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

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 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

ORGANISM(S): Homo sapiens

SUBMITTER: Daria Babushok

PROVIDER: E-GEOD-48482 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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. Illumina Infinium SNP-A genotyping was performed on DNA extracted from bone marrow aspirates using standard manufacturer's protocol

2014-01-01 | E-GEOD-48483 | biostudies-arrayexpress

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]

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.

2014-01-01 | GSE48482 | GEO

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

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Genotyping of paired samples of normal colon and colon adenocarcinoma to estimate copy-number alterations

Project description:22 pairs of normal colon\colon adenocarcinoma samples were genotyped using Illumina HumanOmni1-Quad BeadChip to estimate copy number alterations

2013-02-01 | GSE43933 | GEO

Genotyping of paired samples of normal colon and colon adenocarcinoma to estimate copy-number alterations

Project description:22 pairs of normal colon\colon adenocarcinoma samples were genotyped using Illumina HumanOmni1-Quad BeadChip to estimate copy number alterations Genomic DNA of 22 colon adenocarcinoma samples and 22 corresponding normal colon samples were genotyped using Illumina HumanOmni1-Quad BeadChip to estimate copy number alterations.

2013-02-01 | E-GEOD-43933 | biostudies-arrayexpress

Whole genome SNP array of 16 look-alike human couples

Project description:The Illumina Infinium HumanOmni5-Quad BeadChip was used to obtain genomewide SNP profiling of 16 human couples (32 individuals), selected by their facial resemblance.

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Whole genome SNP array of 32 look-alike human couples

Project description:The Illumina Infinium HumanOmni5-Quad BeadChip was used to obtain genomewide SNP profiling of 32 human couples (64 individuals), selected by their facial resemblance.

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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

Genome-wide Patterns of Population Structure and Admixture among Hispanic/Latino Populations

Project description:Hispanic/Latino populations possess a complex genetic structure that reflects recent admixture among and potentially ancient substructure within Native American, European, and West African source populations. Here, we quantify genome-wide patterns of SNP and haplotype variation among 100 individuals with ancestry from Ecuador, Colombia, Puerto Rico, and the Dominican Republic genotyped using Illumina technology. To investigate variations of continental ancestry between different Hispanic/Latino groups (using self-reported country-specific identification of individual, both parents, and all four grandparents) and within them from healthy controls represented in the New York Health Project Biorepository. Genotyped on the Illumina 610-Quad, which is identical to HumanHap550-v3 SNPs plus an additional ~60,000 SNPs for CNV, no CNV data is provided or was analyzed.

2010-04-07 | E-GEOD-21248 | biostudies-arrayexpress

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