Reference genome and transcriptome informed by the sex chromosome complement of the sample increase ability to detect sex differences in gene expression from RNA-Seq data.

Biology of Sex Differences
Kimberly C OlneyMelissa A Wilson

Abstract

Human X and Y chromosomes share an evolutionary origin and, as a consequence, sequence similarity. We investigated whether the sequence homology between the X and Y chromosomes affects the alignment of RNA-Seq reads and estimates of differential expression. We tested the effects of using reference genomes and reference transcriptomes informed by the sex chromosome complement of the sample's genome on the measurements of RNA-Seq abundance and sex differences in expression. The default genome includes the entire human reference genome (GRCh38), including the entire sequence of the X and Y chromosomes. We created two sex chromosome complement informed reference genomes. One sex chromosome complement informed reference genome was used for samples that lacked a Y chromosome; for this reference genome version, we hard-masked the entire Y chromosome. For the other sex chromosome complement informed reference genome, to be used for samples with a Y chromosome, we hard-masked only the pseudoautosomal regions of the Y chromosome, because these regions are duplicated identically in the reference genome on the X chromosome. We analyzed the transcript abundance in the whole blood, brain cortex, breast, liver, and thyroid tissues from 20 gen...Continue Reading

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Citations

Dec 18, 2020·Frontiers in Oncology·Camila M Lopes-RamosDawn L DeMeo
Apr 22, 2021·Nature Reviews. Cancer·Sue HauptYgal Haupt
Jul 2, 2021·Science Advances·Sarah B CareyStuart F McDaniel
Jul 31, 2021·Human Molecular Genetics·Melissa A Wilson

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Methods Mentioned

BETA
RNA-Seq
MDS

Software Mentioned

GOrilla webtool
tximport
samtools
STAR
HISAT read aligner
linux
Gencode
limma
fasta
Ensemble

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