Matching Items (3)
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- All Subjects: Human Genetics
- All Subjects: Differential Expression
- All Subjects: Genetic Diversity
- Creators: Webster, Timothy
- Creators: Cotter, Daniel Juetten
- Creators: Mathew, Sarah
- Status: Published
Description
There are several challenges to accurately inferring levels of transcription using RNA-sequencing (RNA-seq) data, including detecting and correcting for reference genome mapping bias. One potential confounder of RNA-seq analysis results from the application of a standardized pipeline to samples of different sexes in species with chromosomal sex determination. The homology between the human X and Y chromosomes will routinely cause mismapping to occur, artificially biasing estimates of sex-biased gene transcription. For this reason we tested sex-specific mapping scenarios in humans on RNA-seq samples from the brains of 5 genetic females and 5 genetic males to assess how inferences of differential gene expression patterns change depending on the reference genome. We first applied a mapping protocol where we mapped all individuals to the entire human reference genome (complete), including the X and Y chromosomes, and computed differential expression between the set of genetic male and genetic female samples. We next mapped the genetic female samples (46,XX) to the human reference genome with the Y chromosome removed (Y-excluded) and the genetic male samples (46, XY) to the human reference genome (including the Y chromosome), but with the pseudoautosomal regions of the Y chromosome hard-masked (YPARs-masked) for the two sex-specific mappings. Using the complete and sex-specific mapping protocols, we compared the differential expression measurements of genetic males and genetic females from cuffDiff outputs. The second strategy called 33 additional genes as being differentially expressed between the two sexes when compared to the complete mapping protocol. This research provides a framework for a new standard of reference genome mappings to correct for sex-biased gene expression estimates that can be used in future studies.
ContributorsBrotman, Sarah Marie (Author) / Wilson Sayres, Melissa (Thesis director) / Crook, Sharon (Committee member) / Webster, Timothy (Committee member) / School of Life Sciences (Contributor) / School of Mathematical and Natural Sciences (Contributor) / Barrett, The Honors College (Contributor)
Created2017-05
Description
Unlike the autosomes, recombination on the sex chromosomes is limited to the pseudoautosomal regions (PARs) at each end of the chromosome. PAR1 spans approximately 2.7 Mb from the tip of the proximal arm of each sex chromosome, and a pseudoautosomal boundary between the PAR1 and non-PAR region is thought to have evolved from a Y-specific inversion that suppressed recombination across the boundary. In addition to the two PARs, there is also a human-specific X-transposed region (XTR) that was duplicated from the X to the Y chromosome. Genetic diversity is expected to be higher in recombining than nonrecombining regions, particularly because recombination reduces the effects of linked selection, allowing neutral variation to accumulate. We previously showed that diversity decreases linearly across the previously defined pseudoautosomal boundary (rather than drop suddenly at the boundary), suggesting that the pseudoautosomal boundary may not be as strict as previously thought. In this study, we analyzed data from 1271 genetic females to explore the extent to which the pseudoautosomal boundary varies among human populations (broadly, African, European, South Asian, East Asian, and the Americas). We found that, in all populations, genetic diversity was significantly higher in the PAR1 and XTR than in the non-PAR regions, and that diversity decreased linearly from the PAR1 to finally reach a non-PAR value well past the pseudoautosomal boundary in all populations. However, we also found that the location at which diversity changes from reflecting the higher PAR1 diversity to the lower nonPAR diversity varied by as much as 500 kb among populations. The lack of genetic evidence for a strict pseudoautosomal boundary and the variability in patterns of diversity across the pseudoautosomal boundary are consistent with two potential explanations: (1) the boundary itself may vary across populations, or (2) that population-specific demographic histories have shaped diversity across the pseudoautosomal boundary.
ContributorsCotter, Daniel Juetten (Author) / Wilson Sayres, Melissa (Thesis director) / Stone, Anne (Committee member) / Webster, Timothy (Committee member) / School of Life Sciences (Contributor) / School of International Letters and Cultures (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
Description
Studying human genetic variation opens the possibility of understanding the details of population migrations, how humans develop and function, and why they get sick. To fully understand these things, genetic variation must be comprehensively characterized across globally diverse human populations and evolutionary knowledge can be used to inform studies of disease. In my dissertation I use computational methods to study human genetic variation. Each of my dissertation chapters focuses on a unique topic in the field of human evolutionary genetics. In the first chapter, I present PopInf, a computational pipeline to visualize principal components analysis output and assign ancestry to samples with unknown genetic ancestry, given a reference population panel of known origins. This pipeline facilitates visualization and identification of genetic ancestry across samples, so that this ancestry can be accounted for in studies of health and disease risk. In the next chapter, I investigate factors that shape patterns of genetic variation within and among four small-scale pastoral populations in northern Kenya. I find that geography predominantly shapes patterns of genetic variation in northern Kenyan human populations. In the next chapter, I investigate the extent to which Neanderthal introgression impacts liver cancer etiology. I find a pattern of overall enrichment of somatic mutations on Neanderthal introgressed haplotypes. Finally, through simulations, I investigate the effects of standard autosomal versus sex chromosome complement-informed alignment, variant calling and variant filtering strategies on variants called on the human sex chromosomes. I show that aligning to a reference genome informed on the sex chromosome complement of samples improves variant calling on the sex chromosome compared to aligning to a default reference, and variant calling is improved in males when calling the sex chromosomes haploid rather than diploid and when using haploid-based thresholds for filtering variants on the sex chromosomes. I provide recommendations for alignment, variant calling and filtering on the sex chromosomes based on these findings.
ContributorsOill, Angela Maria (Author) / Wilson, Melissa A (Thesis advisor) / Stone, Anne C (Thesis advisor) / Buetow, Kenneth H (Committee member) / Mathew, Sarah (Committee member) / Pfeifer, Susanne P (Committee member) / Arizona State University (Publisher)
Created2022