title: High-resolution genome-wide copy number analysis of pre-invasive mucinous ovarian tumours

status: Public on Aug 26 2012

city: Melbourne

first: Sally

last: Hunter

state: VIC

address: 7 St Andrew's Pl

department: Research

country: Australia

institute: Peter MacCallum Cancer Centre

summary:
Introduction: Mucinous tumors are the second most common form of epithelial ovarian tumor, yet the cell of origin for this histological sub-type remains undetermined. While these tumors are thought to arise through a stepwise progression from benign cystadenoma to borderline tumor to invasive carcinoma, few studies have attempted to comprehensively characterize the genetic changes specific to this subtype or its precursors.

Methods: To explore the spectrum of genomic alterations common to mucinous tumors we performed high resolution genome-wide copy number analysis, mutation screening by Sanger sequencing and immunohistochemistry on a series of primary ovarian mucinous cystadenomas (n=20) and  borderline tumors (n=22).

Results: Integration of copy number data, targeted mutation screening of RAS/RAF pathway members and immunohistochemistry reveals that p16 loss and RAS/RAF pathway alterations are highly recurrent events that occur early during mucinous tumor development. The frequency of concurrence of these events was observed in 40% of benign cystadenomas and 68% of borderline tumors.

Conclusions: This study is the largest and highest resolution analysis of mucinous benign and borderline tumors performed to date and provides strong support for these lesions being precursors of primary ovarian mucinous adenocarcinoma. The high level of uniformity in the molecular events underlying the pathogenesis of mucinous ovarian tumors provides an opportunity for treatments targeting specific mutations and pathways.

overall_design:
Copy number data was generated for 42 mucinous ovarian tumours (20 benign, 22 borderline). Epithelial and stromal DNA from the tumours and matched-normal lymphocyte DNA were all analysed.

Processed/normalized data for the germline DNA samples are not provided because they themselves are normalised to a diploid copy number, making all the probe values 2, which is not informative.

first: Ian

last: Campbell

first: Kylie

middle: L

last: Gorringe


title: Copy number data from paired primary and relapse ovarian tumours

status: Public on Jun 21 2012

first: Prof David

last: Bowtell PhD.

address: Locked Bag 1 A' Beckett St

department: Research Division

institute: PeterMacCallum Cancer Centre

summary: We used copy number analysis of paired primary and relapse ovarian tumours to identify genes associated with acquired resistance

overall_design:
Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from ovarian tumours.
Copy number profiles of 22 primary and matched ascites samples. Multiple biopsies of four samples were also profiled to assess the intra tumour heterogeneity in samples.

first: Prue

middle: A

last: Cowin

first: Joshy

last: George

first: David

middle: D

last: Bowtell


title: Human lung adenocarcinoma DNA copy number profiling

status: Public on May 17 2012

city: Chapel Hill

first: Matthew

last: Wilkerson

state: NC

address: 450 West Drive

department: Lineberger Comprehensive Cancer Center

country: USA

institute: University of North Carolina at Chapel Hill

summary: Lung adenocarcinoma’s genomic alterations exhibit vast variation.  Lung adenocarcinoma also has previously described intrinsic gene expression subtypes (Hayes et al. 2006, PMID: 17075127).  This study’s aim was to detect and validate subtype-specific alterations.  A portion of these specimens were also assayed for genomewide transcription in GSE26939.

overall_design: 103 tumor samples and 30 normal samples were quantified for DNA copy number using Affymetrix SNP microarrays.

first: D

middle: N

last: Hayes


title: Molecular profiles of pyramidal cell dysfunction in the superior temporal cortex in schizophrenia

status: Public on May 15 2012

city: Belmont

first: Sarah

last: Mauney

state: MA

address: 115 Mill St.

institute: McLean Hospital

summary: Gray matter volume in the cerebral cortex has been consistently found to be decreased in patients with schizophrenia. The superior temporal gyrus (STG) is one of the cortical regions that exhibit the most pronounced volumetric reduction. This reduction is generally thought to reflect, at least in part, decreased number of synapses; the majority of these synapses are believed to be furnished by glutamatergic axon terminals onto the dendritic spines on pyramidal neurons. Pyramidal neurons in the cerebral cortex exhibit layer-specific connectional properties, providing neural circuit structures that support distinct aspects of higher cortical functions. For instance, dendritic spines on pyramidal neurons in layer 3 of the cerebral cortex are targeted by both local and long-range glutamatergic projections in a highly reciprocal fashion. Synchronized activities of pyramidal neuronal networks, especially in the gamma frequency band (i.e. 30-100 Hz), are critical for the integrity of higher cortical functions. Disturbances of these networks may contribute to the pathophysiology of schizophrenia by compromising gamma oscillation. This concept is supported by the following postmortem and clinical observations. First, the density of dendritic spines on pyramidal neurons in layer 3 of the cerebral cortex, including the STG, have been shown to be significantly decreased by 23-66% in subjects with schizophrenia. Second, consistent with these findings, the average somal area of these pyramidal cells is significantly smaller. Third, we have recently found that, in the prefrontal cortex, the density of glutamatergic axonal boutons, of which dendritic spines are their major targets, was significantly decreased by as much as 79% in layer 3 (but not layer 5) in subjects with schizophrenia. Finally, an increasing number of clinical studies have consistently demonstrated that gamma oscillatory synchrony is profoundly impaired in patients with schizophrenia. Furthermore, gamma impairment has been linked to the symptoms and cognitive deficits of the illness and the severity of these symptoms and deficits have in turn been associated with the magnitude of cortical gray matter reduction. Taken together, understanding the molecular underpinnings of pyramidal cell dysfunction will shed important light onto the pathophysiology of cortical dysfunction of schizophrenia. In order to gain insight into the molecular determinants of pyramidal cell dysfunction in schizophrenia, we combined LCM with Affymetrix microarray and high-throughput TaqMan®-based MegaPlex qRT-PCR approaches, respectively, to elucidate the alterations in messenger ribonucleic acid (mRNA) and microRNA (miRNA) expression profiles of these neurons in layer 3 of the STG. We found that transforming growth factor beta (TGFβ) and BMP (bone morphogenetic proteins) signaling pathways and many genes that regulate extracellular matrix (ECM), apoptosis and cytoskeleton were dysregulated in schizophrenia. In addition, we identified 10 miRNAs that were differentially expressed in this illness; interestingly, the predicted targets of these miRNAs included the dysregulated pathways and gene networks identified by microarray analysis. Together these findings provide a neurobiological framework within which we can begin to formulate and test specific hypotheses about the molecular mechanisms that underlie pyramidal cell dysfunction in schizophrenia.

overall_design: Gene epxression microarray from RNA isolated from pyramidal cells in layer III of the STG from 9 normal controls  and 9 subjects with schizophrenia. There was no significant difference between diagnosis groups for age, sex, and post mortem interval (PMI).

first: Charmaine

middle: Y

last: Pietersen

first: Susie

middle: S

last: Kim

first: Maribel

middle: P

last: Lim

first: Robert

middle: J

last: Rooney

first: Jack

last: Chen

middle: M

last: Stephens

first: Jill

last: Goldstein

first: Tracey

last: Petryshen

first: Larry

last: Seidman

first: Martha

middle: E

last: Shenton

middle: W

last: McCarley

first: Kai-C

last: Sonntag

first: T-U

last: Woo


title: Affymetrix SNP 6.0 profiles of 10 Human B-NHL lines

status: Public on Apr 03 2012

city: Cold Spring Harbor

first: Claudio

last: Scuoppo

address: 1 Bungtown Rd

institute: Cold Spring Harbor

summary: B-cell Non Hodgkin Lymphoma are a heterogenous group chracterized by a variety of genetic changes, including translocations, deletions and amplifications. Here we analyzed 10 B-NHL lines  by Affymetrix SNP 6.0 to detect copy number changes. Specifically, we aim to identify cell lines suitable for testing the consequences of acute reintroduction of candidate tumor suppressor genes as they harbor deletions which include the candidate gene(s).

overall_design: 10 BNHL cell lines were grown in standard cell culture conditions. Genomic DNA was exptracted from frozen pellets and analyzed for copy number variations with Affymetrix SNP 6.0 Arrays

first: Scott

last: Lowe


title: Renal Cell Neoplasms Contain Shared Tumor Type-Specific Copy Number Variations

status: Public on Apr 29 2012

city: Pittsburgh

first: John

middle: Michael

last: Krill-Burger

state: PA

address: Rm. WG21.3 Shadyside Hospital

institute: University of Pittsburgh Medical Center

summary: Copy number variant (CNV) analysis was performed on renal cell carcinoma (RCC) specimens (chromophobe, clear cell, oncocytoma, papillary type 1, papillary type 2) using high resolution arrays (1.85 million probes). RCC samples exhibited diverse genomic changes within and across tumor types ranging from 106 CNV segments in a clear cell specimen to 2238 CNV segments in a papillary type 2 specimen. Despite the genomic heterogeneity, distinct CNV segments were common within each of 4 tumor classifications: chromophobe (7 segments), clear cell (3 segments), oncocytoma (9 segments), and papillary type 2 (2 segments). Shared segments ranged from a 6.1 Kb deletion among oncocytomas to a 208.3 Kb deletion common to chromophobes. Among common tumor type-specific variations, chromophobe, clear cell and oncocytomas comprised exclusively non-coding DNA. No CNV regions were common to papillary type 1 specimens although there were 12 amplifications and 12 deletions in 5 of 6 samples. Three microRNAs and 12 mRNA genes had ≥ 98% of their coding region contained within CNV regions including multiple gene families (chromophobe: amylase 1A, 1B, 1C; oncocytoma: general transcription factor 2H2, 2B, 2C, 2D). Gene deletions involved in histone modification and chromatin remodeling affected individual subtypes (clear cell: SFMBT, SETD2; papillary type 2: BAZ1A) as well as the collective RCC group (KDM4C). The genomic amplifications/deletions identified in each renal tumor type represent potential diagnostic and/or prognostic biomarkers.

overall_design: Tissue samples were obtained from the University of Pittsburgh Health Sciences Tissue Bank (HSTB) using an honest broker system and according to IRB approved protocol #970480. Samples were acquired as surgical specimens, flash-frozen in a 1.8 ml cryotube (NalgeNunc, Inc., Rochester, NY) followed by immediate storage at -80C. Each tumor sample (n=27) was classified into one of 5 renal cancer subtypes (chromophobe: n=5, clear cell: n=5, oncocytoma: n=5, papillary type 1: n=6, papillary type 2: n=6) by consensus evaluation of correlative hematoxylin and eosin stained slides performed independently by 3 anatomical pathologists. The three pathologists also confirmed the absence of pathological features in adjacent normal renal samples (n=9) and this normal reference group was expanded by inclusion of 14 normal thyroid samples and 8 normal lung specimens. DNA from each of these specimens was analyzed using genotyping microarrays (SNP 6.0, Affymetrix, Sunnyvale, CA).

first: William

last: LaFramboise


title: Genetic Landscape of Copy Number Alterations in Gastric Cancer

status: Public on Feb 10 2012

city: Singapore

first: Niantao

last: Deng

state: Singapore

address: Center for Computational Biology, level 6, 8 College Road

country: Singapore

institute: Duke NUS Graduate Medical School

summary: Genome-wide DNA copy number profiling of gastric tumors and matched non-maligant samples. The affymetrix SNP6 array was used to obtain DNA copy number profiles in 193 gastric tumors and 98 matched gastric non-malignant samples.

overall_design: Genomic DNA extracted from 193 gastric tumors and 98 matched gastric non-malignant (normal) tissues was hybridized on Affymetrix SNP6 genotyping arrays.

