High-Resolution Genomic Profiling of Philadelphia Chromosome-Positive (Ph+) Acute Lymphoblastic Leukaemia (ALL) Identified Novel Recurrent Copy Number Variations Involved in Both Pathogenesis and Resistance to Tyrosine Kinase Inhibitors.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 230-230
Author(s):  
Ilaria Iacobucci ◽  
E. Ottaviani ◽  
A. Astolfi ◽  
S. Soverini ◽  
N. Testoni ◽  
...  
Keyword(s):  
High Resolution ◽  
Copy Number ◽  
Complex Disease ◽  
B Lymphocyte ◽  
Philadelphia Chromosome ◽  
Snp Array ◽  
Copy Number Variations ◽  
Imatinib Resistance ◽  
Copy Number State ◽  
Monosomy 7

Abstract The Ph chromosome is the most frequent cytogenetic aberration associated with ALL and it represents the single most significant adverse prognostic marker. Despite the encouraging results achieved with imatinib, resistance develops rapidly and is quickly followed by disease progression. Some mechanisms of resistance have been widely described but the full knowledge of contributing factors driving both the disease and resistance remains to be defined. In order to identify at submicroscopic level genetic lesions driving leukemogenesis and resistance, we profiled until now the genomes of 18 patients, out of 55 Ph+ ALL patients treated in our institute, at diagnosis (n=11) or at the time of haematological relapse (n=7) during therapy with imatinib or dasatinib. 250 ng of genomic DNA were processed on 500K single nucleotide polymorphism (SNP) array according to protocols provided by the manufacturer (Affymetrix Inc., Santa Clara, CA, USA). The median SNP call rate of analysed samples was 96%. Raw signal data were analyzed by BRLMM algorithm and copy number state was calculated with respect to a set of 48 Hapmap normal individuals and a diploid reference set of samples obtained from acute leukaemia cases in remission. Regions of amplification and deletion were visualized by Integrated Genome Browser and mapped to RefSeq to identify the specific genes involved in the lesion. Our analysis identified multiple copy number alterations per case, with deletions outnumbering amplification almost 3:1. Lesions varied from loss or gain of complete chromosome arms (trisomy 4, monosomy 7, loss of 9p, 10q, 14q, 16q and gain of 1q and 17q) to microdeletions and microduplications targeting genomic intervals. The recurring microdeletions that we detected in at least 50% of patients (both at diagnosis and at relapse) included 1p36.21 (PRAMEF), 3q29 (TFCR), 7p14.1 (AMPH), 8p23 (DEFB105A), 14q11.2 (DAD1), 16p13.11 (PDXDC1, NTAN1, RRN3), 16p11.2 (SNP) and 19p13.2 (CARM1, SMARCA4). A common microamplification was 4q13.2 (TMPRSS11E) and 17q21.31. Some genomic alterations were identified in genes regulating B-lymphocyte differentiation, such as PAX5 (n=3), BLNK (n=1) and VPREB1 (n=6) and in genes with an established role in leukemogenesis, such as MDS, BTG1, MLLT3 and RUNX1. Furthermore, many of the deletions detected included genes encoded for phosphatase proteins (e.g. PTPRD, PPP1R9B, PTPN18) and for zinc-finger proteins without any difference between diagnosis and resistance. It is noteworthy that some lesions felt in regions lacking annotated genes (loss: 2p11.2, 3p12.3, 7q11.21 and 14q32.33; gain: 8q23.3 and 13q21.1). Using high-resolution genome wide approach we showed that Ph+ ALL is a more complex disease characterized by multiple genomic anomalies which may provide new insights into the mechanisms underlying leukemogenesis and may be used as targets for existing or novel drugs. Supported by: European LeukemiaNet, COFIN 2003, Novartis Oncology Clinical Development, AIL.

