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Description
College students are a niche of young adults, characterized by abnormal sleeping habits and inactive lifestyles. Many students entering college are as young as 18 years old and graduate by 22 years old, a window of time in which their bones are still accruing mineral. The purpose of this cross-sectional study was to determine whether sleep patterns and physical activity observed in college students (N= 52) 18-25 years old at Arizona State University influenced bone biomarkers, osteocalcin (OC) and N-terminal telopeptide of type 1 collagen (NTX-1) concentrations. Students completed various dietary and health history questionnaires including the International Physical Activity Questionnaire short form. Students wore an actigraphy watch for 7 consecutive nights to record sleep events including total sleep time, sleep onset latency and wake after sleep onset. Total sleep time had a significant, negative correlation with OC (r = -0.298, p-value =0.036) while sleep onset latency had a significant, positive correlation with NTX-1 serum concentration (r = 0.293, p-value = 0.037). Despite correlational findings, only sleep percent was found to be significant (beta coefficient = 0.271 p-value = 0.788) among all the sleep components assessed, after adjusting for gender, race, BMI and calcium intake in multivariate regression models. Physical activity alone was not associated with either bone biomarker. Physical activity*sleep onset latency interactions were significantly correlated with osteocalcin (r = 0.308, p-value =0.006) and NTX-1 (r = 0.286, p-value = 0.042) serum concentrations. Sleep percent*physical activity interactions were significantly correlated with osteocalcin (r = 0.280, p-value = 0.049) but not with NTX-1 serum concentrations. Interaction effects were no longer significant after adjusting for covariates in the regression models. While sleep percent was a significant component in the regression model for NTX-1, it was not clinically significant. Overall, sleep patterns and physical activity did not explain OC and NTX-1 serum concentrations in college students 18-25 years old. Future studies may need to consider objective physical activity devices including accelerometers to measure activity levels. At this time, college students should review sleep and physical activity recommendations to ensure optimal healthy habits are practiced.
ContributorsMahmood, Tara Nabil (Author) / Whisner, Corrie (Thesis advisor) / Dickinson, Jared (Committee member) / Petrov, Megan (Committee member) / Adams, Marc (Committee member) / Arizona State University (Publisher)
Created2019
Description
Background In the United States (US), first-year university students typically live on campus and purchase a meal plan. In general, meal plans allow the student a set number of meals per week or semester, or unlimited meals. Understanding how students’ use their meal plan, and barriers and facilitators to meal plan use, may help decrease nutrition-related issues.
Methods First-year students’ meal plan and residence information was provided by a large, public, southwestern university for the 2015-2016 academic year. A subset of students (n=619) self-reported their food security status. Logistic generalized estimating equations (GEEs) were used to determine if meal plan purchase and use were associated with food insecurity. Linear GEEs were used to examine several potential reasons for lower meal plan use. Logistic and Linear GEEs were used to determine similarities in meal plan purchase and use for a total of 599 roommate pairs (n=1186 students), and 557 floormates.
Results Students did not use all of the meals available to them; 7% of students did not use their meal plan for an entire month. After controlling for socioeconomic factors, compared to students on unlimited meal plans, students on the cheapest meal plan were more likely to report food insecurity (OR=2.2, 95% CI=1.2, 4.1). In Fall, 26% of students on unlimited meal plans reported food insecurity. Students on the 180 meals/semester meal plan who used fewer meals were more likely to report food insecurity (OR=0.9, 95% CI=0.8, 1.0); after gender stratification this was only evident for males. Students’ meal plan use was lower if the student worked a job (β=-1.3, 95% CI=-2.3, -0.3) and higher when their roommate used their meal plan frequently (β=0.09, 99% CI=0.04, 0.14). Roommates on the same meal plan (OR=1.56, 99% CI=1.28, 1.89) were more likely to use their meals together.
Discussion This study suggests that determining why students are not using their meal plan may be key to minimizing the prevalence of food insecurity on college campuses, and that strategic roommate assignments may result in students’ using their meal plan more frequently. Students’ meal plan information provides objective insights into students’ university transition.