first: Patrick

last: Tan


title: The invasion promoter Slug is a critical cell cycle regulator

status: Public on Feb 09 2012

city: Taipei

first: Tse-Ming

last: Hong

address: 128 Academia Road, Section 2, Nankang

country: Taiwan

institute: Academia Sinica

summary: Background: The well-characterized function of the transcriptional repressor, Slug, is to promote EMT and tumor invasion/metastasis by down-regulating E-cadherin expression. In this study, we investigated the significance of Slug during the S phase. Method: Slug mRNA expression was isolated from thymidine-arrested CL1-5/AS2neo (control) and CL1-5/AS2neo-Slug-WT stable cells. The Agilent oligonucleotide microarray analysis was performed to identify Slug downstream genes. Results: Overexpression of Slug inhibited lung [3H]-thymidine incorporation and delayed S phase progression. By using Agilent microarray we have identified panel of genes altered by Slug overexpression. Slug can down-regulate target genes about cell cycle networks for DNA replication, DNA replication checkpoint and genomic stability, such as TOP1, ORC4, RFC3, and Rad17. Conclusions: the multifaceted role of Slug in cancer progression by controlling the epithelial-mesenchymal transition and genome stability.

overall_design: Two-condition experiment, Vector vs. Slug overexpression cells. The cDNAs encoding full-length human Slug were amplified and subcloned into lentiviral pLKO_AS2.neo which generated full-length Slug. Vector control or Slug lentivirus were transduced into CL1-5 cells and Gentamycin was used to select stable cells.

first: W

last: Wang

first: Y

middle: C

last: Hsu

first: T

first: P

last: Yang


title: Affymetrix SNP array data for Monoclonal Gammopathies samples

status: Public on Apr 01 2012

city: salamanca

first: Maria

middle: Eugenia

last: Sarasquete

state: salamanca

address: Paseo San Vicente 58-182

department: Hematology

country: Spain

institute: Hospital Universitario de Salamanca

summary: Genetic events mediating transformation from the pre-malignant monoclonal gammopathies (MG) to multiple myeloma (MM) are unknown.

overall_design: To obtain a comprehensive genomic profile of MG from the early to the late stages we performed high resolution analysis on purified plasma cells from 20 MGUS, 20 smoldering MM (SMM) and 34 MM by high density 6.0 SNP-array.

first: Lucía

last: Corral


title: Copy number analysis of high-grade osteosarcoma

status: Public on Mar 28 2012

city: Oslo

first: Marieke

middle: Lydia

last: Kuijjer

address: Gaustadalléen 21

country: Norway

institute: Centre for Molecular Medicine Norway

summary: We performed copy number analysis of high-grade osteosarcoma samples. in order to detect osteosarcoma drivers, we integrated these data with genome-wide gene expression data. We performed two different methods - a non-paired and a paired integrative analysis.

overall_design: Copy number analysis was performed on 32 pre-treatment high-grade osteosarcoma diagnostic biopsies, of which 29 overlapped with the 84 samples used for gene expression analyses.

first: Halfdan

last: Rydbeck

first: Stine

middle: H

last: Kresse

first: Emilie

last: Buddingh

first: Ola

last: Myklebost

first: Horst

last: Bürger

first: Pancras

last: Hogendoorn

first: Leonardo

last: Meza-Zepeda

first: Anne-Marie

last: Cleton-Jansen


title: High-Resolution Genomic Profiling of Adult and Pediatric Core-Binding-Factor Acute Myeloid Leukemia Reveals New Recurrent Genomic Alterations

status: Public on Feb 07 2012

city: Memphis

first: Jeffery

last: Klco

state: TN

address: 262 Danny Thomas Place

department: Pathology

institute: St Jude Children's Research Hospital

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

summary: To identify cooperating lesions in core-binding-factor acute myeloid leukemia (CBF-AML), we performed single-nucleotide polymorphism (SNP)-array analysis on 300 diagnostic and 41 relapse adult and pediatric leukemia samples. We identified a mean of 1.28 copy number alterations (CNAs) per case at diagnosis in both patient populations. Recurrent minimally deleted regions (MDRs) were identified at 7q36.1 (7.7%), 9q21.13 (5%), 11p13 (2.3%), and 17q11.2 (2%). Recurrent focal gains were identified at 8q24.21 (4.7%) and 11q25 (1.7%), both containing a single non-coding RNA. Recurrent regions of copy-neutral loss-of-heterozygosity were identified at 1p (1%), 4q (0.7%), and 19p (0.7%), with known mutated cancer genes present in the minimally altered region. Analysis of relapse samples identified recurrent MDRs at 3q13 (12.2%), 5q (4.9%), and 17p (4.9%).

overall_design: SNP genotyping was performed on 300 adult and pediatric CBF-AMLs; t(8;21), n=157 (adult, n=114; pediatric, n=43); and inv(16), n=143 (adult, n=104; pediatric, n=39). Germline control DNA from remission bone marrow or peripheral blood was available for paired analysis in 175 patients. In addition, for 41 patients, matched relapse samples were analyzed. Data were processed using reference alignment, dChipSNP and circular binary segmentation.

first: Michael

last: Kühn

first: Ina

last: Radtke

first: Lars

last: Bullinger

first: Salil

last: Goorha

first: Jinjun

last: Cheng

first: Jennifer

last: Edelmann

first: Juliane

last: Gohlke

first: Xiaoping

last: Su

first: Peter

last: Paschka

first: Stanley

last: Pounds

first: Jürgen

last: Krauter

first: Arnold

last: Ganser

first: Asmaa

last: Quessar

first: Raul

last: Ribeiro

first: Verena

middle: I

last: Gaidzik

first: Sheila

last: Shurtleff

first: Jan

last: Krönke

first: Karlheinz

last: Holzmann

first: Jing

last: Ma

first: Richard

middle: F

last: Schlenk

first: Jeffrey

last: Rubnitz

first: Konstanze

last: Döhner

first: Hartmut

first: James

middle: R

last: Downing


title: Genome sequencing of childhood medulloblastoma brain tumors links chromothripsis with TP53 mutations

status: Public on Jan 20 2012

city: Toronto

first: David

middle: J. H.

last: Shih

state: ON

address: 686 Bay St

department: Developmental and Stem Cell Biology

country: Canada

institute: Hospital for Sick Children

summary: Genomic rearrangements typically occur progressively during tumor development. Recent findings, however, suggest an alternative mechanism, involving chromosome shattering and reshuffling ('chromothripsis'), for which no genetic basis has yet been described. Whole-genome sequencing of a Sonic-Hedgehog medulloblastoma (SHH-MB) brain tumor from a patient with a germline TP53 mutation (Li-Fraumeni syndrome) revealed massive, complex rearrangements resulting from chromothripsis. Integrating TP53 status with genomic rearrangement data in additional medulloblastomas revealed a striking association between TP53 mutation and chromothripsis in SHH-MBs. Unexpectedly, five seemingly sporadic SHH-MB patients with chromothripsis harbored TP53 germline mutations – findings relevant for clinical management. Analysis of additional tumor entities substantiated a link between TP53 mutation and chromothripsis, beyond general genomic instability. Among these, we observed a strong association between somatic TP53 mutations and chromothripsis in acute myeloid leukemia. These findings implicate p53 in the initiation of, or cellular reaction to, chromothripsis – a novel role for the 'guardian of the genome'.

overall_design: The DNA copy-number profiles of 11 primary medulloblastoma samples were analyzed on the Affymetrix Mapping250K Nsp array, together with data from 70 primary samples taken from GSE14437. Data from diploid reference samples were taken from GSE9222. Additionally, DNA copy-number profiles for 19 additional medulloblastoma samples were generated on the Affymetrix SNP6 platform with matched blood samples.

first: Tobias

last: Rausch

middle: T

last: Jones

first: Marc

last: Zapatka

first: Adrian

last: Stütz

first: Thomas

last: Zichner

first: Joachim

last: Weischenfeldt

first: Natalie

last: Jäger

last: Remke

first: Paul

middle: A

last: Northcott

first: Elke

last: Pfaff

first: Jelena

last: Tica

first: Qi

last: Wang

first: Luca

last: Massimi

first: Hendrik

last: Witt

first: Sebastian

last: Bender

first: Sabrina

last: Pleier

first: Huriye

last: Cin

first: Cynthia

last: Hawkins

first: Christian

last: Beck

first: Andreas

last: von Deimling

first: Volkmar

last: Hans

first: Benedikt

last: Brors

first: Roland

last: Eils

first: Wolfram

last: Scheurlen

first: Jonathon

last: Blake

first: Vladimir

last: Benes

last: Kulozik

first: Olaf

first: Dianna

last: Martin

first: Cindy

last: Zhang

first: Rinnat

last: Porat

first: Diana

last: Merino

first: Jonathan

last: Wasserman

first: Nada

last: Jabado

first: Adam

last: Fontebasso

first: Lars

last: Bullinger

first: Frank

last: Rücker

last: Koster

last: Molenaar

first: Rogier


title: SNP data from blood DNAs of patients with gastric cancer

status: Public on Dec 31 2011

city: daejeon

first: Tae-Wook

last: Kang

address: 111 Gwahangno, Yuseong-gu

country: South Korea

institute: KRIBB

summary: The identification of surrogate single nucleotide polymorphism (SNP) markers that can predict responses to chemotherapy could enable the efficient selection of patients for various regimens. Genome-wide association studies in clinical populations are theoretically capable of identifying markers that are capable of influencing drug responses. We used Affymetrix’s SNP Array 6.0 to detail genetic polymorphism of patient’s group showing differential responsiveness to various regimens and profiled SNP biomarkers for various regimens.

overall_design:
The chemosensitivity of tumor tissue from the initial cohort of 93 patients was assessed using the histoculture drug response assay (HDRA) and the following six established drugs. Then the inhibition rate (IR) cut-off value for a positive response was previously determined as 30%. Blood DNAs were prepared from each patients and hybridized to Affymetrix’s SNP Array 6.0. Genotypes were determined using the Affymetrix Genotyping Console software (version 2.1) based on the BRLMM-P algorithm. We used an ANOVA test to identify SNPs associated with quantitative HDRA drug sensitivity.
Nine different drug regimens were used. For each of the nine regimens, we provided raw drug sensitivity (HDRA) data and binary data (i.e. >= 30 or < 30) at 30% cutoff.
Publication focuses on six drug regimens: CDP, DTAX, FU, OXA, TAX, and TSI.
Publication discusses 93 of the 95 samples contained in this Series.

first: Jin-Cheon

last: Kim

first: Seun-Young

first: Yong-Sung


title: Characterization of FASN knockdown LNCaP cells

status: Public on Jul 10 2012

city: Chiba

first: Yukie

last: Yoshii

address: Anagawa 4-9-1, Inage

country: Japan

institute: National Institute of Radiological Sciences

summary: We examined FASN knockdown LNCaP cells obtained by shRNA transduction with Mission lentiviral transduction particles (SHCLNV-NM 00410, TRCN3128, Sigma) (FASN-RNAi cells). In this study, we used cells transfected with non-targeting shRNA as a control (control-RNAi cells). The expression of genes related to cellular proliferation (phospholipase A2, group IVA, PLA2G4A; tensin 3, TNS3; glypican 4 GPC4), cell adhesion and extracellular matrix organization [peroxidasin homolog (Drosophila) PXDN; sarcoglycan epsilon, SGCE; von Willebrand factor, VWF; hydroxysteroid (17-beta) dehydrogenase 12, HSD17B12; cysteine-rich secretory protein LCCL domain containing 2, CRISPLD2], and cell motility (TNS3, RAP2B member of RAS oncogene family, RAP2B) were shown to be down-regulated by FASN inhibition with RNAi. FASN inhibition led to down-regulation of the PLA2G4A and HSD17B12 genes encoding phospholipase A2 and 17-beta hydroxysteroid dehydrogenase, respectively, which are the key enzymes related to production of an intracellular second messenger arachidonic acid and androgen hormones, both playing roles in promotion of tumor progression. We also found that the genes related to arachidonic acid signalling, including RGS2, SPAG16, VWF and RAP2B, were also suppressed with FASN inhibition. Gene expression profiling therefore demonstrated that FASN inhibition induces down-regulation of genes related to cell proliferation, cell adhesion, migration, and invasion, as well as the production of arachidonic acid and androgen hormones, both of which drive tumor progression.

