title: The utility and limitation of SNP analysis on WGA-amplified tumor DNA in formalin-fixed tumor samples

status: Public on Aug 15 2011

city: Taipei

first: Cher-wei

last: Liang

address: 7 Chung-Shan S. Rd.

department: Pathology

country: Taiwan

institute: National Taiwan University Hospital

summary:
In the study of tumor genetics, formalin-fixed paraffin-embedded (FFPE) tumors are the most readily available tissue samples. While DNA derived from FFPE tissue has been validated for array comparative genomic hybridization (aCGH) application, the suitability of such fragmented DNA for single-nucleotide polymorphism (SNP) array analysis has not been well examined. Furthermore, whole-genome amplification (WGA) has been used in the study of small precursor lesions to produce sufficient amount of DNA for aCGH analysis. It is unclear whether the same approach can be extended to SNP analysis.

In this study, we examined the utility and limitations of genotyping platform performed on whole-genome amplified DNA from FFPE tumor samples for both copy number and SNP analyses. We analyzed the results obtained using DNA derived from matched FFPE and frozen tissue samples on Affymetrix 250K Nsp SNP array. Two widely used WGA methods, Qiagen (isothermal protocol) and Sigma (thermocycling protocol), were used to determine how WGA methods affect the results.

We found that the use of DNA derived from FFPE tumors (without or with WGA) for high-resolution SNP array application can produce a significant amount of false positive and false negative findings.  While some of these misinterpretations appear to cluster in genomic regions with high or low GC contents, the majority appears to occur randomly. Only large-scale chromosome LOH (>10Mb) can be reliably detected from FFPE tumor DNA samples (without or with WGA) but not smaller LOH or copy number alterations. Our findings here indicate a need for caution in SNP array data interpretation when using FFPE tumor-derived DNA, particularly with WGA.

overall_design:
Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from cryopreserved and FFPE mesenchymal tumor samples without or with WGA, as well as genomic snap-frozen non-neoplastic tissue DNA from 5 adult individuals to serve as reference DNA.

WGA was performed using the REPLI-g® FFPE kit (Qiagen, Valencia, CA, USA) and GenomePlex® Tissue Whole Genome Amplification WGA5 kit (Sigma, Saint Louis, MO, USA) in parallel in accordance with the manufacturers’ protocols. A two- to eight-hour individualized reaction time was used in the Qiagen platform for each sample. A gradient amount of initial DNA (10ng, 30ng, 60ng, 100ng and 150ng) was tested followed by gel electrophoresis and qualitative multiplex PCR assay to determine the quality of post-WGA products. At least four independent experiments were concurrently performed per template amplification. Four separateWGA reaction products were pooled for each sample for subsequent microarray analysis to minimize the amplification bias and allele dropout.

One of the Affymetrix GeneChip® Human Mapping 500K Array Set (Nsp 250K SNP array) was used for genotyping analysis. Four gastrointestinal stromal tumors with known cytogenetic aberrations were included. Two cases were sucessfullly amplified and passed the quality tests. A total of 12 samples were compared between each other, including frozen tissue DNA (as reference), frozen tissue DNA with WGA (two platforms), FFPE tissue DNA, and FFPE tissue DNA with WGA (two platforms) from each case.

first: Cheng-Han

last: Lee

first: Adrian

last: Marino-Enriquez

first: Changzhong

last: Chen


title: Impact of cellular miRNAs on the biomarker signatures of circulating miRNAs

status: Public on Jun 17 2011

city: Santa Clara

first: Radha

last: Duttagupta

state: CA

address: 3450 Central Expressway

department: Applied Research

country: USA

institute: Affymetrix

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

overall_design: Refer to individual Series


title: Micro RNA expression from human hepatocellular carcinoma (HCC) specimens from patients undergoing liver transplantation.

status: Public on Oct 15 2011

city: Rochester

first: Christopher

middle: Taylor

last: Barry

state: NY

address: 601 Elmwood Avenue

department: Transplant Surgery

institute: University of Rochester

summary: Current selection criteria for liver transplant in patients with HCC (the Milan criteria) do not incorporate biologic metrics. MiRNA expression profiles correlate with HCC recurrence after transplant and can add significant value to the Milan criteria.

overall_design: MiRNA expression profiles were studied in HCC specimens from patients undergoing liver transplant and correlated with their tumor recurrence status and Milan criteria status.

middle: T


title: Extensive intergenic transcription from loss of Arabidopsis 3’ regulators FCA and FPA

status: Public on Jul 11 2011

city: Lausanne

first: Rene

last: Dreos

state: VD

address: Ecublens

department: CIG

country: Switzerland

institute: UNIL

type: Expression profiling by genome tiling array

summary: The Arabidopsis RNA-binding proteins FCA and FPA were initially identified based on their suppression of the flowering time regulator FLC. Recently, however, they have been found to influence expression of a wide range of targets in the Arabidopsis genome. Here, we use whole-genome tiling arrays to determine the extent of their targets at two stages of seedling development. A wide range of genes and transposable elements were mis-expressed in the fcafpa double mutant with a significant bias for mis-regulated genomic segments mapping to the 3’ region of genes. A large number of previously unannotated (UA) genomic segments, which mapped to intergenic regions, were also mis-expressed in the fcafpa double mutant. We characterized a subset of these UA segments in detail and established them as strand-specific and direct targets of FCA and FPA, with a complex interplay between their functions. Only a few of the UA segments also showed regulation by a histone demethylase previously linked to FCA FPA function; however, others were associated with siRNA production and DNA methylation. Our data suggest that FCA/FPA play important roles in terminating transcription at many loci, often via promotion of proximal polyadenylation, and that in their absence, ectopic transcription and/or extensive read-through transcription occurs. These transcriptional products have the potential to interfere with overlapping transcripts and flanking genes and appear to form the basis for how modulation of FCA FPA function triggers RNA-mediated chromatin silencing mechanisms at a variety of loci in the Arabidopsis genome.

overall_design: We compared genome-wide transcript levels in three biological replicates of Arabidopsis thaliana Columbia (Col-0) and fca-9fpa-7 (fcafpa) double mutant seedlings. Two developmental stages, 7 and 17 days after germination, were analysed.

first: Cagla

last: Sonmez

first: Isabel

last: Bäurle

first: Andreas

last: Magusin

first: Sascha

last: Laubinger

first: Detlef

last: Weigel

first: Caroline

last: Dean


title: Evaluation of copy number alterations in the Ewing's Sarcoma cell line SKES1 with Affymetrix 500k SNP microarray

status: Public on Aug 01 2011

city: Salamanca

first: Carlos

last: Mackintosh

address: Campus Miguel de Unamuno S/N

country: Spain

institute: Centro de Investigación del Cáncer

summary:
As a result of a copy number alterations study (BAC-microarray), the SKES1 cell line was found to harbour a microdeletion in 16q23.2
SNP microarrays were applied in order to accurately delimit this alteration, finding a microdeletion of 1.04 Megabases in size.

overall_design: Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from a SKES1 cell culture


title: A comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants (Mapping250K_Nsp)

status: Public on Jun 30 2011

city: Toronto

first: Stephen

middle: W

last: Scherer

state: Ontario

address: 686 Bay Street

department: Genetics and Genomic Biology

country: Canada

institute: The Hospital for Sick Children

summary: Systematic evaluation of eleven array platforms commonly used for CNV detection to address parameters of quality and CNV calling.

overall_design: 14 Samples

first: Dalila

last: Pinto

first: Jeffrey

middle: R

last: MacDonald


title: Impact on Disease Development, Genomic Location and Biological Function of Copy Number Alterations in Non-Small Cell Lung Cancer

status: Public on Dec 06 2011

city: Boston

first: Yen-Tsung

last: Huang

address: 665 Huntington Avenue

institute: Harvard School of Public Health

summary: Lung cancer, of which more than 80% is non-small cell, is the leading cause of cancer-related death in the United States. Copy number alterations (CNAs) in lung cancer have been shown to be positionally clustered in certain genomic regions. However, it remains unclear whether genes with copy number changes are functionally clustered. Using a dense single nucleotide polymorphism array, we performed genome-wide copy number analyses of a large collection of non-small cell lung tumors (n = 301). We proposed a formal statistical test for CNAs between different groups (e.g., noninvolved lung vs. tumors, early vs. late stage tumors). We also customized the gene set enrichment analysis (GSEA) algorithm to investigate the overrepresentation of genes with CNAs in predefined biological pathways and gene sets (i.e., functional clustering). We found that CNAs events increase substantially from germline, early stage to late stage tumor. In addition to genomic position, CNAs tend to occur away from the gene locations, especially in germline, noninvolved  tissue and early stage tumors. Such tendency decreases from germline to early stage and then to late stage tumors, suggesting a relaxation of selection during tumor progression. Furthermore, genes with CNAs in non-small cell lung tumors were enriched in certain gene sets and biological pathways that play crucial roles in oncogenesis and  cancer progression, demonstrating the functional aspect of CNAs in the context of biological pathways that were overlooked previously. We conclude that CNAs increase with disease progression and CNAs are both positionally and functionally clustered. The potential functional capabilities acquired via CNAs may be sufficient for normal cells to transform into malignant cells.

overall_design: Copy number analysis was performed on 301 non-small cell lung cancer tumor samples using Affymetrix 250K Nsp GeneChip

first: Xihong

last: Lin

first: Lucian

last: Chirieac

first: Ray

last: McGovern

first: John

middle: C

last: Wain

first: Rebecca

middle: S

last: Heist

first: Vidar

last: Skaug

first: Shanbeh

last: Zienolddiny

first: Aage

last: Haugen

first: Li

last: Su

first: David

last: Christiani


title: Analysis of the impact of cellular miRNA signatures on the profiles of circulating miRNA biomarkers (variability data)

first: Radha

last: Duttagupta

summary: Circulating miRNAs are an emerging class of biomarkers correlating their specific expression patterns to disease states. A considerable proportion of hematopoietically-derived miRNAs are present in plasma with the ability to confound the signature of true circulating miRNA species. We use microarray analysis to catalogue a list of 313 haemotopoetic miRNAs and analyze expression profiles of cell-free miRNAs in individual plasma fractions after calibraiting for cellular miRNA signals. Comprehensive global maps of bona fide circulating miRNA species are presented, and inter-individual varibility and gender-specific expession is explored in populations of healthy individuals.

overall_design: Supernatant 1 (S1) fractions from 8 male and 10 female individuals.

first: Roger

last: Jiang

first: Robert

last: Getts

first: Jeremy

last: Gollub

first: Keith

last: Jones


title: miRNA expression data from low nitrate cultures in maize

status: Public on Sep 01 2011

city: Beijing

first: Chuanxiao

last: Xie

address: Zhong-guan-cun South St. No12

department: Institute of Crop Science

country: China

institute: Chinese Academy of Agricultural Sciences

sample_organism:
Zea mays
Zea mays subsp. mays

platform_organism:
Physcomitrium patens
Populus trichocarpa
Arabidopsis thaliana
Glycine max
Medicago truncatula
Oryza sativa
Saccharum officinarum
Sorghum bicolor
Zea mays
synthetic construct


title: Analysis of the impact of cellular miRNA signatures on the profiles of circulating miRNA biomarkers (fractionation data)

summary: Circulating miRNAs are an emerging class of biomarkers correlating their specific expression patterns to disease states. A considerable proportion of hematopoietically-derived miRNAs are present in plasma with the ability to confound the signature of true circulating miRNA species. We use microarray analysis to catalogue a list of 313 haemotopoetic miRNAs and analyze expression profiles of cell-free miRNAs in individual plasma fractions after calibrating for cellular miRNA signals. Comprehensive global maps of bona fide circulating miRNA species are presented, and inter-individual variability and gender-specific expression is explored in populations of healthy individuals.

