Xiaomin Liu

Beijing Genomics Institute

The gut microbiome has been established as a key environmental factor to health. Genetic influences on the gut microbiome have been reported, yet, doubts remain as to the significance of genetic associations. Here, we provide shotgun data for whole genome and whole metagenome from a Chinese cohort, identifying no <20% genetic contribution to the gu...

There is growing interest in studying the genetic contributions to longevity, but limited relevant genes have been identified. In this study, we performed a genetic association study of longevity in a total of 15,651 Chinese individuals. Novel longevity loci, BMPER (rs17169634; p = 7.91 × 10 −15) and TMEM43/XPC (rs1043943; p = 3.59 × 10 −8), were i...

The oral microbiota contains billions of microbial cells, which could contribute to diseases in many body sites. Challenged by eating, drinking, and dental hygiene on a daily basis, the oral microbiota is regarded as highly dynamic. Here, we report significant human genomic associations with the oral metagenome from more than 1915 individuals, for...

The gut microbiome has been implicated in a variety of physiological states, but controversy over causality remains unresolved. Here, we performed bidirectional Mendelian randomization analyses on 3,432 Chinese individuals with whole-genome, whole-metagenome, anthropometric and blood metabolic trait data. We identified 58 causal relationships betwe...

The oral microbiome has been implicated in a growing number of diseases, however, determinants of the oral microbiome and their roles remain elusive. Here, we investigated the oral (saliva and tongue dorsum) metagenome, the whole genome, and other omics data in a total of 4,478 individuals, and demonstrated that the oral microbiome composition and...

Although recent studies have revealed the association between the human microbiome especially gut microbiota and longevity, their causality remains unclear. Here, we assess the causal relationships between the human microbiome (oral and gut microbiota) and longevity, by leveraging bidirectional two-sample Mendelian randomization (MR) analyses based...

Although a few studies have reported the effects of several polymorphisms on major adverse cardiovascular events (MACE) in patients with acute coronary syndromes (ACS) and those undergoing percutaneous coronary intervention (PCI), these genotypes account for only a small fraction of the variation and evidence is insufficient. This study aims to ide...

A Correction to this paper has been published: https://doi.org/10.1038/s41467-021-22613-2

Chromatin organization and transcriptional profiles undergo tremendous reordering during senescence. However, uncovering the regulatory mechanisms between chromatin reconstruction and gene expression in senescence has been elusive. Here, we depicted the landscapes of both chromatin accessibility and gene expression to reveal gene regulatory network...

In this study, we split 2156 individuals from the Chinese Longitudinal Healthy Longevity Survey (CLHLS) data into two groups, establishing a phenotype of exceptional longevity & normal cognition versus cognitive impairment. We conducted a genome-wide association study (GWAS) to identify significant genetic variants and biological pathways that are...

Objective: Human ABO blood groups are determined by the alleles A, B, and O (O01 and O02) of the ABO gene and have been linked to the risks for cardiovascular diseases and cancers that affect lifespan.We examined the genetic associations of the ABO gene and blood groups with longevity. Methods: We inspected the frequencies of the A, B, O, and O0...

The gut microbiome has been implicated in a variety of physiological states. Controversy over causality, however, has always haunted microbiome studies. Here, we utilized the bidirectional Mendelian randomization (MR) approach to address questions that are not yet mature for more costly randomized interventions. From a total of 3,432 Chinese indivi...

Human longevity is heritable, but genome-wide association (GWA) studies have had limited success. Here, we perform two meta-analyses of GWA studies of a rigorous longevity phenotype definition including 11,262/3484 cases surviving at or beyond the age corresponding to the 90th/99th survival percentile, respectively, and 25,483 controls whose age at...

The gut microbiome has been established as a key environmental factor to health. Genetic influences on the gut microbiome have been reported, yet, doubts remain as to the significance of genetic associations. Here, we provide shotgun data for whole genome and whole metagenome from a Chinese cohort, identifying no less than 20% genetic contribution...