High-resolution genome-wide array-CGH reveals copy number variations associated with premature ovarian failure

Placenta ◽  
2011 ◽  
Vol 32 ◽  
pp. S282
Author(s):  
Paola Scaruffi ◽  
Sara Stigliani ◽  
Annamaria Jane Nicoletti ◽  
Pier Luigi Venturini ◽  
Gian Paolo Tonini ◽  
...  
Keyword(s):  
High Resolution ◽  
Premature Ovarian Failure ◽  
Copy Number ◽  
Array Cgh ◽  
Copy Number Variations ◽  
Ovarian Failure ◽  
Genome Wide

scholarly journals Integrating genomic correlation structure improves copy number variations detection

2020 ◽  
Author(s):  
Xizhi Luo ◽  
Fei Qin ◽  
Guoshuai Cai ◽  
Feifei Xiao
Keyword(s):  
Copy Number ◽  
Snp Array ◽  
Copy Number Variations ◽  
Correlation Structure ◽  
Supplementary Information ◽  
Dependence Structure ◽  
Random Pattern ◽  
Genomic Correlation ◽  
Equal Chance ◽  
Cnv Detection

Abstract Motivation Copy number variation plays important roles in human complex diseases. The detection of copy number variants (CNVs) is identifying mean shift in genetic intensities to locate chromosomal breakpoints, the step of which is referred to as chromosomal segmentation. Many segmentation algorithms have been developed with a strong assumption of independent observations in the genetic loci, and they assume each locus has an equal chance to be a breakpoint (i.e. boundary of CNVs). However, this assumption is violated in the genetics perspective due to the existence of correlation among genomic positions, such as linkage disequilibrium (LD). Our study showed that the LD structure is related to the location distribution of CNVs, which indeed presents a non-random pattern on the genome. To generate more accurate CNVs, we proposed a novel algorithm, LDcnv, that models the CNV data with its biological characteristics relating to genetic dependence structure (i.e. LD). Results We theoretically demonstrated the correlation structure of CNV data in SNP array, which further supports the necessity of integrating biological structure in statistical methods for CNV detection. Therefore, we developed the LDcnv that integrated the genomic correlation structure with a local search strategy into statistical modeling of the CNV intensities. To evaluate the performance of LDcnv, we conducted extensive simulations and analyzed large-scale HapMap datasets. We showed that LDcnv presented high accuracy, stability and robustness in CNV detection and higher precision in detecting short CNVs compared to existing methods. This new segmentation algorithm has a wide scope of potential application with data from various high-throughput technology platforms. Availability and implementation https://github.com/FeifeiXiaoUSC/LDcnv. Supplementary information Supplementary data are available at Bioinformatics online.

High-Resolution SNP Microarray Investigation of Copy Number Variations on Chromosome 18 in a Control Cohort

2013 ◽  
Vol 141 (1) ◽  
pp. 16-25
Author(s):  
N.L. Chia ◽  
M. Bryce ◽  
P.E. Hickman ◽  
J.M. Potter ◽  
N. Glasgow ◽  
...  
Keyword(s):  
High Resolution ◽  
Copy Number ◽  
Copy Number Variations ◽  
Control Cohort ◽  
Chromosome 18 ◽  
Snp Microarray

Can Genomic Copy Number Variants Be a Part of Complex Genetic Traits Predisposing to Marrow Failure?.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 106-106
Author(s):  
Christine O’Keefe ◽  
Lukasz Gondek ◽  
Marcin Wlodarski ◽  
Judith Karp ◽  
Michael McDevitt ◽  
...  
Keyword(s):  
Copy Number ◽  
Complex Disease ◽  
Disease Susceptibility ◽  
Disease Risk ◽  
Global Analysis ◽  
Copy Number Variants ◽  
Snp Array ◽  
High Density ◽  
Genetic Traits ◽  
Disease Predisposition