overall_design: Healthy Caucasian individuals were used to segregate blood into 8 subfractions: white blood cells (WBC)/buffy coat, leukocytes, red blood cells (red blood cells (RBC)),  cloudy supernatant (CS), supernatant 1 (S1), supernatant 2 (S2), pellet 1 (P1) and pellet 2 (P2) through differential centrifugation to understand the proportion of cellular miRNAs in each category.


title: miRNA expression profiles of frontal cortex and hippocampus from adult C57BL/6J mice

status: Public on Jun 22 2011

city: University of Helsinki

first: Iiris

last: Hovatta

address: Haartmaninkatu 8

department: Molecular Neurology

country: Finland

institute: University of Helsinki

summary: We used Affymetrix miRNA arrays to analyze the expression of miRNAs in the frontal cortex and hippocampus of 8-week-old C57BL/6J wt mice. We compared these microarray-based expression profiles to ones obtained by miRNA sequencing from the same brain regions of the same mouse strain.

overall_design: miRNA expression profiling of frontal cortex and hippocampus from C57BL/6J mice (N=3) was performed with Affymetrix miRNA array

first: Tessa

last: Sipilä


title: Identification of serum microRNAs associated with prostate cancer in a mouse model of disease

status: Public on May 20 2011

city: Bedford Park

first: Luke

last: Selth

state: SA

address: Flinders Drive

department: College of Medicine and Public Health

country: Australia

institute: Flinders University

summary: There is an urgent need for new biomarkers to enhance the clinical management of prostate cancer. Circulating microRNAs (miRNAs) are emerging as useful non-invasive markers of disease. The objective of this study was to test the utility of a mouse model of prostate cancer as a tool to discover serum miRNAs that could be applied in a clinical setting. Global miRNA profiling using microarrays identified 46 miRNAs at differential levels in the serum of TRansgenic Adenocarcinoma of Mouse Prostate (TRAMP) mice compared to their wild-type littermates.

overall_design: Total RNA extracted from the serum of 9 mice with advanced disease was pooled into 3 groups (TRAMP serum RNA 1, 2 and 3). Serum RNA from age-matched wild-type littermates, pooled as above, served as the control set.

middle: A

first: Lisa

middle: M

last: Butler

first: Waye

middle: D

last: Tilley


title: Affymetrix 500K SNP array data for Primary Effusion Lymphoma samples

status: Public on Jun 23 2011

city: Chapel Hill

first: Dirk

last: Dittmer

state: NC

address: 116 Manning Drive, CB# 7290

department: Microbiology & Immunology

institute: University of North Carolina at Chapel Hill

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary: Affymetrix 500K array was used to determine gross genomic aberrations in a panel of Primary Effusion Lymphoma (PEL) cell lines, specifically focusing on chromosome 10, which includes the Phosphatase and Tensin Homolog (PTEN) locus.

overall_design: 10 PEL cell lines were hybridized to the Affymetrix 500K array where non-PEL B-cell lymphoma cell lines BJAB and DG75 were used as controls. The data was analyzed using Partek Genomic Suite software and compared to normal tonsil controls.

first: Debasmita

last: Roy

middle: P


title: Mesothelioma cell lines SNP data copy number analysis

status: Public on May 19 2011

city: New York

first: Yupu

last: Liang

address: 1230 York Avenue

institute: The Rockefeller University

summary: Malignant pleural mesotheliomas (MPMs) often show CDKN2A and NF2 inactivation but other highly recurrent mutations have not been described. To identify additional driver genes, we used an integrated genomic analysis of 53 MPM tumor samples to guide a focused sequencing effort that uncovered somatic inactivating mutations in BAP1 in 23% of MPM. The BAP1 nuclear deubiquitinase is known to target histones (together with ASXL1 as a Polycomb repressor subunit) and the HCF1 transcriptional co-factor, and we show that BAP1 knockdown in MPM cell lines affects E2F and Polycomb target genes. These findings implicate transcriptional deregulation in the pathogenesis of MPM.

overall_design: Genomic DNA was harvested from untreated malignant pleural mesothelioma (MPM) cell lines and used to generate gain/loss profiles for each line using aCGH.

first: Marc

last: Ladanyi

first: Matthew

last: Bott


title: Expression data in Arabidopsis axe1-5 and met1-3 mutants.

status: Public on May 16 2011

city: Yokohama

first: Motoaki

last: Seki

address: 1-7-22, Suehiro-cho, Tsurumi

country: Japan

institute: RIKEN CSRS

summary: We applied the tiling arrays to study the Arabidopsis whole-genome transcriptome in Arabidopsis axe1-5 and met1-3 mutants.

overall_design: Fifteen-day-old Arabidopsis plants grown on the agar plates were harvested. The total RNA was prepared from 15-day-old Arabidopsis plants (axe1-5 (hda6 mutant), DR5 (parental line of axe1-5), met1-3 and Col) and used for the microarray hybridization. Three replicative hybridization experiments for each strand array were carried out using the independent biological RNA samples.

first: Taiko

middle: K

last: To

first: Jong

last: Kim

first: Akihiro

last: Matsui

first: Yukio

last: Kurihara

first: Taeko

last: Morosawa

first: Junko

last: Ishida

first: Maho

last: Tanaka

first: Yoshiki

last: Mochizuki

first: Hidetoshi

last: Saze

first: Tetsuji

last: Kakutani

first: Kazuo

last: Shinozaki

first: Tetsuro

last: Toyoda


title: Prospective comparison of genome-wide aCGH platforms for the detection of CNVs in MR (Mapping250K_Nsp and Mapping250K_Sty)

status: Public on Feb 17 2011

city: Vancouver

first: Tracy

last: Tucker

address: Box 153 4480 Oak Street

institute: University of British Columbia

summary: Clinical laboratories are adopting array comparative genomic hybridization (AGH) as a standard clinical test. A number of whole genome AGH systems are available, but little is known about the comparative performance in a clinical context.  We prospectively studied 30 children with idiopathic MR and both unaffected parents of each child using Affymetrix 500K GeneChip SNP arrays, Agilent Human Genome 244K oligonucleotide arrays and NimbleGen 385K Whole-Genome oligonucleotide arrays. We determined whether CNVs called on these platforms were detected by Illumina Hap550 beadchips or SMRT 32K BAC whole genome tiling arrays and tested 15 of the 30 trios on Affymetrix 6.0 SNP array.  The Affymetrix 500K, Agilent and NimbleGen platforms identified 3061 autosomal and 117 X chromosome CNVs in 30 trios. 147 of these CNVs were de novo, but only 33 (22%) of the de novo CNVs were found on more than one platform. Performing genotype-phenotype correlations, we identified 7 pathogenic and 4 possibly pathogenic CNVs for MR. All 11 of these CNVs were detected by both the Agilent and NimbleGen arrays, 9 by the Affymetrix 500K and Illumina beadchips, and 5 by the SMRT BAC array. Two of the 4 pathogenic or possibly pathogenic CNVs present in the trios tested with the Affymetrix 6.0 array were identified.   Our findings demonstrate that different results are obtained with different AGH platforms and illustrate the trade-off that exists between sensitivity and specificity. The large number of apparently false positive CNV calls supports the need for validating clinically important findings with a different methodology.

overall_design: 45 trios were analysed consisting of child (proband) and both normal parents.

first: Alexandre

last: Montpetit

first: David

last: Chai

first: Susanna

last: Chan

first: Sébastien

last: Chénier

first: Bradley

last: Coe

first: Allen

last: Delaney

first: Patrice

last: Eydoux

first: Wan

middle: L

last: Lam

first: Sylvie

last: Langlois

first: Emmanuelle

last: Lemyre

first: Marco

last: Marra

first: Hong

last: Qian

first: Guy

last: Rouleau

last: Vincent

first: Jacques

last: Lmichaud

first: Jan

last: Friedman


title: Expression data of distinct organs in Arabidopsis

status: Public on Dec 22 2010

first: Motoaki

last: Seki

summary: We applied the tiling arrays to study the Arabidopsis whole-genome transcriptome in leaf, root, stem, flower, early silique, middle silique and late silique.

overall_design: To obtain approximately 3-week-old leaf and root, plants were grown on a 0.5% gelangum (Wako) containing 0.5% sucrose and 1/2 MS at 22℃ under the continuous light condition. In case of sampling for other tissues (stem, flower, early silique, middle silique, and late silique), plants were grown on soil in pots at 22℃ under 16-h light/8-h dark cycle. Three replicative hybridization experiments for each strand array were carried out using the independent biological RNA samples.

first: Masanori

last: Okamoto

first: Akihiro

last: Matsui

first: Junko

last: Ishida

first: Maho

last: Tanaka

first: Taeko

last: Morosawa

first: Kei

last: Iida

first: Shuji

last: Kawaguchi

first: Norio

last: Kobayashi

first: Yuko

last: Yoshida

first: Manabu

last: Ishii

first: Erimi

last: Harada

first: Kousuke

last: Hanada

first: Tetsuro

last: Toyoda


title: Validation of rapid embryo tracking using cell-free fetal DNA enriched from maternal circulation at 9 weeks gestation

status: Public on Apr 14 2011

city: Morristown

first: Nathan

last: Treff

address: 111 Madison Ave

institute: RMA of New Jersey

summary: Embryo DNA fingerprinting represents an important tool for tracking embryo-specific outcomes after multiple embryo transfer during IVF.  The situation in which 2 embryos are transferred and only one implants represents a unique opportunity for the most well-controlled comparison of competent and incompetent embryos.   Specifically, this design eliminates all patient-related variables from the comparison of embryos with or without reproductive potential.  However, in order to determine which embryo implanted, the investigator must wait until newborn DNA is available upon delivery.  This study validates a non-invasive fetal DNA fingerprinting method that reduces the time to identify which embryo implanted by approximately 31 weeks. Thirty-four patients were studied to determine if fingerprinting of fetal DNA extracted from maternal plasma at 9 gestational weeks concurred with the buccal DNA results obtained from the newborn after delivery. This validation required single nucleotide polymorphism (SNP) profiles on each couples’ preimplantation embryos, enriched fetal DNA from maternal plasma at 9 weeks gestation, and newborn DNA obtained from buccal swabs after delivery. The predictions from fetal DNA-based embryo tracking and gender assignments made at 9 weeks gestation were 100% consistent with standardized methods of assessment performed after term delivery. This study demonstrates the first validated fetal DNA fingerprinting method which predicts both gender and which embryo implanted at 9 weeks gestation following multiple embryo transfer.

overall_design: Affymetrix SNP arrays were processed and successfully completed according to the manufacturer's directions on DNA extracted from 136 embryos, 33 parental blood samples, 17 enriched fetal DNA samples and 21 buccal DNA samples.

