title: Genome-wide gene expression profiling of rice Indica cultivar Zhongxian 3037 and mutant phoenix (pho) panicle

status: Public on Jul 22 2009

first: Wenying

last: Xu

summary: phoenix (pho) is a naturally occurring rice (Oryza sativa L.) mutant that exhibits stable inflorescence reversion. Genetic analysis showed that it was not a simple mendelian mutant. In order to find the major genes contributed to the formation of pho, microarray experiments were carried out to analyze and compare the transcriptional profiles between pho and wild-type panicles.

overall_design: We generated gene expression profiles of rice Indica cultivar Zhongxian 3037 and mutant phoenix (pho) by using 57K Affymetrix rice whole genome array.

first: Kejian

last: Wang

first: Yongbiao

last: Xue

first: Zhukuan

last: Cheng


title: SNP chip data of MDS

status: Public on Aug 01 2009

city: Tokyo

first: Motohiro

last: Kato

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

country: Japan

institute: University of Tokyo

summary:
Myelodysplastic syndromes (MDS) are clonal disorders of hematopoietic progenitors characterized by ineffective hematopoiesis and high propensity to leukemias. Although a number of gene targets have been identified, in many MDS cases, particular genetic targets are unknown. In this study, we performed genome-wide profiling of copy number (CN) abnormalities and allelic imbalances in MDS genomes in order to clarify the distribution of LOH (loss of heterozygosity) and identify their target genes. We analyzed a total of 171MDS and MDS/MPD specimens, including 7 RA/RARS, 23 RCMD/RCMD-RS, 6 5q-syndrome, 30 RAEB-1, 40 RAEB-2, 4 therapy related-MDS/AML, 5 MDSu, 17 CMML-1, 16 CMML-2, 24 overt AML, using high-density SNP arrays. The data were analyzed by CNAG/AsCNAR software we specifically developed for allele-specific CN analysis and sensitive LOH detection. MDS showed characteristic CN profiles in SNP array analysis. Of particular interest is the finding of high frequency of CN-neutral LOH (Uniparental disomy,UPD), which were observed in 51 of 171 (30%) MDS cases. They preferentially involved 1p, 1q, 4q, 7q, 11q, 17p and other chromosomal segments, which were associated with homozygous mutations of both loss-of-function mutations and gain-of function mutations of tumor suppressor genes and cellular oncogenes, including TP53 (17p UPD), AML1/RUNX1 (21q UPD), Nras and cMPL (1p UPD), JAK-2 (9p UPD), and FLT3 (13q UPD). Next we tried to identify a new gene target in 11q UPD, which was most common UPD region in this study and many of these cases were CMML with a normal karyotype. The minimum 11q UPD segment is about 2Mb which existed in 11q23. We sequenced coding exons of c-cbl and detected homozygous mutations in 8 of 9 MDS cases with 11q UPD (CMML= 5, RAEB= 3, overt leukemia= 1), but very rare in cases without 11q UPD (1/162), demonstrating that the mutation is tightly linked to 11q UPD. These mutations were 8 point mutations and 1 micro-deletion, they were accumulated in the linker or RING domain. These c-cbl mutants can transform NIH3T3 in a dominant manner and these mutants are phosphorylated and activate PI3K-Akt pathway. To investigate the functions of these mutants in hematopoietic cells, we introduced these mutants into c-kit(+)Sca1(+)Lin(-) murine bone marrow cells, it prolonged replating capacity of these hematopoietic progenitors.

Keywords: SNP-chip

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

first: Masashi

last: Sanada

first: Takahiro

last: Suzuki

first: Lee-Yung

last: Shih

first: Azusa

last: Tamura

first: Hiroaki

last: Honda

first: Mamiko

last: Sakata-Yanagimoto

first: Keiki

last: Kumano

first: Hideaki

last: Oda

first: Junko

last: Takita

first: Noriko

last: Goto

first: Masaharu

last: Nobuyoshi

first: Norihiko

last: Kawamata

first: Yasuhide

last: Hayashi

first: Hiroshi

last: Harada

first: Mineo

last: Kurokawa

first: Shigeru

last: Chiba

first: Hiraku

last: Mori

first: Keiya

last: Ozawa

first: Mitsuhiro

last: Omine

first: Hisamaru

last: Hirai

first: H

middle: P

last: Koeffler

first: Seishi

last: Ogawa


title: Genes regulating B cell development are mutated in acute lymphoid leukaemia

status: Public on Sep 02 2009

city: Memphis

first: Charles

middle: G

last: Mullighan

state: TN

address: 262 Danny Thomas Place

department: Pathology

country: USA

institute: St Jude Children's Research Hospital

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

summary:
Chromosomal aberrations are a hallmark of acute lymphoid leukaemia (ALL) but alone fail to induce leukaemia. To identify cooperating oncogenic lesions, we performed genome-wide analysis of leukaemic blasts from 242 paediatric ALL patients using high-resolution single nucleotide polymorphism arrays and genomic DNA sequencing. Our analyses revealed deletion, amplification, point mutation and structural rearrangement in genes encoding key regulators of B lymphocyte development and differentiation in 40% of B-progenitor ALL. PAX5 was the most frequent target of somatic mutation, being altered in 31.7% of cases. The identified PAX5 mutations resulted in haploinsufficiency or the generation of hypomorphic alleles. Deletions were also detected in E2A, EBF, LEF1, Ikaros, and Aiolos. These findings demonstrate that direct disruption of pathways controlling B cell development and differentiation contributes to B-progenitor ALL pathogenesis.  Moreover, these data demonstrate the power of high-resolution, genome-wide approaches to identify critical new molecular lesions in cancer.

Keywords: disease state analysis

*** 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: 242 acute lymphoid leukaemia samples, 62 reference samples, and 61-64 remission samples were hybridized to 50K_Hind, 50K_Xba, and 250K_Sty SNP arrays.

last: Mulighan

first: James

middle: R

last: Downing


title: Comparison of transcriptome profile between wild-type and dst mutant plants

status: Public on Jul 30 2009

city: Shanghai

first: Hong-Xuan

last: Lin

address: 300 Fenglin Road

country: China

institute: Shanghai Institute of Plant Physiology and Ecology

summary:
Drought and salinity are two main abiotic-stresses negatively affecting crop growth and productivity worldwide with largely decreasing crop yields. The understanding of plant responses to stresses in physiology, genetics, and molecular biology will be greatly helpful to improve the tolerance of crops to abiotic-stresses through genetic engineering.To identify the genetic loci that control drought and salt tolerance in rice, we performed a large-scale screen for the mutants with altered drought and salt tolerance. A drought and salt tolerance (dst) mutant line was isolated.In this series, we compare the transcriptome of wild-type plant Zhonghua11 and dst mutants under the normal growth conditions.
Keywords: genetic modification

overall_design: 6 samples (3 biological replicates for each line) were used in this experiment.

first: Xin-Yuan

last: Huang

first: Dai-Yin

last: Chao


title: Root-specific transcriptional profiling of contrasting rice genotypes in response to salinity stress

status: Public on Jul 16 2009

city: Glen Osmond

first: Ute

last: Baumann

state: SA

address: Hartley Grove

department: Australian Centre for Plant Functional Genomics

country: Australia

institute: University of Adelaide

summary:
Analysis of root gene expression of salt-tolerant genotypes FL478, Pokkali and IR63731, and salt-sensitive genotype IR29 under control and salinity-stressed conditions during vegetative growth. Results provide insight into the genetic basis of salt tolerance in indica rice.

Keywords: stress response

overall_design: Seedlings were cultured in sand and irrigated with a nutrient solution for 22 d (salt-treated) and 30 d (control) after germination, respectively. Salinity treatment was applied by adding NaCl and CaCl2 (5:1 molar concentration) in two steps over a period of 3 days (final electrical conductivity: 7.4 dS m-1) to prevent osmotic shock. All plants were harvested on day 30.

first: Olivier

last: Cotsaftis

first: Darren

last: Plett

first: Alexander

middle: A

last: Johnson

first: Timothy

middle: J

last: Close

first: Mark

last: Tester

first: Harkamal

last: Walia

first: Clyde

last: Wilson


title: Transcriptome analysis of iron and phosphorus interaction in rice seedlings

city: Hangzhou

first: Luqing

last: Zheng

address: 388 Yuhangtanghe Road

institute: Colledge of Life Sciences, Zhejiang University

summary:
The antagonistic interaction between iron (Fe) and phosphorus (P) has been noted in the area of plant nutrition. To understand the physiology and molecular mechanisms of this interaction, we studied the growth performance, nutrient concentration, and gene expression profiles of root and shoot segments derived from 10-d-old rice (Oryza sativa) seedlings under four different nutrient conditions: (1) full strength of Fe and P (+Fe+P); (2) full strength of P and no Fe (-Fe+P); (3) full strength of Fe and no P (+Fe-P); and (4) without both Fe and P (-Fe-P).
We used Affymetrix genechip to detail the global programme of gene expression underlying different Fe and P supply conditions identified distinct classes of up-regulated genes.

overall_design: The GeneChip analysis experiment was designed as a two-factor experiment  with four treatments: (1) +P+Fe; (2) –Fe+P; (3) +Fe–P; (4) –Fe–P. The  experiment included two biological replicates. Each sample represented root  and shoot material from five to 10 plants.

first: Fangliang

first: Reena

last: Narsai

first: Jiaojiao

last: Wu

first: Estelle

last: Giraud

first: Fei

last: He

first: Longjun

last: Cheng

first: Fang

last: Wang

first: Ping

last: Whelan

first: Huixia

last: Shou


title: Copy number profiling of 45 human breast cancer cell lines on Affymetrix 100K SNP arrays

status: Public on Apr 22 2009

city: South San Francisco

first: Peter

last: Haverty

state: CA

address: 1 DNA Way

department: Bioinformatics

institute: Genentech, Inc.

summary:
Breast cancer cell lines grown in full serum under standard conditions were profiled on Affymetrix GeneChip Mapping 100K Set Arrays

Keywords: Mapping Array

overall_design: Profiling of cell lines grown under standard conditions

first: Guy

last: Cavet

first: Xiaolan

last: Hu

middle: M

last: Lackner


title: Integrated genomics approach to detect allelic imbalances in multiple myeloma, SNP data

status: Public on May 16 2009

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

summary:
A SNP microarray and FISH-based procedure to detect allelic imbalances in multiple myeloma: an integrated genomics approach reveals a wide dosage effect on gene and microRNA expression

Multiple myeloma (MM) is characterized by marked genomic instability. Beyond structural rearrangements, a relevant role in its biology is represented by allelic imbalances leading to significant variations in ploidy status. To better elucidate the genomic complexity of MM, we analyzed a panel of 45 patients using combined FISH and microarray approaches. Using a self-developed procedure to infer exact local copy numbers for each sample, we identified a significant fraction of patients showing marked aneuploidy. A conventional clustering analysis showed that aneuploidy, chromosome 1 alterations, hyperdiploidy and recursive deletions at 1p and chromosomes 13, 14 and 22 were the main aberrations driving samples grouping. Then, we integrated mapping information with gene and microRNAs expression profiles: a multiclass analysis of the identified clusters showed a marked gene-dosage effect, particularly concerning 1q transcripts, also confirmed by correlating gene expression levels and local copy number alterations. A wide dosage effect affected also microRNAs, indicating that structural abnormalities in MM closely reflect in their expression imbalances. Finally, we identified several loci in which genes and microRNAs expression correlated with loss-of-heterozygosity occurrence. Our results provide insights into the composite network linking genome structure and gene/microRNA transcriptional features in MM.