Abstract Individual variability, including disease susceptibility, is determined by the interaction of inherited single base differences (single nucleotide polymorphisms, SNPs) and copy number variants (CNVs) of large genomic regions. A complex combination of these factors may result in a genetic background predisposing to disease. Regions of CNV account for approximately 12% of the human genome, including coding sequences and can range in size from kilobases to megabases. Recent studies have investigated the correlation between CNVs and complex conditions, including mental retardation, lupus and cardiovascular disease. While SNPs have been intensely investigated in many diseases, the influence of CNVs on disease susceptibility is only poorly understood. With the advent of high-throughput, high density array technology, global analysis of complex disease predisposition traits, including CNVs, can be performed. We have applied high-density SNP arrays (SNP-A) for the analysis of somatic chromosomal defects in various hematologic disorders. During our studies we noted a high frequency of germ-line CNVs, complicating our analysis of somatic defects. This observation lead us to the hypothesis that CNVs can themselves constitute predisposition factors to disease and chose to systematically investigate their type and frequency in myeloid disorders including aplastic anemia (AA; N=65), myelodysplastic syndrome (MDS; N=145) and primary and secondary (non-core binding factor) acute myeloid leukemia (AML; N=75). We performed whole genome scanning in patients and a cohort of healthy controls (N=79) using the Affymetrix 250K SNP array. We first identified and catalogued CNVs in controls; their frequency was compared to those reported in the Database of Genomic Variants (http://projects.tcag.ca/variation/) and found to be similar. The CNVs ranged in size from 245.6 Kb to 2.32 Mb (average 805.9 Kb) and were identified on all chromosomes except 5, 13, 16, 18 and 21. We next analyzed copy number changes in patients with myeloid disorders. Using controls (both our cohort and those in the literature) as a reference we determined the frequencies of recurrent CNVs in patients. For most of the CNVs the frequency was <10% within the individual patient groups, similar to what was seen in controls. Nonetheless, four regions (2 distinct loci in the pericentromeric region of 14q, pericentromeric 15q and a locus on 17q21.31) were identified in over 15% of samples studied. We then determined whether a distinct CNV is associated with specific disease risk. While for most CNVs the frequencies found in patients were similar to those in controls, two regions, 3q29 and 14q11.2, were more frequently encountered in patients with AML (3q29, 27/75 vs. 13/79 in controls, p=0.01; 14q11.2, 20/75 vs. 8/79 in controls, p=0.014). The region at 3q29 contains several genes and is a common breakpoint region for hematologic malignancies including MDS and AML, suggesting that this chromosomal area sensitive to physical rearrangement. The locus at 14q11.2 is a known hypervariable region, containing T cell receptor genes. In sum, in addition to SNPs, CNVs may be a part of complex genetic traits in patients with AA, MDS and AML and constitute disease predisposition factors. Beyond their potential role in disease, CNVs have to be excluded in SNP array-based analysis of somatic chromosomal lesions.

SNP Array Analysis Reveals Copy Number Alterations and Uniparental Disomy in Mantle Cell Lymphomas at High Resolution.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 1585-1585
Author(s):  
Elena M. Hartmann ◽  
Itziar Salaverria ◽  
Silvia Bea ◽  
Andreas Zettl ◽  
Pedro Jares ◽  
...  
Keyword(s):  
High Resolution ◽  
Cell Lines ◽  
Copy Number ◽  
Snp Array ◽  
Uniparental Disomy ◽  
Genetic Alterations ◽  
Array Analysis ◽  
Snp Array Analysis ◽  
Copy Number Changes ◽  
500K Array