first: Xin

last: Tao

first: Jing

last: Su

first: Lesley

middle: E

last: Northrop

first: Andrew

last: Ruiz

first: Richard

last: Scott Jr


title: Telomere DNA deficiency is associated with development of human embryonic aneuploidy

status: Public on Jul 04 2011

type:
SNP genotyping by SNP array
Genome variation profiling by SNP array

summary: Aneuploidy represents the most prevalent form of genetic instability found in human embryos and is the leading genetic cause of miscarriage and developmental delay in newborns. Telomere DNA deficiency is associated with genomic instability in somatic cells and may play a role in development of aneuploidy commonly found in female germ cells and human embryos. To test this hypothesis, we developed a method capable of quantifying telomere DNA in parallel with 24-chromosome aneuploidy screening from the same oocyte or embryo biopsy.  Aneuploid human polar bodies possessed significantly less telomere DNA than euploid polar bodies from sibling oocytes (-3.07 fold, P=0.016). This indicates that oocytes with telomere DNA deficiency are prone to aneuploidy development during meiosis. Aneuploid embryonic cells also possessed significantly less telomere DNA than euploid embryonic cells at the cleavage stage (-2.60 fold, P=0.002) but not at the blastocyst stage (-1.18 fold, P=0.340). The lack of a significant difference at the blastocyst stage was found to be due to telomere DNA normalization between the cleavage and blastocyst stage of embryogenesis and not due to developmental arrest of embryos with short telomeres. Heterogeneity in telomere length within oocytes may provide an opportunity to improve the treatment of infertility through telomere based selection of oocytes and embryos with reproductive competence.

overall_design:
Affymetrix SNP arrays were processed according to the manufacturer's directions on DNA extracted from 44 embryos of biopsied blastomere at cleavage stage or biopsied trophectoderm at blastocyst stage and 18 polar bodies biopsied from oocytes,
Afflymetrix SNP array analysis was successfully completed on 18 polar body samples from oocytes, 24 blastomere  and 20 trophectoderm samples from embryos.

first: Deanne

last: Taylor

last: Scott


title: Chao_etal_TSC10A_mapping

status: Public on May 26 2011

city: St. Louis

first: Ivan

last: Baxter

state: MO

address: 975 North Warson Rd

department: PLant Genetics Research Unit

institute: USDA-ARS

type: Genome variation profiling by genome tiling array

summary:
ABSTRACT: Sphingolipid synthesis is initiated by condensation of serine with palmitoyl-CoA to produce 3-ketodihydrosphinganine (3-KDS), which is subsequently reduced by a 3-KDS reductase to dihydrosphinganine (DHS).  Serine palmitoyltransferase was recently shown to be essential for plant viability, but the 3-KDS reductase step of sphingolipid synthesis has not been investigated in plants.  Arabidopsis thaliana contains two genes (At3g06060/TSC10A and At5g19200/TSC10B) that encode proteins with significant homology to the yeast 3-KDS reductase, Tsc10p.  Heterologous expression, in yeast, of either A. thaliana gene restored 3-KDS reductase activity to the yeast tsc10Δ mutant, thereby identifying both as bona fide 3-KDS reductase genes.  Consistent with previous evidence that sphingolipids have essential functions in plants, double mutant progeny lacking both genes were not recovered.  Although the 3-KDS reductase genes are functionally redundant and ubiquitously expressed in A. thaliana, 3-KDS reductase activity was reduced to  approximately 10% of wild-type levels in the loss-of-function tsc10a mutant, leading to an altered sphingolipid profile compared to wild-type plants. Interestingly, this perturbation of sphingolipid biosynthesis in the A. thaliana tsc10a mutant leads to significant alterations in the leaf ionome, including increases in Na, K and Rb (a K analogue), and decreases in Mg, Ca, Fe, and Mo. Reciprocal grafting revealed that these changes in the leaf ionome are driven by the root, and are associated with both increases in root suberin, and elevation of expression in the root of genes involved in Fe homoeostasis, including the Fe-transporter IRT1.

Keywords: genomic hybridization bulked segregant analysis

overall_design: Hybridizations from a set of Bulk Segregant analysis. An F2 population from 7113 in the col-0 background crossed to Ler-0 was analyzed. This series contains the 3 hybs from Ler used to identify Single Feature Polymorphisms, the 3 hybs of Col-0 they were compared to, and 1 hyb for each pool from the BSA mapping(low Ca/Mg Pool and wild type pools).


title: Use of single nucleotide polymorphism microarrays to distinguish between balanced and normal chromosomes in embryos from a translocation carrier

status: Public on May 18 2011

summary:
Objective: To prove the ability to distinguish between balanced and normal chromosomes in embryos from a translocation carrier.
Design: Case report.
Setting: Academic center for reproductive medicine.
Patient: A female with a balanced translocation causing Alagille Syndrome seeking preimplantation genetic diagnosis (PGD).
Interventions: Blastocyst biopsy for PGD.
Main outcome measures: Consistency of 3 methods of embryo genetic analysis (real-time PCR, SNP microarray, and FISH) and normalcy in the newborn derived from PGD.
Results: PGD was applied to 48 embryos.  Real-time PCR, SNP microarray, and FISH demonstrated 100% consistency, although FISH failed to detect aneuploidies observed by comprehensive SNP microarray based analyses.  Two blastocysts were identified to be normal for all 3 factors using SNP microarray technology alone. The two normal embryos were transferred back to the patient resulting in the delivery of a healthy baby boy with a normal karyotype.
Conclusions: This is the first report of validation and successful clinical application of microarray based PGD to distinguish between balanced and normal chromosomes in embryos from a translocation carrier.

overall_design:
Affymetrix SNP arrays were processed according to the manufacturer's directions on DNA extracted from 17 blastocysts on biopsied trophectoderm samples and 31 arrested whole embryos.
Afflymetrix SNP array analysis was successfully completed on 17 trophectoderm, 30 whole embryo and 3 gDNA samples.

first: Paul

last: Bergh

first: Wendy

middle: J

last: Schillings

first: Brynn

last: Levy

first: Tao

last: Xin


title: Expression data for the mom1-2 mutant of Arabidopsis

status: Public on Sep 27 2010

first: Motoaki

last: Seki

summary:
Heterochromatin is an inert region in the genome and composed of mainly remnants of transposons and repetitive elements. In Arabidopsis, the major heterchromatin regions are present at around centromeres (pericentromeric regions) and at a region on the short arm of chromosome 4 (heterochromatin knob). Histones and DNAs in heterochromatin have characteristic features with abundant H3H9me2 and cytosine methylation, respectively. Here, by using a genome tiling array, we showed that a subset of heterochromatin loci are silenced by the action of Morpheus' molecule 1 (MOM1) that is an epigeneic regulator for transcriptional gene silencing independent of global DNA and histone modification. Most of the up-regulated loci in the mom1 mutant carried sequences related to transposable elements but none of them was annotated as functional transposons. No specific subclass of transposons was targeted by MOM1 and loci that were unrelated to transposons but flanked by short tandem repeats were also shown to be under the control of MOM1. The results suggest the presence of an unknown level of regulatory network maintaining the silent state of heterochromain in the genome.

Keywords: Epigenetic regulation of endogenous loci by Morpheus' Molecule 1 (MOM1)

overall_design: Three-week-old Arabidopsis plants (Col-0 and mom1-2) grown on soil were subjected to RNA extraction and the total RNA samples were used for the microarray hybridization. Three replicative hybridization experiments for each strand array were carried out using the independent biological RNA samples.

first: Yoshiki

last: Habu

first: Akihiro

last: Matsui

first: Junko

last: Ishida

first: Taeko

last: Morosawa

last: Mochizuki

first: Norio

last: Kobayashi

first: Kazuo

last: Shinozaki


title: NAKR1 deletion analysis

status: Public on Dec 23 2010

summary: ABSTRACT:The SODIUM POTASSIUM ROOT DEFECTIVE 1 (NaKR1) encodes a soluble metal binding protein that is specifically expressed in companion cells of the phloem. The nakr1-1 mutant phenotype includes high Na+, K+, Rb+ and starch accumulation in leaves, short roots, late flowering and decreased long-distance transport of sucrose. Using traditional and DNA microarray-based mapping, a 7 bp deletion was found in an exon of NaKR1 that caused a premature stop. The mutant phenotypes were complemented by the native gene and by GFP and GUS fusions driven by the native promoter. NAKR1-GFP was mobile in the phloem, it moved into sieve elements and into a novel symplasmic domain of the root meristem. Grafting experiments revealed that the high Na+ accumulation was due primarily to loss of NaKR1 function in the leaves. This supports a role for the phloem in recirculating Na+ to the roots to limit Na+ accumulation in leaves. The onset of root phenotypes coincided with NaKR1 expression after germination. Short root length was primarily due to a decrease in cell division rate in the root meristem indicating a role for NaKR1 expression in the phloem in root meristem maintenance.

overall_design: 3 hybridizations each of mutant NAKR1 and wildtype for deletion identification.


title: An integrative multi-dimensional genetic and epigenetic strategy to identify aberrant genes and pathways in cancer: allelic status

status: Public on Dec 31 2010

first: Raj

last: Chari

state: BC

address: 675 West 10th Avenue

department: Cancer Genetics and Developmental Biology

institute: BC Cancer Research Centre

summary: dChip analysis of 9 breast cancer cell lines. Data obtained from caBIG

overall_design: Part of a multi-dimensional analysis of gene copy number, allelic status, DNA methylation and gene expression data


title: Mapping replication-initiation proteins ORC1 and CDC6 in Arabidopsis thaliana

status: Public on Feb 06 2011

city: Cantoblanco

first: Juan

middle: Carlos

last: Oliveros

state: Madrid

address: Darwin 3

institute: CNB, CSIC

type: Genome binding/occupancy profiling by genome tiling array

summary: Genomic integrity requires faithful chromosome duplication. Origins of replication are the genomic sites where DNA replication initiates in every cell cycle. There are multiple origins scattered throughout the eukaryotic genome whose genome-wide identification has been a hard challenge, especially in multicellular organisms. Thus, very little is known on the distinctive features of origins in terms of DNA sequence and chromatin context at a genomic scale. As part of a project for profiling replication origins in Arabidopsis thaliana, we have performed ChIP-chip analysis of the binding of ORC1 and CDC6, two proteins involved in initiation of DNA replication. Here, we provide the data of the ORC1-bound and CDC6-bound genomic sites using as control genomic DNA.

overall_design:
3 biological replicates of ORC1-binding sites-enriched DNA samples were compared against 3 biological replicates of fragmented genomic DNA (INPUT).
2 biological replicates of CDC6-binding-sites-enriched DNA samples were compared against 3 biological samples of fragmented genomic DNA (INPUT).