overall_design: Total RNA isolation was performed with a Micro-to-Midi total RNA purification system (Invitrogen). The integrity of total RNAs was evaluated using an Agilent 2100 Bioanalyzer (Agilent Technologies). Low Input Quick Amp Labeling Kit, one-color (Agilent Technologies) was used to prepare Cy3-labelled target cRNA according to the manufacturer's instructions. Labeled cRNAs were hybridized with a SurePrint G3 Human GE 8×60K Microarrays (Agilent Technologies). Two separate hybridizations were performed for each sample. Array images were captured using a DNA Microarray Scanner (Agilent Technologies), and data were analyzed using Feature Extraction Software (Agilent Technologies) to obtain background-corrected signal intensities. The data were further analysed with GeneSpring GX Software (Version 11.0, Agilent Technologies). After filtering of data, mRNAs differentially expressed in target versus control were considered using the Fisher exact test, followed by multiple corrections using the Benjamini and Hochberg false discovery rate (FDR) method. Gene sets with a FDR q-value < 0.05 were considered significant.


title: SNP array for CNV calling AUTS2 project [Affymetrix]

status: Public on Jul 12 2012

city: Amsterdam

first: Els

last: Voorhoeve

address: De Boelelaan 1117

department: Clinical Genetics

country: Netherlands

institute: VU medical center

summary: Phenotypic and genotypic description of AUTS2 deletion patients found by Array analysis in an international cohort of intellectual disability (ID) and multiple congenital malformations (MCA).

overall_design: Arrays were hybridized and analysed using manufacturer's  protocols on DNA from patients with ID/MCA.

first: Ingrid

last: Simonic

first: Anath

last: Lionel

first: Gea

last: Beunders


title: Induced pluripotent stem cells from CINCA syndrome patients as a model for dissecting somatic mosaicism and drug discovery

status: Public on Jun 11 2012

city: Kyoto

first: Akira

last: Watanabe

state: Kyoto

address: Rm504, Miyako Bldg, 233, Isa-cho, kamigyo-ku

institute: CyberomiX Inc

summary: Chronic infantile neurological cutaneous and articular (CINCA) syndrome is an IL-1-driven autoinflammatory disorder caused mainly by NLRP3 mutations. The pathogenesis of CINCA syndrome patients who carry NLRP3 mutations as somatic mosaicism has not been precisely described because of the difficulty in separating individual cells based on the presence or absence of the mutation. Here, we report the generation of NLRP3-mutant and non-mutant induced pluripotent stem cell (iPSC) lines from two CINCA syndrome patients with somatic mosaicism, and describe their differentiation into macrophages (iPS-MPs). We found that mutant cells are predominantly responsible for the pathogenesis in these mosaic patients because only mutant iPS-MPs showed the disease relevant phenotype of abnormal IL-1β secretion. We also confirmed that the existing anti-inflammatory compounds inhibited the abnormal IL-1β secretion, indicating that mutant iPS-MPs are applicable for drug screening for CINCA syndrome and other NLRP3-related inflammatory conditions. Our results illustrate that patient-derived iPSCs are useful for dissecting somatic mosaicism, and that NLRP3-mutant iPSCs can provide a valuable platform for drug discovery for multiple NLRP3-related disorders.

overall_design: To characterize iPS and differentiated cells, RNA expression profiles were evaluated by microarray analysis.We analyzed iPC cells and macrophage from healthy volunteers and CINCA syndrome patients. Human ES cella and fibroblasts were used as control.

first: Takayuki

last: Tanaka

first: Kazutoshi

last: Takahashi

first: Mayu

last: Yamane

first: Shota

last: Tomida

first: Saori

last: Nakamura

first: Koichi

last: Oshima

last: Niwa

first: Ryuta

last: Nishikomori

first: Naotomo

last: Kambe

first: Hideki

last: Hara

first: Masao

last: Mitsuyama

first: Nobuhiro

last: Morone

first: John

last: Heuser

first: Takuya

last: Yamamoto

first: Aiko

last: Matsubara

first: Seishi

last: Ogawa

first: Isao

last: Asaka

first: Toshio

last: Heike

first: Shinya

last: Yamanaka

first: Tatsutoshi

last: Nakahata

first: Megumu

middle: K

last: Saito


title: Age-dependent gene expression in isolated small intestinal epithelial cells (IECs)

city: Hannover

first: Mathias

middle: W.

last: Hornef

address: Carl Neuberg Str. 1

department: Inst. of Medical Microbiology

country: Germany

institute: Hannover Medical School

summary: Intestinal epithelial cells were isolated from total small intestine of each four 3- and 21-day-old C57BL/6 mice (protocol according to: Lotz et al., J. Exp. Med. 2006). Each two 3- and 21-day-old animals were obtained from one litter. Total RNA was isolated by TriZol and ist purity was examined using a Bioanalyszer. We used microarrays to detail the global gene expression in primary total isolated intestinal epithelial cells of 3- versus 21-day-old mice.

overall_design: Four biological replicates from isolated intestinal epithelial cells obtained from 3- and 21-day-old mice (each two animals from one litter). Colour change.


title: Spt6 Levels are Modulated by PAAF1 and 26S Proteasome to Regulate the HIV-1 LTR and a Subset of Cellular Genes involved in Cancer.

status: Public on May 29 2012

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

country: France

institute: IPMC/CNRS

summary: Effect of PAAF1 and Spt6 knock-down on gene expression. Total RNAs were extracted from HeLa-LTR-Luc cells in which PAAF1 or Spt6 had been knock down by a specific siRNA or HeLa-LTR-Luc cells that had been transfected with a control siRNA (“si Neg”). Differentially expressed genes in PAAF1 knock-down cells were identified by microarray.

overall_design: Two biological replicates (A / B) in 3 experimental conditions (si-Neg, si-PAAF1, si-Spt6) were analyzed in a single channel experiment.

first: B

last: Mari

first: P

last: Barbry

first: K

first: R

last: Kiernan

first: M

last: Nakamura


title: Analysis of gene expression change by gefitinib treatment in gefitinib sensitive PC9 and resistant PC9.

status: Public on Jul 01 2012

city: Tokyo

first: Junko

last: Hamamoto

address: 35 Shinanomachi, Shinjuku-ku

department: Pulmonary Medicine

institute: School of Medicine, Keio University

summary: We established a gefitinib-resistant cell line (PC-9GR), by serial exposure of gefitinib to PC-9, an originally gefitinib-sensitive lung cancer cell line (PC-9na), for long period.We collected total RNA from both PC-9 and PC-9GR and examined mRNA expression profile, comprehensively.

overall_design: Gefitinib induced gene expression was measured in human lung cancer cell line was measured at 48 hours after exposure to 1uM Gefitinib.

first: Hideki

last: Terai

first: Kenzo

last: Soejima


title: Dominant Th2 differentiation of human regulatory T cells upon loss of FOXP3 expression

status: Public on Dec 14 2011

city: Regensburg

first: Christian

last: Schmidl

address: Franz-Josef-Strauss-Allee 11

institute: Rengensburg Center for Interventional Immunology

summary: CD4+CD25+FOXP3+ regulatory T cells (Treg) are pivotal for peripheral self-tolerance. They prevent immune responses to auto- and alloantigens and are thus under close scrutiny as cellular therapeutics for autoimmune diseases and the prevention or treatment of alloresponses after organ or stem cell transplantation. We previously showed that human Treg cells with a memory cell phenotype, but not those with a naïve phenotype, rapidly down-regulate expression of the lineage-defining transcription factor forkhead box P3 (FOXP3) upon in vitro expansion. We now compared the transcriptomes of stable FOXP3+ Treg and converted FOXP3- 'ex-Treg' cells by applying a newly developed intranuclear staining protocol that permits the isolation of intact mRNA from fixed, permeabilized and FACS-purified cell populations. Whole genome microarray analysis revealed strong and selective upregulation of Th2 signature genes, including GATA-3, IL-4, IL-5 and IL-13, upon downregulation of FOXP3. Th2 differentiation of converted, FOXP3- ex-Treg cells occurred even under non-polarizing conditions and could not be prevented by IL-4 signaling blockade. Thus, our studies identify Th2 differentiation as the default developmental program of human Treg cells after downregulation of FOXP3.

overall_design: RNA preparations from FOXP3 stained in vitro expanded CD4+CD25highCD45RA- “memory” Treg cells from five independent donors were analyzed using Whole Human Genome Oligo Microarrays (Agilent). An adapted FOXP3 staining procedure to stain FOXP3 in human regulatory T cells to isolate intact RNA for microarray hybridization was developed (see extract protocol).

first: Leo

last: Hansmann

first: Reinhard

last: Andreesen

first: Janina

last: Kett

first: Lena

last: Steger

first: Petra

last: Hoffmann

first: Michael

last: Rehli

first: Matthias

last: Edinger


title: Programming human pluripotent stem cells into adipocytes [Agilent]

status: Public on Dec 25 2011

city: NYC

first: Tim

middle: D

last: Ahfeldt

state: NY

address: 1425 Madison Ave

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary: The utility of human pluripotent stem cells as a tool for understanding disease and as a renewable source of cells for transplantation therapies is dependent on efficient differentiation protocols that convert these cells into relevant adult cell types. Here we report the robust and efficient differentiation of human pluripotent stem cells into adipocytes. We found that inducible expression of PPARG2 in pluripotent stem cell-derived mesenchymal progenitor cells programmed their development towards an adipocyte cell fate. Using this approach, multiple human pluripotent cell lines were differentiated into adipocytes with efficiencies of 85% to 90%. These pluripotent stem cell-derived adipocytes retained their identity independent of transgene expression, could be maintained in culture for several weeks, expressed mature markers, and exhibited mature functional properties such as lipid catabolism in response to a beta-adrenergic stimulus. Global transcriptional and lipid metabolomic analyses further confirmed the identity and maturity of these pluripotent stem cell-derived adipocytes.

overall_design:
Mesenchymal progenitor cells (MPCs) derived from human embryonic stem cells hESCs and induced pluripotent stem cells (iPSCs) along with adipose-derived stromal vascular cells (ADSVCs) were subjected to induction of PPAR2 and compared to primary fat samples. Overall 2 ADSVC (ADSVC 24 nd 49) lines, 1 hESC (HUES9) line and 1 iPSC (BJRiPS) line were differentiated into MPCs, PPAR2 programmed, and compared to untreated MPCs and primary fat samples from 2 individuals. Each condition is either represented in duplicate or triplicate and there are two universal reference spots to aid in slide-dependant batch effects (24 samples total).

