4.3 Article

Who's afraid of the X? Incorporating the X and Y chromosomes into the analysis of DNA methylation array data

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Biochemical Research Methods

InterpolatedXY: a two-step strategy to normalize DNA methylation microarray data avoiding sex bias

Yucheng Wang et al.

Summary: This article presents a new two-step strategy to address the bias issue in normalizing sex chromosome data, and proposes a concept to quantitatively measure the normalization effect. The method can be applied to all quantile-based and non-quantile-based normalization methods, as well as other array-based data types.

BIOINFORMATICS (2022)

Article Multidisciplinary Sciences

Sex-specific multi-level 3D genome dynamics in the mouse brain

Devin Rocks et al.

Summary: This study provides evidence that 3D chromatin structure differs between male and female mouse brains and undergoes dynamic remodeling during the female ovarian cycle. The study also shows that female-specific 3D genome dynamics affect neuronal gene expression and brain disorder-relevant genes, and could play a role in reproductive hormone-induced brain plasticity and female-specific risk for brain disorders.

NATURE COMMUNICATIONS (2022)

Review Biotechnology & Applied Microbiology

Meta-analysis of epigenome-wide association studies in newborns and children show widespread sex differences in blood DNA methylation

Olivia Solomon et al.

Summary: This study conducted a meta-analysis to investigate sex differences in DNA methylation in newborns and older children. The findings revealed numerous DNA methylation sites associated with sex in newborn blood, where most of these sites had lower methylation levels in males. Furthermore, the study replicated these findings in older children and identified additional autosomal sites with sex-specific differences in DNA methylation. These differentially methylated sites were enriched in genes associated with cancer, psychiatric disorders, and cardiovascular phenotypes.

MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH (2022)

Article Biochemistry & Molecular Biology

Sex-differential DNA methylation and associated regulation networks in human brain implicated in the sex-biased risks of psychiatric disorders

Yan Xia et al.

Summary: The study expanded the regulatory networks related to sex-differential methylation and psychiatric disorders by integrating methylation quantitative trait loci, gene expression, and protein-protein interaction data. It found significant enrichment of sex-associated genes in psychiatric disorder-associated gene sets, suggesting that sex-differential genes in neuronal pathways may contribute to the sex-bias of psychiatric disorders.

MOLECULAR PSYCHIATRY (2021)

Article Cell Biology

Male-specific age estimation based on Y-chromosomal DNA methylation

Athina Vidaki et al.

Aging-US (2021)

Article Multidisciplinary Sciences

Skewness of X-chromosome inactivation increases with age and varies across birth cohorts in elderly Danish women

Jonas Mengel-From et al.

Summary: Mosaicism in blood varies with age, with skewness of X-chromosomal mosaicism increasing for women as they age. Longitudinal studies of septuagenarians and centenarians showed that 16% of women developed skewed X-inactivation over a 10-year period. Additionally, cross-birth cohort comparisons indicated that older birth cohorts had a higher degree of skewness in X-inactivation, possibly due to improved living conditions and medical treatment in more recent birth cohorts.

SCIENTIFIC REPORTS (2021)

Editorial Material Public, Environmental & Occupational Health

Stop 'controlling' for sex and gender in global health research

Janna R. Shapiro et al.

BMJ GLOBAL HEALTH (2021)

Article Genetics & Heredity

Ageing-associated changes in DNA methylation in X and Y chromosomes

Laura Kananen et al.

Summary: The study identified significant overlap in X chromosomal age-associated CpGs between males and females, while showing differences in age-associated DNA methylation changes in the Y chromosome. Despite consistent findings in X chromosomal CpGs in both sexes, it is unlikely to be a major contributor to sexual dimorphism in ageing, with Y chromosome potentially playing a significant role in the aging process.

EPIGENETICS & CHROMATIN (2021)

Review Medicine, General & Internal

Sex Differences Are Here to Stay: Relevance to Prenatal Care

Amy M. Inkster et al.

Summary: Sex differences in perinatal complications, influenced by gene expression and gonadal steroid hormones, play a significant role in placental function and pregnancy outcomes. Consideration of sex differences is important when developing diagnostic or risk prediction tools for such complications.

JOURNAL OF CLINICAL MEDICINE (2021)

Article Biotechnology & Applied Microbiology

Revisiting genetic artifacts on DNA methylation microarrays exposes novel biological implications

Benjamin Planterose Jimenez et al.

