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Creators: Barrett, The Honors College
Creators: Webster, Timothy
Member of: Barrett, The Honors College Thesis/Creative Project Collection
Resource Type: Text
Status: Published

Standard mapping protocols misestimate sex-biased gene expression

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

Genetic diversity across the pseudoautosomal boundary varies across human populations

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

Sex-biased gene expression and pathway activation in hepatitis-associated HCC.

Description

Hepatocellular Carcinoma (HCC) is one of the main types of liver cancer accounting for 75% of cases and is the second deadliest cancer worldwide. Chronic Hepatitis B (HBV) and Hepatitis C (HCV) remain one of the most important global risk factors and account for 80% of all HCC cases. HCC also exhibits sex-differences with significantly higher incidence and worse prognosis in males. The mechanistic basis of these sex-differences is poorly understood. To identify genes and pathways that are sex-differentially expressed in viral-mediated HCC, we performed differential expression analysis on tumor vs. tumor adjacent samples that were stratified based on sex, viral etiology, and both. The differentially expressed genes were then used in a pathway enrichment analysis to identify potential pathways of interest. We found differentially expressed genes in both sexes and both etiologies. 65 genes were unique to females and 184 genes unique to males. 381 genes are unique to HBV and 195 genes are unique to HCV. We also found pathways that were significantly enriched by the differentially expressed genes. Ten pathways unique to the female tumor tumor-adjacent comparison and a majority of those pathways were a part of the cell cycle. Four enriched pathways unique to male tumor tumor-adjacent and three of them were a part of the immune system. There were no pathways unique to either etiology, but seven pathways shared by both etiologies. Two were a part of the cell cycle and one involved lipid metabolism. These differentially expressed genes and significant pathways are potential targets for individualized therapeutics and diagnostics for HCC.

ContributorsJorgensen, Annika (Author) / Wilson, Melissa (Thesis director) / Buetow, Kenneth (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor) / Department of Physics (Contributor)

Created2023-05