Keywords: Integrated genomics approach based on SNP microarray and FISH procedures to detect allelic imbalances in multiple myeloma.

overall_design: Pathological bone marrow specimens from 41 MM and four plasma cell leukemia (PCL) patients at diagnosis. 250 nanograms of genomic DNA was processed and, in accordance with the manufacturer's protocols, 40 micrograms of fragmented biotin-labelled DNA were hybridized on GeneChip Human Mapping 50K XbaI Arrays (Affymetrix Inc.). The arrays were scanned using the GeneChip Scanner 3000 7G. The images were acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares. Genomic Smoothing analysis was performed by using the smoothing window of 0 Mb, and inferred copy number states were derived from a Hidden Markov Model (HMM) based algorithm implemented in CNAT 4.0.1. Circular Binary Segmentation (Ohlsen et al., 2004) was applied using DNAcopy package for R Bioconductor on raw data. FBN procedure was finally applied to infer exact local copy number as described in the mentioned Reference.

first: Agnelli

last: Luca

first: Mosca

last: Laura

first: Fabris

last: Sonia

first: Lionetti

last: Marta

first: Andronache

last: Adrian

first: Kwee

last: Ivo

first: Todoerti

last: Katia

first: Verdelli

last: Donata

first: Battaglia

last: Cristina

first: Bertoni

last: Francesco

first: Lambertenghi

middle: D

last: Giorgio

first: Neri

last: Antonino


status: Public on Jun 03 2009

city: New Delhi

first: Akhilesh

middle: Kumar

last: Tyagi

state: Delhi

address: Benito Juarez Road

department: Plant Molecular Biology

country: India

institute: University of Delhi South Campus,  Benito Juarez Road  India

summary:
Glycinebetaine-induced water-stress tolerance in codA-expressing transgenic indica rice is associated with up-regulation of several stress responsive genes.
Rice (Oryza sativa L.), a non-accumulator of glycinebetaine (GB), is highly susceptible to abiotic stress. Transgenic rice with chloroplast-targeted choline oxidase encoded by the codA gene from Arthrobacter globiformis has been evaluated for inheritance of transgene up to R5 generation and water-stress tolerance. During seedling, vegetative and reproductive stages, transgenic plants could maintain higher activity of photosystem II and they show better physiological performance, e.g. enhanced detoxification of reactive oxygen species compared to wild-type plants under water-stress. Survival rate and agronomic performance of transgenic plants is also better than wild-type following prolonged water-stress. Choline oxidase converts choline into glycinebetaine and H2O2 in a single step. It is possible that H2O2 /GB might activate stress response pathways and prepare transgenic plants to mitigate stress. To check this possibility, microarray-based transcriptome analysis of transgenic rice has been done. It unraveled altered expression of many genes involved in stress responses, signal transduction, gene regulation, hormone signaling and cellular metabolism. Overall, 165 genes show more than 2 folds up-regulation at P value <0.01 in transgenic rice. Out of these, at least 50 genes are known to be involved in plant stress response. Exogenous application of H2O2 or GB to wild-type plants also induces such genes. Our data show that metabolic engineering for GB is a promising strategy for introducing stress tolerance in crop plants and which could be imparted, in part, by H2O2- and/or GB-induced stress response genes.

overall_design: Rice (Oryza sativa L.), transgenic plants expressing codA gene from Arthrobacter globiformis were compared with untransformed plants at seedling level

first: Jitender

last: Giri

middle: K


title: Rice seedling hormone treatment

status: Public on Jun 08 2009

first: Mukesh

last: Jain

state: New Delhi

address: New Mehrauli Road

institute: Jawaharlal Nehru University

summary:
Indica rice seedlings of IR64 variety were grown hydroponically for 7-days in a culture room with a daily photoperiodic cycle of 14h light and 10h dark. Seedlings were incubated in 0.1% dimethyl sulfoxide (control) or 50 micromolar solutions of indole-3-acetic acid (IAA treatment) and benzyl aminopurine (BAP treatment) for 1h and 3h. Equal amounts of 1h and 3h samoles were pooled for each treatment before RNA isolation. The 5 micrograms of each total RNA sample was processed for microarray analysis according to Affymetrix protocol.
Keywords: Rice, seedling, IAA, BAP, hormone response

overall_design: Two biological replicates for each sample (control, IAA treated, BAP treated) were used for microarray analysis. The experiment involves the identification of differentially expressed genes in IAA and BAP treated samples as compared to control.

first: Jitendra

last: Khurana


title: SNP data from lymphoma samples

status: Public on May 01 2009

first: Motohiro

last: Kato

summary: B cell non-Hodgkin's lymphoma (B-NHL) consists of different pathological entities that are frequently characterized by distinct genetic alterations. However, the knowledge on these genetic lesions in B-NHL is still limited. In order to obtain a more comprehensive view of genetic lesions in B-NHL, we performed genome-wide analysis of copy number (CN) alterations as well as allelic imbalances using Affymetrix SNP arrays with B-NHL cases, including SNP array data were analyzed with CNAG/AsCNAR software, which enabled sensitive detection of CN alterations in allele-specific manner, and thus allelic imbalances, without depending on availability of paired normal controls. Most frequent numerical abnormalities in B-NHL were gains of chromosomes 3 and 18, although gains of chromosome 3 were less prominent in FL. Chromosomal deletions that lead to loss of heterozygosity (LOH) were commonly found in 1p, 6q and 10q. High-grade amplifications and homozygous deletions frequently provide a clue to identify relevant gene targets. In our series, 12 loci of high-grade amplifications and 14 loci of homozygous deletions were identified, and helped to specify the candidate genes. These regions included, FCGR2B amplified in 5 cases of DLBCL, RERE amplified in 2 cases of FL and CDKN2A/CDKN2B deleted in 9 cases of DLBCL.

overall_design: To identify oncogenic lesions in neuroblastoma, we performed a genome-wide analysis of primary tumor samples from 241 lymphoma samples (238 fresh tumors and 3 cell lines) using high-density 50K and/or 250K SNP arrays (Affymetrix GeneChip).

first: M

last: Sanada

first: J

last: Takita

first: Y

last: Sato

first: K

last: Takeuchi

last: Chen

last: Nakazaki

last: Nomoto

last: Asakura

first: S

last: Muto

first: A

last: Tamura

last: Akatsuka

last: Hayashi

first: T

last: Igarashi

last: Kurokawa

last: Chiba

last: Mori

last: Ishikawa

last: Tobinai

last: Yoshino

last: Kobayashi

last: Ogawa'


title: SNEP: Simultaneous detection of nucleotide and expression polymorphisms using Affymetrix GeneChip

status: Public on Jun 09 2009

city: Mishima

first: Nori

last: Kurata

address: 1111 Yata

institute: National Institute of Genetics

summary: Nucleotide polymorphisms can potentially influence the hybridization of mRNA to 25-mer oligonucleotides. Because Affymetrix Rice Genome Array was designated mainly for Nipponbare genome of Oryza sativa, the expression level of other varieties could not be estimated correctly. We tried to apply new approaches to estimate expression level by discerning the probe-level differential hybridization.

sample_organism:
Oryza sativa Indica Group
Oryza sativa Japonica Group

overall_design: Nipponbare and 93-11 replicates were analyzed.

first: Youko

last: Horiuchi

first: Yoshiaki

last: Harushima


title: Multi-dimensional genomic analysis in breast cancer patients

status: Public on May 05 2009

city: San Diego

first: Jack

last: Yu

address: 3210 Merryfield Row

institute: Veridex, LLC

summary:
Multi-dimensional genomic analysis identifies a class of breast cancer patients with high metastatic outcome and differential response to chemotherapeutic drugs
The application of multi-dimensional genomic analyses might provide a more refined risk assessment of breast tumor aggressiveness and improve the selection of patients for personalized medicine.
Our study demonstrates the feasibility of using CNAs to predict patient outcome. In combination with gene expression profiles, the clinical implication for such prognostic assays is the identification of breast cancer patients at different risks and sensitivities to chemotherapeutic drugs.
Keywords: survival time

overall_design: try to find the association between genomic DNA copy number changes with breast cancer patients survival time.

first: Yi

last: Zhang

first: John

middle: W

last: Martens

middle: X

last: Jiang

first: Anieta

last: Sieuwerts

first: Marcel

last: Smid

first: Jan

last: Klijn

first: Yixin

last: Wang

last: Foekens


title: Transcriptome analysis of gibberellin-signaling mutants in rice [Oryza sativa]

status: Public on Apr 21 2009

city: Yokohama

first: Hitoshi

last: Sakakibara

address: 1-7-22 Suehiro, Tsurumi

department: Plant Science Center

institute: RIKEN

summary: Gibberellins control a wide range of aspects of plant growth and development. Although a series of mutant of the signaling pathway has been identified, the global regulatory network underlying gibberellin signal transduction has not been revealed. To address this issue, we performed microarray analysis with rice gibberellin signaling mutants, gid1, gid2, slr, and the parental cultivar Taichung 65.

overall_design: We analyzed gid1-3, gid2-1, slr1 (k1001), and their parental cultiver Taichung 65. In each line, we prepared 3 biological replicates. Thus, 12 samples were analyzed in this experiment

first: Tomoe

last: Kamada-Nobusada

first: Miyako

last: Ueguchi-Tanaka

first: Makoto

last: Matsuoka


title: SNP data of acute promyelocytic leukemia samples

status: Public on Apr 01 2009

first: Motohiro

last: Kato

summary:
Acute promyelocytic leukemia (APL) is a hematopoietic malignant disease characterized by the chromosomal translocation t(15;17), resulting in the formation of the PML-RARA gene.  Here, 47 t(15;17) APL samples were analyzed with high-density single-nucleotide polymorphism microarray (50K and 250K SNP-chips) using the new algorithm AsCNAR (allele-specific copy-number analysis using anonymous references).  Copy-number-neutral loss of heterozygosity (CNN-LOH) was identified at chromosome 10q (3 cases), 11p (3 cases) and 19q (1 case).  Twenty-eight samples (60%) did not have an obvious alteration (normal-copy-number [NC] group).  Nineteen samples (40%) showed either one or more genomic abnormalities: 8 samples (17%) had trisomy 8 either with or without an additional duplication, deletion, or CNN-LOH (+8 group); and 11 samples (23%) had genomic abnormalities without trisomy 8 (other abnormalities group).  These chromosomal abnormalities were acquired somatic mutations.  Interestingly, FLT3-ITD mutations (11/47 cases) only occurred in the group with no genomic alteration (NC group).  Taken together, these results suggest that the pathway of development of APL differs in each group: FLT3-ITD, trisomy 8, and other genomic changes.  Here, we showed for the first time hidden abnormalities and novel disease-related genomic changes in t(15;17) APL.