Results files linked below: Enrichment ratio calculated from normalized intensities and averaged over all replicates. Positive values indicate enrichment of the ChIP fraction versus the INPUT sample.

first: C

last: Gutierrez

first: S

last: Jacobsen


title: Expression of JNK target genes during dorsal closure of the Drosophila embryo

status: Public on Jul 07 2010

city: Nice

first: Raphaël

last: Rousset

address: Parc Valrose, Centre de Biochimie

department: Institut Biologie Valrose, iBV

country: France

institute: CNRS, INSERM, Université Côte d'Azur

summary: Tissue morphogenesis relies on proper differentiation of morphogenetic domains, adopting specific cell behaviours. Yet, how signalling pathways interact to determine and coordinate these domains remains poorly understood. Dorsal closure (DC) of the Drosophila embryo represents a powerful model to study epithelial cell sheet sealing. In this process, JNK (JUN N-terminal Kinase) signalling controls leading edge (LE) differentiation generating local forces and cell shape changes essential for DC. The LE represents a key morphogenetic domain in which, in addition to JNK, a number of signalling pathways converges and interacts (anterior/posterior -AP- determination; segmentation genes, such as Wnt/Wingless; TGFβ/Decapentaplegic). To better characterize properties of the LE morphogenetic domain, we used microarrays to identify genes whose expression is regulated by the JNK pathway during dorsal closure of the Drosophila embryo.

overall_design: Three genetic conditions were compared: wild-type (WT), gain of function (GOF) and loss of function (LOF). For the GOF embryos, the JNK pathway was strongly activated by expressing HepACT in the ectoderm using the UAS-GAL4 system (69B-GAL4). For the LOF embryos, we used a combination of 2 alleles, heprev75 and hep1. Carefully staged embryos, corresponding to stages 13 and 14, were collected and for each condition, three independent RNA samples were prepared to be hybridized on the microarrays.

first: Fabrice

last: Carballès

first: Stéphane

last: Noselli


title: Copy number alterations in pleural mesothelioma

status: Public on Jul 01 2010

city: Hanover

first: Brock

middle: Clarke

last: Christensen

state: NH

address: 7650 Remsen

institute: Dartmouth Medical School

summary: Integrated profiling of somatic molecular alterations present in tumors is necessary to further our understanding of the tumorigenic process. We investigated the potential relationships between gene copy number alterations and DNA methylation profiles in a case series of pleural mesotheliomas (n=23). Gene copy number (CN) alterations profiled with 500K SNP arrays and DNA methylation measured at over 750 cancer-related genes with methylation bead-arrays were examined concomitantly. Considering each probed locus, there were no instances of significantly correlated CN alteration and methylation (no loci with Q < 0.05) and averaging loci over their associated genes revealed only two genes with significantly correlated CN and methylation alterations (Q < 0.04). In contrast to the lack of discrete correlations, the overall extent of tumor CN alteration was significantly associated with DNA methylation profile when comparing CN alteration extent among methylation profile classes (P < 0.02), and there was evidence that this association was partially attributable to prevalent allele loss observed at the maintenance DNA methyltransferase DNMT1. Taken together, this work indicates a strong association between global genetic and global epigenetic dysregulation in mesothelioma rather than a discrete, local coordination of gene inactivation, and further highlights the utility and necessity of integrative genomics approaches in cancer biology.

overall_design:
From the total study population, 23 tumors from the incident case series were chosen for copy number alteration profiling by hybridizing 5ml containing  ≥ 50ng/ml of tumor or matched peripheral blood DNA to each of the two  GeneChips® that comprise the Human Mapping 500K single-nucleotide polymorphism array set (Affymetrix, Santa Clara, CA), following manufacturer protocols and standard operating procedures at the Harvard Partners Microarray Core servicing facility. Probe intensities at each locus were determined in the GCOS software and genotypes calls were generated using the Genotyping Analysis Software (Affymetrix). Probe signals were normalized to their matched referent peripheral blood sample data using the Copy Number Analysis Tool v4.0.1 software (CNAT) (Affymetrix) with median scaling and default tuning parameters, and copy number states were inferred by Hidden Markov Model analysis.

The supplementary file 'GSE21057_tumor_copy_number.txt' contains the (blood-normalized) copy number calls for each tumor sample.

first: Karl

last: Kelsey

first: Heather

middle: H

last: Nelson


title: Integrated profiling reveals a global correlation between epigenetic and genetic alterations in mesothelioma

type:
Methylation profiling by array
Genome variation profiling by SNP array
SNP genotyping by SNP array

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

overall_design: Refer to individual Series


title: Efect of neonatal nutrition on adipose tissue remodeling genes during early development and in adult mice

status: Public on Jan 01 2011

city: Baton Rouge

first: Robert

middle: A.

last: Koza

state: LA

department: Genomics Core Facility

institute: Pennington Biomedical Research Center

summary: While the phenomenon linking the early nutritional environment to disease susceptibility exists in many mammalian species, the underlying mechanisms are unknown. We hypothesized that nutritional programming is a variable quantitative state of gene expression, fixed by the state of energy balance in the neonate, that waxes and wanes in the adult animal in response to changes in energy balance. We tested this hypothesis with an experiment, based upon global gene expression, to identify networks of genes in which expression patterns in inguinal fat of mice have been altered by the nutritional environment during early post-natal development. Gene expression patterns in inguinal fat was assessed at 5, 10, 21 days of age and as adults fed chow (56 days of age) followed by high fat diet for 8 weeks (112 days of age) for C57BL/6J mice reared by lactating dams fed either a control diet (CONT), lactating dams fed a diet in which food intake was restricted to cause under-nourishment (lactation under-nutrition; LUN); and, lactating dams fed a high fat diet in where the number of progeny was limited to four (lactation over-nutrition; LON) .

overall_design: 15 samples with 3 technical replicates of each sample. Each of the 15 samples consisted of pooled total RNA from 12 male mice. Dietary control samples are included for each time period.

first: Leslie

last: Kozak

first: Susan

last: Newman

first: Pei-Min

last: Chao

first: Tamra

last: Mendoza


title: Affymetrix SNP array data for Chronic Lymphocytic Leukemia_diagnostic sample_patient samples

status: Public on Apr 28 2011

city: Uppsala

first: Anders

last: Isaksson

address: Akademiska sjukhuset ing61 3tr

country: Sweden

institute: Uppsala University

summary: High-resolution genomic microarrays provides simultaneous detection of copy-number aberrations such as the known recurrent aberrations in Chronic Lymphocytic Leukemia_diagnostic sample_patient (del(11q), del(13q), del(17p) and trisomy 12),  and copy-number neutral loss of heterozygosity. We screened 369 newly diagnosed Chronic Lymphocytic Leukemia_diagnostic sample_patient patient samples from a population-based cohort using 250K single nucleotide polymorphism-arrays.

overall_design: Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from peripheral blood samples.

first: Rebeqa

last: Gunnarsson

first: Markus

last: Rasmussen


title: Rat life cycle liver gene expression

status: Public on Jun 24 2010

city: Jefferson

first: Vikrant

last: Vijay

state: AR

address: 3900 NCTR Road

department: Division of Systems Biology

institute: US FDA National Center for Toxicological Research

summary: Age- and sex-related susceptibility to adverse drug reactions is a key concern in understanding drug safety and disease progression. We hypothesize that the underlying suite of hepatic genes expressed at various developmental and life-cycle stages will impact susceptibility to adverse drug reactions. Thus, understanding the basal expression patterns of genes throughout the life span of the rat model species in both sexes will inform our assessments of adverse drug reactions. The liver plays a central role in the metabolism and biotransformation of drugs via key cellular pathways. Untreated, male and female F344 rats were sacrificed at 2, 5, 6, 8, 15, 21, 52, 78, and 104 weeks of age. Liver tissues were collected for histology and gene expression analysis. Whole-genome rat microarrays (44,000 features) were used to query global expression profiles. An initial list of active genes was selected using a 2-way ANOVA with a p-value cutoff of 0.05 and 1.5 fold-change difference from mean expression. Three dimensional principal component analyses revealed notable expression profile divergence between males and females after 5 weeks with greatest differences observed at 21 and 52 weeks before converging again at 104 weeks. Furthermore, k-means clustering identified groups of genes that displayed specific developmental and age-related patterns of expression. Various adult aging-related clusters included genes involved in pathways related to susceptibility to adverse drug effects such as xenobiotic metabolism, DNA damage repair, and oxidative stress.  These results suggest an underlying role for genes in these specific clusters in potentiating age- and sex-related susceptibilities to adverse health effects.

overall_design: time course, 9 time points, 2 sexes, n=5 per group, total of 90 samples

first: Joshua

last: Kwekel


title: SNP microarray based 24 chromosome aneuploidy screening is significantly more consistent than FISH

status: Public on May 19 2010

first: Nathan

last: Treff

summary: Many studies estimate that chromosomal mosaicism within the cleavage stage human embryo is high.  However, comparison of two unique methods of aneuploidy screening of blastomeres within the same embryo has not been conducted and may indicate whether mosaicism is overestimated due to technical inconsistency rather than biological phenomena.  The present study investigates the prevalence of chromosomal abnormality and mosaicism found with two different single cell aneuploidy screening techniques.Thirteen arrested cleavage stage embryos were studied. Each was biopsied into individual cells (n=160). The cells from each embryo were randomized into two groups. Those destined for FISH based aneuploidy screening (n=75) were fixed, 1 cell per slide. Cells for SNP microarray based aneuploidy screening (n=85) were put into individual tubes. Microarray was significantly more reliable (96%) than FISH (83%) for providing an interpretable result (P=0.004). Markedly different results were obtained when comparing microarray and FISH results from individual embryos.  Mosaicism was significantly less commonly observed  by microarray (4 of 13 embryos; 31%) than by FISH (13 of 13 embryos; 100%)(P=0.0005).  Although FISH evaluated fewer chromosomes per cell and fewer cells per embryo, FISH still displayed significantly more unique genetic diagnoses per embryo (3.2+0.2) than microarray (1.3+0.2)(P<0.0001).  This is the first prospective, randomized, blinded, and paired comparison between microarray and FISH based aneuploidy screening. Aneuploidy and mosaicism were less common with microarray. While evaluating a smaller number of chromosomes with a proportionally smaller opportunity for finding mosaicism, FISH still had a dramatically higher level of inter-cell variation in diagnosis. SNP microarray based 24 chromosome aneuploidy screening provides more complete and consistent results than FISH.

overall_design:
Affymetrix SNP arrays were processed according to the manufacturer's directions on DNA extracted from 13 arrested cleavage stage embryos and biopsied into individual blastomere cells.  Individual blastomeres were randomized and blinded for SNP microarray analysis (n = 85).
Afflymetrix SNP array analysis was successfully completed on 82 blastomeres.

first: Brynn

last: Levy

first: Jing

last: Su

first: Lesley

last: Northrop

first: Michael

last: Drews

first: Richard

middle: T

last: Scott


title: Affymetrix SNP array data for Marginal Zone Lymphoma samples

status: Public on Feb 01 2011

city: Bellinzona

first: Francesco

last: Bertoni

state: Ticino

address: Via V. Vela 6

department: Lymphoma & Genomics Research Program

institute: IOR

summary: Marginal zone B-cell lymphomas (MZL) have been divided into three distinct subtypes (extranodal MZL of MALT type, nodal MZL; splenic MZL). Nevertheless, the relationship between them is still unclear. We performed a comprehensive analysis of genomic DNA copy number changes in a very large series of MZL cases with the aim of addressing this question. Samples from 218 MZL patients (25 nodal, 57 MALT, 134 splenic and two not better specified MZL) were analyzed with the Affymetrix Human Mapping 250K SNP arrays, and the data combined with matched gene expression in 33/218 cases. MALT lymphoma presented significantly more frequently gains at 3p, 6p, 18p and del(6q23) (TNFAIP3/A20), whilst splenic MZL was associated with del(7q31), del(8p). Nodal MZL did not show statistically significant differences when compared with MALT lymphoma while lacked the splenic MZL-related 7q losses. Gains of 3q and 18q gains were common to all three subtypes. Del(8p) was often present together with del(17p) (TP53). While del(17p) did not determine a worse outcome and del(8p) was only of borderline significance, the presence of both deletions had a highly significant negative impact on the outcome of splenic MZL.