Methods First-year students’ meal plan and residence information was provided by a large, public, southwestern university for the 2015-2016 academic year. A subset of students (n=619) self-reported their food security status. Logistic generalized estimating equations (GEEs) were used to determine if meal plan purchase and use were associated with food insecurity. Linear GEEs were used to examine several potential reasons for lower meal plan use. Logistic and Linear GEEs were used to determine similarities in meal plan purchase and use for a total of 599 roommate pairs (n=1186 students), and 557 floormates.
Results Students did not use all of the meals available to them; 7% of students did not use their meal plan for an entire month. After controlling for socioeconomic factors, compared to students on unlimited meal plans, students on the cheapest meal plan were more likely to report food insecurity (OR=2.2, 95% CI=1.2, 4.1). In Fall, 26% of students on unlimited meal plans reported food insecurity. Students on the 180 meals/semester meal plan who used fewer meals were more likely to report food insecurity (OR=0.9, 95% CI=0.8, 1.0); after gender stratification this was only evident for males. Students’ meal plan use was lower if the student worked a job (β=-1.3, 95% CI=-2.3, -0.3) and higher when their roommate used their meal plan frequently (β=0.09, 99% CI=0.04, 0.14). Roommates on the same meal plan (OR=1.56, 99% CI=1.28, 1.89) were more likely to use their meals together.
Discussion This study suggests that determining why students are not using their meal plan may be key to minimizing the prevalence of food insecurity on college campuses, and that strategic roommate assignments may result in students’ using their meal plan more frequently. Students’ meal plan information provides objective insights into students’ university transition.
Contributorsvan Woerden, Irene (Author) / Bruening, Meg (Thesis advisor) / Hruschka, Daniel (Committee member) / Schaefer, David (Committee member) / Vega-Lopez, Sonia (Committee member) / Adams, Marc (Committee member) / Arizona State University (Publisher)
Created2019
Description
Salad bars are promoted as a means to increase fruit and vegetable consumption among school-age children; however, no study has assessed barriers to having salad bars. Further, it is not known if barriers differ across school level. This cross-sectional study investigated the barriers to having salad bars across school level among schools without salad bars in Arizona (n=177). Multivariate binominal regression models were used to determine differences between the barriers and school level, adjusting for years at current job, enrollment of school, free-reduced eligibility rate and district level clustering. The top five barriers were not enough staff (51.4%), lack of space for salad bars (49.7%), food waste concerns (37.9%), sanitation/food safety concerns (31.3%), and time to get through the lines (28.3%) Adjusted analyses indicated two significant differences between barriers across school level: time to get through lines (p=0.040) and outside caterer/vendor (p=0.018) with time to get through lines reported more often by elementary and middle school nutrition managers and outside caterer/vendor reported most often by high school nutrition managers. There were several key barriers reported and results indicate that having an outside vendor/caterer for their meal programs and time to get through the service lines varied across school level. High schools report a higher percent of the barrier outside caterer/vendors and elementary and middle schools report a higher percent of the barrier time to get through the lines. Results indicate that research determining the approximate time it takes students to get through salad bar lines will need to be considered. More research is needed to determine if the barrier time to get through the service lines is due to selection of food items or if it is due to the enrollment size of the lunch period. Future research interventions may consider investigating food safety and sanitation concerns of middle school nutrition managers. Findings may be used to guide ways to decrease barriers in schools without salad bars.