Keywords: SNP-chip

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

first: Tadayuki

last: Akagi

first: Lee-Yung

last: Shih

first: Norihiko

last: Kawamata

first: Go

last: Yamamoto

first: Masashi

last: Sanada

first: Ryoko

last: Okamoto

first: Carl

last: Miller

first: Der-Cherng

last: Liang

first: Seishi

last: Ogawa

first: H

last: Koeffler


title: High-resolution copy number analysis of medulloblastoma

status: Public on Apr 15 2009

city: HEIDELBERG

first: Paul

middle: A.

last: Northcott

address: Im Neuenheimer Feld 280

country: Germany

institute: German Cancer Research Center (DKFZ)

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

summary:
We used high-resolution SNP genotyping to identify regions of genomic gain and loss in the genome of 212 medulloblastomas, a malignant pediatric brain tumor.  Focal amplifications of fifteen known oncogenes and focal deletions of twenty known tumor suppressor genes (TSG) were revealed, most not previously implicated in medulloblastoma.  Importantly, we identified novel amplifications and homozygous deletions, including recurrent, mutually exclusive, highly focal genetic events in genes targeting histone lysine methylation, particularly histone 3, lysine 9 (H3K9).  Post-translational modification of histone proteins is critical for regulation of gene expression, can participate in determining stem cell fates, and has been implicated in carcinogenesis. Consistent with our genetic data, restoration of expression of genes controlling H3K9 methylation greatly diminishes proliferation of medulloblastoma in vitro.  Copy number aberrations of genes with critical roles in writing, reading, removing, and blocking the state of histone lysine methylation, particularly H3K9, suggest that defective control of the histone code contributes to the pathogenesis of medulloblastoma.

Keywords: Affymetrix SNP array

overall_design: Genomic DNA isolated from fresh frozen primary human medulloblastomas and medulloblastoma cell lines were subjected to SNP genotyping using either Affymetrix 100K or 500K GeneChip Mapping array sets for the purpose of obtaining genome-wide copy number and LOH profiles.

first: Yukiko

last: Nakahara

first: Xiaochong

last: Wu

first: Lars

last: Feuk

first: David

last: Ellison

first: Sid

last: Croul

first: Stephen

last: Mack

middle: N

last: Kongkham

first: John

last: Peacock

first: Adrian

last: Dubuc

first: Young-Shin

last: Ra

first: Karen

last: Zilberberg

first: Jessica

last: Mcleod

first: Steve

last: Scherer

first: J

middle: S

last: Rao

first: Charles

last: Eberhart

first: Wesia

last: Grajkowska

first: Yancey

last: Gillespie

first: Boleslaw

last: Lach

first: Richard

last: Grundy

first: Ian

middle: F

last: Pollack

first: Ronald

middle: L

last: Hamilton

first: Timothy

middle: V

last: Meter

first: Carlos

last: Carlotti

first: Frederick

last: Boop

first: Darrell

last: Bigner

last: Gilbertson

first: James

middle: T

last: Rutka

first: Michael

last: Taylor


title: Expression information of splicing factor OsSKIPa knock-down and overexpressed rice

status: Public on Mar 18 2009

city: Wuhan

first: Kabin

last: Xie

state: Hubei

address: Shizi Shan Street

department: National Key Laboratory of Crop Genetic Improvement

institute: Huazhong Agriculture University

summary:
OsSKIPa is an SNW/SKIP protein in rice, which homolog to SKIP(human) and PRP45(yeast). OsSKIPa can rescue the lethal of yeast prp45 mutants. OsSKIPa-suppressed plants (S59R) show decrease of cell viability. Overexpression of OsSKIPa (S58S) increase the osmotic stresses tolerance. OsSKIPa is an important regulator and interacting with a lot of proteins which have varient functions. In order to find the genes expression information when OsSKIPa changed. We use microarray to find changed genes in S59R and S58S plants in the normal condition.
Keywords: gene expression array-based (RNA / in situ oligonucleotide)

overall_design: Whole plants were collected from 1-month-old S58S (two replicates), S59R (three replicates) and wild type (three replicates).

first: Xin

last: Hou

first: Jialing

last: Yao

first: Zhuyun

last: Qi

first: Lizhong

last: Xiong


title: SNP copy number data from glioblastoma subcutaneous xenografts

status: Public on Mar 07 2009

city: San Francisco

first: Graeme

last: Hodgson

department: Neurological Surgery

institute: UCSF

summary:
Development of model systems that recapitulate the molecular heterogeneity observed amongst GBM tumors will expedite the testing of targeted molecular therapeutic strategies for GBM treatment. In this study, we profiled DNA copy number and mRNA expression in 21 independent GBM tumor lines maintained as subcutaneous xenografts (GBMX), and compared GBMX molecular signatures to those observed in GBM clinical specimens derived from The Cancer Genome Atlas (TCGA). The predominant copy number signature in both tumor groups was defined by chromosome-7-gain/chromosome-10-loss, a poor prognosis genetic signature. We also observed, at frequencies similar to that detected in TCGA GBMs genomic amplification and overexpression of known GBM oncogenes such as EGFR, MDM2, CDK6 and MYCN, and novel genes including NUP107, SLC35E3, MMP1, MMP13 and DDX1. The transcriptional signature of GBMX tumors, which was stable over multiple subcutaneous passages, was defined by overexpression of genes involved in M-phase, DNA Replication, and Chromosome organization (MRC) and was highly similar to the poor-prognosis mitosis-and-cell-cycle-module (MCM) in GBM. Assessment of gene expression in TCGA-derived GBMs revealed overexpression of MRC cancer genes AURKB, BIRC5, CCNB1, CCNB2, CDC2, CDK2, and FOXM1, which form a transcriptional network important for G2/M- progression and/or -checkpoint activation. In conclusion, our study supports propagation of GBM tumors as subcutaneous xenografts as a useful approach for sustaining key molecular characteristics of patient tumors, and highlights therapeutic opportunities conferred by this GBMX tumor panel for testing targeted therapeutic strategies for GBM treatment.
Disease state analysis

overall_design: DNA copy number was assessed in 21 independent GBM xenograft tumors

first: J

middle: G

first: Ru-Fang

last: Yeh


status: Public on Mar 24 2009

city: Boston

first: Rameen

last: Beroukhim

state: MA

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

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

summary:
Integrated genomic profiling of endometrial carcinoma associates aggressive tumors with indicators of PI3 kinase activation

Although 75% of endometrial cancers are treated at an early stage, 15% to 20% of these recur. We performed an integrated analysis of genome-wide expression and copy-number data for primary endometrial carcinomas with extensive clinical and histopathological data to detect features predictive of recurrent disease. Unsupervised analysis of the expression data distinguished 2 major clusters with strikingly different phenotypes, including significant differences in disease-free survival. To identify possible mechanisms for these differences, we performed a global genomic survey of amplifications, deletions, and loss of heterozygosity, which identified 11 significantly amplified and 13 significantly deleted regions. Amplifications of 3q26.32 harboring the oncogene PIK3CA were associated with poor prognosis and segregated with the aggressive transcriptional cluster. Moreover, samples with PIK3CA amplification carried signatures associated with in vitro activation of PI3 kinase (PI3K), a signature that was shared by aggressive tumors without PIK3CA amplification. Tumors with loss of PTEN expression or PIK3CA overexpression that did not have PIK3CA amplification also shared the PI3K activation signature, high protein expression of the PI3K pathway member STMN1, and an aggressive phenotype in test and validation datasets. However, mutations of PTEN or PIK3CA were not associated with the same expression profile or aggressive phenotype. STMN1 expression had independent prognostic value. The results affirm the utility of systematic characterization of the cancer genome in clinically annotated specimens and suggest the particular importance of the PI3K pathway in patients who have aggressive endometrial cancer.

overall_design: 84 endometrial cancers (including 9 cell lines) were subject to 100K SNP analysis. 57 endometrial cancers were subject to expression analysis.

first: Helga

last: Salvesen


title: Comparative analyses of gene copy number and mRNA expression in GBM tumors and GBM xenografts

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

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

overall_design: Refer to individual Series


title: Expression data for heat shock in rice seedlings

status: Public on Jan 08 2009

first: Bin

last: Han

address: 500 Cao Bao Road

institute: National Center for Gene Research，Chinese Academy of Sciences

summary:
In this study, we have analyzed the expression profiles of rice genes under control and heat shock conditions using microarray technology to identify the genes differentially expressed.
Keywords: Heat shock

overall_design: 14-day-old light-grown rice seedlings grown under controlled conditions and those subjected to heat shock were used for RNA extraction and hybridization on Affymetrix microarrays. Three technical replicates of each sample were used for microarray analysis. For heat shock treatment, the seedlings were kept in a chamber at 42 degree C. The seedlings kept at 28-30 degree C, served as control (Seedling).

first: Wenhuo

last: Hu

first: Guocheng


title: Detection of genomic deletions in rice by genomic DNA hybridization to oligonucleotide microarrays

status: Public on Mar 06 2009

city: Los Banos

first: Ramil

middle: Paner

last: Mauleon

state: Laguna

address: IRRI Campus, Pili Drive

department: Crop Research Informatics Laboratory

country: Philippines

institute: International Rice Research Institute

summary:
Rice deletion mutants have not been widely used in functional genomics, because the mutated genes are not tagged and therefore, difficult to identify
We present a microarray-based approach to identify deleted genomic regions in rice mutants selected from a large collection generated by gamma ray or fast neutron treatment.
Our study focuses not only on the utility of this method for forward genetics, but also its potential as a reverse genetics tool through accumulation of hybridization data for a collection of deletion mutants harboring multiple genetic lesions.
We demonstrate that hybridization of labeled genomic DNA directly onto the Affymetrix Rice GeneChip® allows rapid localization of deleted regions in rice mutants.  Deletions ranged in size from one gene model to ~500 kb and were predicted on all 12 rice chromosomes.  The utility of the technique as a tool in forward genetics was demonstrated in combination with an allelic series of mutants to rapidly narrow the genomic region, and eventually identify a candidate gene responsible for a lesion mimic phenotype.
We demonstrate the utility of oligonucleotide arrays to discover deleted genes in rice.  The density and distribution of deletions suggests the feasibility of a database saturated with deletions across the rice genome.  This community resource can continue to grow with further hybridizations, allowing researchers to quickly identify mutants that harbor deletions in candidate genomic regions, for example, regions containing QTL of interest.
MS Accepted at BMC Genomics, MS ID : 2798701382204393

Note: 14 of the 16 mutants deposited are reported in the published manuscript (mutants d1137 & g6989 are not discussed).