overall_design: Copy number analysis of Affymetrix 250K Nsp SNP arrays was performed for a total of 218 MZL samples were analyzed by high resolution genome wide-DNA profiling: 57 MALT lymphoma, 134 splenic MZL, 25 nodal MZL and two MZL where allocation to a specific category was not possible.

first: Andrea

last: Rinaldi

first: Ivo

last: Kwee


title: A genotype-first approach for the molecular and clinical characterization of uncommon de novo microdeletion of 20q13.33

city: Spokane

first: Blake

middle: C.

last: Ballif

state: WA

address: 2820 North Astor Street

department: Research & Development

institute: Signature Genomic Laboratories

summary: Molecular cytogenetic techniques such as microarray analysis have allowed for a “genotype-first” approach to the characterization of chromosome abnormalities: in the absence of clinical features suggestive of a specific syndrome, patients with similar copy number imbalances can be examined for common clinical features. Using a genotype-first approach, we characterized microdeletions at 20q13.33 in six patients referred for genetic evaluation of developmental delay, mental retardation, and/or congenital anomalies. These deletions are relatively rare, with only 11 cases reported.  A comparison to previously reported cases of 20q13.33 microdeletion shows phenotypic overlap, with clinical features that include mental retardation, developmental delay, speech and language deficits, seizures, and behavior problems such as autistic spectrum disorder. Based on analysis of the smallest region of overlap (SRO) among cases reported here and in previous studies, we discuss several possible candidate genes for specific clinical features, including ARFGAP1, CHRNA4, KCNQ2, and MYT1. Deletion of this region may play an important role in cognitive development.

overall_design: aCGH control vs. patient, total of 6 patients

first: Ryan

middle: N

last: Traylor

first: Damien

last: Bruno

first: Trent

last: Burges

first: Robert

last: Wildin

first: Anne

last: Spencer

first: Devika

last: Ganesamoorthy

first: David

last: Amor

first: Matthew

last: Hunter

first: Jill

last: Rosenfeld

first: Aaron

last: Theisen

first: Beth

last: Torchia

first: Lisa

middle: G

last: Shaffer

first: Howard

last: Slater


title: MicroRNA expression data from human prostate cancer

status: Public on Jul 20 2010

city: Erlangen

first: Sven

last: Wach

address: Glueckstrasse 6

department: Dept. of Urology

country: Germany

institute: University Hospital, Friedrich-Alexander-University Erlangen-Nuernberg

summary: MicroRNAs are small RNA molecules of about 21-25 nucleotides that regulate gene expression via posttranscriptional inhibition of protein synthesis. They play a vital role in the process of tumorigenesis. To identify and characterize the diagnostic potential of miRNAs in prostate cancer, a leading cause of tumor mortality, we performed microarray based screening of miRNA expression profiles.

overall_design: We selected 20 cases of moderately differentiated prostate cancer and generated pairs of tumor and corresponding normal tissue by microdissection

first: Arif

middle: B

last: Ekici

first: Andre

last: Reis

first: Elke

last: Eltze


title: Pooled genome-wide analysis to identify novel risk loci for pediatric allergic asthma

status: Public on Mar 17 2011

city: Bologna

first: Giampaolo

last: Ricci

state: BO

address: Massarenti 9

department: Pediatric Allergologic Center

country: Italy

institute: University of Bologna

summary: We performed a pooled GWAS and individual genotyping in 269 children with allergic respiratory diseases comparing allergic children with and without asthma. We used a modular approach to identify the most significant loci associated with asthma by combining silhouette statistics and physical distance method with cluster-adapted thresholding. We found 97% concordance between pooled GWAS and individual genotyping, with 36 out of 37 top-scoring SNPs significant at individual genotyping level. The most significant SNP is located inside the coding sequence of C5, an already identified asthma susceptibility gene, while the other loci regulate functions that are relevant to bronchial physiopathology, as immune- or inflammation-mediated mechanisms and airway smooth muscle contraction. Integration with gene expression data (from mouse experimental asthma model taken from GSE6858 and GSE1301) showed that almost half of the putative susceptibility genes are differentially expressed in experimental asthma mouse models.

overall_design: Affymetrix SNP arrays (Mapping 250K NspI and StyI) were performed according to the manufacturer's directions on pooled DNA extracted from peripheral blood samples.The design is a pooled-GWAS. DNA samples were assigned to the Asthma group if displaying symptoms of asthma, alone or associated to other allergic phenotypes, including rhinoconjunctivitis (RC), and assigned to the RC group if displaying rhinitis or rhinoconjunctivits alone or associated to other allergic phenotypes, excluding asthma. Each of the two groups was subdiveded into 4 independent groups of samples, each containing 31-36 individuals. Individual DNA samples were then added to their respective pools in equivalent molar amounts. Each pool was labeled and hybridized independently on three different arrays (3 technical replicates for each pool).

first: Annalisa

last: Astolfi


title: Expression data in Arabidopsis aba2-1 mutant, cyp707a1-1a2-1a3-1 triple mutant seeds, embryo and endosperm tissues

status: Public on Apr 16 2010

first: Motoaki

last: Seki

summary: We applied the tiling arrays to study the Arabidopsis whole-genome transcriptome in aba2-1, cyp707a1-1a2-1a3-1 triple mutants seeds, embryo and endosperm tissues

overall_design: Freshly harvested seeds were imbibed in 8.5 cm Petri dishes containing two filter papers (approximately 7 cm diameter) and 2 mL of water and harvested. Dissection of embryo and endosperm from 24-h-imbibed seeds was carried out under a stereoscopic microscope. Three replicative hybridization experiments for each strand array were carried out using the independent biological RNA samples.

first: Masanori

last: Okamoto

first: Kiyoshi

last: Tatematsu

first: Akihiro

last: Matsui

first: Taeko

last: Morosawa

first: Junko

last: Ishida

first: Maho

last: Tanaka

first: Takaho

last: Endo

first: Yoshiki

last: Mochizuki

first: Tetsuro

last: Toyoda

first: Kazuo

last: Shinozaki

first: Eiji

last: Nambara


title: Single Cell Whole Genome Amplification Technique Impacts the Accuracy of SNP Microarray Based Genotyping and Copy Number Analyses

status: Public on Dec 20 2010

first: Nathan

last: Treff

summary: Methods of comprehensive microarray based analyses of single cell DNA are rapidly emerging.  Whole genome amplification (WGA) remains a critical component for these methods to be successful.  A number of commercially available WGA kits have been independently utilized in previous single cell microarray studies.  However, direct comparison of their performance on single cells has not been conducted.  The present study demonstrates that among previously published methods, a single cell GenomePlex WGA protocol provides the best combination of speed and accuracy for SNP microarray based copy number analysis when compared to a REPLI-g or GenomiPhi based protocol.  Alternatively, for applications that do not have constraints on turn-around time and that are directed at accurate genotyping rather than copy number assignments, a REPLI-g based protocol may provide the best solution.

overall_design:
Affymetrix SNP arrays were processed according to the manufacturer's directions on DNA extracted from human fibroblast cell lines and single fibroblast cells.
Afflymetrix SNP array analysis was successfully completed on 46 lymphocyte single cell samples, 8 gDNA extracted from cell lines, 11 reference gDNA extracted from cell lines and 3 reference gDNA samples from the RMA of New Jersey DNA bank.

GSM617116 to GSM617129: CEL files were processed using GTYPE version 4 (Affymetrix Inc., Genotyping Console 4.0 Manual) using the DM algorithm for genotype calls.  Copy number and loss of heterozygosity were calculated from CHP files using CNAT version 4.1 (Affymetrix Inc., Genotyping Console 4.0 Manual)  analysis against a reference set consisting of three normal females from in house gDNA  bank, 11 normal females from Coriel cell lines and 16 normal females from the HapMap database (www.hapmap.org). The 16 normal females are NA10855, NA10863, NA11832, NA12057, NA12234, NA12717, NA12813, NA18505, NA18508, NA18517, NA19137, NA19152, NE00088, NE00091, NE00403, and NE01119.

middle: R

first: Jing

last: Su

first: Xin

last: Tao

first: Lesley

last: Northrop

first: Richard

last: Scott


title: Affy SNP-array data for 23 ETV6/RUNX1-positive ALL patient samples and one cell line

city: Lund

first: Henrik

last: Lilljebjörn

address: Lund University Hospital

department: Dept of Clinical Genetics

institute: Lund University

summary: The ETV6/RUNX1 fusion gene, present in 25% of B-lineage childhood acute lymphoblastic leukemia (ALL), is thought to represent an initiating event, which requires additional genetic changes for leukemia development. To identify additional genetic alterations, 24 ETV6/RUNX1-positive ALLs were analyzed using 500K single nucleotide polymorphism arrays. The results were combined with previously published data sets, allowing us to ascertain genomic copy number aberrations (CNAs) in 164 cases. In total, 45 recurrent CNAs were identified with an average number of 3.5 recurrent changes per case (range 0-13). Twenty-six percent of cases displayed a set of recurrent CNAs identical to that of other cases in the data set. The majority (74%), however, displayed a unique pattern of recurrent CNAs, indicating a large heterogeneity within this ALL subtype. As previously demonstrated, alterations targeting genes involved in B-cell development were common (present in 28% of cases). However, the combined analysis also identified alterations affecting nuclear hormone response (24%) to be a characteristic feature of ETV6/RUNX1-positive ALL. Studying the correlation pattern of the CNAs allowed us to highlight significant positive and negative correlations between specific aberrations. Furthermore, oncogenetic tree models identified ETV6, CDKN2A/B, PAX5, del(6q), and +16 as possible early events in the leukemogenic process.

overall_design: Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from 23 leukemic bone marrow samples and one ETV6/RUNX1-positive cell line.

first: Thoas

last: Fioretos


title: Relationship between nucleosome positioning and DNA methylation: ChIP-chip

status: Public on May 29 2010

city: Los Angeles

first: matteo

last: Pellegrini

address: 621 Charles Young Drive South

department: MCD Biology

institute: UCLA

summary: Nucleosomes compact and regulate access to DNA in the nucleus, and are composed of approximately 147 bases of DNA wrapped around a histone octamer1, 2. Here we report a genome-wide nucleosome positioning analysis of Arabidopsis thaliana utilizing massively parallel sequencing of mononucleosomes.  By combining this data with profiles of DNA methylation at single base resolution, we identified ten base periodicities in the DNA methylation status of nucleosome-bound DNA and found that nucleosomal DNA was more highly methylated than flanking DNA.  These results suggest that nucleosome positioning strongly influences DNA methylation patterning throughout the genome and that DNA methyltransferases preferentially target nucleosome-bound DNA.  We also observed similar trends in human nucleosomal DNA suggesting that the relationships between nucleosomes and DNA methyltransferases are conserved.  Finally, as has been observed in animals, nucleosomes were highly enriched on exons, and preferentially positioned at intron-exon and exon-intron boundaries. RNA Pol II was also enriched on exons relative to introns, consistent with the hypothesis that nucleosome positioning regulates Pol II processivity.  We also found that DNA methylation enriched on exons, consistent with the targeting of DNA methylation to nucleosomes.