Abstract Importance Sex differences in genetic associations with human longevity remain largely unknown; investigations on this topic are important for individualized health care. Objective To explore sex differences in genetic associations with longevity. Design, Setting, and Participants This population-based case-control study used sex-specifi...

eAppendix. Supplementary Material eReferences eTable 1. Sample Size and Ages of the Sex-Specific CLHLS GWAS Datasets eTable 2. The 11 Male-Specific Pathways Significantly Enriched and Associated With Longevity (P<0.005 and FDR<0.05) and the Significant Genes in These Pathways eTable 3. The 34 Female-Specific Pathways Significantly Enriched and As...

Copy number variations (CNVs) have been shown to cause numerous diseases, however, their roles in human lifespan remain elusive. In this study, we investigate the association of CNVs with longevity by comparing the Han Chinese genomes of long-lived individuals from 90 to 117 years of age and the middle-aged from 30 to 65. Our data demonstrate that...

Approximately 15 genes have been directly associated with skin pigmentation variation in humans, leading to its characterization as a relatively simple trait. However, by assembling a global survey of quantitative skin pigmentation phenotypes, we demonstrate that pigmentation is more complex than previously assumed, with genetic architecture varyin...

Objective: To identify potential causative markers involved in the development of early-onset myasthenia gravis (EOMG) in the MHC and non-MHC regions that may interact with the HLA-B*08:01 allele. Methods: We analyzed 583 MG patients and identified 5 patients homozygous for the disease-associated ancestral haplotype 8.1 (HLA-A*01:01, B*08:01, DR...

De novo mutations (DNMs) are important in autism spectrum disorder (ASD), but so far analyses have mainly been on the ~1.5% of the genome encoding genes. Here, we performed whole-genome sequencing (WGS) of 200 ASD parent–child trios and characterised germline and somatic DNMs. We confirmed that the majority of germline DNMs (75.6%) originated from...

The human major histocompatibility complex (MHC) region has been shown to be associated with numerous diseases. However, it remains a challenge to pinpoint the causal variants for these associations because of the extreme complexity of the region. We thus sequenced the entire 5-Mb MHC region in 20,635 individuals of Han Chinese ancestry (10,689 con...

Only two genome-wide significant loci associated with longevity have been identified so far, probably because of insufficient sample sizes of centenarians, whose genomes may harbor genetic variants associated with health and longevity. Here we report a genome-wide association study (GWAS) of Han Chinese with a sample size 2.7 times the largest prev...

Based on the genotypic/phenotypic data from Chinese Longitudinal Healthy Longevity Survey (CLHLS) and Cox proportional hazard model, the present study demonstrates that interactions between carrying FOXO1A-209 genotypes and tea drinking are significantly associated with lower risk of mortality at advanced ages. Such significant association is repli...

The major histocompatibility complex (MHC) is one of the most variable and gene-dense regions of the human genome. Most studies of the MHC, and associated regions, focus on minor variants and HLA typing, many of which have been demonstrated to be associated with human disease susceptibility and metabolic pathways. However, the detection of variants...

Coverage of whole gene body and exome of the MHC genes by capture sequencing data. (XLSX)

Comparison of MHC capture genotypes and HapMap genotypes for sample NA18532. (XLSX)

The accuracy of HLA typing method using simulated data at different sequencing depth with different sequencing error rate. (XLSX)

HLA alleles typed by PCR based Sanger sequence method and target capture sequence method. (XLSX)

Distribution of variations within different genomics functional regions for three samples. (XLSX)

Comparison of MHC capture genotypes and HapMap genotypes for sample NA18555. (XLSX)

Coverage of the MHC region using 200 bp insert size library. (XLSX)

Comparison of MHC capture SNPs and Illumina 2.5 M genotyping alleles for sample YH. We classified both the MHC capture alleles and the alleles that were called by genotyping into three categories: (1) Hom ref (homozygotes where both alleles are identical to the reference); (2) Hom mut (homozygotes where both alleles differ from the reference); (3)...