overall_design: Genomic DNA from 16 rice deletion mutants (induced by treatment of the indica variety IR64 with DEB-treatment, Fast Neutron or gamma ray (GR) exposure) and wildtypes were hybridized to affymetrix-rice oligonucleotide array

first: Myron

last: Bruce

first: Jan

last: Leach


title: Comparative transcriptional profiling of two contrasting rice genotypes in response to rice stripe virus infection

status: Public on Apr 02 2009

city: Fuzhou

first: Xiaoting

last: Zhang

state: Fujian

address: Jinshan

department: Plant Protection Department

institute: Fujian Agriculture and Forestry University

summary:
During the pathogenesis of virus disease, lots of changes occur in plant hosts including the altered gene expression profiles. Rice stripe virus (RSV) is the type member of Tenuivirus, transmitted by Laodelphax striatellus in a circulative propagative man
To investigate the molecular differences in two japonica rice genotypes WuYun3 and KT95-418 in response to RSV infection, Affymetrix rice genome array were used to analyze and compare their transcriptional profiles.
Keywords: disease state analysis

overall_design: Nine-day old 20 rice seedlings were exposed to approximately 100 viruliferous small brown planthoppers (Laodelphax striatellus Fall) for two days to be innoculated by RSV. Then they were transplanted in insect-free greenhouse at 25±3C with a daily photope

first: Zujian

last: Wu

first: Liyan

first: Qiying

last: Lin

first: Lianhui


title: Prevalence of Copy-number neutral LOH in glioblastomas revealed by analysis of laser-microdissected tissues

status: Public on Mar 01 2009

city: Fukuoka

first: DAISUKE

last: KUGA

state: Fukuoka

address: 3-1-1, Maidashi, Higashi-ku

institute: Kyushu University

summary:
We have employed a laser capture microdissection technique and single nucleotide polymorphism arrays to characterize genomic alterations associated with the development of glioblastomas.  Combined analysis of LOH and copy number revealed that more than half of the identified 254 LOH loci showed no copy number alteration, indicating the presence of copy-number neutral LOH
Keywords: DNA copy number, Loss of heterozygosity

overall_design: Affymetrix 50K SNP mapping arrays were used to profile 14 primary glioblastomas (GBMs) with matched blood DNA samples. Loss of heterozygosity (LOH) and copy number abnormality (CNA) profiles were derived from each tumour-blood pair.

first: Daisuke

last: Kuga

first: Yoji

last: Kukita

first: Kenshi

last: Hayashi


title: SNP array analysis of neuroblastic tumor NB99

status: Public on Oct 16 2008

city: Paris

first: Olivier

last: Delattre

address: 26 rue d'Ulm

department: Genetics

country: France

institute: Institut Curie

summary: The genetic aberrations of NB tumor NB99 were determined using the Affymetrix SNP chip 50K array (Hind III).

overall_design: DNA copy number change of NB tumor NB99


title: Expression data from rice embryo,endosperm,root,leaf and seedling

status: Public on Feb 02 2009

city: Shanghai

first: Hong-Wei

last: Xue

address: 300 Fenglin Road

institute: Institute of Plant Physiology and Ecology,Shanghai Institutes of Biological Sciences

summary:
Expression profiles of protein coding genes were characterized using Affymetrix rice genome array to compare with expression profiles of miRNAs.

Keywords: tissue

overall_design: Five tissues (embryo, endosperm, leaf and root of 7-day-old seedlings, 10-day-old seedling) were analyzed, each has two biological repeats.

first: Liang-Jiao

first: Jing-Jing


title: Rice cultivars undergoing a susceptible and resistant interaction with the parasitic plant Striga hermonthica

status: Public on Sep 22 2008

city: Sheffield

first: Julie

last: Scholes

address: Western Bank

department: Animal and Plant Sciences

country: United Kingdom

institute: University of Sheffield

summary:
Using rice cultivars Nipponbare, which exhibits resistance to Striga hermonthica (a root parasitic plant that causes devastating loss of yield), and IAC165, which is susceptible, we aim to identify suites of genes underlying susceptibility and resistance to S. hermonthica by profiling changes in gene expression using rice whole genome microarrays.  In addition to a functional categorisation of changes in gene expression, genes that were significantly differentially regulated within regions predicted to contain Nipponbare quantitative trait loci for resistance were identified.
Keywords: Infected material vs. comparable control tissue, time course

overall_design: Root tissue was harvested from two cultivars of rice that had been infected with Striga hermonthica (or from uninfected control tissue).  Three timepoints were used (2, 4 and 11 days after infection or mock-inoculation) using two replicate chips per treatment/timepoint.

first: Philip

last: Swarbrick

first: Kan

last: Huang

first: Jon

last: Slate

first: Malcolm

middle: C

last: Press


title: 50K SNP Copy Number Analysis of Ovarian Carcinomas

status: Public on Feb 17 2009

city: East Melbourne

first: Dariush

last: Etemadmoghadam

address: St Andrew's Place

institute: Peter MacCallum Cancer Centre

summary:
Genome-wide copy number variation was measured in primary tumours of the ovary, Fallopian tube and peritoneum. A well-defined subset of advanced-stage serous tumors was then used to relate CNV to primary resistance to treatment.

Analysis is described in: Etemadmoghadam, D., et al. (2009). "Integrated genome-wide DNA copy number and expression analysis identifies distinct mechanisms of primary chemoresistance in ovarian carcinomas." Clin Cancer Res 15(4): 1417-27.

overall_design: 118 needle-dissected or whole tumours (>80% tumour content) were analysed.

first: Anna

last: deFazio

first: Rameen

last: Beroukhim

first: Craig

last: Mermel

first: Joshy

last: George

first: Gad

last: Getz

first: Richard

last: Tothill

first: Aikou

last: Okamoto

first: Maria

middle: B

last: Raeder

first: Study

last: AOCS

first: Paul

last: Harnett

first: Stephen

last: Lade

first: Lars

middle: A

last: Akslen

last: Tinker

first: Bianca

last: Locandro

first: Kathryn

last: Alsop

first: Yoke-Eng

last: Chiew

first: Nadia

last: Traficante

first: Sian

last: Fereday

first: Daryl

last: Johnson

last: Fox

first: William

last: Sellers

first: Mitsuyoshi

last: Urashima

first: Helga

last: Salvesen

first: Matthew

last: Meyerson

first: David

last: Bowtell


title: Molecular and transcriptional characterization of chromosome 17p loss in chronic lymphocytic leukemia, experiment B

status: Public on Nov 11 2008

first: Luca

last: Agnelli

address: Venezian 1

institute: IRCCS Istituto Nazionale dei Tumori

summary:
Distinct genetic abnormalities such as TP53 deletion at 17p13.1, have been identified as having an adverse prognostic relevance in B-cell chronic lymphocytic leukemia (B-CLL). Conventional cytogenetic studies have shown that TP53 deletion in B-CLL is associated predominantly with 17p loss resulting from complex chromosomal rearrangements. We performed genome-wide DNA (SNPs arrays), fluorescence in situ hybridization (FISH) and gene expression profiling (GEP) analyses to investigate the significance of 17p loss in a panel of 71 genetically well-characterized B-CLLs in Binet stage A, 18 of which carried a TP53 monoallelic deletion. Combined SNP arrays and FISH approaches showed 17p loss in all of the TP53-deleted cases, with breakpoints scattered along the 17p11.2 region. Mutations in exons 5 to 9 of TP53 were found in 9/12 deleted samples. GEP of 60 B-CLLs, including 7 patients with 17p loss, identified 40 differentially expressed genes in 17p- versus 17p normal samples, 35 of which were down-regulated in 17p- tumors. The majority (30/35) of these transcripts, including putative tumor suppressor genes, mapped to 17p. Overall, these data indicate that, beside TP53 deletion, the concomitant loss of 17p arm may contribute to the strong negative prognostic impact known to be associated with this lesion in B-CLL.
Keywords: genomic analysis of B-CLL with 17p loss patients

overall_design: This series of microarray experiments contains the genome-wide profiles of purified B-cell chronic lymphocytic leukemia (B-CLL) cells obtained from 12 newly diagnosed patients (Binet stage A). Peripheral blood mononuclear cells from B-CLL patients were isolated by Ficoll-Hypaque density-gradient centrifugation and the proportion of CD5/CD19/CD23 triple positive B cells in the suspension was determined by direct immunofluorescence performed using a FACS-sort flow cytometer with antibodies to: CD19 FITC/PE, CD23 PE and CD5 Cy-Chrome. If B-CLL cells were less than 90%, T cells, NK cells and monocytes were removed by negative selection using CD3, CD56, CD16, and CD14 monoclonal antibody treatment followed by magnetic beads. 250 nanograms of genomic DNA was processed and, in accordance with the manufacturer's protocols, 40 micrograms of fragmented biotin-labelled DNA were hybridized on GeneChip Human Mapping 50K XbaI Arrays (Affymetrix Inc.). The arrays were scanned using the GeneChip Scanner 3000 7G. The images were acquired using Affymetrix GeneChip® Operating Software (GCOS version 1.4). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using GTYPE 4.1 and Affymetrix Copy Number Analysis Tool (CNAT 4.0.1) softwares. Genomic Smoothing analysis was performed by using the smoothing window of 1 Mb, and inferred copy number states were derived from a Hidden Markov Model (HMM) based algorithm implemented in CNAT 4.0.1.