Supplementary file(s):
GeneSymbol-collapsed data represent the final normalized data used for analyses in the manuscript.


title: Identification of novel sub-microscopic copy number aberrations in adult acute myeloid leukemia

status: Public on Mar 08 2012

city: London

first: Manu

last: Gupta

address: Charterhouse Sq.

department: Medical Oncology

country: United Kingdom

institute: Queen Mary University of London

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

summary: In this study we have screened 56 pairs of AML samples for cryptic copy number aberration and loss-of-heterozygosity. We have identified 80 CNAs among 56 patient samples; 21 containing <5 genes while 11 contained or were present within a single gene. Four (7%) patients carried gains at sub-telomeres on multiple chromosomes. Some of the cryptic regions are common with other recent studies while most are novel. Also, we show that it is better to analyse sample at diagnosis and sample at remission (paired control) both against a common unrelated control and then compare the two results than analysing the diagnostic sample directly against the paired control.

overall_design: Genomic DNA from 56 diagnostic AML samples were analysed using Affymetrix SNP 6.0 arrays.  Genomic DNA at the time of remission from each patient served as paired-control. Prevalence of copy number aberrations and regions of homozygosity were identified.

first: Sabah

last: Khalid

first: Manoj

last: Raghavan

first: Tracy

last: Chaplin

first: Gael

last: Molloy

first: Sindhu

last: Subramaniam

first: Silvana

last: Debernardi

first: Finlay

last: MacDougall

first: Kajsa

last: Paulsson

first: Jean-Baptiste

last: Cazier

first: T

last: Lister

first: Bryan

last: Young


title: Human lung adenocarcinoma

status: Public on May 17 2012

city: Chapel Hill

first: Matthew

last: Wilkerson

address: 450 West Drive

institute: University of North Carolina at Chapel Hill

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

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

overall_design:
Refer to individual Series

Note: The Sample name (i.e. tumor #) is consistent among all three SubSeries.  For example, Samples GSM663336, GSM889665, GSM89347 represent various datatypes for tumor 53.


title: Genome wide analysis of acral melanoma (Affymetrix)

status: Public on Dec 13 2011

first: Simon

last: Furney

address: 237 Fulham Road

institute: Institute of Cancer Research

summary: Genotyping of  a matched  normal, primary and metastatic acral melanoma

overall_design: DNA from blood and one matched Primary and one metastatic acral melanoma was genotyped on Affmetrix SNP6

first: S

middle: J

last: Turajlic


title: Clonal Selection Drives Genetic Divergence of Metastatic Medulloblastoma

city: HEIDELBERG

first: Paul

middle: A.

last: Northcott

address: Im Neuenheimer Feld 280

institute: German Cancer Research Center (DKFZ)

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

overall_design: Refer to individual Series


title: Genome wide analysis of tumours in individuals with p53-germline mutations

status: Public on Jan 19 2012

first: Diana

middle: M

last: Merino

state: Ontario

address: 686 Bay St.

department: Genetics and Genome Biology

institute: The Hospital for Sick Children

summary: Copy number analysis of Affymetrix GW6.0 SNP/CNV arrays was performed for 7 tumours (4 adrenocortical carcinomas, 2 rhabdomyosarcoma and 1 extra-renal rhabdoid tumour) derived from individuals with germline p53-mutations.

overall_design: Affymetrix CNV/SNP arrays were performed according to the manufacturer's directions on DNA extracted from fresh frozen tumour samples

first: D

last: Malkin

first: J

last: Wasserman


title: Complete OATP1B1 and OATP1B3 deficiency underlies human Rotor syndrome.

status: Public on Jan 16 2012

city: Prague

first: Viktor

last: Stranecky

address: Ke Karlovu 2

department: 1st Faculty of Medicine

country: Czech Republic

institute: Charles University

summary:
Rotor syndrome is an autosomal recessive disorder characterized by conjugated hyperbilirubinemia, near-absent hepatic uptake of anionic diagnostics, and coproporphyrinuria.
The mechanistic basis of other hyperbilirubinemia syndromes is largely understood, but that of Rotor syndrome has remained enigmatic. The existing paradigm of hepatic bilirubin excretion postulates a unidirectional elimination pathway: Uptake of conjugated bilirubin from blood by hepatocytes, glucuronidation of bilirubin, and excretion of conjugated bilirubin into bile by ABCC2, a canalicular bilirubin-glucuronide and xenobiotic export pump. An analogous view holds for drugs conjugated in the liver.
Here we demonstrate by molecular-genetic analysis of 8 Rotor-syndrome families that Rotor syndrome is a two-gene disorder, with impaired hepatic re-uptake of bilirubin-glucuronide caused by complete deficiencies in the hepatic organic anion transporting polypeptides OATP1B1 and OATP1B3.

overall_design: SNP genotyping was performed on 22 samples - 10 affected and 12 healthy siblings from 8 Rotor-syndrome families. Affymetrix GeneChip Command Console software was used for image processing and CEL files were processed by Affymetrix GTC using the BRLMM-P-Plus algorithm and regional GC correction configuration for Copy Number/LOH analysis. The HapMap270 file supplied by Affymetrix was used as the reference.

first: Milan

last: Jirsa

first: Stanislav

last: Kmoch


title: Pediatric Hepatocellular Carcinoma Celll Line

status: Public on Dec 01 2011

city: Tuebingen

first: Michael

last: Bonin

state: BW

address: CAlwerstr. 7

department: Medical Genetics

institute: University Tuebingen

summary:
Development of a new carcinoma cell line (HC-AFW1) derived from a pediatric liver tumor

The cell line HC-AFW1 was derived  from a 4 year old boy suffering from HCC through culturing and passage into immuno-deficient mice. The cell line is stable now for over 8 months of culture with a doubling time of 40 h. The tumor cells show an epithelial histology and express hepatoma proteins such as Alpha-fetoprotein (AFP), Glypican 3, E-cadherin, CD10, CD326, HepPar1, Vimentin and Desmin. Catenin beta shows a deletion of 49 amino acids in the exon 3 involving the phosphorylation sites of GSK3 and is detectable in the cell nuclei. Cytogenetic analysis revealed large anomalies in the chromosomal map including chromosomal aberrations found in hepatoblastoma as well as in adult HCC.

overall_design:
Copy number analysis of two different passages of HC-AFW1 cells

Two tumor specimens were used for tissue culture and xenotransplantation into NSG mice. Tumor cells derived from xenografts were cultured and designated as HC-AFW1. DNA was analyzed from the passage 2 (2P2).

HC-AFW2 was derived from tissue culture without transfer in to mice. Primary tissue samples were minced into pieces of 3x3 mm and cultured on 6 well plates (Becton Dickenson, Frankfurt, Germany) in DMEM (GIBCO BRL, Carlsbad, CA) supplemented with 10% FCS (growth medium). Cell cultures were maintained in a humidified atmosphere containing 5% CO2 at 37°C. For subculturing cells were detached from the culture surface using accutase in Dulbecco´s PBS containing 0.5mM EDTA (PAA Laboratories GmbH, Cölbe, Germany) for 2-3 minutes at 37°C. A sub-cultivation ratio of 1:4 and 1:6 was performed twice per week. Cells were stored in liquid nitrogen as a suspension in complete growth medium with 10% DMSO.

DNA from patient blood and tumor samples was isolated with the QiaAmp DNA mini Kit according to manufacturer's instructions (Qiagen, Hilden, Germany). Single nucleotide polymorphism (SNP) and copy number polymorphism (CNP) genotyping were performed  using the Genome-Wide Human SNP Array 6.0 and Genotyping Console (GTC) software (Affymetrix, Santa Clara, CA).

first: Sorin

last: Armeanu-Ebinger


title: High-resolution genome-wide copy-number analysis suggests a monoclonal origin of multi-focal prostate cancer

first: Xueying

last: Mao

address: Charterhouse Square

institute: Queen Mary

summary: Many human cancers present as multi-focal lesions. Understanding the clonal origin of multi-focal cancers is of both etiological and clinical importance. The molecular basis of multi-focal prostate cancer has previously been explored using only a limited number of isolated markers and, although independent origin is widely believed, the clonal origin of multi-focal prostate cancer is still debatable. We attempted to address clonal origin using a genome-wide copy-number analysis of individual cancer and high-grade prostatic intraepithelial neoplasia (HGPIN) lesions. Using Affymetrix array 6.0 copy-number analysis, we compared the genomic changes detected in 54 individual cancer and HGPIN lesions, isolated from 20 clinically localized prostate cancer cases. Identical genomic copy-number changes, shared by all same-case cancer foci, were detected in all 16 informative multi-tumor cases. In addition, both HGPIN lesions in the two multi-HGPIN cases available shared identical genomic changes. Commonly known genomic alterations, including losses at 6q15, 8p21.3-8p21.2, 10q23.2-10q23.31, 13q21.31-13q21.32, 16q22.3, 16q23.2-16q23.3 and 21q22.2-21q22.3 regions and gain of 8q24.3 were the most frequently detected changes in this multi-focal prostate cancer study, occurring in all same-case foci in at least one case. Microarray data were confirmed by fluorescence in situ hybridization in selected foci. Our high-resolution genome-wide copy-number data suggest that many multi-focal cases derive from a single prostate cancer precursor clone and that this precursor may give rise to separate HGPIN foci, which through clonal expansion may progress to multi-focal invasive prostate cancer. These findings, which demonstrate the monoclonal origin of multi-focal prostate cancer, should significantly enhance our understanding of prostate carcinogenesis and potentially improve clinical management of the disease.

overall_design:
Copy number analysis of Affymetrix SNP 6.0 array was performed for a total of 48 cancer and HGPIN lesions from 18 prostate cancer cases. All samples have case-matched normal controls.
PL = high grade PIN from left side, PR = high grade PIN from right side, PM = high grade PIN from middle of the tissue, TL = tumour from left side, TR = tumour from right side.

first: Lara

last: Boyd

first: Liyan

last: Xue

first: Dongmei

last: Lin

first: Tracy

last: Chaplin

last: Kudahetti

first: E

last: Stankiewicz

first: Yongwei

last: Yu

first: Luis

last: Belran

first: Greg

last: Shaw

first: John

last: Hines

first: R

last: Oliver

first: Daniel

last: Berney

first: Yong-Jie

last: Lu


title: Acquired genomic copy number aberrations and survival in chronic lymphocytic leukemia

status: Public on Nov 29 2011

city: Ann Arbor

first: Sami

middle: N

last: Malek

state: MI

address: 4410 Cancer Center; 1500 E Medical Center Dr

department: Internal Medicine, Hematology-Oncology

institute: University of Michigan

summary: Genomic aberrations are of predominant importance to the biology and clinical outcome of patients with chronic lymphocytic leukemia (CLL), and FISH-based genomic risk classifications are routinely used in clinical decision making in CLL.  One of the known limitations of CLL FISH is the inability to comprehensively interrogate the CLL genome for genomic changes.  In an effort at overcoming the existing limitations in CLL genome analysis, we have  analyzed high-purity DNA isolated from FACS-sorted CD19+ cells and paired CD3+ or buccal cells from 255 CLL patients for acquired genomic copy number aberrations (aCNA) using ultra-high-density Affymetrix SNP 6.0 arrays.  Overall, two or more subchromosomal aCNA were found in 39% (100/255) of all cases analyzed, while ≥3 subchromosomal aCNA were detected in 20% (50/255) of cases.  Subsequently, we have correlated genomic lesion loads (genomic complexity) with the clinical outcome measures time to first therapy (TTFT) and overall survival (OS).  Using multivariate analyses incorporating the most important prognostic factors in CLL together with SNP 6.0 array-based genomic lesion loads at various thresholds, we identify elevated CLL genomic complexity as an independent and powerful marker for the identification of CLL patients with aggressive disease and short survival.

