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Structural genomic variation analysis in patients with bone marrow failure using Illumina Infinium SNP Arrays [Illumina Quad610 Beadchip]

ABSTRACT: To better understand the natural history of bone marrow failure syndromes, we analyzed 124 single nucleotide polymorphism arrays (SNP-A) from a comprehensively characterized cohort of 91 patients who had SNP-A for clinical evaluation of BMFS. 67 samples from 51 patients were genotyped with the Quad610, and 57 samples from 54 patients were genotyped with the Omni1-Quad. This submission includes 67 samples from 51 patients that were genotyped with Illumina Quad610 Beadchip. Illumina Infinium SNP-A genotyping was performed on DNA extracted from bone marrow aspirates using standard manufacturer's protocol

ORGANISM(S): Homo sapiens

SUBMITTER: Daria Babushok

PROVIDER: E-GEOD-48483 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Structural genomic variation analysis in patients with bone marrow failure using Illumina Infinium SNP Arrays [Omni1-Quad]

Project description:To better understand the natural history of bone marrow failure syndromes, we analyzed 124 single nucleotide polymorphism arrays (SNP-A) from a comprehensively characterized cohort of 91 patients who had SNP-A for clinical evaluation of BMFS. 67 samples from 51 patients were genotyped with the Quad610, and 57 samples from 54 patients were genotyped with the Omni1-Quad. This submission includes 55 samples from 54 patients that were genotyped with Omni1-Quad. Illumina Infinium SNP-A genotyping was performed on DNA extracted from bone marrow aspirates using standard manufacturer's protocol

2014-01-01 | E-GEOD-48482 | biostudies-arrayexpress

Structural genomic variation analysis in patients with bone marrow failure using Illumina Infinium SNP Arrays [Illumina Quad610 Beadchip]

Project description:To better understand the natural history of bone marrow failure syndromes, we analyzed 124 single nucleotide polymorphism arrays (SNP-A) from a comprehensively characterized cohort of 91 patients who had SNP-A for clinical evaluation of BMFS. 67 samples from 51 patients were genotyped with the Quad610, and 57 samples from 54 patients were genotyped with the Omni1-Quad. This submission includes 67 samples from 51 patients that were genotyped with Illumina Quad610 Beadchip.

2014-01-01 | GSE48483 | GEO

Structural genomic variation analysis in patients with bone marrow failure using Illumina Infinium SNP Arrays

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2014-01-01 | E-GEOD-48484 | biostudies-arrayexpress

Structural genomic variation analysis in patients with bone marrow failure using Illumina Infinium SNP Arrays [Omni1-Quad]

2014-01-01 | GSE48482 | GEO

Genotyping by array: Human Developmental Biology Resource (HDBR) expression resource of prenatal human brain development-SNP data

Project description:The Human Developmental Biology Resource (HDBR) expression resource is a new resource for studying prenatal human brain development. It consists of two parts which have been uploaded as two submissions: HDBR expression resource- RNAseq (E-MTAB-4840) and HDBR expression resource- SNP data (E-MTAB-4843, this submission). It is unique in the age range (4 post conception weeks [PCW] to 17PCW) and number of brains studied, particularly those under 8PCW. It is also unique in that both the large-scale data sets and the corresponding RNA and DNA samples are available, the latter via the MRC-Wellcome Trust Human Developmental Biology Resource (HDBR; www.hdbr.org). There are 628 RNA-seq datasets from different regions of the brains studied. The number of regions depends on the stage and size of the sample and/or the tissue available. Embryos (4-8PCW) have been staged using a modified Carnegie staging system, details can be found at http://database.hudsen.eu/. All the RNAseq datasets from the same embryo/fetus have the same ID number (e.g. RNAseq datasets HDBR251-HDBR254 are from different tissues from embryo number 1406). The embryo/fetus ID number is recorded in the âindividualâ column. The majority of the brains studied are between 4 and 12PCW. During this time the major brain regions are established and there are the early stages of cortex development. DNA was prepared from all the tissues used for RNA-seq analysis and SNP genotype data generated from one tissue from each brain. RNA-seq data and SNP-data from the same tissue and individual embryo or fetus have the same name (e.g. HDBR469). There are also SNP genotype data from 229 additional specimens in paraffin wax blocks available for individual gene expression studies. For the specimens in wax blocks, the SNP genotype data was generated from DNA from either skin or placenta. The tissues present in the corresponding wax block(s) are given in the biosource type column.

2016-10-12 | E-MTAB-4843 | biostudies-arrayexpress

Genotyping of SNP array in individuals with San ancestry in southeastern Africa

Project description:Only a few scattered groups with oral traditions of Khoe-San hunter-gatherer ancestry remain in southeastern Africa. We investigate genomic variation of remaining individuals from two South African groups with oral histories connecting them to eastern San groups, i.e., the San from Lake Chrissie and the Duma San of the uKhahlamba-Drakensberg. Using ~2.2 million genetic markers, combined with comparative published datasets, we show that the Lake Chrissie San have genetic ancestry from both Khoe-San (likely the ||Xegwi San) and Bantu-speakers. Specifically, we found that the Lake Chrissie San are closely related to current southern San groups (i.e. the Karretjie People). Duma San individuals, on the other hand, were genetically similar to southeastern Bantu speakers from South Africa. Samples were genotyped on the Illumina Omni2.5M (HumanOmni25-8v1-2_A1) SNP chip. Results were analyzed using the software GenomeStudio 2011.1 and the data were exported to Plink format, aligned to Human Genome build version 37.

2016-09-21 | E-MTAB-5119 | biostudies-arrayexpress

SNP genotyping analyses for the Chinese indigenous pig breeds and commercial pig breeds

Project description:Genome-wide SNP genotyping array can genotyped SNP highthroughly. It can be used in many aspects, such as phylogeny relationships, genome-wide association studies, copy number identification.