Abstract Mantle Cell Lymphoma (MCL) is an aggressive B-Cell Non Hodgkin Lymphoma which is genetically characterized by the translocation t(11;14). This translocation leads to juxtaposition of the Cyclin D1 gene and the IgH locus, resulting in constitutive overexpression of Cyclin D1 and consecutive cell cycle dysregulation. Apart from this typical structural genetic alteration, several studies using conventional or array-based comparative genomic hybridization (CGH) reported a high number of secondary numerical genetic alterations contributing to MCL lymphomagenesis and influencing the clinical behavior. Increasingly, there is evidence that loss of heterozygosity (LOH) without copy number changes (e.g. caused by mitotic recombination between the chromosomal homologues, also referred to as acquired (partial) uniparental disomy (a(p)UPD), is an important alternative mechanism for tumor suppressor gene inactivation. However, this phenomenon is undetectable by CGH techniques. Single Nucleotide Polymorphism (SNP) based arrays allow - in addition to high resolution copy number (CN) analyses and SNP genotyping - in the same experiment the analysis of loss of heterozygosity (LOH) events and hereby enable the detection of copy neutral LOH. We analyzed the 3 t(11;14)-positive MCL cell lines Granta 519, HBL-2 and JVM-2 and 5 primary tumor specimens from untreated MCL patients with both the Affymetrix GeneChip®Human Mapping 100K and 500K array sets. In the 3 cell lines, we found an excellent agreement between the copy number changes obtained by SNP array analysis and previously published array CGH results. Extending published results (Nielaender et al., Leukemia 2006), we found regions of pUPD in all 3 MCL cell lines, which often affected regions reported as commonly deleted in MCL. Intriguingly, HBL-2 that is characterized by relatively few chromosomal losses, carries an increased number of large regions showing copy neutral LOH. Furthermore, we compared the results obtained by the 100K and 500K mapping array sets from 5 primary MCL tumor specimens with previously published conventional CGH data. All cases showed genetic alterations in both conventional CGH and SNP array analysis. The total number of copy number alterations detected by conventional CGH was 35, including 23 losses, 10 gains and 2 amplifications. The total number of CN alterations detected by the mapping 100K and 500K array sets was 81 (50 losses, 26 gains and 5 amplifications) and 82 (50 losses, 27 gains and 5 amplifications), respectively. We found an excellent agreement in the large CN alterations detected by conventional CGH and both SNP array platforms. Furthermore, we identified &gt;40 mostly small CN alterations that have not been detected by conventional CGH (median size &lt;5MB for losses and &lt;3Mb for gains). The CN alterations detected by the 100k and the 500K array sets were highly identical. Importantly, we discovered regions of partial UPD in 4 of the 5 MCL cases (size range from around 2Mb up to a single region &gt;40Mb). In conclusion, the results demonstrate the capability of SNP array analysis for identifying CN alterations and partial UPD at high resolution in MCL cell lines as well as in primary tumor samples.

Identification of Novel Genetic Lesions in Myelodysplastic Syndromes Using High Density SNP-Arrays.

Blood ◽  
2007 ◽  
Vol 110 (11) ◽  
pp. 2430-2430
Author(s):  
Saskia Langemeijer ◽  
Roland Kuiper ◽  
Peter Vandenberghe ◽  
Estelle Verburgh ◽  
Jan Boezeman ◽  
...  
Keyword(s):  
Copy Number ◽  
Single Gene ◽  
Snp Array ◽  
Gene Copy Number ◽  
Gene Copy ◽  
Trisomy 8 ◽  
Entire Genome ◽  
Monosomy 7 ◽  
Snp Arrays ◽  
Copy Number Changes

Abstract Conventional cytogenetics and FISH reveal chromosomal defects in approximately 50% of MDS patients. These mostly consist of gross gains and losses of specific chromosomal regions or entire chromosomes like 5q-, monosomy 7 and trisomy 8. Currently, the genes that are critical for MDS development remain largely unknown, which hampers both a proper diagnosis of clonal disease as well as development of targeted therapy. To identify the affected genetic loci and to map the critical regions and genes in MDS, we performed high-resolution (250k) SNP-based CGH. So far, 231 controls and 87 MDS patients from various subclasses were analyzed. In all patients and controls, loss of heterozygosity (LOH) without copy number changes was observed at multiple loci across the entire genome. Although large areas of LOH encompassing the main part of the p- or q-arm of chromosomes were only seen in MDS patients, no genomic regions were identified that were statistically more often affected in patients compared to control DNA. Copy number changes (excluding known regions of normal variation) were seen in 53% of patients with a normal karyotype (n=54). In 231 controls and in non-malignant T cells of a subset of patients, these areas were not affected, indicating that they were disease-specific. The number of affected regions per patient ranged from 0–7. The majority (82%) of karyotypic aberrations were confirmed using SNP-arrays. Only balanced translocations and some subclonal aberrations could not be detected. Importantly, SNP-array analysis revealed additional copy number changes in 70% of patients with an abnormal karyotype. Copy number changes that were observed in only one patient might reflect general genomic instability in the tumor cells and may not represent genes that are implicated in the pathogenesis of MDS. Therefore, we selected areas that were affected in at least two patients. In total, we found 51 different recurrent genomic loci. This indicates that MDS is genetically diverse, which is in agreement with its diverse clinical and morphological presentation. Among the 51 recurrent loci, 15 contained only a single gene (Table). Among these genes, there were several known to be implicated in MDS (e.g. ETV6 and RUNX1), whereas others represent novel genes that are potentially implicated in the pathogenesis of MDS. For several of these, a biological function has been described that may be linked to control of differentiation and proliferation, like the transcription- and proliferation-regulating gene JARID2 and the transcription factor DMTF1. Currently, we are performing a high thoughput mutation- and expression-analysis of these genes in a larger group of patients. Single gene copy number changes in MDS Chr Cytoband Loss/Gain Cases Size (Mb) Gene 1 p35.1 loss 2 0.01 CSMD2 3 p24.2 loss 2 0.07 LRRC3B 6 p22.3 loss 3 0.02 JARID2 8 p23.2-1 gain 2 0.14 MCPH1 9 p13.2 gain 2 0.23 MELK 9 p24.3 gain 2 1.14 SMARCA2 11 q22.3 gain 2 0.05 SLC35F2 12 p12.1 loss 3 0.08 ST8SIA1 12 p13.2 loss 4 0.08 ETV6 12 q23.2 loss 2 0.03 IGF1 16 q23.3 loss 2 0.06 MPHOSPH6 21 q22.12 loss 3 0.07 RUNX1 21 q22.2 gain 2 0.62 DSCAM 22 q12.2 gain 2 0.00 PES1 X q13.1 loss 2 0.17 EDA