ContributorsKebric, Kelsey (Author) / Bruening, Meg (Thesis advisor) / Ohri-Vachaspati, Punam (Committee member) / Adams, Marc (Committee member) / Arizona State University (Publisher)
Created2016
Description
Background: Childhood obesity is one of the most serious public health concerns in the United States and has been associated with low levels of physical activity. Schools are ideal physical activity promotion sites but school physical activity opportunities have decreased due the increased focus on academic performance. Before-school programs provide a good opportunity for children to engage in physical activity as well as improve their readiness to learn. Purpose: The purpose of this study was to examine the effect of a before-school running/walking club on children's physical activity and on-task behavior. Methods: Participants were third and fourth grade children from two schools in the Southwestern United States who participated in a before-school running/walking club that met two times each week. The study employed a two-phase experimental design with an initial baseline phase and an alternating treatments phase. Physical activity was monitored using pedometers and on-task behavior was assessed through systematic observation. Data analysis included visual analysis, descriptive statistics, as well as multilevel modeling. Results: Children accumulated substantial amounts of physical activity within the before-school program (School A: 1731 steps, 10:02 MVPA minutes; School B: 1502 steps, 8:30 MVPA minutes) and, on average, did not compensate by decreasing their physical activity during the rest of the school day. Further, on-task behavior was significantly higher on days the children attended the before-school program than on days they did not (School A=15.78%, pseudo-R2=.34 [strong effect]; School B=14.26%, pseudo-R2=.22 [moderate effect]). Discussion: Results provide evidence for the positive impact of before-school programs on children's physical activity and on-task behavior. Such programs do not take time away from academics and may be an attractive option for schools.
ContributorsStylianou, Michalis (Author) / Kulinna, Pamela H. (Thesis advisor) / Van Der Mars, Hans (Committee member) / Amazeen, Eric (Committee member) / Adams, Marc (Committee member) / Mahar, Matthew T. (Committee member) / Arizona State University (Publisher)
Created2014
Effect of a Wii Fit® intervention on balance, muscular fitness, and bone health in middle-aged women
Description
Sustaining a fall can be hazardous for those with low bone mass. Interventions exist to reduce fall-risk, but may not retain long-term interest. "Exergaming" has become popular in older adults as a therapy, but no research has been done on its preventative ability in non-clinical populations. The purpose was to determine the impact of 12-weeks of interactive play with the Wii Fit® on balance, muscular fitness, and bone health in peri- menopausal women. METHODS: 24 peri-menopausal-women were randomized into study groups. Balance was assessed using the Berg/FICSIT-4 and a force plate. Muscular strength was measured using the isokinetic dynamometer at 60°/180°/240°/sec and endurance was assessed using 50 repetitions at 240°/sec. Bone health was tracked using dual-energy x-ray absorptiometry (DXA) for the hip/lumbar spine and qualitative ultrasound (QUS) of the heel. Serum osteocalcin was assessed by enzyme immunoassay. Physical activity was quantified using the Women's Health Initiative Physical Activity Questionnaire and dietary patterns were measured using the Nurses' Health Food Frequency Questionnaire. All measures were repeated at weeks 6 and 12, except for the DXA, which was completed pre-post. RESULTS: There were no significant differences in diet and PA between groups. Wii Fit® training did not improve scores on the Berg/FICSIT-4, but improved center of pressure on the force plate for Tandem Step, Eyes Closed (p-values: 0.001-0.051). There were no significant improvements for muscular fitness at any of the angular velocities. DXA BMD of the left femoral neck improved in the intervention group (+1.15%) and decreased in the control (-1.13%), but no other sites had significant changes. Osteocalcin indicated no differences in bone turnover between groups at baseline, but the intervention group showed increased bone turnover between weeks 6 and 12. CONCLUSIONS: Findings indicate that WiiFit® training may improve balance by preserving center of pressure. QUS, DXA and osteocalcin data confirm that those in the intervention group were experiencing more bone turnover and bone formation than the control group. In summary, twelve weeks of strength /balance training with the Wii Fit® shows promise as a preventative intervention to reduce fall and fracture risk in non-clinical middle aged women who are at risk.