2013-05-09 | GSE46733 | GEO

Genome-wide SNP array data from Human Variation Panel by Illumina 510S

Project description:Radiation therapy is used to treat half of all cancer patients. Response to radiation therapy varies widely among patients. Therefore, we performed a genome-wide association study (GWAS) to identify biomarkers to help predict radiation response using 277 ethnically defined human lymphoblastoid cell lines (LCLs). Basal gene expression levels (Affymetrix) and 1.3 million genome-wide SNP markers (Illumina) were assayed for all 277 human LCLs. MTS (3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium) assays for radiation cytotoxicity were also performed to obtain area under the curve (AUC) as a radiation response phenotype for use in the association studies. Functional validation of candidate genes, selected from an integrated analysis that used SNP, expression and AUC data, was performed with multiple cancer cell lines using specific siRNA knockdown, followed by MTS and colony-forming assays. 27 loci, each containing at least 2 SNPs within 50kb with p-values <10-4, were associated with radiation AUC. 270 expression probe sets were associated with radiation AUC with p<10-3. The integrated analysis identified 50 SNPs in 14 of the 27 loci that were associated with both AUC and the expression of 39 genes that were also associated with radiation AUC (p<10-3). Functional validation using siRNA knockdown in multiple tumor cell lines showed that C13orf34, MAD2L1, PLK4, TPD52 and DEPDC1B each significantly altered radiation sensitivity in at least 2 cancer cell lines. Studies performed with LCLs can help to identify novel biomarkers that might contribute to variation in response to radiation therapy and enhance our understanding of mechanisms underlying that variation. EBV-transformed LCLs from 96 African-American (AA), 96 Caucasian-American (CA), and 96 Han Chinese-American (HCA) unrelated healthy subjects (sample sets HD100AA, HD100CAU, HD100CHI) were purchased from the Coriell Cell Repository (Camden, NJ).

2010-09-24 | E-GEOD-24245 | biostudies-arrayexpress

Genome-wide SNP array data from Human Variation Panel by Illumina 550K

Project description:Radiation therapy is used to treat half of all cancer patients. Response to radiation therapy varies widely among patients. Therefore, we performed a genome-wide association study (GWAS) to identify biomarkers to help predict radiation response using 277 ethnically defined human lymphoblastoid cell lines (LCLs). Basal gene expression levels (Affymetrix) and 1.3 million genome-wide SNP markers (Illumina) were assayed for all 277 human LCLs. MTS (3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium) assays for radiation cytotoxicity were also performed to obtain area under the curve (AUC) as a radiation response phenotype for use in the association studies. Functional validation of candidate genes, selected from an integrated analysis that used SNP, expression and AUC data, was performed with multiple cancer cell lines using specific siRNA knockdown, followed by MTS and colony-forming assays. 27 loci, each containing at least 2 SNPs within 50kb with p-values <10-4, were associated with radiation AUC. 270 expression probe sets were associated with radiation AUC with p<10-3. The integrated analysis identified 50 SNPs in 14 of the 27 loci that were associated with both AUC and the expression of 39 genes that were also associated with radiation AUC (p<10-3). Functional validation using siRNA knockdown in multiple tumor cell lines showed that C13orf34, MAD2L1, PLK4, TPD52 and DEPDC1B each significantly altered radiation sensitivity in at least 2 cancer cell lines. Studies performed with LCLs can help to identify novel biomarkers that might contribute to variation in response to radiation therapy and enhance our understanding of mechanisms underlying that variation. EBV-transformed LCLs from 96 Caucasian-American (CA), and 96 Han Chinese-American (HCA) unrelated healthy subjects (sample sets HD100CAU, HD100CHI) were purchased from the Coriell Cell Repository (Camden, NJ).

2010-09-24 | E-GEOD-24260 | biostudies-arrayexpress

Genome-wide SNP array data from Human Variation Panel by Illumina 650K

Project description:Radiation therapy is used to treat half of all cancer patients. Response to radiation therapy varies widely among patients. Therefore, we performed a genome-wide association study (GWAS) to identify biomarkers to help predict radiation response using 277 ethnically defined human lymphoblastoid cell lines (LCLs). Basal gene expression levels (Affymetrix) and 1.3 million genome-wide SNP markers (Illumina) were assayed for all 277 human LCLs. MTS (3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium) assays for radiation cytotoxicity were also performed to obtain area under the curve (AUC) as a radiation response phenotype for use in the association studies. Functional validation of candidate genes, selected from an integrated analysis that used SNP, expression and AUC data, was performed with multiple cancer cell lines using specific siRNA knockdown, followed by MTS and colony-forming assays. 27 loci, each containing at least 2 SNPs within 50kb with p-values <10-4, were associated with radiation AUC. 270 expression probe sets were associated with radiation AUC with p<10-3. The integrated analysis identified 50 SNPs in 14 of the 27 loci that were associated with both AUC and the expression of 39 genes that were also associated with radiation AUC (p<10-3). Functional validation using siRNA knockdown in multiple tumor cell lines showed that C13orf34, MAD2L1, PLK4, TPD52 and DEPDC1B each significantly altered radiation sensitivity in at least 2 cancer cell lines. Studies performed with LCLs can help to identify novel biomarkers that might contribute to variation in response to radiation therapy and enhance our understanding of mechanisms underlying that variation. EBV-transformed LCLs from 95 African-American (AA) unrelated healthy subjects (sample sets HD100AA) were purchased from the Coriell Cell Repository (Camden, NJ).

2010-09-25 | E-GEOD-24274 | biostudies-arrayexpress

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