Genome-Wide DNA Copy Number Analysis by SNP Arrays of B-Cell Chronic Lymphocytic Leukemia: Correlation with Known Biological and Molecular Prognostic Markers.

Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 1061-1061
Author(s):  
Laura Mosca ◽  
Sonia Fabris ◽  
Giovanna Cutrona ◽  
Luca Agnelli ◽  
Serena Matis ◽  
...  
Keyword(s):  
High Resolution ◽  
Copy Number ◽  
Prognostic Markers ◽  
Snp Array ◽  
Lymphocytic Leukemia ◽  
Array Analysis ◽  
Genome Wide ◽  
Trisomy 12 ◽  
Snp Array Analysis ◽  
Cell Chronic Lymphocytic Leukemia

Abstract B-cell chronic lymphocytic leukemia (B-CLL) is a genetically heterogeneous disease with a variable clinical course. Chromosomal changes have been identified by FISH in approximately 80% of patients, and the presence of specific lesions, such as trisomy 12 and 13q14, 11q23, 17p13.1 and 6q23 deletions represent prognostic markers for disease progression and survival. In order to characterize further the complexity of B-CLL genomic lesions, we performed high density, single nucleotide polymorphism (SNP) array analysis in highly purified neoplastic cells (&gt;92%) from a panel of 100 untreated, newly diagnosed patients (57 males and 43 females; age, median 63 years, range 30–87) in Binet stage A. All patients were investigated by FISH for the presence of trisomy 12 (21 cases); 13q14 deletion (44 cases, 34 as the sole abnormality); 11q22.3, 17p13.1 and 6q23 (15, 7 and 2 patients, respectively). In addition, ZAP-70 and CD38 expression resulted positive in 42 and 46 patients, whereas IgVH genes were mutated in 45 patients. Genome-wide DNA profiling data were generated on GeneChip® Human Mapping 250K NspI arrays (Affymetrix); copy number alterations (CNA) were calculated using the DNA copy Bioconductor package, which looks for optimal breakpoints using circular binary segmentation (CBS) (Olshen et al, 2004). A total of 782 CNAs (ranging from 1 to 31 per sample, mean and median values 7.82 and 7, respectively) were detected; DNA losses (365/782=46.67% loss; 194/782=24.81% biallelic deletion) were found to be more frequent than gains (148/782=18.93% gain; 75/782=9.59% amplification). The most recurrent alterations detected by FISH were all confirmed by SNP array analysis, strengthening further the good reliability of such high-resolution technology. We identified 12 minimally altered regions (MARs) larger than 100 kb with a frequency higher than 5%. Among well known alterations, the largest was represented by chromosome 12 trisomy, followed by 6q, 17p and 11q23 deletions (32.87, 19.09 and 10.43 Mb, respectively) and 13q14 deletion (635 kb). Gain of 2p25.3 involves a common region of 4.39 Mb region in 7 patients, although it was extended to the whole short arm of chromosome 2 in 3 cases. Among those alterations previously described in B-CLL, we found losses at 14q32.33 (12 pts) and 22q11.2 (5 pts) involving the IGH and IGLλ loci, respectively. With regard to novel regions, we identified losses at 4q35.2 (5 pts) and 11q25 (6 pts). In addition we found a high frequency of losses/gains at 14q11.2 (42 pts) and 15q11.2 (33 pts), two genomic regions reported to be affected by DNA copy number variations in normal individuals. As regards correlations between CNAs and biological markers, we found that the number of CNAs is significantly higher in cases with unmutated IgVH (9.4; range 2–31) as compared with mutated IgVH (6; range 1–13) (p=0.002), while neither CD38 nor ZAP-70 expression showed significant correlation. In addition, a significant higher number of either CNAs (p=0.001), total MARs (p&lt;0.0001) or even only novel MARs (p=0.009) was significantly associated with cases with 17p deletion or multiple cytogenetic aberrations as evaluated by FISH analysis. Our data indicate that genetic abnormalities involving chromosomal gains and losses are very common in early-stage B-CLL and further support the application of high resolution SNP array platforms in the characterization of genetic changes in the disease. In addition, we detected novel altered chromosomal regions that warrant further investigations to better define their pathogenetic and prognostic role in B-CLL.