Summary: Our study introduces UMtools, an R-package with novel methods for quantifying and qualifying genetic artifacts based on fluorescence intensity signals. Through modeling and validation on a dataset of monozygotic twins, we estimate minor allele frequency from DNA methylation data and empirically detect variants not included in dbSNP. Furthermore, we identify interactions between genetic artifacts and imprinting, X-inactivation, or tissue-specific regulation. Overall, our study provides an atlas to navigate through the vast diversity of genetic artifacts encountered on DNA methylation microarrays, setting the stage for a paradigm shift in studying the genetic component of epigenetic variation.

GENOME BIOLOGY (2021)

Article Genetics & Heredity

Human methylome variation across Infinium 450K data on the Gene Expression Omnibus

Sean K. Maden et al.

Summary: The study analyzed a large number of publicly available DNAm array samples, with approximately two-thirds from blood, one-quarter from brain, and one-third from cancer patients. It was found that some samples did not pass quality assessments, and modifying the failure thresholds was suggested to make assessments more informative. Finally, a database containing DNAm array data and metadata, including learned and predicted sample labels, was compiled for access.

NAR GENOMICS AND BIOINFORMATICS (2021)

Article Biochemical Research Methods

CoMeBack: DNA methylation array data analysis for co-methylated regions

Evan Gatev et al.

BIOINFORMATICS (2020)

Article Endocrinology & Metabolism

SeXY chromosomes and the immune system: reflections after a comparative study

Irene Meester et al.

BIOLOGY OF SEX DIFFERENCES (2020)

Article Medicine, General & Internal

Sex and gender: modifiers of health, disease, and medicine

Franck Mauvais-Jarvis et al.

LANCET (2020)

Review Behavioral Sciences

Four Core Genotypes and XY mouse models: Update on impact on SABV research

Arthur P. Arnold

NEUROSCIENCE AND BIOBEHAVIORAL REVIEWS (2020)

Editorial Material Neurosciences

Analysis of sex differences in pre-clinical and clinical data sets

Adriene M. Beltz et al.

NEUROPSYCHOPHARMACOLOGY (2019)

Article Biochemical Research Methods

A framework for analyzing DNA methylation data from Illumina Infinium HumanMethylation450 BeadChip

Zhenxing Wang et al.

BMC BIOINFORMATICS (2018)

Article Genetics & Heredity

Adjusting for Batch Effects in DNA Methylation Microarray Data, a Lesson Learned

E. M. Price et al.

FRONTIERS IN GENETICS (2018)

Review Psychiatry

Exposure to childhood abuse is associated with human sperm DNA methylation

Andrea L. Roberts et al.

TRANSLATIONAL PSYCHIATRY (2018)

Article Biochemical Research Methods

Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi

Jean-Philippe Fortin et al.

BIOINFORMATICS (2017)

Article Multidisciplinary Sciences

Landscape of X chromosome inactivation across human tissues

Taru Tukiainen et al.

NATURE (2017)

Article Biochemical Research Methods

Comparison of pre-processing methods for Infinium HumanMethylation450 BeadChip array

Yu-Jia Shiah et al.

BIOINFORMATICS (2017)

Article Biotechnology & Applied Microbiology

An evaluation of processing methods for HumanMethylation450 BeadChip data

Jie Liu et al.

BMC GENOMICS (2016)

Article Multidisciplinary Sciences

Epigenetic Pattern on the Human Y Chromosome Is Evolutionarily Conserved

Minjie Zhang et al.

PLOS ONE (2016)

Review Immunology

Sex differences in immune responses

Sabra L. Klein et al.

NATURE REVIEWS IMMUNOLOGY (2016)

Article Genetics & Heredity

Characterization of whole-genome autosomal differences of DNA methylation between men and women

Paula Singmann et al.

EPIGENETICS & CHROMATIN (2015)

Article Medicine, Research & Experimental

The Human Placental Methylome

Wendy P. Robinson et al.

COLD SPRING HARBOR PERSPECTIVES IN MEDICINE (2015)

Article Oncology

Association of DNA methylation with age, gender, and smoking in an Arab population

Shaza B. Zaghlool et al.

CLINICAL EPIGENETICS (2015)

Article Biochemistry & Molecular Biology

Landscape of DNA methylation on the X chromosome reflects CpG density, functional chromatin state and X-chromosome inactivation

Allison M. Cotton et al.

HUMAN MOLECULAR GENETICS (2015)

Article Biotechnology & Applied Microbiology

Meta-analysis of human methylation data for evidence of sex-specific autosomal patterns

Nina S. McCarthy et al.