first: Sonia

last: Fabris

first: Laura

last: Mosca

first: Katia

last: Todoerti

first: Giovanna

last: Cutrona

first: Marta

last: Lionetti

first: Daniela

last: Intini

first: Serena

last: Matis

first: Monica

last: Colombo

first: Massimo

last: Gentile

first: Gianluca

last: Festini

first: Vincenzo

last: Callea

last: Spriano

first: Stefano

last: Molica

first: Giorgio

last: Lambertenghi-Deliliers

first: Fortunato

last: Morabito

first: Manlio

last: Ferrarini

first: Antonino

last: Neri


title: Gastric Cancer Cell Lines

status: Public on Dec 29 2008

city: Singapore

first: Wu

last: Yonghui

address: 11 Hospital Drive

country: Singapore

institute: National Cancer Center of Singapore

type: Genome variation profiling by genome tiling array

summary:
Regions of recurrent genomic amplification and deletion are frequently observed in primary gastric cancers (GC). However, identifying specific oncogenes and tumor suppressor genes within these regions can be challenging, as they often cover tens to hundreds of genes. Here, we combined high-resolution array-based comparative genomic hybridization (aCGH) with gene expression profiling to target genes lying within focal high-level amplifications in GC cell lines, and identified RAB23 as an amplified and overexpressed Chr 6p11p12 gene in Hs746T cells. High RAB23 protein expression was also observed in some lines lacking RAB23 amplification, suggesting additional mechanisms besides gene amplification for up-regulating RAB23. siRNA silencing of RAB23 reduced the invasive potential of both amplified and nonamplified GC cell lines. RAB23 gene amplifications were observed in 13% of primary gastric carcinomas. In two independent patient cohorts, RAB23 transcript and protein expression was significantly associated with diffuse-type gastric cancer (dGC) compared to intestinal-type gastric cancer (iGC), providing further evidence that dGC and iGC likely represent two molecularly distinct tumor types. Our study demonstrates that investigating focal chromosomal amplifications by combining highresolution aCGH with expression profiling is a powerful general strategy for identifying novel cancer genes in recurrent regions of chromosomal aberration.
Keywords: gastric cancer cell lines, comparative genomic hybridization, gene expression profiling

overall_design: Affy 100K SNP profiling and 32K BAC Array profiling for 7 Gastric Cancer Cell Lines

first: Yonghui

last: Wu

first: Patrick

last: Tan


title: Comparison of primary neuroblastoma tumors and derivative early-passage cell lines using genome-wide SNP array analysis

status: Public on Jan 31 2009

city: Chicago

first: Samuel

last: Volchenboum

state: IL

address: 5640 S. Ellis RI405

institute: University of Chicago

summary:
Stromal contamination is one of the major confounding factors in the analysis of primary solid tumor samples by single nucleotide polymorphism (SNP) arrays. As we propose to employ genome-wide SNP microarray analysis as a diagnostic platform for neuroblastoma, the sensitivity, specificity, and accuracy of these studies must be optimized.
In order to investigate the effects of stroma, we derived early passage cell lines from nine primary tumors and compared their genomic signature with that of the primary tumors by 100K SNP array analysis. The average concordance between tumor and cell line for raw LOH (loss of heterozygosity) calls was 96% (range 91%-99%) and for raw copy number alterations (CNA), 71% (range 43%-87%). In general, there were a larger number of LOH events identified in the cell lines compared to the matched tumor samples (mean increase 3.2% ± 1.9%).
We have developed an algorithm that shows that the presence of stroma contributes to under-reporting of LOH and copy number loss (CNL). Notable findings in this sample set were uniparental disomy (UPD) of chromosome arms 11p, 1q, 14q, and 15q and a novel area of amplification on chromosome band 11p15. Our analysis demonstrates that LOH was identified significantly more often in derived cell lines compared to the original tumor samples. While these may in part be due to clonal selection during adaptation to tissue culture, our study indicates contamination by normal stromal elements may be a major contributing factor in underestimation of LOH and CNL events.

Keywords: genome wide SNP analysis

overall_design: Nine human neuroblastoma tumor samples with paired blood samples and derivative cell lines

first: Rani

middle: E

last: George


title: antiOsLIC collar chip

status: Public on Dec 22 2008

city: Beijing

first: Lei

last: Wang

state: Beijing

address: Nanxincun 20, Development center 214,Haidian district

institute: Institute of Botany, CAS

summary: 30 collars were taken from wild type plants or antiOsLIC transgenic plants respectively. One collar from one plant only. The leaves are just sprout 2-3 cm (about 1-2 days) from the stem. For measuring the genes expression level, Wild type plants were taken as control. The developing collar from both line2 of OsLIC antisense transgenic plants and wild type were harvested at the heading stage. The position of the collar was about 1cm above the last developed collar. Total RNA was extracted from the collars using TRIzol regeant (Invitrogen, P/N 15596-018, USA) and purified by using Qiagen RNeasy columns (QIAGEN, Cat. NO. 74104). All the processes for cDNA and cRNA synthesis, cRNA fragmentation, hybridization, washing and staining, and scanning, were conducted according to the GeneChip Standard Protocol (Eukaryotic Target Preparation, Affymetrix). Poly-A RNA Control Kit and the One-Cycle cDNA Synthesis kit were used in this experiment as described in the website: http://www.affymetrix.com/products/arrays/specific/rice.affx.

overall_design: To identify genes differentially expressed between the OsLIC antisense transgenic lines and the wild-type plants.The developing collar from both lines of OsLIC antisense transgenic plants and the wild type was harvested at the heading stage. The chip experiments were performed according to standard protocol from Affymetrix.The overall intensity of all probe sets of each array was scaled to 500 to ensure equal hybridization intensity; each probe set was assigned “P”, “A” or “M” and a p-value from the algorithm in GCOS, a log2 transformed signal ratio of each gene was calculated with use of the GCOS baseline tool, and log2 (ratio) ≥1 (2-fold change) was used as a cut-off.

first: Hong

last: Yan

first: Kang

last: Chong


title: Chromophobe and Oncocytoma Renal Cell Carcinomas: gene expression and SNP analysis

status: Public on Aug 13 2008

city: Grand Rapids

first: Karl

last: Dykema

state: MI

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

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

summary:
Chromosomal abnormalities, such as structural and numerical abnormalities, are a common occurrence in cancer. The close association of homologous chromosomes during interphase, a phenomenon termed somatic chromosome pairing, has been observed in cancerous cells, but the functional consequences of somatic pairing have not been established. Gene expression profiling studies revealed that somatic pairing of chromosome 19 is a recurrent chromosomal abnormality in renal oncocytoma, a neoplasia of the adult kidney. Somatic pairing was associated with significant disruption of gene expression within the paired regions and resulted in the deregulation of the prolyl-hydroxylase EGLN2, a key protein that regulates the oxygen-dependent degradation of hypoxia-inducible factor (HIF). Overexpression of EGLN2 in renal oncocytoma increased ubiquitin-mediated destruction of HIF and concomitantly suppressed the expression of several HIF-target genes, including the pro-death BNIP3L gene. The transcriptional changes that are associated with somatic pairing of chromosome 19 mimic the transcriptional changes that occur following DNA amplification. Therefore, in addition to numerical and structural chromosomal abnormalities, alterations in chromosomal spatial dynamics should be considered as genomic events that are associated with tumorigenesis. The identification of EGLN2 as a significantly deregulated gene that maps within the paired chromosome region directly implicates defects in the oxygen-sensing network to the biology of renal oncocytoma.
Keywords: Gene expression profiling, SNP analysis, renal, tumor

overall_design: Oncocytoma and Chromophobe RCC samples - expression profiling and SNP chip analysis


title: SNP data from Neuroblastoma samples

status: Public on Oct 10 2008

city: Tokyo

first: Yuyan

last: Chen

address: Hongo7-3-1, Bunkyo-ku

department: Pediatrics

institute: University of Tokyo

summary: Neuroblastoma in advanced stages is among the most intractable pediatric cancers, even with the recent therapeutic advances. Neruroblastoma harbours a variety of genetic changes, including a high frequency of MYCN amplification, loss of heterozygosity in 1p36 and 11q, and gain of genetic material from 17q, all of which have been implicated in the pathogenesis of neuroblastoma. However, the scarcity of reliable molecular targets has hampered the development of effective therapeutic agents targeting neuroblastoma. We performed a genome-wide analysis of a large number of neuroblastoma samples, consisting of varying disease stages, permitted us to obtain a comprehensive registry of genomic lesions in neuroblastoma.

overall_design: To identify oncogenic lesions in neuroblastoma, we performed a genome-wide analysis of primary tumor samples from 215 neuroblastoma patients using high-density SNP arrays (Affymetrix GeneChip 250K NspI). Twenty-two neuroblastoma-derived cell lines were also analyzed by SNP array analysis using Affymetrix GeneChip 250K NspI as well as Affymetrix GeneChip 50K HindIII or Affymetrix GeneChip 50K XbaI.

first: Junko

last: Takita

first: Young

last: Choi

first: Motohiro

last: Kato

first: Miki

last: Ohira

first: Masashi

last: Sanada

first: Lili

first: Manabu

last: Soda

first: Akira

last: Kikuchi

first: Takashi

last: Igarashi

last: Nakagawara

first: Yasuhide

last: Hayashi

first: Hiroyuki

last: Mano

first: Seishi

last: Ogawa


title: Genomic profiling of TP53 and non-TP53 Li-Fraumeni syndrome tumors reveals hits in the p53 and overlapping pathways

status: Public on Jul 16 2008

city: Houston

first: Ralf

last: Krahe

state: TX

address: 1515 Holcombe Blvd., Unit #1010

department: Cancer Genetics

institute: University of Texas M.D. Anderson Cancer Center

summary:
Li-Fraumeni syndrome (LFS) is a rare, clinically and genetically heterogeneous inherited cancer syndrome.  Most cases are due to mutations in TP53.  CHK2 is a minor predisposing locus; we recently mapped a third locus to 1q23.  In both TP53 and non-TP53 LFS, there is evidence for risk heterogeneity within and between kindreds, suggesting additional risk modifiers.  Using BAC- and SNP-based microarrays, we performed genomic profiling of primary soft tissue sarcomas, osteosarcomas and matching constitutive samples of 10 LFS patients (6 with and 4 without TP53 mutations), to identify genome-wide patterns of copy number changes and loss-of-heterozygosity (LOH).  Our complementing global approaches revealed several interesting patterns for TP53 and non-TP53 LFS tumors, including positive (1q/7, 3p/15, 4q/9q, 8q/19p, 9p/10q, 13/14 and 15q/18q) and negative (2q/9q, 3q/14q and 4q/6q) associations between chromosomal regions.  The region containing the oncogene TWIST1 (7p21.1) was the most common gain independent of TP53 status and tumor type, while LOH of 8q11.2 with the tumor suppressor ST18 was the only region exclusively associated with non-TP53 soft tissue sarcomas.  We resequenced known mutations in BRAF, KRAS and NRAS and identified somatic NRAS mutations in 2 of 10 tumors.  TP53 and non-TP53 LFS tumors shared multiple hits in genes of the p53 and overlapping pathways.  Although common dogma in cancer genetics holds that multiple hits in the same pathway are redundant and thus unlikely, we show that different combinations of genetic alterations in both TP53 and non-TP53 LFS tumors appear to act together in the p53 network in LFS tumorigenesis
Keywords: Comparative genomic hybridization

overall_design: Using the Spectral Genomics dye-swap BAC arrays we studied 10 Li Fraumeni syndrome tumor cases

first: M

last: Tuna

first: F

last: Wright

first: L

last: Bachinski

first: B

last: Zhang

first: K

last: Baggerly

first: R

last: Luthra

first: G

last: Lozano

last: Strong


title: Whole-Genome Profiling in Liposarcomas Reveals Genetic Alterations Common to Specific Telomere Maintenance Mechanisms

status: Public on May 01 2008

city: Savannah

first: Jay

last: Johnson

state: GA

address: 4700 Waters Ave

institute: Memorial Health University Medical Center

summary:
 Telomere attrition ultimately leads to the activation of protective cellular responses such as apoptosis or senescence.  Impairment of such mechanisms can allow continued proliferation despite the presence of dysfunctional telomeres.  Under such conditions, high levels of genome instability are often engendered.  Data from both mouse and human model systems indicate that a period of genome instability might facilitate tumorigenesis.  Here, we employ a liposarcoma model system to assay telomere maintenance mechanism-specific genetic alterations.  A multiassay approach was used to assess the telomere maintenance mechanism(s) active in tumors.  Genomic DNA from these samples was then analyzed by high resolution DNA mapping array in order to identify genetic alterations.  Our data reveal a higher level of genome instability in ALT-positive tumors as compared with telomerase-positive tumors, whereas tumors lacking both mechanisms have relatively low levels of genome instability.  The bulk of the genetic changes are amplifications, regardless of the mode of telomere maintenance employed.  We also identified genetic changes specific to the ALT mechanism, e.g., deletion of chromosome 1q32.2-q44, as well as changes that are underrepresented amongst ALT-positive tumors, such as amplification of chromosome 12q14.3-q21.2.  Taken together, these studies provide insight into the molecular pathways involved in the regulation of ALT and reveal several loci that might be exploited either as prognostic markers or targets of chemotherapeutic intervention.
Keywords: genotype, genome instability, copy number alteration, liposarcoma, ALT, telomerase, telomere

overall_design:
Goal: To study telomere maintenance and genetic alterations in liposarcoma using Affymetrix Mapping 50K Xba 240 GeneChip.