Whole-transcriptome paired-end sequencing and the pancreatic cancer genetic landscape.

2013 ◽  
Vol 31 (15_suppl) ◽  
pp. 4048-4048
Author(s):  
Marina Macchini ◽  
Annalisa Astolfi ◽  
Valentina Indio ◽  
Silvia Vecchiarelli ◽  
Elisa Grassi ◽  
...  
Keyword(s):  
Pancreatic Cancer ◽  
High Resolution ◽  
Copy Number ◽  
Massively Parallel Sequencing ◽  
Rna Extraction ◽  
Snp Array ◽  
Single Nucleotide Variants ◽  
Kras Mutations ◽  
Mesenchymal Transition ◽  
Whole Transcriptome

4048 Background: A deeper knowledge of the pancreatic cancer (PDAC) biology is needed to improve the prognosis of the disease. Methods: 17 PDAC samples were collected by ultrasound-guided biopsy used for DNA and RNA extraction. 14 samples were analyzed by high resolution copy number analysis (CNA) on Affymetrix SNP array 6.0 and with segmentation algorithm against a reference of 270 Ceu HapMap individuals (Partek Genomic Suite). 17 samples were analyzed by whole transcriptome massively parallel sequencing, performed at 75x2 bp on a HiScanSQ Illumina platform. An average of 7, 3x107 reads per sample were generated, with a mean read depth of 50X. Single nucleotide variants (SNVs) were detected with SNVMix2 and compared with genetic variation databases (dbSNP, 1000genomes, Cosmic). Non-synonimous SNVs were analyzed with the predictors SNPs and GO and PROVEAN. Results: CNA results in 9/14 samples exhibited both macroscopic and cryptic cytogenetic alterations, with a mean of 10 CNA per patient. Most frequent gains were observed in 18q11.2 involving GATA6 (3/14) and 19q13 targeting AKT2 (3/14) while hotspot deletions were found on 18q21 (7/14), 17p13 (6/14), 9p21.3 (6/14), 15q (5/14) and 1q35 (4/14). RNAseq showed that samples exhibited a mean of 145 (range: 61-240) non-synonimous SNVs, of which 16 on average are potentially disease-related. Merging copy number and RNAseq data we highlighted the major oncogenic hits of PDAC, confirming the prevalence (14/17) of KRAS mutations, in one case also NRAS (G13D), and the three oncosuppressor CDKN2A (mutated in 3 cases and deleted in 6 cases, in hetero- or homozygosity), SMAD4 (altered by point mutation or gene deletion in 7/14), and TP53 (lost in 6/14 and mutated in 5/17). The signaling pathways affected were: KRAS/MAPK, TGFbeta and integrin signaling, proliferation and apoptosis, DNA damage response, and epithelial to mesenchymal transition. Moreover we found new oncogenic alterations, such as HMGCR, that displayed mutations in 17% of the analyzed patients (3/17). Conclusions: NGS combined with high resolution cytogenetic analysis can improve the understanding of pancreatic carcinogenesis.

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