ArticleGigaScience2019
Identifying, understanding, and correcting technical artifacts on the sex chromosomes in next-generation sequencing data.
Article in GigaScience, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 64 papers, 1 of them a synthesis that pooled it.
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Who cites it
64 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A lizard is never late: Squamate genomics as a recent catalyst for understanding sex chromosome and microchromosome evolution.The Journal of heredity · 2023Pooled it
- Assessing Hardy-Weinberg equilibrium in T2T-aligned 1000 genomes project.PLoS genetics · 2026Article
- A study of sex-specific genetic effects underlying risk of orofacial clefts also highlights the potential impact of sequencing errors due to short read mis-mapping.medRxiv : the preprint server for health sciences · 2026Article
- A Novel Network Approach to Identify Sample-Specific Context-Informed Metabolic Signatures During Developmental Processes.bioRxiv : the preprint server for biology · 2026Article
- Modeling rare coding variation on chromosome X provides insight into the genetics and differential sex prevalence of autism spectrum disorder.medRxiv : the preprint server for health sciences · 2026Article
- Best practices for improving alignment and variant calling on human sex chromosomes.American journal of human genetics · 2026Article
- ONYX: an alignment-free biological sex inference from high-throughput sequencing data.Frontiers in bioinformatics · 2026Article
- XhetRel: a pipeline for X heterozygosity and relatedness analysis of sequencing data.Bioinformatics advances · 2026Article
- Sex-specific placental transcriptome alterations in late-onset preeclampsia reveal male-biased immune and metabolic dysregulation.Biology of sex differences · 2025Observational
- Genetic diversity of the Y-chromosome in domestic animals: from evolutionary insights to functional implications.Molecular biology reports · 2025Review
- Methodological opportunities in genomic data analysis to advance health equity.Nature reviews. Genetics · 2025Review
- Sex Bias in Autoimmunity: New Findings and New Opportunities.JID innovations : skin science from molecules to population health · 2025Review
- An iPSC-based model of 47,XYY Jacobs syndrome reveals a DNA methylation-independent transcriptional dysregulation shared with male X aneuploid cells.Genome research · 2025Article
- Establishing genome sequencing and assembly for non-model and emerging model organisms: a brief guide.Frontiers in zoology · 2025Review
- Evolutionary divergence between homologous X-Y chromosome genes shapes sex-biased biology.Nature ecology & evolution · 2025Article
- Small variant benchmark from a complete assembly of X and Y chromosomes.Nature communications · 2025Article
- Decoding sex differences in human immunity through systems immunology.Oxford open immunology · 2025Review
- Sequence-Based Machine Learning Reveals 3D Genome Differences between Bonobos and Chimpanzees.Genome biology and evolution · 2024Article
- Regulation of Sex-biased Gene Expression by the Ancestral X-Y Chromosomal Gene PairbioRxiv : the preprint server for biology · 2024Article
- Evolutionary and biomedical implications of sex differences in the primate brain transcriptome.Cell genomics · 2024Article
4 more citing papers are in PubMed but not listed here.
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Authors and funding
8 authors.
Funding
Abstract
backgroundMammalian X and Y chromosomes share a common evolutionary origin and retain regions of high sequence similarity. Similar sequence content can confound the mapping of short next-generation sequencing reads to a reference genome. It is therefore possible that the presence of both sex chromosomes in a reference genome can cause technical artifacts in genomic data and affect downstream analyses and applications. Understanding this problem is critical for medical genomics and population genomic inference.
resultsHere, we characterize how sequence homology can affect analyses on the sex chromosomes and present XYalign, a new tool that (1) facilitates the inference of sex chromosome complement from next-generation sequencing data; (2) corrects erroneous read mapping on the sex chromosomes; and (3) tabulates and visualizes important metrics for quality control such as mapping quality, sequencing depth, and allele balance. We find that sequence homology affects read mapping on the sex chromosomes and this has downstream effects on variant calling. However, we show that XYalign can correct mismapping, resulting in more accurate variant calling. We also show how metrics output by XYalign can be used to identify XX and XY individuals across diverse sequencing experiments, including low- and high-coverage whole-genome sequencing, and exome sequencing. Finally, we discuss how the flexibility of the XYalign framework can be leveraged for other uses including the identification of aneuploidy on the autosomes. XYalign is available open source under the GNU General Public License (version 3).
conclusionsSex chromsome sequence homology causes the mismapping of short reads, which in turn affects downstream analyses. XYalign provides a reproducible framework to correct mismapping and improve variant calling on the sex chromsomes.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.