly as a vehicle to transfer pathogen fragments between nestmates. Second, I show that Vg is localized and expressed in the honey bee digestive tract and suggest possible immunological functions it may be performing there. Finally, I show that Vg enters to nucleus and binds to deoxyribonucleic acid (DNA), acting as a potential transcription factor to regulate expression of many genes pertaining to behavior, metabolism, and signal transduction pathways. These findings represent a significant advance in the understanding of Vg functionality and honey bee biology, and set the stage for many future avenues of research.
ContributorsHarwood, Gyan (Author) / Amdam, Gro V (Thesis advisor) / Kusumi, Kenro (Committee member) / Rabeling, Christian (Committee member) / Chang, Yung (Committee member) / Arizona State University (Publisher)
Created2019
Description
Intracerebral hemorrhage (ICH) is a devastating type of acute brain injury with high mortality and disability. Acute brain injury swiftly alters the immune reactivity within and outside the brain; however, the mechanisms and influence on neurological outcome remains largely unknown. My dissertation investigated how ICH triggers focal and systemic immune responses and their impact hemorrhagic brain injury. At the focal level, a significant upregulation of interleukin (IL)-15 was identified in astrocytes of brain sections from ICH patients. A transgenic mouse line where the astrocytic IL-15 expression is controlled by a glial fibrillary acidic protein promoter (GFAP-IL-15tg) was generated to investigate its role in ICH. Astrocyte-targeted expression of IL-15 exacerbated brain edema and neurological deficits following ICH. Aggravated ICH injury was accompanied by an accumulation of pro-inflammatory microglia proximal to astrocytes in perihematomal tissues, microglial depletion attenuated the augmented ICH injury in GFAP-IL-15tg mice. These findings suggest that IL-15 mediates the crosstalk between astrocytes and microglia, which worsens ICH injury.Systemic immune response was investigated by leveraging the novel method of obtaining and analyzing bone marrow cells from the cranial bone flaps of ICH patients. A swift increase of hematopoietic stem cell (HSCs) population in the bone marrow was identified, along with a shift towards the myeloid cell lineage. Human findings were mirrored in an ICH mouse model. Fate mapping these HSCs revealed increased genesis of Ly6Clow monocytes in the bone marrow, which transmigrate into the hemorrhagic brain and give rise to alternative activation marker bearing macrophage. Blockade of the β3-adrenergic receptor or inhibition of Cdc42 abolished ICH-induced myeloid bias of HSCs. Importantly, mirabegron, a Food and Drug Administration-approved β3 adrenergic receptor agonist, and a Cdc42 activator, IL-3, enhanced bone marrow generation of Ly6Clow monocytes and improved recovery. These results suggest that brain injury modulates HSC lineage destination to curb distal brain inflammation, implicating the bone marrow as a unique niche for self-protective neuroimmune interactions. Together, these results demonstrate how acute brain injury exerts a profound yet distinct effect on immune responses within and outside the brain and sheds new light on neuroimmune interactions with potential clinical implications.
ContributorsShi, Samuel Xiang-yu (Author) / Chang, Yung (Thesis advisor) / Liu, Qiang (Committee member) / Gonzales, Rayna J (Committee member) / Ducruet, Andrew F (Committee member) / Arizona State University (Publisher)
Created2020
Description
Alzheimer’s disease (AD) is the world’s leading cause of dementia and is the sixthleading cause of death in the United States. While AD has been studied for over a century, little progress has been made in terms of treating or preventing disease progression; therefore, new therapeutic drug targets must be identified. Current clinical trials focus on inhibiting Beta- Secretase 1 (BACE1), the major enzyme involved in the formation of the amyloid beta (Abeta) peptide fragments that aggregate to form insoluble plaques in the brains of AD patients. However, many of these clinical trials have been halted due to neurological effects or organ damage with no substantial cognitive improvements. Because the current leading theory of AD is that the buildup of amyloid plaques leads to metabolic changes that result in the intraneuronal accumulation of hyperphosphorylated Microtubule Associated Protein Tau (TAU, encoded by the MAPT gene), which causes cell death resulting in brain atrophy and dementia (known as the Amyloid Cascade Hypothesis), identifying drug targets that modulate Amyloid Precursor Protein (APP) processing – without directly inhibiting BACE1 – may prove to be a viable treatment. In this work, the role of the Adenosine triphosphate Binding Cassette subfamily C member 1 (ABCC1) was studied in the context of AD. Rare mutations in ABCC1 were identified in a familial case of late-onset AD and in a sporadic case of early-onset AD, and previous laboratories have demonstrated that Abeta is a substrate for ABCC1-mediated export. Although the final experiments reveal no significant difference between the mutant and reference alleles, the data demonstrate that overexpression of ABCC1 modulates APP processing, resulting in decreased Abeta formation and increased alpha- secretase cleavage of the APP molecule, likely via transcriptional modulation of genes that are capable of altering APP metabolism. Therefore, pharmacological interventions that increase either ABCC1 expression or activity may be capable of halting, reversing, or preventing disease progression. Many cancer drug development pipelines have been employed to identify compounds that decrease ABCC1 expression or activity, and it is likely that compounds have been identified that have the opposite effect. These drugs should be studied in the context of Alzheimer’s disease.