first: Peter

last: Ouillette

first: Roxane

last: Collins

first: Sajid

last: Shakhan

first: Jinghui

last: Li

first: Edward

last: Peres

first: Lisa

last: Kujawski

first: Moshe

last: Talpaz

first: Mark

last: Kaminski

first: Cheng

first: Kerby

last: Shedden


title: Discovery of novel recurrent mutations and rearrangements in early T-cell precursor acute lymphoblastic leukaemia by whole genome sequencing

status: Public on Jan 10 2012

city: Memphis

first: Charles

middle: G

last: Mullighan

address: 262 Danny Thomas Place, MS 342

institute: St. Jude Children's Research Hospital

summary: Acute lymphoblastic leukaemia with early T-cell precursor immunophenotype (ETP ALL) is a highly aggressive subtype of ALL of unknown aetiology. To gain insights into the genetic basis of this disease, we performed whole genome sequencing of tumour and normal DNA of 12 children with ETP ALL. Analysis of structural and sequence variants in this discovery cohort, and mutation recurrence screening in a panel of 51 ETP and 43 non ETP ALL samples identified a high frequency of activating mutations in genes regulating cytokine receptor and Ras signalling, including IL7R, NRAS, KRAS, FLT3, BRAF, JAK1 and JAK3 in ETP ALL. Moreover, we identified multiple new targets of mutation in including GATA3, EP300, RUNX1, DNM2, ECT2L, HNRNPA1 and HNRNPR, as well as genes known to be mutated in T-ALL, including NOTCH1, PHF6, and WT1.. Five of 12 ETP ALL cases harboured novel chromosomal translocations, several of which accompanied complex multichromosomal rearrangements and resulted in the expression of chimeric in-frame fusion genes disrupting hematopoietic regulators, including ETV6-INO80D, NAP1L1-MLLT10 and RUNX1-EVX1. These results indicate that although ETP ALL is genetically heterogeneous, activation of Ras and cytokine receptor signalling distinguishes this disease from non-ETP ALL. These findings suggest that targeting this pathway may improve the currently dismal outcome of this disease.

overall_design: Gene expression profiling of an extended panel of childhood B-lineage and T-lineage acute lymphoblastic leukemia samples was performed using Affymetrix U133A arrays.

first: Guangchun

last: Song

first: Shann-Ching

last: Chen

first: Sheila

last: Shurtleff

first: Dario

last: Campana

first: James

last: Downing


title: Primary tumor grafts as advanced models for breast cancer that authentically reflect tumor histopathology, growth, metastasis, and patient outcomes (copy number)

status: Public on Oct 23 2011

city: Salt Lake City

first: Alana

last: Welm

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: Huntsman Cancer Institute / University of Utah

summary:
Development and pre-clinical testing of new cancer therapies is limited by the scarcity of in vivo models that authentically
reproduce tumor growth and metastatic progression. We report new models for breast tumor growth and metastasis, in the form
of transplantable tumors derived directly from individuals undergoing treatment for breast cancer. These tumor grafts represent
the diversity of human breast cancer and maintain essential features of the original tumors, including metastasis to specific
sites.  Co-engraftment of primary human mesenchymal stem cells maintains phenotypic stability of the grafts and increases tumor
growth by promoting angiogenesis. We also report that tumor engraftment is a prognostic indicator of disease outcome for newly
diagnosed women; orthotopic breast tumor grafting marks a step toward individualized models for tumor growth, metastasis,
and prognosis. This bank of tumor grafts also serves as a publicly available resource for new models in which to study the biology of
breast cancer.

overall_design: Single replicates of genomic DNA from 12 human breast cancer tumors and xenografts of those tumors in immunodeficient mice were hybridized to Affymetrix Human SNP 6.0 genotyping arrays.

first: Yoko

middle: S

last: DeRose

first: Guoying

last: Wang

first: Yi-Chun

last: Lin

first: Philip

last: Bernard

first: Saundra

last: Buys

last: Ebbert

first: Rachel

last: Factor

first: Cindy

last: Matsen

first: Brett

last: Milash

last: Nelson

first: Leigh

last: Neumayer

first: Lor

last: Randall

first: Inge

last: Stijleman

first: Bryan

middle: E

middle: L


title: CDKN1B encoding the cyclin-dependent kinase inhibitor 1B (p27) is located in the minimally deleted region of 12p abnormalities in myeloid malignancies and its low expression is a favorable prognostic marker in acute myeloid leukemia

status: Public on Dec 16 2011

city: New York

first: Hans-Ulrich

last: Klein

department: Neurology

institute: Columbia University Medical Center

summary: Alterations of the short arm of chromosome 12 (12p) occur in various hematological malignancies and ETV6 and CDKN1B, which are located on 12p, have been implicated as leukemogenic genes of interest. Design and Methods: We selected 7 patients with myeloid malignancies and small 12p deletions by FISH encompassing only the region centromeric of ETV6 and further evaluated them by SNP microarrays. Results: The minimal deleted region (MDR) contained nine genes only. These genes were subsequently analyzed by microarray expression profiling in an independent cohort of 781 cases mostly with different hematological malignancies or without any hematological malignancy: CREBL2, MANSC1, and CDKN1B were expressed in >25% of cases, while the other 6 genes were expressed in a minority of cases only. As CDKN1B is a cell cycle regulator and functions as a tumor suppressor gene, this gene was selected for further expression studies in 286 AML patients. In cases with low CDKN1B expression (expression level <1,160; 1st quartile), RUNX1-RUNX1T1 (11/83; 13.3%; vs. 5/203; 2.5%; p=0.001), PML-RARA rearrangements (11/83; 13.3%; vs. 4/203; 2.0%; p<0.001), 11q23/MLL rearrangements (6/83; 7.2%; vs. 4/203; 2.0%; p=0.038), and FLT3-TKD mutations (7/63; 11.1% vs. 6/167; 3.6%; p=0.047) were more frequently observed than in patients with intermediate/high expression (2nd-4th quartiles). Low CDKN1B expressers had longer median OS and EFS (not reached vs. 14.9 months; p=0.005 and 31.0 vs. 9.7 months; p=0.013, respectively) than intermediate/high expressers. Conclusions: CDKN1B is an interesting candidate gene as a potential biomarker for acute myeloid leukemia prognostication.

overall_design: Affymetrix SNP arrays were performed according to the manufacturer's directions using DNA extracted from mononuclear cells after Ficoll density centrifugation from bone marrow or peripheral blood samples.

first: Claudia

last: Haferlach

first: Ulrike

last: Bacher

first: Alexander

last: Kohlmann

first: Sonja

last: Schindela

first: Tamara

last: Alpermann

first: Wolfgang

last: Kern

first: Susanne

last: Schnittger

first: Torsten


title: MERLION LUNG CANCER STUDY_2_DNA

status: Public on Nov 22 2011

city: Evry

first: Cyril

last: Dalmasso

address: 23 bd de France

department: Mathématiques

institute: Université d'Evry Val d'Essonne

summary:
East-Asian (EA) patients with Non Small Cell Lung Cancer (NSCLC) are associated with a high proportion of non-smoking women, EGFR activating somatic mutations, and clinical responses to tyrosine kinase inhibitors. We identify copy number alterations specific to EA and Western European (WE) NSCLCs and conducted an integrative analysis using transcritomic data for identifying copy-number-driven candidate genes.
Samples were hybridized to Affymetrix Genome-Wide Human SNP 6.0 arrays according to the manufacturer’s specifications in the same center.

overall_design: 226 lung adenocarcinomas (90 East-Asian and 136 Western-European)  were analyzed for copy-number aberrations (CNAs) using a common high resolution SNP microarray platform.

first: Philippe

last: Broët

first: Eng-Huat

last: Tan

first: Marco

last: Alifano

first: Shenli

last: Zhang

first: Jeanie

last: Wu

first: Ming-Hui

last: Lee

first: Jean-François

last: Régnard

first: Darren

last: Lim

first: Heng-Nung

last: Koong

first: Thirugnanam

last: Agasthian

first: Lance

last: Miller

first: Elaine

first: Sophie

last: Camilleri-Broët

first: Patrick


title: CNV analysis for Generation of isogenic pluripotent stem cells differing exclusively at two early onset Parkinson point mutations

status: Public on Jul 26 2011

city: Cambridge

first: Albert

middle: W

last: Cheng

address: Room 453, 9 Cambridge Center

institute: Whitehead Institute

summary: Patient-specific induced pluripotent stem cells (iPSCs) derived from somatic cells provide a unique tool for the study of human disease in disease relevant cells, as well as a promising source for cell replacement therapies for degenerative diseases. However one of the crucial limitations before realizing the full promise of this “disease in a dish” approach has been the inability to do controlled experiments under genetically defined conditions. This is particularly relevant for disorders with long latency periods, such as Parkinson’s disease (PD), where in vitro phenotypes of patient-derived iPSCs are predicted to be subtle and susceptible to significant epistatic effects of genetic background variations. By combining zinc-finger nuclease (ZFN)-mediated genome editing and iPSC technology we provide a generally applicable solution to this key problem by generating isogenic pairs of disease and control human embryonic stem cells (hESCs) and hiPSCs lines that differ exclusively at a susceptibility variant for PD by modifying a single point mutation (A53T) in the α-synuclein gene. The robust capability to genetically correct disease causing point mutations in patient-derived hiPSCs represents not only a significant progress for basic biomedical research but also a major advancement towards hiPSC-based cell replacement therapies using autologous cells.

overall_design: ZFN-mediated genome edited human iPS cells or ES cells were assayed for genomic variation

first: Frank

last: Soldner


title: SNP array analysis of lung cancer NCI-H1395, diluted to different tumor cell concentrations

status: Public on Sep 09 2011

city: Uppsala

first: Anders

last: Isaksson

address: Akademiska sjukhuset ing61 3tr

country: Sweden

institute: Uppsala University

summary: In vitro mix of DNA from patient-matched lung cancer and blood cell lines, representing 30,50,70,100% tumor cell tissue, analyzed on Affymetrix 6.0 arrays.

overall_design: Lung cancer cell line H-1395 and patient-matched blood cell line BL1395 were obtained from ATCC and cultured according to their recommendations. DNA extraction was performed using the DNeasy Tissue Kit (Qiagen, Hilden, Germany). DNA from patient-matched Lung cancer and Blood cell lines NCI-H1395 and NCI-BL1395 were mixed to simulate tumor tissue with 30,50,70,100% cancer cells. The DNA ratio was adjusted to compensate for NCI-H1395 being nearly triploid. DNA was analyzed on Affymetrix SNP6.0 microarrays according to the manufacturer's protocol.

first: Markus

last: Rasmussen


title: Affymetrix SNP6.0 on Ollier disease-related tumors

status: Public on Aug 26 2011

city: Leiden

first: Twinkal

middle: Chandubhai

last: Pansuriya

state: Zuid-Holland

address: Albinusdreef 2

institute: LUMC

summary: Mutations in the PTH1R gene were reported but these mutations are limited to a small subgroup of patients. The etiology of Ollier disease is unknown. We therefore undertook genome-wide copy number and loss of heterozygosity (LOH) analysis using Affymetrix SNP 6.0 arrays on 37 tumors of 28 Ollier patients in combination with expression array using Illumina Beadarray v3.0 for 7 tumors of 6 patients. We used Affymetrix SNP 6.0 to find out LOH and copy number alterations in Ollier tumors.