ContributorsWherry, Sarah Jo (Author) / Swan, Pamela D (Thesis advisor) / Adams, Marc (Committee member) / Der Ananian, Cheryl (Committee member) / Sweazea, Karen (Committee member) / Vaughan, Linda (Committee member) / Arizona State University (Publisher)
Created2014
Description
Research indicates that adults are not acquiring enough physical activity. Increasing the use of stairs is an accessible way to weave high intensity physical activity into the daily routine. The purpose of this study is to test the effect of four environmental changes on ascending stair use in a mixed population of college students, faulty, and staff on a southwest college campus. The study design included a 10-week time series design with alternating baseline and intervention phases, including a directional cue represented by footprints on the ground, a positive prompt, a deterrent prompt and a combination phase. Data was collected with both an in-person tally and a video recording device. The study included 6,140 observations and coded variables included stair use, sex, number of bags carried, temperature, and volume. Rater reliability ranged from .81 to 1.0. Multivariate logistic regression was used to perform the statistic analysis. Stair use increased significantly from Washout 1 and the positive prompting phase with a 7% absolute increase and an odds ratio of 1.35 (95% CI 1.080-1.696). Stair use during the footprint phase, deterrent phase and combination phase did not increase significantly compared to the previous baseline or washout phases. Day of the week (Monday=reference, Tuesday CI=1.626, 95% CI 1.298-2.011, Wednesday OR=0.457, 95% CI 0.248-0.841, Thursday OR=1.434, 95% CI 1.164-1.766), sex (OR=1.376, 95% CI 1.173-1.613) and volume (OR=1.007, 95% CI 1.005-1.008) were significantly correlated to stair use. Women used the stairs more than men and higher volume situations were related to increased stair use. Temperature and baggage number were not related to stair use. The results of this study indicate that positive prompting with an environmental message theme is an effective method to increase stair use in a university setting.
ContributorsFord, Marley (Author) / Adams, Marc (Thesis advisor) / Der Ananian, Cheryl (Committee member) / Vaughan, Linda (Committee member) / Arizona State University (Publisher)
Created2015
Description
Chronic diseases are the leading causes of death in the United States. Dietary behaviors influence the risk of developing multiple chronic diseases. The U.S. population consumes too few fruits and vegetables and too much sugar sweetened beverages (SSB) and fast food. The Social Ecological Model (SEM) was created as a framework for health promotion interventions. The SEM organizes factors that can influence health into five layers: intrapersonal factors, interpersonal processes, institutional/organizational factors, community factors, and public policy. Each layer can influence dietary behaviors and other layers.
This work aims to understand how the community layer, represented by the food environment, moderates the association of two other layers and dietary behaviors: the interpersonal layer, represented by receiving health care provider’s (HCP) advice to lose weight, and the policy layer, represented by participation in the Supplemental Nutrition Assistance Program (SNAP), and a policy change within the Special Supplemental Nutrition Program for Women, Infants, and Children (WIC).
Participant data were obtained from a household telephone survey of 2,211 adults in four cities in New Jersey from two cross-sectional panels in 2009-10 and 2014. Community food data were purchased and classified according to previously established protocol. Interaction and stratified analyses determined the differences in the association between HCP advice, SNAP participation, and time (for WIC participants) and eating behaviors by the food environment.
Interaction and stratified analyses revealed that HCP advice was associated with a decrease in SSB consumption when participants lived near a small grocery store, or far from a supermarket, limited service restaurant (LSR), or convenience store. SNAP participation was associated with a higher SSB consumption when respondents lived close to a small grocery store, supermarket, and LSR. There were no differences in fruit and vegetable consumption between two time points among WIC participants, or by food outlet.
The food environment, part of the community layer of SEM, moderated the relationship between the interpersonal layer and dietary behaviors and the policy layer and dietary behaviors. The association between HCP advice and dietary behaviors and SNAP participation and dietary behaviors were both influenced by the food environment in which participants lived.
This work aims to understand how the community layer, represented by the food environment, moderates the association of two other layers and dietary behaviors: the interpersonal layer, represented by receiving health care provider’s (HCP) advice to lose weight, and the policy layer, represented by participation in the Supplemental Nutrition Assistance Program (SNAP), and a policy change within the Special Supplemental Nutrition Program for Women, Infants, and Children (WIC).
Participant data were obtained from a household telephone survey of 2,211 adults in four cities in New Jersey from two cross-sectional panels in 2009-10 and 2014. Community food data were purchased and classified according to previously established protocol. Interaction and stratified analyses determined the differences in the association between HCP advice, SNAP participation, and time (for WIC participants) and eating behaviors by the food environment.
Interaction and stratified analyses revealed that HCP advice was associated with a decrease in SSB consumption when participants lived near a small grocery store, or far from a supermarket, limited service restaurant (LSR), or convenience store. SNAP participation was associated with a higher SSB consumption when respondents lived close to a small grocery store, supermarket, and LSR. There were no differences in fruit and vegetable consumption between two time points among WIC participants, or by food outlet.
