Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Ribosomal Protein Gene Deletions in Diamond Blackfan Anemia

ABSTRACT: Diamond Blackfan anemia is a congenital bone marrow failure syndrome characterized by hypoproliferative anemia, often with associated physical abnormalities. Perturbations of the ribosome appear critically important to the development of DBA, as alterations in 9 different ribosomal protein genes have been identified in multiple unrelated families, along with rarer abnormalities of additional ribosomal proteins. However, presently only 50-60% of patients have an identifiable genetic lesion by ribosomal protein gene sequencing. Using genome-wide SNP array to evaluate for regions of recurrent copy variation, we identified deletions at known DBA-related ribosomal protein gene loci in 17% (9/51) of patients without an identifiable mutation, including RPS19, RPS17, RPS26, and RPL35A [Illumina platforms] A total of 68 samples were analyzed on Illumina Omni1_Quad or Illumina OmniExpress Genotyping bead arrays; 51 affected probands, 1 affected sibling, 1 unaffected sibling, and 15 parents. [NimbleGen platform] 5 samples where a deletion was identified by SNP array and one sample where no deletion was identified were run on Nimblegen Human CGH 3x720K Whole-Genome Exon-Focused arrays for confirmation.

ORGANISM(S): Homo sapiens

SUBMITTER: Jason Farrar

PROVIDER: E-GEOD-31575 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Ribosomal protein gene deletions in Diamond-Blackfan anemia.

Farrar Jason E JE Vlachos Adrianna A Atsidaftos Eva E Carlson-Donohoe Hannah H Markello Thomas C TC Arceci Robert J RJ Ellis Steven R SR Lipton Jeffrey M JM Bodine David M DM

Blood 20111101 26

Diamond-Blackfan anemia (DBA) is a congenital BM failure syndrome characterized by hypoproliferative anemia, associated physical abnormalities, and a predisposition to cancer. Perturbations of the ribosome appear to be critically important in DBA; alterations in 9 different ribosomal protein genes have been identified in multiple unrelated families, along with rarer abnormalities of additional ribosomal proteins. However, at present, only 50% to 60% of patients have an identifiable genetic lesio ...[more]

PMID: 22045982

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Project description:A genome-wide eQTL analysis was performed in whole blood samples collected from 76 Japanese subjects. RNA microarray analysis was performed for 3 independent samples that were genotyped in a genome-wide scan. The correlations between the genotypes of 534,404 autosomal single nucleotide polymorphisms (SNPs) and the expression levels of 30,465 probes were examined for each sample. The SNP-probe pairs with combined correlation coefficients of all 3 samples corresponding to P < 3.10 × 10-12 (i.e., Bonferroni-corrected P < 0.05) were considered significant. SNP-probe pairs with a high likelihood of cross-hybridization and SNP-in-probe effects were excluded to exclude false positive results. We identified 102 cis-acting and 5 trans-acting eQTL regions. The cis-eQTL regions were widely distributed both upstream and downstream of the gene, as well as within the gene. RNA microarray data obtained from 3 independent samples originally recruited for other studies investigating the gene expression levels in psychiatric disorders were used in the present study. For the purpose of the present analyses, genomic DNA was collected from 24 subjects (13 men and 11 women, mean age [SD] = 39.9 [7.6] years) in sample 1, 24 subjects in sample 2 (12 men and 12 women, 34.1 [11.5] years), and 28 subjects (14 men and 14 women, 41.4 [11.8] years) in sample 3. Some of the subjects had depressive symptoms, but all were physically healthy and without clinically significant systemic disease (e.g., malignant disease, diabetes mellitus, hypertension, renal failure, or endocrine disorders). Subjects were recruited from the outpatient clinic of the National Center of Neurology and Psychiatry Hospital, Tokyo, Japan, through advertisements in free local information magazines or through our website announcement. All the subjects were biologically unrelated Japanese individuals who resided in the same geographical area (western Tokyo). The study protocol was approved by the ethics committee at the National Center of Neurology and Psychiatry, Japan. Written informed consent was obtained from every subject after the study was explained to them. Venous blood was collected between 1100 and 1200 h in PAXgene tubes (Qiagen, Valencia) from each subject and was incubated at room temperature for 24 h for RNA stabilization. RNA was extracted from whole blood according to the manufacturer’s guidelines by using the PAXgene Blood RNA System Kit (PreAnalytix GmbH, Hombrechtikon, Switzerland). The RNA was quantified by optical density readings at A260nm by using the NanoDrop ND-1000 (Thermo Scientific, Rockford). Gene expression analysis was performed using Agilent Human Genome 4 × 44 K arrays (Agilent Technologies, Santa Clara). Raw signal data for each of the 3 independent samples were analyzed separately by the GeneSpring GX software (Agilent Technologies). Data were filtered according to the expression level for quality control to eliminate genes that were below the 20th percentile threshold. The expression value of each gene was normalized to the median expression value of all genes in each chip. A total of 30,465 probes were included in the analysis. Genomic DNA was obtained from venous blood samples. Genotyping was performed by Riken Genesis (Yokohama, Japan) using the Illumina HumanOmni1-Quad BeadChip (Illumina, Inc., San Diego). A total of 713,495 autosomal SNPs were assessed for quality using the PLINK v1.07 software. All SNPs with a call rate below 95%, a deviation from Hardy-Weinberg equilibrium at an error level of P < 0.001, or a minor allele frequency of less than 10% were excluded. The remaining 534,404 SNPs were used for further analysis.

Project description:Contemporary Jews comprise an aggregate of ethno-religious communities whose worldwide members identify with each other through various shared religious, historical, and cultural traditions1,2. Historical evidence suggests common origins in the Middle East, followed by migrations leading to the establishment of communities of Jews in Europe, Africa, and Asia - in what is termed the Jewish Diaspora3-5. This complex demographic history imposes special challenges in attempting to address the genetic structure of the Jewish people6. While many genetic studies have shed light on Jewish diseases and origins, including those focusing on uniparentally- and biparentally-inherited markers7-16, genome-wide patterns of variation across the vast geographic span of Jewish Diaspora communities and their respective neighbors have yet to be addressed. Here we use high-density bead arrays to genotype individuals from 14 Jewish Diaspora communities, and compare these patterns of genome-wide diversity with those from 69 Old World non-Jewish populations, of which 25 have not been previously reported. These samples were carefully chosen to provide comprehensive comparisons between Jewish and non-Jewish populations in the Diaspora, as well as with non-Jewish populations from the Middle East and North Africa. Principal component and structure-like analyses identify previously unrecognized genetic substructure within the Middle East. Most Jewish samples form a remarkably tight sub-cluster that overlies Druze and Cypriot samples, but not samples from other Levantine populations or paired Diaspora host populations. In contrast, Ethiopian Jews (Beta Israel) and Bene Israel Indian Jews cluster with neighbouring autochthonous populations in Ethiopia and western India, respectively; despite a clear paternal link between the Bene Israel and the Levant. These results cast light on the variegated genetic architecture of the Middle East, and trace the origins of most Jewish Diaspora communities to the Levant. 466 samples are analysed on three different Illumina platforms.

Dataset Information

Ribosomal Protein Gene Deletions in Diamond Blackfan Anemia

Publications

Ribosomal protein gene deletions in Diamond-Blackfan anemia.

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