Brief description:  Telomere attrition ultimately leads to the activation of protective cellular responses such as apoptosis or senescence.  Impairment of such mechanisms, however, can allow continued proliferation despite the presence of dysfunctional telomeres.  Under such conditions, high levels of genome instability are often engendered.  Data from both mouse and human model systems indicate that a period of genome instability might facilitate tumorigenesis.  The high-density SNP-based microarrays (e.g., Affymetrix 100K arrays) can detect deletions, amplifications, and loss-of-heterozygosity on a genome in the liposarcoma samples.  Chromosomal alterations of liposarcoma should provide insight into the molecular pathways involved in the regulation of ALT and reveal several loci that might be exploited either as prognostic markers or targets of chemotherapeutic intervention.

Quality control steps taken:
a.	PCR-based quality assessment of liposarcoma tissue genomic DNA
b.	Nanodrop analysis of preprocessed DNA prior to array hybridization
c.	Analysis of array call rates following hybridization (array experiments giving call rates of less than 80% were routinely repeated)

Data extraction and processing protocols
a.	Image scanning hardware and software, and processing procedures and parameters:  SNP array hybridization was detected using a GCS3000 scanner (Affymetrix).  SNP calls and signal quantification were obtained with Gene Chip Operating System (GCOS) 1.2 and Affymetrix GDAS 3.0 with Dynamic Model Mapping Analysis by default settings (0.25) for both homozygote and heterozygote call thresholds. Copy number analyses were carried out using Affymetrix Chromosome Copy Number Analysis Tool (CNAT) 2.1 with a default genomic smoothing window setting of 0.5 Mb.
b.	Normalization, transformation and data selection procedures and parameters.  Array data was normalized by a reference data set with CNAT.
c.	Definition of chromosomal aberration, amplification, deletion and LOH used for data interpretation: These definitions and their algorithms were described in detail by Huang, et al: Whole genome DNA copy number changes identified by high density oligonucleotide arrays. Hum Genomics. 2004 May;1(4):287-99.


title: Variations in stress sensitivity and genomic expression in diverse S. cerevisiae strains (CGH)

status: Public on Sep 05 2008

city: Madison

first: Audrey

middle: P.

last: Gasch

state: WI

address: 425-g Henry Mall

department: Laboratory of Genetics

institute: University of Wisconsin Madison

summary:
Gene expression variation was measured in 17 non-laboratory strains compared to the sequenced S288c lab strain
Keywords: comparative genomic hybridizations (CGH) comparing different yeast strains

overall_design: Each strain was grown in at least biological triplicate to log phase in rich (YPD) medium.  Extracted total RNA was compared to that collected from the diploid S288C strain, DBY8268 (ura3-52/ura3-delta, ho/ho, GAL2/GAL2)

first: Daniel

middle: J

last: Kvitek

first: Jessica

last: Will

middle: P


title: SNP-based mapping and gene expression profiling identifies novel chromosomal imbalances and candidate genes in T-PLL

status: Public on Feb 07 2008

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

institute: Institut fuer Zellbiologie

summary:
T-cell prolymphocytic leukemia (T-PLL) is a rare aggressive lymphoma derived from mature T cells, which is, in most cases, characterized by the presence of an inv(14)(q11q32)/t(14;14)(q11;q32) and a characteristic pattern of secondary chromosomal aberrations. DNA microarray technology was employed to compare the transcriptomes of eight immunomagnetically purified CD3+ normal donor-derived peripheral blood cell samples, with five highly purified inv(14)/t(14;14)-positive T-PLL blood samples. Between the two experimental groups, 734 genes were identified as differentially expressed, including functionally important genes involved in lymphomagenesis, cell cycle regulation, apoptosis and DNA repair. Notably, the differentially expressed genes were found to be significantly enriched in genomic regions affected by recurrent chromosomal imbalances. Upregulated genes clustered on chromosome arms 6p and 8q, and downregulated genes on 6q, 8p, 10p, 11q and 18p. High-resolution copy-number determination using single nucleotide polymorphism chip technology in 11 inv(14)/t(14;14)-positive T-PLL and 1 without the inv(14) including those analyzed for gene expression, refined chromosomal breakpoints as well as regions of imbalances. In conclusion, combined transcriptional and molecular cytogenetic profiling identified novel specific chromosomal loci and genes that are likely to be involved in disease progression and suggests a gene dosage effect as a pathogenic mechanism in T-PLL.
Each Sample has its raw data file linked as a supplementary file.
Keywords: disease state analysis

overall_design: 12 T-cell prolymphocytic leukaemia samples were hybridized to 50K_Xba SNP arrays.

first: Jan

last: Dürig

first: Reiner

last: Siebert


title: Genome-wide DNA copy number predictors of lapatinib sensitivity in tumour-derived cell lines

status: Public on Mar 11 2008

city: King of Prussia

first: Joel

last: Greshock

state: PA

address: 2301 Renaissance Blvd.

department: Translational Medicine, Oncology

institute: GlaxoSmithKline

summary:
A common aim of pharmacogenomic studies that employ genome-wide assays on panels of cancers is the unbiased discovery of genomic alterations that are associated with clinical outcome and drug response.  Previous investigations of lapatinib, a selective dual-kinase inhibitor of EGFR and HER2 tyrosine kinases, have demonstrated predictable relationships between the activity of these genes and response.  Under the hypothesis that additional genes may play a role in promoting sensitivity, a predictive model for lapatinib sensitivity was constructed from genome-wide DNA copy number data from 24 cancer cell lines. An optimal predictive model, which consists of aberrations at nine distinct genetic loci, includes gains of HER2, EGFR, and loss of CDKN2A. This model, which achieved area under the Receiver Operating Characteristic (ROC) curve of ~0.85 (80% confidence interval: 0.70–0.98;  P<0.01), and correctly classified the sensitivity status of 8/10 head and neck cancer cell lines.  This study demonstrates that previously described biomarkers of lapatinib sensitivity, including copy number gains of EGFR and HER2, can be discovered as powerful predictors of response using novel genomic assays in an unbiased manner. Further, these results demonstrate the utility of DNA copy number profiles in pharmacogenomic studies.
Keywords: Comparative Genomic Hybridization

overall_design:
Basal DNA copy number profiles were derived from Affymetrix 'SNP chips' for a panel of 34 tumor derived cell lines. Each of these cell lines were tested for their degree of sensitivity to lapatinib. Specific DNA alterations associating with lapatinib sensitivity were identified using a training set consisting of 24 of these lines.  A predictive model was constructed from these loci. The remaining 10 lines were used to test the model performance.

A panel of chips (n = 12) assayed with germline DNA served as a reference in order to calculate the test/reference ratios reported in the Sample table VALUE columns. The 'reference' Samples for the 500K and 100K assays are as follows:

500K: GSM188024, GSM188025, GSM188026, GSM188027, GSM188028, GSM188029,     GSM188030, GSM188031, GSM188032, GSM188033, GSM188034, GSM188035, GSM188048, GSM188049, GSM188050, GSM188051, GSM188052, GSM188053,     GSM188054, GSM188055, GSM188056, GSM188057, GSM188058, GSM188059

100K: GSM187950, GSM187951, GSM187952, GSM187953, GSM187954, GSM187955, GSM187956, GSM187957, GSM187958, GSM187959, GSM187960, GSM187961, GSM187949, GSM187948, GSM187946, GSM187947, GSM187945, GSM187944,     GSM187943, GSM187942, GSM187941, GSM187940, GSM187939, GSM187938

first: Barbara

last: Weber

first: Tal

middle: Z

last: Zaks


title: Chromosome copy number and LOH analysis of colorectal carcinoma specimens

status: Public on Aug 21 2008

city: Shimotsukeshi

first: Hiroyuki

last: Mano

state: Tochigi

address: 3311-1 Yakushiji

department: Division of Functional Genomics

institute: Jichi Medical University

summary:
Structural changes of chromosomes play important roles in the carcinogenesis of colorectal carcinoma (CRC). Here, by using SNP-typing arrays, we have tried to screen for recurrent chromosome copy number changes and loss-of-heterozygosity in the genome of colorectal carcinoma.
Genomic DNA was isolated from tumor and paired normal tissues of CRC (n=94), and was hybridized to Affymetrix Mapping 50K Xba 240 arrays. Chromosome copy number and LOH likelihood score was inferred at every SNP locus with CNAG2.0 software (http://www.genome.umin.jp).
Keywords: Comparative genomic hybridization

overall_design: Tumor samples and paired normal tissues (n=94 for each) were hybridized to the microarrays. Signal intensity data as well as genotype data were compared between a pair of tumor and normal samples with CNAG2.0. The resultant copy number and LOH likelihood score for each sample are thus calculated from two datasets (tumor and normal).


title: Epigenetic-Mediated Dysfunction of the BMP Pathway Inhibits Differentiation of Human Glioblastoma Initiating Cells

status: Public on Jan 07 2008

city: Bethesda

first: Howard

last: Fine

state: MD

address: 9030 Old Georgetown Rd

department: Neurological Disorders and Stroke

institute: National Cancer Institute

summary:
Despite similarities between tumor initiating cells with stem-like properties (TICs) and normal neural stem cells, we hypothesized that there may be differences in their differentiation potentials. We now demonstrate that both bone morphogenetic protein (BMP)-mediated and ciliary neurotrophic factor (CNTF)-mediated Jak/STAT-dependent astroglial differentiation is impaired due to EZH2-dependent epigenetic silencing of BMP receptor 1B (BMPR1B) in a subset of glioblastoma TICs. Forced expression of BMPR1B either by transgene expression or demethylation of the promoter restores their differentiation capabilities and induces loss of their tumorigenicity. We propose that deregulation of the BMP developmental pathway in a subset of glioblastoma TICs contributes to their tumorigenicity both by desensitizing TICs to normal differentiation cues, and by converting otherwise cytostatic signals to pro-proliferative signals.
Keywords: Genomic alterations

overall_design: DNA extracted from four glioma cell lines were hybridized to 50K mapping arrays (Xba only) to detect and summarize chromosomal aberrations in those samples.