overall_design: Genomic DNA associated with RNAP II was isolated by ChIP using an anti-PolII antibody.

first: Ramakrishna

last: Chodavarapu

first: Suhua

last: Feng

first: Yana

last: Bernatavichute

first: Pao-Yang

last: Chen

first: Hume

last: Stroud

first: Yanchun

last: Yu

first: Jonathan

last: Hetzel

first: Frank

last: Kuo

first: Jin

last: Kim

first: Shawn

last: Cokus

first: David

last: Casero

first: Maria

last: Bernal

first: Peter

last: Huijser

first: Amander

last: Clark

first: Ute

last: Krämer

first: Sabeeha

middle: S

last: Merchant

first: Xiaoyu

last: Zhang

first: Matteo

first: Steven

last: Jacobsen


title: Genetic variegation of clonal architecture and stem cells in leukaemia

status: Public on Dec 16 2010

city: Belmont

first: Frederik

last: van Delft

address: 15 Cotswold Road

department: Haemato-oncology

country: United Kingdom

institute: ICR

summary: Little is known of the genetic architecture of cancer at the subclonal and single cell level or in the stem-like cells responsible for cancer clone maintenance and propagation. We have examined this issue in ALL in which ETV6-RUNX1 gene fuson is an early or initiating genetic lesion followed by a modest number of driver copy number alterations. By multiplexing FISH probes for these mutations, up to eight genetic abnormalities can be detected in single cells, a genetic signature of sub-clones identified and a composite picture of sub-clonal architecture and putative ancestral trees assembled. Sub-clones in ALL have variegated genetics and complex, non-linear or branching evolutionary histories. CNA are independently and recurrently acquired in sub-clones of individual patients, and in no preferential order. Clonal architecture is dynamic and changes in the lead up to a diagnosis and in relapse. Leukaemic stem cells, assayed by transplantation in NOD/SCID IL2Rgamma deficient mice, are also genetically variegated, mirroring sub-clonal patterns. These findings have significant implications for the cancer stem cell concept, for interpretation of cancer genome data and for therapeutic targetting in cancer.

overall_design:
Mononuclear cells were isolated at diagnosis of ALL for patient #3 and #7. Transplantation of 2 000 - 2 000 000 unsorted leukaemia cells was performed by intra-tibial injection into 7 - 14 week old NOD/SCID IL2Rgamma deficient mice. Mice were sacrificed when peripheral blood engraftment was >2%. An equivalent of 2 000 - 200 000 CD45 cells were used for serial transplantation. DNA was extracted from mononuclear cells at initial diagnosis and after second transplantation.
Copy number analysis of Affymetrix 500K SNP arrays was performed in CNAG 3.0 for patients #3 and #7 at initial diagnosis and after second transplantation. Reference files were 9 samples from leukemia in remission.

first: Kristina

last: Anderson

first: Christoph

last: Lutz

middle: W

first: Caroline

middle: M

last: Bateman

first: Yanping

last: Guo

first: Susan

last: Colman

first: Helena

last: Kempski

first: Anthony

middle: V

last: Moorman

first: Ian

last: Titley

first: John

last: Swansbury

first: Lyndal

last: Kearney

first: Tariq

last: Enver

first: Mel

last: Greaves


title: Affymetrix SNP array data for Burkitt lymphoma samples

status: Public on Dec 07 2010

city: Essen

first: Rene

last: Scholtysik

address: Virchowstrasse 173

department: IFZ

institute: University Hospital Essen

summary: For sporadic Burkitt lymphoma (BL) few genetic lesions are known besides the pathognomonic IG-MYC translocations. Thirtynine molecularly-defined BL were analyzed with high-resolution single-nucleotide polymorphism chips for genomic imbalances and uniparental disomy (UPD). Imbalances were correlated to transcript profiling and selected miRNA analysis. Translocations affecting the MYC locus were studied by fluoresence in situ hybridization. We detected 528 copy number changes, defining 29 recurrently imbalanced regions. 518 regions of UPD were found, but these were rarely recurrent. Combined imbalance mapping and transcript profiling revealed a profound correlation between copy number and expression. Several recurrent imbalances affected the MYC pathway: The miRNA-supercluster 17-92 was frequently gained and the transcription factor E2F2 was recurrently deleted. Molecular BL lacking MYC translocations showed MYC gains. Amplifications of the polymerase iota gene were associated with increased genomic instability. The present findings suggests that UPDs play no major role in the pathogenesis of BL, whereas some genes may contribute to BL development through gene dosage effects. Amplifications of the polymerase iota gene may be functionally linked with increased genomic instability in BL. The pattern and rarity of chromosomal changes detectable even at the high resolution employed here, together with aberrations of genes regulating MYC activity, support that deregulation of the MYC pathway is the major force driving BL pathogenesis, but show that this deregulation is more complex than previously known.

overall_design: Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from whole tissue. Copy number and LOH analysis of 500K SNP arrays was performed for 30 molecularly-defined Burkitt lymphomas. Genotyping was performed using the BRLMM-algorithm. Only a single 250k Chip was performed for nine additional Burkitts. 20 normal references (10 of those hybridized to nsp-chips) extracted from healthy blood donors, used as normals in the analysis in addition to the HapMap references provided by Affymetrix, are included in the set.

first: René


title: Affymetrix SNP array analysis of the breast cell lines MCF10A, MCF10AT, MCF10CA1h and MCF10CA1a

status: Public on Feb 15 2010

city: Rockville

first: Robert

last: Clifford

state: MD

address: 2115 E Jefferson

department: CCR

institute: NCI

summary: To characterize genomic instability in breast cancer progression, we examined copy number loss and copy number gain in the MCF10A series of cell lines.

overall_design:
Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from breast cell lines.
The resulting CEL files were normalized individually to a set of CEL files from 127 female CEPH lymphoblastoid cell lines (see linked supplementary file GSE19920_ceph_controls.txt.gz).
Copy number variations were determined by an unpaired analysis.

first: Maxwell

middle: P

last: Lee

first: Lalage

last: Wakefield


title: Expression data in Arabidopsis ago1-25 and hyl1-2 mutants.

status: Public on Dec 02 2009

city: Yokohama

first: Motoaki

last: Seki

address: 1-7-22, Suehiro-cho, Tsurumi

institute: RIKEN CSRS

summary: We applied the tiling arrays to study the Arabidopsis whole-genome transcriptome in Arabidopsis ago1-25 and hyl1-2 mutants.

overall_design: Fifteen-day-old Arabidopsis plants grown on the agar plates were . The total RNA was prepared from 15-day-old Arabidopsis plants (wild type (WT), ago1-25 and hyl1-2) and used for the microarray hybridization. Three replicative hybridization experiments for each strand array were carried out using the independent biological RNA samples.

first: Yukio

last: Kurihara

first: Akihiro

last: Matsui

first: Junko

last: Ishida

first: Makiko

last: Kawashima

first: Maho

last: Tanaka

first: Taeko

last: Morosawa

first: Yoshiki

last: Mochizuki

first: Kazuo

last: Shinozaki

first: Tetsuro

last: Toyoda


title: Global effects of the small RNA biogenesis machinery on the Arabidopsis thaliana transcriptome

status: Public on May 08 2010

city: Oldenburg

first: Sascha

last: Laubinger

address: Carl-von-Ossietzky-Str. 9-11

institute: University of Oldenburg

type: Non-coding RNA profiling by genome tiling array

summary: In Arabidopsis thaliana, four different DICER-LIKE (DCL) proteins have distinct, but  partially overlapping functions in the biogenesis of microRNAs (miRNAs) and small  interfering RNAs (siRNAs) from longer, non-coding precursor RNAs. To analyze the  impact of different components of the small RNA (sRNA) biogenesis machinery on the  transcriptome, we subjected dcl and other mutants impaired in sRNA biogenesis to  whole-genome tiling array analysis. We compared both protein-coding genes and noncoding  transcripts, including most pri-miRNAs, in two tissues and several stress  conditions. We discovered distinct effects of dcl1, hyl1 and se mutations on the  transcriptome, as well as a number of common genes affected in dcl1 and dcl2 dcl3 dcl4  triple mutants. Our results furthermore suggest that the DCL1 is not only involved in  miRNA action, but can also contribute to silencing of certain transposons, apparently  through an effect on DNA methylation. Together, our findings contribute to the  knowledge of both specialization and overlap between different RNA silencing pathways.

overall_design: Wild type and dcl1-100, se-3, hyl1-2, rdr6-15 ans dcl2,3,4 mutants were grown on MS or soil at 23°C and LL. 7 day old seedlings (grown on MS plates) and inflorescences from 28 (>40) day old plants (dcl1) were used for RNA extraction. For stress treatments, seedlings had been grown for 10 days on solid MS medium at 21°C, they were transferred to liquid MS medium containing no additives (mock control), 200 mM NaCl (salt stress), 300 mM mannitol (osmotic stress) or 100 μM ABA. For cold and heat stress, seedlings were transferred to pre-chilled or pre-warmed liquid MS medium and incubated at 8°C and 30°C, respectively. Samples were taken after 1 h and 12 h of continuous stress treatment. RNA was extracted from whole seedlings. All RNA samples were converted into double stranded DNA targets that were hybridized to whole genome tiling arrays (Affymetrix Arabidopis Tiling1.0R®). All hybridizations were performed with 3 biological replicates.

first: Georg

last: Zeller

first: Stefan

last: Henz

first: Sabine

last: Buechel

first: Timo

last: Sachsenberg

first: Jia-Wei

last: Wang

first: Gunnar

last: Rätsch

first: Detlef

last: Weigel


title: Affymetrix SNP array data for pediatric acute myeloid leukemia (AML) samples at diagnosis: Nsp SNP Array

status: Public on Jan 04 2010

city: Memphis

first: Jeffery

last: Klco

state: TN

address: 262 Danny Thomas Place

department: Pathology

institute: St Jude Children's Research Hospital

summary:
Genome-wide profiling of Copy Number Alterations (CNA) and Loss of Heterozygosity (LOH), gene expression and resequencing of pediatric AML.
This study characterizes the CNA and LOH in a representative cross-section through subtypes of pediatric AML. Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from cryopreserved diagnostic bone marrow or peripheral blood samples.

overall_design:
111 pediatric AML samples were studied using either Affymetrix 100K + 500K 5.0 SNP arrays, 65 of the samples had paired germ line material.

The supplemental files 'GSE15730_AML_175_SNP_Nsp_signal.txt' and 'GSE15730_AML_176_SNP_Nsp_signal.txt' contain the raw signals generated by dChip without normalization.