BMC GENOMICS (2014)

Article Biochemistry & Molecular Biology

Sex-biased methylome and transcriptome in human prefrontal cortex

Hongqin Xu et al.

HUMAN MOLECULAR GENETICS (2014)

Article Biotechnology & Applied Microbiology

Functional normalization of 450k methylation array data improves replication in large cancer studies

Jean-Philippe Fortin et al.

GENOME BIOLOGY (2014)

Article Biotechnology & Applied Microbiology

A data-driven approach to preprocessing Illumina 450K methylation array data

Ruth Pidsley et al.

BMC GENOMICS (2013)

Review Oncology

Review of processing and analysis methods for DNA methylation array data

C. S. Wilhelm-Benartzi et al.

BRITISH JOURNAL OF CANCER (2013)

Article Biochemistry & Molecular Biology

Low-level processing of Illumina Infinium DNA Methylation BeadArrays

Timothy J. Triche et al.

NUCLEIC ACIDS RESEARCH (2013)

Article Biochemical Research Methods

The sva package for removing batch effects and other unwanted variation in high-throughput experiments

Jeffrey T. Leek et al.

BIOINFORMATICS (2012)

Article Obstetrics & Gynecology

Outcomes of preterm infants <29 weeks gestation over 10-year period in Canada: a cause for concern?

P. S. Shah et al.

JOURNAL OF PERINATOLOGY (2012)

Article Obstetrics & Gynecology

The relationship between blastocyst morphology, chromosomal abnormality, and embryo gender

Samer Alfarawati et al.

FERTILITY AND STERILITY (2011)

Article Biochemistry & Molecular Biology

DNA methylation profiles of human active and inactive X chromosomes

Andrew J. Sharp et al.

GENOME RESEARCH (2011)

Article Genetics & Heredity

Chromosome-wide DNA methylation analysis predicts human tissue-specific X inactivation

Allison M. Cotton et al.

HUMAN GENETICS (2011)

Article Biochemistry & Molecular Biology

The UCSC Genome Browser database: update 2011

Pauline A. Fujita et al.

NUCLEIC ACIDS RESEARCH (2011)

Article Genetics & Heredity

Evaluation of the Infinium Methylation 450K technology

Sarah Dedeurwaerder et al.

EPIGENOMICS (2011)

Review Endocrinology & Metabolism

What does the four core genotypes mouse model tell us about sex differences in the brain and other tissues?

Arthur P. Arnold et al.

FRONTIERS IN NEUROENDOCRINOLOGY (2009)

Article Biochemistry & Molecular Biology

Inactive X chromosome-specific reduction in placental DNA methylation

Allison M. Cotton et al.

HUMAN MOLECULAR GENETICS (2009)

Article Genetics & Heredity

Blastocyst transfer and gender: IVF versus ICSI

Martha Agnes Hentemann et al.

JOURNAL OF ASSISTED REPRODUCTION AND GENETICS (2009)

Editorial Material Cell Biology

Discovering NF-κB

David Baltimore

COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY (2009)

Article Biochemistry & Molecular Biology

New binary polymorphisms reshape and increase resolution of the human Y chromosomal haplogroup tree

Tatiana M. Karafet et al.

GENOME RESEARCH (2008)

Article Obstetrics & Gynecology

Blastocyst embryo transfer is associated with a sex-ratio imbalance in favor of male offspring

Martha Luna et al.

FERTILITY AND STERILITY (2007)

Article Mathematical & Computational Biology

Adjusting batch effects in microarray expression data using empirical Bayes methods

W. Evan Johnson et al.

BIOSTATISTICS (2007)

Article Cell Biology

Increased skewing of X chromosome inactivation with age in both blood and buccal cells

G. P. S. Knudsen et al.

CYTOGENETIC AND GENOME RESEARCH (2007)

Article Genetics & Heredity

The dynamics of X-inactivation skewing as women age

C Hatakeyama et al.

CLINICAL GENETICS (2004)

Article Biochemistry & Molecular Biology

Identification of a nuclear protein that promotes NF-κB activation

DY Chen et al.

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS (2003)

Article Biochemistry & Molecular Biology

The human genome browser at UCSC

WJ Kent et al.

GENOME RESEARCH (2002)

Article Multidisciplinary Sciences

Molecular evidence for a relationship between LINE-1 elements and X chromosome inactivation: The Lyon repeat hypothesis

JA Bailey et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2000)