overall_design: To understand the genetic mechanism behind the development of enchondroma, we mainly focus on enchondromas and found alterations were validated. We used 14 enchondromas and 23 chondrosarcomas of 28 Ollier patients. We also used 30 controls (blood, saliva or frozen tissue). As controls, normal DNA derived from fresh frozen muscle tissue (n=3), peripheral blood lymphocytes (n=4) or saliva (n=4) was available for 11 Ollier patients and 3 patients with unrelated bone diseases. We used blood lymphocyte DNA from 12 healthy controls and 1 HapMap sample. We also isolated DNA from saliva for 3 of these controls to validate the use of saliva DNA in this study.

middle: C


title: Role of miR-30 miRNAs during adipogenesis

status: Public on Jul 04 2011

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

summary: Analysis of human adipose tissue-derived stem cells (hMADS cells) overexpressing either miR-30a or miR-30d, as well as knocked-down for the whole miR-30 family. Gene expression was analyzed after 4 days in adipogenic medium. Data give insight into the role of miR-30 during adipogenesis, and identifies enriched predicted targets for miR-30.

overall_design: Human adipose tissue-derived stem cells (hMADS cells) were transfected with one of the following: premiR-30a (Ambion), premiR-30d (Ambion), premiR negative control #1 (Ambion). Three days after transfection, cells were submitted to adipogenic differentiation for 4 days. In a separate experiment, hMADS cells were transfected with either antimiR-30 or antimiR-neg (mismatch control), and then submitted to differentiation as described above. For each experimental condition, 2 hMADS cell clones were used independently (clone B7 and B9).

first: L

last: Zaragosi

first: B

last: Wdzieknoski

first: K

first: P

last: Villageois

last: Mari

first: C

last: Dani

last: Barbry


title: Gene expression signatures in GIST-T1 cells transfected with siRNA targeting HOTAIR

city: Sapporo

first: Hiromu

last: Suzuki

state: Hokkaido

address: S1, W17, Chuo-ku

department: Department of Molecular Biology

institute: Sapporo Medical University

summary: To analyze the effect of HOTAIR depletion in a gastrointestinal stromal tumor (GIST) cells, RNAi-mediated knockdown of HOTAIR was carried out using GIST-T1 cells. Gene expression microarray analysis revealed that a number of reported HOTAIR target genes were upregulated by knockdown of HOTAIR.   Moreover, we found that 1424 genes were upregulated by siHOT (>2-fold), and Gene Ontology analysis revealed enrichment of genes related to “nucleus”, “chromosome” and “membrane-bounded organelle.”

overall_design: For RNAi-mediated knockdown of HOTAIR, three different Stealth siRNAs against HOTAIR were generated by Invitrogen, after which a mixture of the three was used for transfection.  GIST-T1 cells in 6-well plates were transfected with 100 pmol of Stealth siRNA (Invitrogen) or a Stealth RNAi Negative Control Medium GC (Invitrogen) using Lipofectamine2000 (Invitrogen).  Total RNA was extracted 48 h after transfection.

first: Yasuhisa

last: Shinomura


title: A comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants (GenomeWideSNP_6)

status: Public on Jun 30 2011

city: Toronto

first: Stephen

last: Scherer

address: 686 Bay Street

department: Genetics and Genomic Biology

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

overall_design: 36 Samples

first: Dalila

last: Pinto

first: Jeffrey

middle: R

last: MacDonald


title: Human PC-3 prostate cancer cells: Control (shNTC; non-target shRNA) vs. shETV4 knock down (shETV4)

status: Public on Dec 06 2011

city: Zürich

first: Daniel

middle: Philipp

last: Stiehl

address: Winterthurerstr. 190

department: Physiology

country: Switzerland

institute: University of Zurich

summary: Transcriptional profiling of human PC-3 prostate cancer cells lentivirally infected with non-target control (NTC) short hairpin (sh)RNA comparing with lentivirally shRNA mediated human ETV4 knock-down. Cells were either cultured for 24 hours at 20% oxygen tension or 0.2% oxygen. Goal was to determine (i) genes affected by hypoxia in PC-3 NTC cells and (ii) identification of hypoxically induced genes requiring ETV4 for hypoxic regulation.

overall_design: four condition experiment, shNTC at 20% and 0.2% oxygen and shETV4 at 20% and 0.2% oxygen for 24 hours. Biological replicates: 3 for each of the 4 conditions

first: Kristin

last: Wollenick

first: Roland

middle: H

last: Wenger

middle: P


title: Clonal Selection Drives Genetic Divergence of Metastatic Medulloblastoma [Affymetrix SNP6 Arrays]

status: Public on Dec 09 2011

first: Paul

last: Northcott

summary: Medulloblastoma, the most common malignant pediatric brain tumour, disseminates by shedding cells into the cerebrospinal fluid, which then re-implant to cover the surface of the brain and spinal cord.  Metastases are a very poor prognostic sign at presentation and are usually lethal at recurrence.  Mechanisms driving dissemination have been described in the bulk primary tumour, with the underlying assumption that primary tumour and metastases are biologically similar.  Here we show that in both mouse and human medulloblastoma, multiple metastases from a single animal are extremely similar, but are genetically highly divergent from the primary tumour. Clonal genetic events in the metastases can be demonstrated in a restricted sub-clone of the primary tumour, suggesting that only rare cells within the primary tumour have the ability to metastasize.  Failure to account for the bicompartmental nature of primary and metastatic medulloblastoma represents a major barrier to the development of effective targeted therapies.

overall_design:
Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from cryopreserved human medulloblastoma tissue samples.
Copy number analysis of Affymetrix SNP6 arrays was performed for 17 pediatric medulloblastoma samples.  Samples comprise a series of 7 patient-matched primary/metastatic cases.

middle: A

first: Xiaochong

last: Wu

first: Michael

last: Taylor


title: Intellectual disability and mood disorder associated with partial deletion of the Neurexin 1 Gene

status: Public on Jun 25 2011

city: Las Vegas

first: Patricia

last: Bray-Ward

state: NV

address: 1707 W Charleston Blvd, 110B

department: Pediatrics

institute: University of Nevada School of Medicine

summary:
Abstract
Background
Neurexins are proteins located in the presynaptic membrane that bind postsynaptic ligands, neuroligins, neurexophilins, and dystrophoglycan. They exert profound effects on neurological function by mediating signalling across synapses and determining synaptic characteristics through the recruitment of additional proteins for synapse formation. Alterations in neurexin-encoding genes cause cognitive disorders such as autism, developmental delay and schizophrenia. The three neurexin genes in the human genome (NRXN1, NRXN2, and NRXN3) each have two different functional promoters, producing a large (alpha) and small (beta) transcript with corresponding proteins. NRXN1 produces hundreds, perhaps thousands, of different transcripts with differential localization in the CNS.
Results
We report here the identification of an individual (53825) with mild dysmorphia, severe language disorder, mild intellectual disability, attention deficit hyperactivity disorder (ADHD), and a mood disorder. Genomic analysis by Affymetrix 6.0 Gene Chip and FISH (fluorescence in situ hybridization) using probes specific for NRXN1 revealed a hemizygous deletion of approximately 190 Kb, which includes exons 3-5 of NRXN1. This deletion should result in the absence of the vast majority of different NRXN1 alpha transcripts from one of the NRXN1 gene copies, without effecting NRXN1 beta transcription.

overall_design:
Copy number analysis of Affymetrix 6.0 SNP arrays was performed according to the manufacturer's directions on DNA extracted from cryopreserved diagnostic bone marrow or peripheral blood samples for pediatric patients.
One sample showed partial deletion of NRXN1 alpha; data presented in this Series.


title: Affymetrix SNP array data for Primary Effusion Lymphoma samples

status: Public on Jun 23 2011

city: Chapel Hill

first: Dirk

last: Dittmer

address: 116 Manning Drive, CB# 7290

department: Microbiology & Immunology

institute: University of North Carolina at Chapel Hill

summary: Primary Effusion Lymphoma (PEL) is a Diffuse-Large B-cell Lymphoma (DLBCL) with poor prognosis. 100% of PEL carry the genome of Kaposi's Sarcoma-associated herpesvirus (KSHV) and approximately half are co-infected with Epstein-Barr virus (EBV). We profiled genomic aberrations in PEL using the Affymetrix 6.0 SNP array. This identified for the first time individual genes that are altered in PEL. 10/13 (76%) samples were deleted for both the fragile site tumor suppressors WWOX and FHIT. Alterations were also observed in: DERL1, ETV1, RASA4, TPK1, TRIM56 and VPS41 genes, which are yet to be characterized for their roles in cancer. Co-infection with EBV was associated with significantly fewer gross genomic aberrations. PEL could be segregated into EBV positive and EBV negative clusters on the basis of host chromosome alterations. The genomic signature of PEL cells in culture was analogous to those explanted from xenograft tumors. This suggests a model in which both host and virus contribute to the PEL phenotype.

overall_design: 17 samples (no replicates) were analyzed using Partek Genomic Suite software

first: Debasmita

last: Roy

first: Sang-Hoon

last: Sin

first: Blossom

last: Damania


title: Notch/HES1-mediated PARP1 activation: A cell-type specific mechanism for tumor suppression

status: Public on Dec 12 2011

first: Charles

last: Mullighan

address: 262 Danny Thomas Place

department: Pathology

institute: St Jude Children's Research Hospital

summary: Notch signaling plays both oncogenic and tumor suppressor roles, depending on cell type. In contrast to T cell acute lymphoblastic leukemia (T-ALL), where Notch activation promotes leukemogenesis, induction of Notch signaling in B-ALL leads to growth arrest and apoptosis. The Notch target Hairy/Enhancer of Split1 (HES1) is sufficient to reproduce this tumor suppressor phenotype in B-ALL, however the mechanism is not yet known. Here we report that HES1 regulates pro-apoptotic signals via the novel interacting protein Poly ADP-Ribose Polymerase1 (PARP1) in a cell type-specific manner. The interaction of HES1 with PARP1 inhibits HES1 function, induces PARP1 activation and results in PARP1 cleavage in B-ALL. HES1-induced PARP1 activation leads to self-ADP ribosylation of PARP1, consumption of NAD+, diminished ATP levels, and translocation of the Apoptosis Inducing Factor (AIF) from mitochondria to the nucleus, resulting in apoptosis in B-ALL, but not T-ALL. Importantly, induction of Notch signaling via the Notch agonist peptide DSL can reproduce these events and leads to BALL apoptosis. The novel interaction of HES1 and PARP1 in B-ALL modulates the function of the HES1 transcriptional complex and signals through PARP1 to induce apoptosis. This mechanism reveals a cell type-specific pro-apoptotic pathway which may lead to Notch agonist-based cancer therapeutics.

overall_design: Study involved the gene expression profiling of human acute lymphoblastic leukemia samples, and comparison of the levels of expression NOTCH1 pathway genes and targets across ALL subtypes

first: Sankaranarayanan

last: Kannan

first: Wendy

last: Fang

first: Guangchun

last: Song

first: Richard

last: Hammitt

first: John

last: McMurray

first: Patric

last: Zwiedler-McKay


title: Allele-specific copy number analysis of tumor samples with aneuploidy and tumor heterogeneity

first: Anders

last: Isaksson

summary: Chromosomal aberrations were studied both in a lung cancer cell line and colorectal cancer tumor samples. Results were verified by SKY karyotypes and by DNA ploidy analysis. The sensitivity of detecting chromosomal aberrations in tumor samples was evaluated by analyzing data from simulated mixtures of the lung cancer cell line H1395 and the normal cell line 1395BL from the same patient.

overall_design: Copy number analysis is presented on 12 colorectal cancer tumor samples and on in silico dilutions of a lung cancer cell line and its patient-matched blood cell line.