The CNA and LOH data can be found in the Supplemental Information of the associated manuscript.

first: Ina

last: Radtke

first: James

last: Downing


title: SNP microarray based 24 chromosome aneuploidy screening demonstrates that cleavage stage FISH poorly predicts aneuploidy in embryos that develop to morphologically normal blastocysts

city: Morristown

first: Nathan

last: Treff

address: 111 Madison Ave

institute: RMA of New Jersey

summary: Preimplantation genetic diagnosis (PGD) of aneuploidy by fluorescence in situ hybridisation (FISH) has not delivered the expected clinical benefit.  Many previous re-analysis studies of embryos deemed aneuploid by FISH on day 3 have found a high degree of chromosomal normalcy at the blastocyst stage.  While most have interpreted this as “self correction,” there remains a lack of evidence for such a phenomenon.  A more comprehensive technique for 24 chromosome aneuploidy screening was utilised here to re-evaluate blastocysts previously diagnosed as abnormal by FISH and investigate possible self correction mechanisms, including extrusion or duplication of aneuploid chromosomes resulting in uniparental isodisomy (UPID), and preferential segregation of aneuploidy to the trophectoderm (TE).  Embryos that developed to a morphologically normal blastocyst after an aneuploidy diagnosis by cleavage stage FISH were biopsed into 4 sections, 3 TE and 1 inner cell mass (ICM), and randomised for evaluation by single nucleotide polymorphism (SNP) microarray based 24 chromosome aneuploidy screening (MA-PGD).  Fifty-eight percent of blastocysts were euploid for all 24 chromosomes despite an aneuploid FISH result on day 3.  Only 18% were consistent with the original FISH diagnosis, while the remaining 24% identified abnormalities that were different from the original FISH diagnosis.  Abnormalities did not preferentially segregate to the TE and aneuploid chromosome extrusion or duplication resulting in UPID did not occur. Cleavage stage FISH is poorly predictive of aneuploidy in an embryo that develops into a morphologically normal blastocyst.  Clinicians should consider re-evaluating embryos diagnosed as aneuploid by FISH that form morphologically normal blastocysts using a validated comprehensive 24 chromosome aneuploidy screening method.

overall_design:
Affymetrix SNP arrays were processed according to the manufacturer's directions on DNA extracted from 50 cryopreserved blastocysts that were biopsied into 3 sections of trophectoderm and 1 inner cell mass section.

Affymetrix SNP array analysis was successfully completed on 145 trophectoderm samples and 47 ICM samples from embryos, 8 lymphocyte samples from cell lines and 6 mixed male and female samples.

first: Lesley

middle: E

last: Northrop

first: Brynn

last: Levy

first: Richard

last: Scott


title: Genotype and expression profiling of primitive neuroectodermal tumours

status: Public on Dec 22 2009

city: Toronto

first: David

middle: J. H.

last: Shih

state: ON

address: 686 Bay St

department: Developmental and Stem Cell Biology

institute: Hospital for Sick Children

type:
Genome variation profiling by SNP array
Expression profiling by array

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

overall_design: Refer to individual Series


title: Affymetrix SNP array data for esophageal squamous cell carcinoma (ESCC) samples

status: Public on Jul 06 2010

city: Bethesda

first: Howard

last: Yang

address: 37 CONVENT DR, Room 5120

summary:
We demonstrate that blood and esophageal tissues shared similar DNA methylation patterns within the same individual,suggesting an influence of genetic background on DNA methylation.

Recent studies have shown a genetic influence on gene expression variation, chromatin, and DNA methylation.  However, the effects of genetic background and tissue types on DNA methylation at the genome-wide level have not been characterized extensively.  To study the effect of genetic background and tissue types on global DNA methylation, we performed DNA methylation analysis using the Affymetrix 500K SNP array on tumor, adjacent normal tissue, and blood DNA from 30 patients with esophageal squamous cell carcinoma (ESCC).  The use of multiple tissues from 30 individuals allowed us to evaluate variation of DNA methylation states across tissues and individuals.  Our results demonstrate that blood and esophageal tissues shared similar DNA methylation patterns within the same individual, suggesting an influence of genetic background on DNA methylation.  Furthermore, we showed that tissue types are important contributors of DNA methylation states.

overall_design: Methylation and gDNA intensity data derived from Affymetrix 500k array. 30 individuals with blood, normal and tumor esophageal tissues.

last: Hu

first: Maxwell

last: Lee


title: GRO analysis of topoisomerase mutants

status: Public on Feb 16 2010

city: Burjassot

first: Jose

middle: E.

last: Perez-Ortin

state: Valencia

address: Dr. Moliner 50

department: Bioquimica y Biologia Molecular

institute: Universitat de Valencia

summary:
Genomic Run-on analysis of topoisomerase mutants (top1-delta/top2ts or top2ts) has been conducted at reference temperature for wt strain and at non-permissive temperature for wt and mutant strains.

Keywords: Genomic Run On

overall_design: The analysis includes 3 repeats of the wild type strain (JCW25) at 30ºC and 3 more at 37ºC, 3 repeats of the top2ts mutant (JCW26) at 37ºC and 3 repeats of the double top1 (delta) top2ts mutant at 37ºC. A single genomic DNA hybridization on one of the filters can be used for normalization between gene probes if needed.

last: Garcia-Martinez

first: Ignacio

last: Bermudez


title: Genotype profiling of a primitive neuroectodermal tumour identifies a non-constitutive chr19q13.41 amplicon

summary:
Primitive neuro-ectodermal tumours (PNET) of the supratentorial region are rare, highly malignant embryonal brain tumours affecting young children. Although supratentorial PNET (sPNET) are histologically similar to infratentorial PNET/medulloblastoma, sPNET have more aggressive clinical phenotypes, which suggest sPNET represents distinct biological entities. In contrast to considerable progress in understanding the signalling pathways involved in medulloblastoma, little is known about sPNET pathogenesis. Here we identify a focal amplicon on chr19q13.41 that houses two polycistronic microRNA clusters. Functional analysese indicates that the microRNA clusters may promote oncogenesis in part by modulating cell survival.
Copy number analysis was also performed on an overlapping set of PNET tumours, also available on GEO with accession code GSE14087.

Keywords: single nucleotide polymorphism array, pediatric brain cancer

overall_design: A primitive neuroectodermal tumour sample with matched blood from the University of Cambridge was analyzed on the Affymetrix GeneChip Mapping 250K Nsp SNP array.

first: Mei

last: Li

first: Kyle

middle: F

first: Yun

last: Lu

middle: J

first: Charles

last: Eberhart

first: Ching

last: Lau

first: Scott

last: Pomeroy

first: Peter

last: Collins

first: Piergiorgio

last: Modena

first: Amar

last: Gajjar

first: Michael

middle: D

last: Taylor

first: Eric

last: Bouffet

first: Cynthia

last: Hawkins

first: Annie

last: Huang


title: Copy-number alterations correlate to high-risk genomic aberrations and survival in chronic lymphocytic leukemia

status: Public on Nov 23 2009

city: Uppsala

first: Anders

last: Isaksson

address: Akademiska sjukhuset ing61 3tr

institute: Uppsala University

summary:
Large but not small copy-number alterations correlate to high-risk genomic aberrations and survival in chronic lymphocytic leukemia: a high-resolution genomic screening of newly diagnosed patients.

Single nucleotide polymorphism (SNP)-arrays allow simultaneous detection of copy-number aberrations (CNAs) and copy-number neutral loss-of-heterozygosity (CNN-LOH). In this study we investigated the presence of CNAs and CNN-LOH in newly diagnosed CLL samples from a Swedish chronic lymphocytic leukemia (CLL) cohort. In this study we could detect the known recurrent aberrations in CLL (i.e. deletions of 13q, 11q, 17p and trisomy 12). We also detected other both large and small CNAs which were mostly non-recurrent. CNN-LOH was detected on chromosome 13q in patients that carried homozygous deletion of 13q.

overall_design: In this study, we applied 250K SNP-arrays and screened samples from 203 newly diagnosed chronic lymphocytic leukemia (CLL) patients from a population-based Scandinavian cohort. All samples contained >70% CLL cells.


title: Genetic and Epigenetic Somatic Alterations in Head and Neck Squamous Cell Carcinomas Are Globally Coordinated but Not Locally Targeted (Affymetrix Copy Number)

status: Public on Mar 18 2010

city: Providence

first: Graham

last: Poage

state: RI

address: 70 Ship St

institute: Brown University

summary: Solid tumors, including head and neck squamous cell carcinomas (HNSCC), arise as a result of genetic and epigenetic alterations in a sustained stress environment. Since it has been hypothesized that epigenetic alterations may act by providing the second carcinogenic hit in gene silencing, we sought to identify genome-wide DNA copy number alterations and CpG dinucleotide methylation events and examine the global/local relationships between these types of alterations in HNSCC. Importantly, we found that the global pattern of copy number alterations in these tumors was significantly associated with tumor methylation profiles. However, at the local level, gene promoter regions did not exhibit a correlation between copy number and methylation , and the spectrum of genes affected by each type of alteration was unique. A case-series of 19 tumors and matched blood references were hybrizided to Affymetrix Human Mapping 500k arrays and copy number was determined via HMM with Copy Number Analysis Tool v4.0.1.

overall_design:
This study was designed to investigate the relationship between copy number and DNA methylation alterations in head and neck squamous cell carcinoma. Data in this submission relates to the copy number portion only. Each patient tumor has been de-identified and assigned a number (1-19) and the blood samples with the same number correspond to the respectively-numbered tumor.

The supplementary file 'GSE20939_tumor_copy_number.txt' contains the (blood normalized) copy number calls for each tumor sample.

first: Karl

middle: T

last: Kelsey

first: E

middle: A

last: Houseman


title: SNP chip data of CML, resistant with tyrosine kinase inhibitor

status: Public on Feb 09 2010

city: Tokyo

first: Motohiro

last: Kato

address: 7-3-1, Hongo, Bunkyo-ku

institute: University of Tokyo

summary:
To elucidate whether tyrosine kinase inhibitor (TKI) resistance in CML is associated with characteristic genomic alterations, we analyzed DNA samples from 45 TKI resistant CML patients with 250K single nucleotide polymorphism (SNP) arrays. From 20 patients, matched serial samples of pre-treatment and TKI resistance time points were available. 11 of the 45 TKI resistant patients had mutations of BCR-ABL1, including two T315I mutations. Besides known TKI resistance associated genomic lesions such as duplication of the BCR-ABL1 gene (n=8) and trisomy 8 (n=3), recurrent submicroscopic alterations including acquired uniparental disomy were detectable on chromosomes 1, 8, 9, 17, 19 and 22. On chromosome 22, newly acquired and recurrent deletions of the IGLC1 locus were detected in three patients, who had previously presented with lymphoid or myeloid blast crisis. This may support a hypothesis of TKI induced selection of subclones differentiating into immature B-cell progenitors as a mechanism of disease progression and evasion of TKI sensitivity.

