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Methyaltion array and RNA-Seq analysis of response to P.falciparum infection in Fulani and Mossi ethnic groups, Burkina Faso

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE100563 | GEO | 2017/10/02

SECONDARY ACCESSION(S): PRJNA392115

REPOSITORIES: GEO

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DNA-methylation analysis of response to P.falciparum infection in Fulani and Mossi ethnic groups, Burkina Faso

Project description:The Fulani ethnic group is relatively protected from Plasmodium falciparum malaria, however a genetic basis for this is unknown. Therefore, we have performed a pilot study to examine global transcription and DNA methylation patterns in specific immune cell populations in the Fulani, compared to a sympatric ethnic group, the Mossi. When we compared uninfected and infected individuals in Fulani and Mossi, a strong transcriptional response was only detected in the monocyte fraction of Fulani, and this was not related to differences in DNA methylation.

2017-10-02 | GSE100561 | GEO

RNA-sequencing analysis of response to P.falciparum infection in Fulani and Mossi ethnic groups, Burkina Faso

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Methyaltion array and RNA-Seq analysis of response to P.falciparum infection in Fulani and Mossi ethnic groups, Burkina Faso

Project description:Methyaltion array and RNA-Seq analysis of response to P.falciparum infection in Fulani and Mossi ethnic groups, Burkina Faso

| PRJNA392115 | ENA

DNA methyaltion analysis in decidualization

Project description:DNA methylation status was examined by Illumina 450k in non-decidualized and decidualized ESCs.

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DNA Methyaltion of Human Cortical Organoids

Project description:Assesing DNA methylation patterns of human cortical organoids during long term (>600 days) maturation.

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Genetic differences among ethnic groups.

Project description:BackgroundMany differences between different ethnic groups have been observed, such as skin color, eye color, height, susceptibility to some diseases, and response to certain drugs. However, the genetic bases of such differences have been under-investigated. Since the HapMap project, large-scale genotype data from Caucasian, African and Asian population samples have been available. The project found that these populations were located in different areas of the PCA (Principal Component Analysis) plot. However, as an unsupervised method, PCA does not measure the differences in each single nucleotide polymorphism (SNP) among populations.ResultsWe applied an advanced mutual information-based feature selection method to detect associations between SNP status and ethnic groups using the latest HapMap Phase 3 release version 3, which included more sub-populations. A total of 299 SNPs were identified, and they can accurately predicted the ethnicity of all HapMap populations. The 10-fold cross validation accuracy of the SMO (sequential minimal optimization) model on training dataset was 0.901, and the accuracy on independent test dataset was 0.895.ConclusionsIn-depth functional analysis of these SNPs and their nearby genes revealed the genetic bases of skin and eye color differences among populations.

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Hepatitis B virus infection and genotype in asymptomatic people from 10 ethnic groups in Yunnan, China.

Project description:AimTo evaluate the infection and genotype distribution of hepatitis B virus (HBV) in ethnic groups in Yunnan, China.MethodsTwo thousand five hundred and eighty-four asymptomatic local people from 10 ethnic groups were investigated in Yunnan, China. Infection and genotype distribution were evaluated by serological and genetic methods. Genotyping was verified by sequencing. Ethnic genotype distribution was compared by proportion test.ResultsFour types of infection model based on HBV serum markers were identified, and the average HBV infection rate was 5.7% in those asymptomatic local people. The genotype prevalence was 59.6% for B, 21.1% for C and 19.3% BC; subgenotypes Ba, Cs and Ce were identified in this study. Hepatitis B surface antigen-positive rate and the proportion of genotype B were significantly lower in ethnic groups with a northern origin compared to those with a southern origin (50% vs 73.9%, P = 0.037; 4.2% vs 10.5%, P = 0.000).ConclusionGenotype B is dominant and genotype BC has high occurrence in asymptomatic local ethnic groups in Yunnan. HBV infection status and genotype distribution may associate with ethnic origin.

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Microsatellite stable Left Colon Cancer distinct in Indigenous African patients versus other ethnic groups

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The multigroup ethnic identity measure-revised: measurement invariance across racial and ethnic groups.

Project description:The Multigroup Ethnic Identity Measure-Revised (MEIM-R), a brief instrument assessing affiliation with one's ethnic group, is a promising advance in the ethnic identity literature. However, equivalency of its measurement properties across specific racial and ethnic groups should be confirmed before using it in diverse samples. We examined (a) the psychometric properties of the MEIM-R, including factor structure, measurement invariance, and internal consistency reliability, and (b) levels of and differences in ethnic identity across multiple racial and ethnic groups and subgroups. Asian (n = 630), Black/African American (n = 58), Hispanic (n = 240), multiethnic (n = 160), and White (n = 375) women completed the MEIM-R as part of the "Gestational diabetes' Effect on Moms" diabetes prevention trial in the Kaiser Permanente Northern California health care setting (N = 1,463; M age = 32.5 years, SD = 4.9). Multiple-groups confirmatory factor analyses provided provisional evidence of measurement invariance, i.e., an equal, correlated 2-factor structure, equal factor loadings, and equal item intercepts across racial and ethnic groups. Latent factor means for the 2 MEIM-R subscales, exploration and commitment, differed across groups; effect sizes ranging from small to large generally supported the notion of ethnic identity as more salient among people of color. Pending replication, good psychometric properties in this large and diverse sample of women support the future use of the MEIM-R. Preliminary evidence of measurement invariance suggests that the MEIM-R could be used to measure and compare ethnic identity across multiple racial and ethnic groups.

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Gene activation precedes DNA demethylation in response to infection in human dendritic cells

Project description:This SuperSeries is composed of the SubSeries listed below.

2018-07-03 | GSE116412 | GEO