first: Markus

last: Rasmussen

first: Magnus

last: Sundström

first: Hanna

last: Kultima

first: Johan

last: Botling

first: Patrick

last: Micke

first: Helgi

last: Birgirsson

first: Bengt

last: Glimelius


title: Genomic exploration of monozygotic twins discordant (MZD) for schizophrenia uncovers de novo mutations (DNM) and reveals candidate genes

status: Public on Nov 11 2011

city: London

first: Christina

last: Castellani

address: Biological and Geological Sciences Building

department: Biology

institute: The University of Western Ontario

summary: We examined six pairs of monozygotic twins discordant (MZD) for schizophrenia and identified copy number variation (CNV) and single nucleotide polymorphism (SNP) differences between affected and unaffected co-twins using the Affymetrix Genome Wide SNP 6.0.

overall_design:
Affymetrix SNP arrays were performed according to the manufacurer's protocol on DNA extracted from whole blood
CNV analysis was done using Affymetrix Genotyping Console 4.0 and Partek Genotyping Suite

first: Shiva

last: Singh


title: Assessment of palindromes as platforms for DNA amplification in breast cancer

status: Public on Jun 13 2011

city: Seattle

first: Jamie

last: Guenthoer

state: WA

address: 1100 Fairview Ave N

department: Human Biology

institute: Fred Hutchinson Cancer Research Center

type: Genome variation profiling by genome tiling array

summary: DNA amplification, particularly of chromosomes 8 and 11, occurs frequently in breast cancer and is a key factor in tumorigenesis, often associated with poor prognosis. The mechanisms involved in the amplification of these regions are not fully understood.  Studies from model systems have demonstrated that palindrome formation can be an early step in DNA amplification, most notably seen in the breakage-fusion-bridge (BFB) cycle. Therefore, palindromes might be associated with gene amplicons in breast cancer. To address this possibility, we coupled high-resolution palindrome profiling by the Genome-wide Analysis of Palindrome Formation (GAPF) assay with genome-wide copy-number analyses on a set of breast cancer cell lines and primary tumors to spatially associate palindromes and copy-number gains. We identified GAPF-positive regions distributed non-randomly throughout cell line and tumor genomes, often in clusters and associated with copy-number gains. Commonly amplified regions in breast cancer, chromosomes 8q and 11q, had GAPF-positive regions flanking and throughout the copy-number gains. We also identified amplification-associated GAPF-positive regions at similar locations in subsets of breast cancers with similar characteristics (e.g., ERBB2 amplification). These shared positive regions offer the potential to evaluate the utility of palindromes as prognostic markers, particularly in premalignant breast lesions. Our results implicate palindrome formation in the amplification of regions with key roles in breast tumorigenesis, particularly in subsets of breast cancers.

overall_design: DNA palindrome profiles generated using the Genome-wide Analysis of Palindrome Formation (GAPF) assay. Whole genome profiling was performed on Colo320DM vs HF and MCF7 vs HF. Prolifing of chromosomes 8, 11, and 12 was performed on BT474 vs PBL, MCF7 vs PBL, MDA231 vs PBL, UACC893 vs PBL and 4 primary invasive ductal carcinomas (IDCs) vs PBL. Copy-number analysis on SNP 6.0 arrays was performed on Colo320DM and the 4 primary IDCs. The CEL files for the 4 breast cancer cell lines were obtained from the Wellcome Trust Sanger Institute Cancer Genome Project web site (http://www.sanger.ac.uk/genetics/CGP). All SNP arrays were compared to the HapMap cellection reference.

first: J

first: S

last: Diede

first: H

last: Tanaka

first: X

last: Chai

first: L

last: Hsu

last: Tapscott

first: P

last: Porter


title: Gene expression profiling in acute myeloid leukemia with mutated NPM

status: Public on Jan 05 2012

city: Milan

first: Myriam

last: Alcalay

address: Via Adamello 16

department: Experimental Oncology

country: Italy

institute: European Institute of Oncology

summary: Approximately one third of acute myeloid leukemias (AMLs) are characterized by aberrant cytoplasmic localization of Nucleophosmin (NPMc+ AML), consequent to mutations in the NPM putative nucleolar localization signal.  These events are mutually exclusive with the major AML-associated chromosomal rearrangements, and are frequently associated with normal karyotype, Fms-like tyrosine kinase (FLT3) mutations and multilineage involvement. We report the gene expression profiles of 78 de novo AMLs (72 with normal karyotype; 6 with non-major chromosomal abnormalities) that were characterized for the subcellular localization and mutation status of NPM. Unsupervised clustering clearly separated NPMc+ from NPMc- AMLs, regardless of the presence of FLT3 mutations or non-major chromosomal rearrangements, supporting the concept that NPMc+ AML represents a distinct entity. The molecular signature of NPMc+ AML includes up-regulation of several genes putatively involved in the maintenance of a stem cell phenotype, suggesting that NPMc+ AML may derive from a multipotent hematopoietic progenitor.

overall_design: 78 de novo AMLs, negative for AML-associated chromosomal translocations at the cytogenetic and/or molecular level.


title: Genetic analysis of ancestry, admixture, and selection in Bolivian and Totonac populations of the New World

status: Public on Jun 09 2011

first: Scott

last: Watkins

department: Human Genetics

institute: University of Utah

summary:
The genetic structure of some native Bolivians has been substantially influenced by admixture from Europeans, which we estimate to have occurred approximately 360 – 384 years ago.  Consistent with historical accounts of male admixture, Y-chromosome haplogroups typical of Europeans were found in 39% of our Bolivian samples.  No evidence of African admixture was found in native Bolivians. The Mesoamerican Totonacs have little evidence of European or African admixture.  Our analysis indicates that some admixed Bolivians have Native American mtDNA and Y-chromosomes but harbor up to 30% European autosomal ancestry, demonstrating the need for autosomal markers to assess ancestry in admixed populations.
From a dense genome-wide panel of 815,377 markers, we developed a set of 324 AIMs, specific for Native American ancestry.  As few a 40-50 of these markers successfully predict New World ancestry in the ascertainment panel of Bolivians and Totonacs.  The markers easily distinguish New World from Old World ancestry, even for populations more closely related to the Americas such as central and eastern Asians, and were effective for New World vs. Old World comparisons in five other geographically and culturally distinct populations of the Americas.  SNPs demonstrating very high divergence between the two Native American populations and major Old World populations are found on haplotypes that are shared and occur at similar frequencies in other indigenous low-admixture American populations examined here (i.e. Pima, Maya, Colombian, Karitiana, and Surui).   After excluding the possibility of recent relatedness, our results indicate that native Bolivians and Totonacs share ancestry with other American populations through a substantial contribution from a common founding population, population bottlenecks, and possible natural selection on functional variation.

overall_design: Population structure, admixture, and selection were assessed with a genome-wide panel of 815,377 autosomal markers, Y-chromosome STR and SNPs, and mtDNA sequence data.

first: Jin

last: Xing

first: Chad

last: Huff

first: David

last: Witherspoon

first: Yuhua

last: Zhang

first: Ugo

last: Perego

last: Woodward

first: Lynn

middle: B

last: Jorde


title: New markers for minimal residual disease detection in acute lymphoblastic leukemia

status: Public on Apr 20 2011

first: Jeffery

last: Klco

summary: To identify new markers for minimal residual disease (MRD) detection in acute lymphoblastic leukemia (ALL), we compared genome-wide gene expression of lymphoblasts from 270 patients with newly  diagnosed childhood ALL to that of normal CD19 CD10  B-cell progenitors (n=4). Expression of 30 genes differentially expressed by > 3-fold in at least 25% of cases of ALL (or 40% of ALL subtypes) was tested by flow cytometry in 200 B-lineage ALL and 61 nonleukemic BM samples, including samples containing hematogones. Of the 30 markers, 22 (CD44, BCL2, HSPB1, CD73, CD24, CD123, CD72, CD86, CD200, CD79b, CD164, CD304, CD97, CD102, CD99, CD300a, CD130, PBX1, CTNNA1, ITGB7, CD69, CD49f) were differentially expressed in up to 81.4% of ALL cases; expression of some markers was associated with the presence of genetic abnormalities. Results of MRD detection by flow cytometry with these markers correlated well with those of molecular testing (52 follow-up samples from 18 patients); sequential studies during treatment and diagnosis-relapse comparisons documented their stability. When incorporated in 6-marker combinations, the new markers afforded the detection of 1 leukemic cell among 105 BM cells. These new markers should allow MRD studies in all B-lineage ALL patients, and substantially improve their sensitivity.

overall_design: Study involved the gene expression profiling of human acute lymphoblastic leukemia samples. We first screened for genes expressed at different levels in ALL cells and their normal counterparts by comparing genome-wide gene expression profiles of 270 cases of newly diagnosed B-lineage ALL to those of highly purified normal CD19 CD10  cells. Genes that had a substantially abnormal expression in leukemic cells were then tested by flow cytometry to assess levels of protein expression. The most promising molecules were examined in detail for their usefulness as MRD markers.

first: Elaine

last: Coustan-Smith

first: Guangchun

last: Song

first: Christopher

last: Clark

first: Laura

last: Key

first: Peixin

last: Liu

first: Mohammad

last: Mehrpooya

first: James

last: Downing

first: Dario

last: Campana


title: SNP array analysis on Maffucci tumours

status: Public on Jul 19 2011

first: Twinkal

last: Pansuriya

summary: Here we have used four enchondromas and two chondrosarcomas of Maffucci patients. We also had one normal sample available for paired analysis in one of the chondrosarcoma II. We did not find any LOH or coomon copy number variation in all Maffucci enchondromas while chondrosarcomas are genetically unstable.

overall_design: Affymetrix SNP 6.0 array was performed using 4 EC and 2CS of Maffucci patients. Illumina expression v3 array was possible to perform using only 1 EC and 2 CS due to rarity of the disease. For SNP array, we used 29 control samples submitted previously (GSE22965) to creat baseline.

first: Jan

last: Oosting

first: Judith

last: Bovee


title: Chromothripsis identifies a rare and aggressive entity among newly diagnosed multiple myeloma patients

status: Public on Jun 06 2011

city: Saint Herblain

first: Wilfried

last: Gouraud

address: bd Jacques Monod

department: Integrated Center of Oncology René Gauducheau

institute: ICO (Integrated Center of Oncology Nantes)

summary: Comment on published article "Massive genomic rearrangement acquired in a single catastrophic event during cancer development." by Stephens, P.J., Greenman, C.D., Beiyuan, F., Yang, F., Bignell, G.R., Mudie, L.J., Pleasance, E.D., Lau, K.W., Beare, D., Stebbings, L.A., et al. (2011). Cell 144, 27-40. [PMID: 21215367]

overall_design:
10 myeloma patients examined with high resolution genome-wide chip
SUPPLEMENTARY FILE: Copy number table.

first: Florence

last: Magrangeas

first: Hervé

last: Avet-Loiseau

first: Stéphane

last: Minvielle


title: Affymetrix copy number data for melanoma cell line mapping

status: Public on Apr 07 2011

city: Vienna

first: Mario

last: Mikula

address: Waehringergürtel 18-20

department: General Dermatology

country: Austria

institute: Medical University Vienna

summary: We searched for putative phenotypic and genotypic differences between primary lesions and melanoma metastasis. Therefore, we investigated melanoma cells derived either from the primary tumor or from lymph node metastasis of the same individual patient. In vitro studies revealed high migratory and anchorage-independent growth of metastasis-derived cells. Unexpectedly, whole genome DNA analysis displayed a total of 10 homozygous losses in the primum-derived cell line, whereas the metastasis–derived cell line only shared 5 of those losses. We further tested these cells in a mouse model for intradermal melanoma growth and detected fast growth of the metastasis-derived cell line and delayed growth of primum-derived cells. However, after re-grafting of primum-derived cells, tumor growth kinetic was accelerated and therefore comparable to metastasis-derived cells. Moreover, re-grafted primum-derived cells now also harboured the same reduced DNA deletion pattern, identical to human metastasis-derived cells. We conclude that our xenotransplantation model mimics clonal selection from a heterogeneous starting population, and we suggest that tumor cell progression at the metastatic niche can occur parallel and independently from the primary tumor. Therefore, we propose that for mutation-targeted therapy approaches, the genotyping procedure should include primary as well as metastatic melanoma biopsies.