The food environment, part of the community layer of SEM, moderated the relationship between the interpersonal layer and dietary behaviors and the policy layer and dietary behaviors. The association between HCP advice and dietary behaviors and SNAP participation and dietary behaviors were both influenced by the food environment in which participants lived.
ContributorsLorts, Cori Elizabeth (Author) / Ohri-Vachaspati, Punam (Thesis advisor) / Adams, Marc (Committee member) / Hooker, Steven (Committee member) / Roberto, Anthony (Committee member) / Tasevska, Natasha (Committee member) / Arizona State University (Publisher)
Created2017
Description
Background: Children’s fruit and vegetable consumption in the United States is lower than recommended. School lunch is an opportunity for students to be exposed to fruits and vegetables and potentially increase their daily intake. The purpose of this study is to examine the relationship between tray color and fruit and vegetable selection, consumption, and waste at lunch.
Methods: Study participants (n=1469) were elementary and middle school students who ate school lunch on the day of data collection. Photographs and weights (to nearest 2 g) were taken of fruits and vegetables on students’ trays before and after lunch. Trained research assistants viewed photographs and sorted trays into variable categories: color of main tray, presence/absence of secondary fruit/vegetable container, and color of secondary fruit/vegetable container. Fruit and vegetable selection, consumption, and waste were calculated using tray weights. Negative binomial regression models adjusted for gender, grade level, race/ethnicity, free/reduced price lunch status, and within-school similarities were used to examine relationships between tray color and fruit and vegetable selection, consumption, and waste.
Results: Findings indicated that students with a light tray selected (IRR= 0.44), consumed (IRR=0.73) and wasted (IRR=0.81) less fruit and vegetables. Students without a secondary fruit/vegetable container selected (IRR=0.66) and consumed (IRR=0.49) less fruit and vegetables compared to those with a secondary container. Light or clear secondary fruit and vegetable containers were related to increased selection (IRR=2.06 light, 2.30 clear) and consumption (IRR=1.95 light, 2.78 clear) compared to dark secondary containers, while light secondary containers were related to decreased waste (IRR= 0.57).
Conclusion: Tray color may influence fruit and vegetable selection, consumption, and waste among students eating school lunch. Further research is needed to determine if there is a cause and effect relationship. If so, adjusting container colors may be a practical intervention for schools hoping to increase fruit and vegetable intake among students.
Methods: Study participants (n=1469) were elementary and middle school students who ate school lunch on the day of data collection. Photographs and weights (to nearest 2 g) were taken of fruits and vegetables on students’ trays before and after lunch. Trained research assistants viewed photographs and sorted trays into variable categories: color of main tray, presence/absence of secondary fruit/vegetable container, and color of secondary fruit/vegetable container. Fruit and vegetable selection, consumption, and waste were calculated using tray weights. Negative binomial regression models adjusted for gender, grade level, race/ethnicity, free/reduced price lunch status, and within-school similarities were used to examine relationships between tray color and fruit and vegetable selection, consumption, and waste.
Results: Findings indicated that students with a light tray selected (IRR= 0.44), consumed (IRR=0.73) and wasted (IRR=0.81) less fruit and vegetables. Students without a secondary fruit/vegetable container selected (IRR=0.66) and consumed (IRR=0.49) less fruit and vegetables compared to those with a secondary container. Light or clear secondary fruit and vegetable containers were related to increased selection (IRR=2.06 light, 2.30 clear) and consumption (IRR=1.95 light, 2.78 clear) compared to dark secondary containers, while light secondary containers were related to decreased waste (IRR= 0.57).
Conclusion: Tray color may influence fruit and vegetable selection, consumption, and waste among students eating school lunch. Further research is needed to determine if there is a cause and effect relationship. If so, adjusting container colors may be a practical intervention for schools hoping to increase fruit and vegetable intake among students.