first: Jeongwu

last: Lee

first: Myung

last: Son

first: Kevin

last: Woolard

first: Nicholas

middle: M

last: Donin

first: Aiguo

last: Li

first: Chui

middle: H

last: Cheng

first: Svetlana

last: Kotliarova

first: Yuri

last: Kotliarov

first: Jennifer

last: Walling

first: Susie

last: Ahn

first: Misuk

last: Kim

first: Mariam

last: Totonchy

first: Thomas

last: Cusack

first: Chibawanye

last: Ene

first: Hilary

last: Ma

first: Qin

last: Su

first: Jean-Claude

last: Zenklusen

first: Wei

first: Dragan

last: Maric


title: Identification of candidate neuroblastoma genes by combining genomic and expression microarrays: SNP data

status: Public on Oct 09 2008

city: Newcastle upon Tyne

first: Michael

middle: Stewart

last: Jackson

address: Central Parkway

department: Institute of Genetic Medicine

institute: Newcastle University

summary:
Gene expression analysis was performed on 30 Neuroblastomas to identify genes whose transcription is significantly altered by recurrent chromosomal alterations. Genomic copy number losses and gains had been delineated in the tumours using FISH and SNP arrays. We have identified genes significantly altered by 7 recurrent alterations: 1p, 3p, 4p, 10q and 11q loss, 2p and 17q gain, and genes co-amplified and over-expressed as a result of MYCN amplification. Subsequently, correlation of microarray data with survival and expression within rodent neuroblastomas were used to identify genes likely to be involved in the disease progression, and identified a significant excess of differentially expressed genes which correlated with survival within the minimally altered regions on 17q and 4p
Identifying genes whose expression is consistently altered by chromosomal gains or losses is an important step in defining genes of biological relevance in a wide variety of tumour types. However, additional criteria are needed to discriminate further among the large number of candidate genes identified. This is particularly true for neuroblastoma, where multiple genomic copy number changes of proven prognostic value exist. We have used Affymetrix microarrays and a combination of fluorescent in-situ hybridisation and single nucleotide polymorphism (SNP) microarrays to establish expression profiles and delineate copy number alterations in 30 primary neuroblastomas. Correlation of microarray data with patient survival and analysis of expression within rodent neuroblastoma cell lines were then used to further define genes likely to be involved in the disease process. Using this approach we identify >1000 genes within 8 recurrent genomic alterations (loss of 1p, 3p, 4p, 10q and 11q, 2p gain, 17q gain, and the MYCN amplicon) whose expression is consistently altered by copy number change. Of these, 84 correlate with patient survival, with the minimal regions of 17q gain and 4p loss being significantly enriched for such genes. Orthologues of all but one of these genes on 17q are overexpressed in rodent neuroblastoma cell lines. A significant excess of SNPs whose copy number correlates with survival is also observed on proximal 4p in stage 4 tumours, and we find that deletion of 4p is associated with improved outcome in an extended cohort of tumours. These results define the major impact of genomic copy number alterations upon transcription within neuroblastoma, and highlight genes on distal 17q and proximal 4p for downstream analyses. They also suggest that integration of discriminators such as survival and comparative gene expression with microarray data may be useful in the identification of critical genes within regions of loss or gain in many human cancers.

Keywords: Disease State Analysis

overall_design: Chromosomal gains and losses were delineated in Stage 4 neuroblastomas to facilitate, in combination with expression array data, the identification of genes within regions of gain and loss whose expression is significantly altered by copy number change.

middle: S

first: Maria

last: Lastowska


title: Molecular characterization and genetic analysis reveal SA0420 as an early senescing rice mutant with pleotropic

status: Public on Mar 21 2008

city: Taichung

first: Angeline

address: Kuo Kuang road

country: Taiwan

institute: NCHU

summary:
  SA0420 is a stable rice (Oryza sativa L.) mutant exhibits multiple traits including a leaf-tip yellowing (YLT), a taro fragrance (or aroma, A), a reduced panicle number (PN), spikelet number (SN), plant height (PH), days to heading (DH), filled grain weight (FGW), and fertility rate (FR), different from those of a local cultivar TNG67. Correlation analysis on F2 progenies of SA0420 and TNG67 revealed that except for aroma which is inheritated independently, phenotypes including YLT, PN, SN, PH, and FGW are tightly associated with each others, indicating a control simultaneously by pleotropic gene. Among those phenotypes, YLT appears the earliest at vegetative stage, therefore may act as a predisposing factor that give rise to other phenotypes. Genetic analysis suggested that YLT is controlled by a single recessive gene. By analyzing the recombinant inbreed lines (RILs) that produce YLT and normal green (G) progenies in a 1:3 ratio, the phenotypes associated with YLT were further confirmed. To investigate the molecular events of leaf-tip yellowing, microarray analyses were performed to compare the gene expression profiles between YLT and G plants of RILs. Clustering of genes according to their involved metabolic pathways revealed that various photosynthesis and carbon fixation gene expressions are lower (~55~75%) in YLT than in G plants, consistent with the observation that photosynthesis rate of SA0420 was only 60% to that of TNG67. Moreover, higher expressions of oxidative phosphorylation-related genes indicated that not only the reduced synthesis rate but also the elevated energy consumptions may synergistically decrease the growth vigor of SA0420. Dissection of the mature leaf revealed that chlorophyll is drastically reduced in the leaf-tip of SA0420 while carotenoids remain stable. This explains the appearance of leaf-tip yellowing and recall an analogy of early senescence. Indeed, many senescence-associated genes (SAG) were found to be up-regulated in SA0420.
Keywords: rice (Oryza sativa), yellow and green leaves, molecular functions, signal-microarray, vegetative stage

first: Hsing-Min

first: Wei-Ming

last: Leu

first: Ching-Chi

last: Tsai

first: Wan-Ju

first: Yu-Ying

last: Tseng

first: Tung-Hai

first: Chiang-Sheng

last: Wang


title: Identification of rice genes differentially expressed upon virulent infection by Magnaporthe grisea

status: Public on Jan 01 2008

city: Beaucouze

first: sandrine

last: balzergue

address: Rue G. Morel

institute: INRA

summary:
Two-week old rice plants (cultivar Nipponbare) were treated with either Magnaporthe grisea (virulent isolate FR13) spore suspension in gelatine or gelatine alone. Two time points were taken (3 and 4 days post inoculation- dpi). Disease symptoms were not visible at 3 dpi whereas they were at 4 dpi. Two biological repeats were done.
Keywords: normal vs disease comparison,time course,treated vs untreated comparison

overall_design: 8 arrays - rice

first: Sandrine

last: Balzergue

first: Jean-benoit

last: Morel

first: Marie-Laure

middle: L

last: Martin-Magniette


title: Assessing the significance of chromosomal aberrations in cancer: Methodology and application to glioma

status: Public on Dec 11 2007

city: Boston

first: Rameen

last: Beroukhim

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute

summary:
Comprehensive knowledge of the genomic alterations that underlie cancer is a critical foundation for diagnostics, prognostics and targeted therapeutics.  Systematic efforts to analyze cancer genomes are underway, but the analysis is hampered by the lack of a statistical framework to distinguish meaningful events from random background aberrations. Here, we describe a systematic method called Genomic Identification of Significant Targets in Cancer (GISTIC) designed for analyzing chromosomal aberrations in cancer. We use it to study chromosomal aberrations in 141 gliomas and compare the results with two prior studies.
Traditional methods highlight hundreds of altered regions with little concordance between studies. The new approach reveals a highly concordant picture involving ~35 significant events, including 16-18 broad events near chromosome-arm size and 16-21 focal events. About half of these events correspond to known cancer-related genes, only some of which have been previously tied to glioma. We also show that superimposed broad and focal events may have different biological consequences. Specifically, gliomas with broad amplification of chromosome 7 have different properties than those with overlapping focal EGFR amplification: the broad events act in part through effects on MET and its ligand HGF and correlate with MET dependence in vitro. Our results support the feasibility and utility of systematic characterization of the cancer genome.
Keywords: SNP analysis, gliomas, chromosomal aberrations

overall_design: 141 gliomas and 33 normal tissue samples were subject to 100K SNP analysis.

first: Gad

last: Getz


title: Identification of human minor H antigens based on genotyping of pooled DNA

first: Yasuhito

last: Nannya

address: BUnkyo-ku Hongo 7-3-1

department: Department of Hematology/Oncology

institute: Tokyo University

summary:
Minor histocompatibility (H) antigens are the molecular targets of allo-immunity responsible both for the development of anti-tumor effects and for graft-versus-host disease (GVHD) in allogeneic hematopoietic stem cell transplantation (allo-HSCT).  However, despite their potential clinical use, our knowledge of human minor H antigens is largely limited by the lack of efficient methods of their characterization.  Here we report a robust and efficient method of minor H gene discovery that combines whole genome association scans (WGAS) with cytotoxic T-lymphocyte (CTL) assays, in which the genetic loci of minor H genes recognized by the CTL clones are precisely identified using pooled-DNA analysis of immortalized lymphoblastoid cell lines with/without susceptibility to those CTLs.  Using this method, we have successfully mapped two loci: one previously characterized (HMSD encoding ACC-6), and one novel.  The novel minor H antigen encoded by the BCL2A1 was identified within a 26 kb linkage disequilibrium block on chromosome 15q25, which had been directly mapped by WGAS.  The pool size required to identify these regions was no more than 100 individuals.  Thus, once CTL clones are generated, this method should substantially facilitate discovery of minor H antigens applicable to targeted allo-immune therapies and also contribute to our understanding of human allo-immunity.
Keywords: pooled DNA, minor histocompatibility antigen, genotype array

overall_design: For CTL-2A12, we collected 44 cytotoxicity-positive (CTX+) and 44 cytotoxicity-negative (CTX-) B-LCLs. For  CTL-1B9, 57 CTX+ and 38 CTX- B-LCLs were collected. Pools of DNA were generated and subjected to analysis on Affymetrix® GeneChip® 100K and 500K microarrays in duplicates.Genetic mapping of the minor H locus was performed by identifying marker SNPs that showed statistically significant deviations in allele-frequencies between CTX+ and CTX- pools based on the observed allele-specific signals in the microarray experiments.