ContributorsJepsen, Wayne Mathew (Author) / Huentelman, Matthew (Thesis advisor) / Kusumi, Kenro (Thesis advisor) / Jensen, Kendall (Committee member) / Newbern, Jason (Committee member) / Arizona State University (Publisher)
Created2021
Description
Next-generation sequencing is a powerful tool for detecting genetic variation. How-ever, it is also error-prone, with error rates that are much larger than mutation rates.
This can make mutation detection difficult; and while increasing sequencing depth
can often help, sequence-specific errors and other non-random biases cannot be de-
tected by increased depth. The problem of accurate genotyping is exacerbated when
there is not a reference genome or other auxiliary information available.
I explore several methods for sensitively detecting mutations in non-model or-
ganisms using an example Eucalyptus melliodora individual. I use the structure of
the tree to find bounds on its somatic mutation rate and evaluate several algorithms
for variant calling. I find that conventional methods are suitable if the genome of a
close relative can be adapted to the study organism. However, with structured data,
a likelihood framework that is aware of this structure is more accurate. I use the
techniques developed here to evaluate a reference-free variant calling algorithm.
I also use this data to evaluate a k-mer based base quality score recalibrator
(KBBQ), a tool I developed to recalibrate base quality scores attached to sequencing
data. Base quality scores can help detect errors in sequencing reads, but are often
inaccurate. The most popular method for correcting this issue requires a known
set of variant sites, which is unavailable in most cases. I simulate data and show
that errors in this set of variant sites can cause calibration errors. I then show that
KBBQ accurately recalibrates base quality scores while requiring no reference or other
information and performs as well as other methods.
Finally, I use the Eucalyptus data to investigate the impact of quality score calibra-
tion on the quality of output variant calls and show that improved base quality score
calibration increases the sensitivity and reduces the false positive rate of a variant
calling algorithm.
This can make mutation detection difficult; and while increasing sequencing depth
can often help, sequence-specific errors and other non-random biases cannot be de-
tected by increased depth. The problem of accurate genotyping is exacerbated when
there is not a reference genome or other auxiliary information available.
I explore several methods for sensitively detecting mutations in non-model or-
ganisms using an example Eucalyptus melliodora individual. I use the structure of
the tree to find bounds on its somatic mutation rate and evaluate several algorithms
for variant calling. I find that conventional methods are suitable if the genome of a
close relative can be adapted to the study organism. However, with structured data,
a likelihood framework that is aware of this structure is more accurate. I use the
techniques developed here to evaluate a reference-free variant calling algorithm.
I also use this data to evaluate a k-mer based base quality score recalibrator
(KBBQ), a tool I developed to recalibrate base quality scores attached to sequencing
data. Base quality scores can help detect errors in sequencing reads, but are often
inaccurate. The most popular method for correcting this issue requires a known
set of variant sites, which is unavailable in most cases. I simulate data and show
that errors in this set of variant sites can cause calibration errors. I then show that
KBBQ accurately recalibrates base quality scores while requiring no reference or other
information and performs as well as other methods.
Finally, I use the Eucalyptus data to investigate the impact of quality score calibra-
tion on the quality of output variant calls and show that improved base quality score
calibration increases the sensitivity and reduces the false positive rate of a variant
calling algorithm.
ContributorsOrr, Adam James (Author) / Cartwright, Reed (Thesis advisor) / Wilson, Melissa (Committee member) / Kusumi, Kenro (Committee member) / Taylor, Jesse (Committee member) / Pfeifer, Susanne (Committee member) / Arizona State University (Publisher)
Created2020