Keywords: SNP-chip

overall_design: To identify oncogenic lesions in CML, we performed a genome-wide analysis of primary CML samples using high-density SNP arrays (Affymetrix GeneChip).

first: Daniel

last: Nowak

first: Seishi

last: Ogawa

first: Markus

last: Muschen

first: Norihiko

last: Kawamata

first: Antonie

last: Meixel

first: Verena

first: Han

last: Kim

first: Sharon

last: Kang

first: Ronald

last: Paquette

first: Mi-Sook

last: Chang

first: Nils

middle: H

last: Thoenissen

first: Max

last: Mossner

first: Wolf-Karsten

last: Hofmann

first: Alexander

last: Kohlmann

first: Tamara

last: Weiss

first: Torsten

last: Haferlach

first: Claudia

first: H

last: Koeffler


title: SNP array data for 56 chronic myeloid leukemia samples.

status: Public on Sep 02 2009

first: Charles

middle: G

last: Mullighan

summary:
Copy number and LOH analysis was performed for 56 chronic myeloid leukemia cases obtained from 23 CML cases obtained atchronic phase, accelerated phase, blast crisis, or remission. All caseswere genotyped with Affymetrix 250k Sty and Nsp arrays.
Keywords: Acute leukemia, BCR-ABL1, chronic myeloid leukemia, copy number analysis, loss-of-heterozygosity, genomics

*** Due to privacy concerns, the primary SNP array data is no longer available with unrestricted access. Individuals wishing to obtain this data for research purposes may request access using the Web links below. ***

overall_design: All assays were performed on DNA extracted fromcryopreserved, mononuclear cell preparations of diagnostic peripheralblood or bone marrow samples. All blast crisis samples were flow sortedprior to DNA extraction. SNP calls were generated using AffymetrixGTYPE. Probe intensity data was extracted and used for DNA copy numberanalysis using dChip, a karyotype-guided normalization algorithm(Reference normalization, Mullighan et al Nature 2007;446:758), dChipand circular binary segmentation (implemented as DNAcopy in R).

first: James

last: Downing


title: Identification of novel gene amplification events in breast cancer

status: Public on Sep 16 2009

first: Robert

last: Clifford

summary:
To identify novel gene amplification events that may contribute to breast cancer  progression, we examined copy number variation
in 161 primary breast cancer samples using the Affymetrix 250K_Nsp and 250K_Sty microarrays or the Affymetrix SNP5.0 microarray.

overall_design:
Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from primary breast cancer samples.
Copy number variations were determined from probeset signal intensities.

first: Maxwell

last: Lee

first: Wakefield

last: Lalage


title: SNP array data for 36 acute myeloid and lymphoblastic leukemia cell lines

summary:
Copy number and LOH analysis was performed for 36 acute leukemia cell lines. All cases were genotyped with Affymetrix 250k Sty and Nsp arrays.
Keywords: Acute leukemia, BCR-ABL1, cell lines, copy number analysis, loss-of-heterozygosity, genomics

*** Due to privacy concerns, the primary SNP array data is no longer available with unrestricted access. Individuals wishing to obtain this data for research purposes may request access using the Web links below. ***

overall_design: All assays were performed on DNA extracted from cell lines growing in log phase under recommended conditions. All blast crisis samples were flow sorted prior to DNA extraction. SNP calls were generated using Affymetrix GTYPE. Probe intensity data was extracted and used for DNA copy number analysis using dChip, a karyotype-guided normalization algorithm (Reference normalization, Mullighan et al Nature 2007;446:758), dChip and circular binary segmentation (implemented as DNAcopy in R). To select reference chromosomes for normalization, existing cytogenetic information was curated from the literature, and karyotyping repeated for a subset of cell lines (manuscript in preparation). Prior to copy number inference, summarized, normalized SNP probe values were corrected from ploidy in triploid or tetraploid cell lines. Copy number inferences were made using a set of 50 acuteleukemia remission samples (GSE9111).


title: Mutations in ABHD12 cause the neurodegenerative disease PHARC: An inborn error of endocannabinoid metabolism

status: Public on Aug 27 2010

city: Bergen

first: Torunn

last: Fiskerstrand

address: Jonas Lies vei

department: Center for medical genetics and molecular medicine

country: Norway

institute: Haukeland University Hospital

summary: PHARC is a neurodegenerative disease comprising early onset cataract and hearing loss, retinitis pigmentosa, and involvement of both the central and peripheral nervous systems; including demyelinating sensorimotor polyneuropathy and cerebellar ataxia. Previously, we mapped this Refsum-like disorder to a 16 Mb region on chromosome 20. Here we report that mutations in the ABHD12 gene cause PHARC disease and we describe the clinical manifestations in a total of 19 patients from four different countries. The ABHD12 enzyme was recently shown to hydrolyse 2-arachidonoyl glycerol (2-AG), the main endocannabinoid lipid transmitter that acts on cannabinoid receptors CB1 and CB2. Our data therefore represent an example of an inherited disorder related to endocannabinoid metabolism. The endocannabinoid system is involved in a wide range of physiological processes including neurotransmission, mood, appetite, pain appreciation, addiction behaviour and inflammation, and several potential drugs targeting these pathways are in development for clinical applications. Our findings show that ABHD12 performs essential functions in both the central and peripheral nervous systems and the eye. Any future drug-mediated interference with this enzyme should consider the potential risk of long-term adverse effects.

overall_design:
Homozygosity mapping using Affymetrix 250K SNP arrays were performed according to the manufacturer's directions on DNA extracted from  peripheral blood samples. This accession number contains the data for families 1-5 plus 7 in the article.

Supplementary files linked below.
The region of interest on chromosome 20 was found using families 1 and 2. The patients in families 3,4 and 5 were then recruited and the patients were homozygous for the same region on chromosome 20 as those in families 1 and 2, showing that all these patients are distantly related. All affected are homozygous for the same mutation. The rest of the chromosomes fall outside the scope of our study.

Mutations in ABHD12 Cause the Neurodegenerative Disease PHARC: An Inborn Error of Endocannabinoid Metabolism, Fiskerstrand et al. The American Journal of Human Genetics, 26 August 2010
http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B8JDD-50W2K9M-3&_user=6129429&_coverDate=08%2F26%2F2010&_rdoc=1&_fmt=high&_orig=search&_sort=d&_docanchor=&view=c&_acct=C000000150&_version=1&_urlVersion=0&_userid=6129429&md5=234296648f66debd3e2b08e795f2179f


title: Genotype profiling of primitive neuroectodermal tumours (250K_Nsp_SNP and 250K_Sty_SNP)

first: David

last: Shih

summary:
Primitive neuro-ectodermal tumours (PNET) of the supratentorial region are rare, highly malignant embryonal brain tumours affecting young children. Although supratentorial PNET (sPNET) are histologically similar to infratentorial PNET/medulloblastoma, sPNET have more aggressive clinical phenotypes, which suggest sPNET represents distinct biological entities. In contrast to considerable progress in understanding the signalling pathways involved in medulloblastoma, little is known about sPNET pathogenesis. Prior low resolution CGH (comparative genomic hybridization) studies indicate sPNET have frequent genomic imbalances and copy number aberrations (CNAs). To define genes involved in sPNET pathogenesis, we utilized the Affymetrix 250K Nsp SNP (single nucleotide polymorphism) analysis to identify genes targeted by recurrent CNAs in primary human sPNET samples.
Copy number analysis was conducted on 39 primary PNET samples. Select target genes were validated by genomic and/or RT-PCR. Our analysis revealed frequent CNA across the sPNET genome, encompassing large and focal chromosome segments, and corroborated previous reports that isochromosome 17q, an abnormality found in ~ 30% of medulloblastoma, is rare in sPNET.

Keywords: single nucleotide polymorphism array, disease state analysis

overall_design:
A total of 56 primary sPNET samples were collected for this study from The Hospital for Sick Children, John Hopkins University, St. Jude Research Hospital, University of Cambridge, Children’s Hospital Boston, Virginia Commonwealth University, Instituto nazionale per lo studio e la cura dei tumori, and Texas Children’s Hospital, with local Institutional Research Ethics Board approval. Pineoblastoma and rhaboid tumours were specifically excluded, leaving 52 samples, 39 of which had good quality DNA available. These samples, in addition to 28 diploid reference samples (a gift from Dr. S. Scherer, University of Toronto), were analyzed on the Affymetrix GeneChip Mapping 250K Nsp SNP array.

Due to sample availability at the time the arrays were run, the diploid reference samples analyzed on the Sty arrays are different from reference samples analyzed on the Nsp arrays.

first: Kyle

first: Mei

last: Li

first: Yun

last: Lu

last: Eberhart

first: Ching

last: Lau

first: Scott

last: Pomeroy

first: Peter

last: Collins

first: Piergiorgio

last: Modena

first: Amar

last: Gajjar

first: Michael

last: Taylor

first: Eric

last: Bouffet

first: Cynthia

last: Hawkins

first: Annie

last: Huang


title: High-resolution SNP-array profiling in myeloproliferative neoplasms

status: Public on Oct 01 2009

city: Ulm

first: Frank

last: Stegelmann

address: Albert-Einstein-Allee 23

department: Internal Medicine III

institute: University Hospital of Ulm

summary: SNP arrays allow for genome-wide profiling of copy-number alterations (CNAs) and copy-neutral runs of homozygosity (ROH) at high resolution. To identify novel genetic lesions in myeloproliferative neoplasms (MPN), a large series of 151 clinically well-characterized patients was analyzed in our study. CNAs were rare in essential thrombocythemia and polycythemia vera. In contrast, approximately one third of myelofibrosis patients exhibited small genomic losses (< 5 Mb). In two secondary myelofibrosis cases the tumor suppressor gene NF1 in 17q11.2 was affected. Sequencing analyses revealed a mutation in the remaining NF1 allele of one patient. In terms of ROH, no chromosomes other than 9p were recurrently affected. In conclusion, in our study we identified novel genomic aberrations in MPN, in particular in patients with myelofibrosis. Further analyses on single-gene level are necessary to uncover the mechanisms that are involved in the pathogenesis of MPN.

overall_design:
Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from cryopreserved diagnostic peripheral blood samples.
Copy number analysis of Affymetrix 250K SNP arrays was performed for 151 myeloproliferative neoplasm samples [essential thrombocythemia, n=45; polycythemia vera, n=45; secondary myelofibrosis, n=14; primary myelofibrosis, n=47]. There are also 60 samples from acute myeloid leukemia patients in remission which were used as references for unpaired analysis.

first: Lars

last: Bullinger

first: Martin

last: Griesshammer

first: Karlheinz

last: Holzmann

first: Marianne

last: Habdank

first: Susanne

last: Kuhn

first: Carmen

last: Maile

first: Stefanie

last: Schauer

first: Hartmut

last: Döhner

first: Konstanze


title: Interspecies hybridization between Arabidopsis thaliana and Arabidopsis arenosa

city: Lincoln

first: Harkamal

last: Walia

state: NE

address: Agronomy and Horticulture

institute: University of Nebraska

summary:
Hybrid matings between A. thaliana and A. arenosa result in post zygotic seed lethality resulting in hybridization barrier between the two species. This barrier can be overcome to a large degree by increasing the genome dosage of the maternal genome (i.e. A. thaliana) in a cross between the two species. In this experiment we assayed the transcriptome of an incompatible cross (2x At x 2x Aa) with high seed lethality and a compatible cross (4x At x 2x Aa) using silique tissue at 5 days after pollination.
We used microarrays to identify dosage responsive gene in interspecies hybridization

Keywords: differential expression

sample_organism: Arabidopsis arenosa x Arabidopsis thaliana

overall_design: Total RNA was derived from the compatible and incompatible siliques for hybridization using the Affymetrix protocol. The experiment was performed in 3 independent biological replicates.

first: Luca

last: Comai

first: Caroline

last: Josefsson