first: Takakazu

last: Kawase

first: Hiroki

last: Torikai

first: Go

last: Yamamoto

first: Makoto

last: Onizuka

first: Satoko

last: Morishima

first: Kunio

last: Tsujimura

first: Koichi

last: Miyamura

first: Yoshihisa

last: Kodera

first: Yasuo

first: Toshitada

last: Takahashi

first: Kiyotaka

last: Kuzushima

first: Seishi

last: Ogawa

first: Yoshiki

last: Akatsuka


title: Genome-wide gene expression profiling of rice stigma

status: Public on Jun 30 2007

first: Wenying

last: Xu

address: Datun Road, Chaoyang District

institute: Institute of Genetics and Developmental Biology of the Chinese Academy of Sciences

summary:
In angiosperms, stigma provides initial nutrients and guidance cues for pollen grain germination and tube growth. However, little is known about genes that regulate these processes in rice. Here we generate rice stigma-specific gene expression profiles through comparing genome-wide expression patterns of hand dissected unpollinated stigma at anthesis with seven tissues including seedling shoot, seedling root, mature anther, ovary at anthesis, seeds of five days after pollination, 10-day-old embryo, 10-day-old endosperm as well as suspension cultured cells by using 57K Affymetrix rice whole genome array. In total, we identified 665 probe sets (550 genes) to be expressed specifically or predominantly in the stigma papillar cells of rice. Real-Time quantitative RT-PCR analysis of 34 selected genes confirmed their stigma-specific expression. The expression of five selected genes was further validated by RNA in situ hybridization. Gene annotation shows that several auxin-signaling components, transporters and stress-related genes are significantly overrepresented in the rice stigma gene set. We also found that genes involved in cell wall metabolism and cellular communication appear to be conserved in the stigma between rice and Arabidopsis. Our results indicate that the stigmas appear to have conserved and novel molecular functions between rice and Arabidopsis.
Keywords: rice (Oryza sativa L.), pollination and fertilization, stigma, molecular functions, signaling£¬microarray, stress response

overall_design: We generate rice stigma-specific gene expression profiles through comparing genome-wide expression patterns of hand dissected unpollinated stigma at anthesis with seven tissues including seedling shoot, seedling root, mature anther, ovary at anthesis, seeds of five days after pollination, 10-day-old embryo, 10-day-old endosperm as well as suspension cultured cells by using 57K Affymetrix rice whole genome array.

first: Meina

last: Li

first: Wenqiang

last: Yang

first: Zhaosheng

last: Kong

first: Yongbiao

last: Xue


title: Pancreatic cancer_Affymetrix 100K SNP arrays

status: Public on Oct 22 2007

city: London

first: Tomohiko

last: Harada

address: Charterhouse Square

department: Centre for Molecular Oncology

institute: Cancer Research UK

summary:
To identify genomic abnormalities characteristic of pancreatic ductal adenocarcinoma (PDAC) in vivo, a panel of 27 microdissected PDAC specimens were analyzed using high-density microarrays representing ~116 000 single nucleotide polymorphism (SNP) loci. We detected frequent gains of 1q, 2, 3, 5, 7p, 8q, 11, 14q and 17q (>78% of cases), and losses of 1p, 3p, 6, 9p, 13q, 14q, 17p and 18q (>44%). Although the results were comparable with those from array CGH, regions of those genetic changes were defined more accurately by SNP arrays. Integrating the Ensembl public data, we have generated "gene" copy number indices that facilitate the search for novel candidates involved in pancreatic carcinogenesis. Copy numbers in a subset of the genes were validated using quantitative real-time PCR. The SKAP2/SCAP2 gene (7p15.2), which belongs to the src family kinases, was most frequently (63%) amplified in our sample set and its recurrent over-expression (67%) was confirmed by reverse transcription-PCR. Furthermore, fluorescence in situ hybridization and in situ RNA hybridization analyses for this gene have demonstrated a significant correlation between DNA copy number and mRNA expression level in an independent sample set (p<0.001). These findings indicate that the dysregulation of SKAP2/SCAP2, which is mostly caused by its increased gene copy number, is likely to be associated with the development of PDAC.
Keywords: pancreatic cancer; tissue microdissection; SNP array; DNA copy number; LOH

overall_design:
A total of 27 fresh-frozen PDAC tissue specimens were obtained surgically or at autopsy from Yamaguchi University School of Medicine, Japan. All the tissues were confirmed histologically by a pathologist. Tissue microdissection was manually performed to collect more than 90% of tumor cells in all cases and DNA was extracted using a DNA extraction kit (SepaGene). Reference DNA was obtained from lymphocytes of total 13 healthy volunteers (six males and seven females). To assess DNA copy number alterations and LOH, we used the Copy Number Analyzer for Affymetrix GeneChip® (CNAG, Ver2.0) software (Nannya et al. Cancer Res. 2005 Jul 15;65(14):6071-9).

The following Samples were added to the Series after this study was published: PC5_Hind (GSM278031), PC5_Xba (GSM278032), PC11-Hind (GSM278043), and PC19_Hind (GSM278057). A supplementary file describing the clinical data of 28 microdissected PDAC samples is linked at the bottom of the Series.

first: Claude

last: Chelala

first: Vipul

last: Bhakta

first: Tracy

last: Chaplin

first: Krishna

last: Caulee

first: Patrick

last: Baril

first: Bryan

middle: D

last: Young

first: Nicholas

middle: R

last: Lemoine


title: Mycroarray analyses reveal that plant mutagenesis may induce more transcriptomic changes than transgene insertion

status: Public on Jul 31 2008

city: Lisbon

first: Rita

middle: Maria

last: Batista

address: Av Padre Cruz

department: Food safety and nutrition

country: Portugal

institute: Instituto Nacional de Saude Dr. Ricardo Jorge

summary:
Controversy regarding genetically modified (GM) plants and their potential impact on human health contrasts with the tacit acceptance
of other plants that were also modified, but not considered as GM products (e.g., varieties raised through conventional breeding such as mutagenesis). What is beyond the phenotype of these improved plants? Should mutagenized plants be treated differently from transgenics? We have evaluated the extent of transcriptome modification occurring during rice improvement through transgenesis versus mutation breeding. We used oligonucleotide microarrays to analyze gene expression in four different pools of four types of rice plants and respective controls: (i) a
gamma-irradiated stable mutant, (ii) the M1 generation of a 100-Gy gamma-irradiated plant, (iii) a stable transgenic plant obtained for production of an anticancer antibody, and (iv) the T1 generation of a transgenic plant produced aiming for abiotic stress improvement, and all of the unmodified original genotypes as controls. We found that the improvement of a plant variety through the acquisition of a new desired trait, using either mutagenesis or transgenesis, may cause stress and thus lead to an altered expression of untargeted genes. In all of the cases studied, the observed alteration was more extensive in mutagenized than in transgenic plants. We propose that the safety assessment of improved plant varieties should be carried out on a case-by-case basis and not simply restricted to foods obtained through genetic engineering.

overall_design:
Plant Materials
Two genetically stable Oryza sativa L. ssp. japonica lines: a gamma-irradiated ricemutant(cv. EstrelaA)and a well characterized transgenic rice line (cv. Bengal) were used as well as controls. The stable mutant was obtained in 1988 by gamma-irradiation, had already gone over 10 generations of self-pollination, and had a mature average height about 45 cm lower than the wild type. The stable transgenic line, which was already in the third generation of self-pollination after transformation, expresses a ScFV antibody (ScFvT84.66) against carcinoembryonic antigen, a well characterized tumor-associated marker antigen.
We have also used two genetically unstable rice lines: the M1 generation of a 100-Gy gamma-irradiated line (98% survival after mutagenesis) and the T1 generation of an Agrobacterium-transformed transgenic line (both cv. Nipponbare) containing one copy of the BCBF1 gene driven by the AtRD29A promoter from Arabidopsis and one copy of the hpt II gene. We used seeds from the same self-pollinated panicle for control and irradiation/transgenesis. The unstable mutant line chosen for this experiment was the one showing a phenotype more similar to that of the nonirradiated control.
In the case of the transgenic lines, stability was based on the stable
inheritance of the introduced transgenes in the homozygous progeny. Regarding the mutagenized plants we have defined as genetically stable plants those that, after mutagenesis, had already gone through several cycles of self-pollination while maintaining the desirable traits.

RNA Extraction and Microarrays
Two pools of six whole seedlings were prepared for each condition under test, and RNA was isolated with the RNeasy Plant Mini Kit (Qiagen) following the manufacturer’s instructions. Total RNA was kept at -80°C and sent to the Affymetrix core facility (Instituto Gulbenkian de Ciência,
Oeiras, Portugal), where quality-control analysis was carried out before cDNA synthesis from themRNA[with appropriate oligo(dT) primers], labeling (through synthesis of cRNA with incorporation of biotinylated ribonucleotide analogs), and hybridization to the GeneChip Rice Genome Array (Affymetrix). This array contains probes to query 51,279 transcripts representing two rice subspecies (48,564 japonica transcripts and 1,260 transcripts of indica subspecies).
Data Analysis
Microarrays data analysis was performed with Partek Genomics Suite software. Affymetrix CEL files were imported by using the Robust Multichip Average method, which involves four steps: background correction of the perfect match values, quintile normalization across all of the chips in the experiment, Log2 transformation, and median polish summarization. The logged data were used for hierarchical cluster analysis and statistical analysis.
Hierarchical cluster analysis was performed by using Pearson’s dissimilarity product moment correlation coefficient and Ward’s algorithm.
For the identification of differentially expressed genes we used ANOVA
and a false discovery rate with a 0.05 threshold.

first: Nelson

last: Saibo

first: Tiago

last: Lourenço

first: Maria

last: Oliveira


title: Genomic profiling data of 40 childhood leukemia patients

status: Public on May 01 2007

city: Nijmegen

first: Roland

last: Kuiper

address: Geert Grooteplein 10

department: Human Genetics

country: Netherlands

institute: Radboud University Nijmegen Medical Centre

summary:
In this study, we performed an inventory of copy number changes present in childhood acute lymphoblastic leukemias. The cohort contains a total of 40 diagnosis samples, including 7 T-lineage ALLs and 33 precursor B-cell ALLs. High resolution genomic profiling was perfomed using Affymetrix SNP arrays. We detected multiple de novo genetic lesions, including gross aneuploidies and segmental gains and losses, some of which were subtle and affected single genes. Many of these lesions involved recurrent (partially) overlapping deletions and duplications, containing various established leukemia-associated genes, such as ETV6, RUNX1, and MLL. Importantly, the most frequently affected genes were those controlling G1/S cell cycle progression (e.g. CDKN2A, CDKN1B, and RB1), followed by genes associated with B-cell development. The latter group includes microdeletions of the B-lineage transcription factors PAX5, EBF, E2-2, and IKZF1 (Ikaros), as well as genes with other established roles in B-cell development, i.e., RAG1 and RAG2, FYN, PBEF1, or CBP/PAG. The fact that we frequently encountered multiple lesions affecting genes involved in cell cycle regulation and B-cell differentiation, strongly suggests that both these processes need to be targeted independently and simultaneously in order to trigger ALL-development.
Keywords: comparative genome hybridization

overall_design: Genomic DNA from 40 bone marrow or periphearal blood was hybridized on Affymetrix Nsp, Xba or Hind SNP-based arrays according to manufacturer's procedures. Copy number detection was performed using CNAG2.0 software, Reference genomes are included in this data set

first: Simon

middle: V

last: vanReijmersdal

first: Eric

middle: F

last: Schoenmakers

first: Ad

last: GeurtsvanKessel

first: Peter

last: Hoogerbrugge