overall_design: DNA was extracted from in vitro grown cell lines, and Affymetrix SNP6.0 arrays were performed according to the manufacturer's instructions. Intensity Log2 ratios were used to manually search for homozygous deletions via the genotyping console.

first: Alexander

last: Swoboda


title: Tissue samples from the same individual patient

summary: We searched for putative phenotypic and genotypic differences between primary lesions and melanoma metastasis. Therefore we investigated melanoma cells derived either from the primary tumor or from lymph node metastasis of the same individual patient. In vitro studies revealed high migratory and anchorage independent growth of metastasis-derived cells. Unexpectedly, whole genome DNA analysis displayed a total of 10 homozygous losses in the primum-derived cell line, whereas the metastasis–derived cell line only shared 5 of those losses. We further tested these cells in a mouse model for intradermal melanoma growth and detected fast growth of the metastasis-derived cell line and no growth of primum-derived cells. Therefore we suggest that tumor cell progression at the metastatic niche can occur parallel and independently from the primary tumor. Additionally we screened melanoma samples isolated from patients and could identify one case were the primum harboured deletions not present in the metastatic lesion. We propose that for mutation-targeted therapy genotyping should be performed not only from primary, but foremost from metastatic melanoma cells.

overall_design: Blood samples as well tumor samples were directly processed for DNA isolation and subsequent chip hybridization. Each sample was hybridized onto a single affymetrix SNP 6.0 chip.

first: Oliver

last: Schanab


title: Analysis of the gene expression pattern of bovine blastocysts at three stages of development

status: Public on Feb 17 2011

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

institute: Université Laval

summary: Blastocyst formation is a primordial event of pre-implantation development since it is required for pregnancy establishment and progression. The blastocyst plays a pivotal role because it is the stage at which the embryo is transferred and starts coordinated cross-talks with the mother. It is also the terminal step of pre-implantation developmentbefore transfer; it reflects all stresses the embryo may have faced during the process of in-vitro treatment. Achieving the formation of a morphologically healthy blastocyst following normal kinetics is a good sign but remains a poor indicator of embryo quality. Considering the limitation of the invasive methods for competence assessment, the analysis of blastocysts’ gene expression is a promising way to improve our understanding of blastocyst formation and to study the effects of different treatments on gene expression. Methods: Early, expanded and hatched blastocysts were collected for RNA extraction, amplification, and cDNA microarray hybridization. Gene candidates (IFNt, PLAC8, SSLP1, AKR1B1, HNRNPA2B1, ARGFX, NANOS, CCNB1) were selected and confirmed using Q-RT-PCR to validate the microarray data. Results: Our analysis show that hatched blastocysts are enriched in genes transcripts implicated in implantation, cell adhesion and extracellular matrix digestion. Early blastocysts expressed genes mainly involved in cell cycle control, transcription and translation. Q-RT-PCR validated most microarray results (87.5%). Some of the differentially expressed genes are interesting as potential markers of competence. Conclusions: Overall, our study provides new insights into the molecular regulation of blastocyst formation. In addition, it could help assess blastocyst staging and select better embryos based on the expression of quality markers.

overall_design: In the present study the Laval/Sirard_bovine_embryo_3K_V3.0 array was used to conduct a series of 18 hybridizations (for three Blastocysts stages (early, expended, hatched) with three biological replicates and dye swaps) in a loop design experiment.

first: Wiem

last: Rekik

first: Isabelle

last: Dufort


title: ENPP1 deletion and infantile arterial calcification

status: Public on Jan 26 2011

city: Salt Lake City

first: Scott

last: Watkins

country: USA

summary: The goal of this study was to identify new mutations in the ENPP1 gene that produce infantile arterial calcification and fetal demise.  A stillborn (proband) was diagnosed with infantile arterial calcification.  Mutations in the ENPP1 gene account for ~80% of the cases of infantile arterial calcification through loss of function in both alleles (recessive inheritance).

overall_design:
The proband and parents were screened for mutations by sequencing.  The male parent was analyzed by microarray to verify and map a deletion suspected by sequence data analysis. The sample was called with a Europeans reference. ENPP1 position is located at chr6:132,170,849-132,257,988 (hg18).

The matrix data provided contains only the deleted region and flanking probes.


title: Genomic alterations of chromosome 11 induce transcriptome dysregulation in aggressive and malignant prolactin tumours

status: Public on Sep 16 2011

city: BRON

first: Joël

last: LACHUER

address: 16 avenue du Doyen Lépine

institute: INSERM

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

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

overall_design: Refer to individual Series


title: Genome-wide survey reveals predisposing diabetes type 2-related DNA methylation variations in human peripheral blood

status: Public on Oct 18 2011

city: Jerusalem

first: Asaf

last: Hellman

address: Hadassah Medical School

department: Developmental Biology and Cancer Research

country: Israel

institute: Hebrew University

summary: Inter-individual DNA methylation variations were frequently hypothesized to alter individual susceptibility to Type 2 Diabetes Mellitus (T2DM). Sequence-influenced methylations were described in T2DM-associated genomic regions, but evidence for direct, sequence-independent association with disease risk is missing. Here we explore disease-contributing DNA methylation through a stepwise study design: first, a pool-based, genome-scale screen among 1,169 case and control individuals revealed an excess of differentially methylated sites in genomic regions that were previously associated with T2DM through genetic studies. Next, in-depth analyses were performed at selected top-ranked regions. A CpG site in the first intron of the FTO gene showed small (3.35%) but significant (p=0.000021) hypomethylation of cases relative to controls. The effect was independent of the sequence polymorphism in the region and persists among individuals carrying the sequence risk alleles. The odds of belonging to the T2DM group increased by 6.1% for every 1% decrease in methylation (OR=1.061, 95% CI: 1.032-1.090), and the sensitivity (AUC = 0.638, 95% CI: 0.586-0.690), (Males=0.675, Females=0.609), was better than of the strongest known sequence variant. Furthermore, a prospective study in an independent population cohort revealed significant hypomethylation of young individuals that later progressed to T2DM, relative to the individuals that stayed healthy. Further genomic analysis revealed co-localization with gene enhancers and with binding sites for methylation-sensitive transcriptional regulators. The data showed that low methylation level at the analyzed sites is an early marker of T2DM, and suggest a novel mechanism by which early-onset, inter-individual methylation variation at isolated non-promoter genomic sites predisposes to T2DM.

overall_design: Five pools of DNA samples consist of 710 T2DM patients and 459 control individuals were analyzed for average methylation levels at 1,461,753 DNA genomic fragments containing 3,359,645 CpG methylation sites using four SNP arrays for each sample, two 'genomic' (before treatment) replicates and two MSRE (treatment with a cocktail of five methyl-sensitive-restriction-enzyme) replicates. The analysis was done using the Affymetrix SNP 6.0 array.


title: SNP arrays in matched diagnosis/remission samples of normal karyotype-acute myeloid leukemia

status: Public on Dec 31 2010

city: Catania

first: Vincenza

last: Barresi

address: V.le A Doria, 6

institute: University of Catania

summary: We analysed, by last-generation high-resolution SNP arrays, Normal Karyotype (NK)-AML patients at diagnosis (Dx) and remission (R) phases, in order to determine the number of tumor-associated copy number abnormalities (CNAs) and copy neutral-loss of heterozygosity (CN-LOH) regions per patient and to identify possible recurring genomic abnormalities. The number of tumor-associated CNAs was detemined after comparison of 11 matched Dx/R samples using stringent conditions able to reduce the number of false positive CNAs. 8 additional unmatched Dx samples were included in the analysis of recurring CNAs and for detection of broad CN-LOH segments. With the exception of a single outlier case, a low number of CNAs per patient was detected (median value of 1 somatic loss or gain per patient). However, a high prevalence of CNAs (60-70% of the patients showed at least 1 tumor-associated gain or loss) and few recurring CNAs were observed, thus providing new hints towards identification of cooperating mutations.  An extensive search of all CN-LOH regions > 1 Mb revealed only 3 broad regions (terminal 12Mb of 22q, terminal 27Mb of 1p and the whole chromosome 21) in three patients out of 19 (16%). CN-LOH of the whole chromosome 21 was responsible for homozygosity of a missense mutation (R80C) of RUNX1/AML1. Our study suggests that a relative submicroscopic copy number stability NK-AML genomes is associated with low recurrence of specific CNAs and CN-LOH in NK-AML patient population.

overall_design: Nineteen AML bone marrow samples were collected at the time of diagnosis (>90% blasts), defined as karyotypically-normal on the basis of standard metaphase cytogenetics (MC) and analysed by the Affymetrix SNP 6.0 arrays. In 11 of such cases (matched Dx) we obtained a bone marrow sample at the remission phase (matched R) of comparable high quality as evaluated by Contrast QC and MAPD values. In 8 cases (unmatched Dx) the corresponding R sample was not available or was not of comparable quality. As a reference set the publicly available data from 270 HapMap individuals were used.

first: Daniele

middle: F

last: Condorelli


title: Genome-Wide Analysis of Somatic Copy Number Alterations (CGH, SNP) and Gene Expression (RNA-seq) in Metastatic Melanoma

city: Lausanne

first: Armand

last: Valsesia

address: Bâtiment Génopode

institute: Ludwig Institute for Cancer Research

summary: All cancers are diseases of the genome. A combination of somatic point mutations, focal amplifications and deletions, and chromosome level aberrations conspire to disrupt gene expression and the interplay between signaling pathways that control normal growth and tissue homeostasis. Here we investigate somatic copy number abberations in metastatic melanomas.

overall_design: A metastatic melanoma was assayed on Affymetrix SNP arrays to detect copy number abberations. 7 cutaneous melanomas as well as their matched control ( peripheral blood lymphocytes (PBL) or Epstein-Barr virus transformed lymphoblastoid cell lines ) and 2 control melanocytes were assayed on Illumina SNP arrays. 7 metastatic melanomas were hybridized on Agilent CGH arrays using donor matched control as reference.

first: Brian

middle: J

last: Stevenson

first: Christian

last: Iseli

first: Donata

last: Rimoldi


title: Orthotopic xenografts of RCC retain histological, immunophenotypic and genetic features of tumors in patients

status: Public on May 05 2011

city: Boston

first: Chiara

last: Grisanzio

address: 44 Binney Street

department: Medical Oncology

institute: DFCI

summary:
Development of a clinically relevant animal models of RCC for preclinical investigations.
For DNA copy number analysis, the Sty I (250K) SNP array of the 500K Human Mapping Array (Affymetrix) was used. Arrays were scanned by GeneChip Scanner 3000 7G. Probe-level signal intensities were normalized to a baseline array with median intensity using invariant set normalization and SNP-level signal intensities were obtained using a model-based (PM/MM) method.
Keywords: SNP array data, renal cell carcinoma

overall_design: To ensure at least 70% contribution from tumor cells, enriched tumor areas from 10 original RCCs and 10 corresponding xenografts were isolated from 7 µm-thick tissue frozen sections using a fine needle with the aid of an optical microscope. DNA was then extracted using phenol chloroform

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