ContributorsWeight, Raquelle (Author) / Bruening, Meg (Thesis advisor) / Adams, Marc (Committee member) / Martinelli, Sarah (Committee member) / Arizona State University (Publisher)
Created2020
Description
Background: Exercise is Medicine (EIM) is a health promotion strategy for addressing physical inactivity in healthcare. However, it is unknown how to successfully implement the processes.
Purpose: The purpose of this study was to understand how implementing EIM influenced provider behaviors in a university-based healthcare system, using a process evaluation.
Methods: A multiple baseline, time series design was used. Providers were allocated to three groups. Group 1 (n=11) was exposed to an electronic medical record (EMR) systems change, EIM-related resources, and EIM training session. Group 2 (n=5) received the EMR change and resources but no training. Group 3 (n=6) was only exposed to the systems change. The study was conducted across three phases. Outcomes included asking about patient physical activity (PA) as a vital sign (PAVS), prescribing PA (ExRx), and providing PA resources or referrals. Patient surveys and EMR data were examined. Time series analysis, chi-square, and logistic regression were used.
Results: Patient survey data revealed the systems change increased patient reports of being asked about PA, χ2(4) = 95.47, p < .001 for all groups. There was a significant effect of training and resource dissemination on patients receiving PA advice, χ2(4) = 36.25, p < .001. Patients receiving PA advice was greater during phase 2 (OR = 4.7, 95% CI = 2.0-11.0) and phase 3 (OR = 2.9, 95% CI = 1.2-7.4). Increases were also observed in EMR data for PAVS, χ2(2) = 29.27, p <. 001 during implementation for all groups. Increases in PA advice χ2(2) = 140.90, p < .001 occurred among trained providers only. No statistically significant change was observed for ExRx, PA resources or PA referrals. However, visual analysis showed an upwards trend among trained providers.
Conclusions: An EMR systems change is effective for increasing the collection of the PAVS. Training and resources may influence provider behavior but training alone increased provider documentation. The low levels of documented outcomes for PA advice, ExRx, resources, or referrals may be due to the limitations of the EMR system. This approach was effective for examining the EIM Solution and scaled-up, longer trials may yield more robust results.
Purpose: The purpose of this study was to understand how implementing EIM influenced provider behaviors in a university-based healthcare system, using a process evaluation.
Methods: A multiple baseline, time series design was used. Providers were allocated to three groups. Group 1 (n=11) was exposed to an electronic medical record (EMR) systems change, EIM-related resources, and EIM training session. Group 2 (n=5) received the EMR change and resources but no training. Group 3 (n=6) was only exposed to the systems change. The study was conducted across three phases. Outcomes included asking about patient physical activity (PA) as a vital sign (PAVS), prescribing PA (ExRx), and providing PA resources or referrals. Patient surveys and EMR data were examined. Time series analysis, chi-square, and logistic regression were used.
Results: Patient survey data revealed the systems change increased patient reports of being asked about PA, χ2(4) = 95.47, p < .001 for all groups. There was a significant effect of training and resource dissemination on patients receiving PA advice, χ2(4) = 36.25, p < .001. Patients receiving PA advice was greater during phase 2 (OR = 4.7, 95% CI = 2.0-11.0) and phase 3 (OR = 2.9, 95% CI = 1.2-7.4). Increases were also observed in EMR data for PAVS, χ2(2) = 29.27, p <. 001 during implementation for all groups. Increases in PA advice χ2(2) = 140.90, p < .001 occurred among trained providers only. No statistically significant change was observed for ExRx, PA resources or PA referrals. However, visual analysis showed an upwards trend among trained providers.
Conclusions: An EMR systems change is effective for increasing the collection of the PAVS. Training and resources may influence provider behavior but training alone increased provider documentation. The low levels of documented outcomes for PA advice, ExRx, resources, or referrals may be due to the limitations of the EMR system. This approach was effective for examining the EIM Solution and scaled-up, longer trials may yield more robust results.
ContributorsBirchfield, Natasha R (Author) / Der Ananian, Cheryl (Thesis advisor) / Krasnow, Aaron (Committee member) / Doebbeling, Bradley (Committee member) / Adams, Marc (Committee member) / Swan, Pamela (Committee member) / Arizona State University (Publisher)
Created2019
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