scholarly journals Genome-Wide Somatic Copy Number Alterations and Mutations in High-Grade Pancreatic Intraepithelial Neoplasia

2018 ◽  
Vol 188 (7) ◽  
pp. 1723-1733 ◽  
Author(s):  
Tatsuo Hata ◽  
Masaya Suenaga ◽  
Luigi Marchionni ◽  
Anne Macgregor-Das ◽  
Jun Yu ◽  
...  
Keyword(s):  
Copy Number ◽  
Intraepithelial Neoplasia ◽  
High Grade ◽  
Copy Number Alterations ◽  
Pancreatic Intraepithelial Neoplasia ◽  
Genome Wide ◽  
Somatic Copy Number Alterations

scholarly journals Molecular profiling and genome-wide analysis based on somatic copy number alterations in advanced colorectal cancers

2017 ◽  
Vol 57 (3) ◽  
pp. 451-461 ◽  
Author(s):  
Tamotsu Sugai ◽  
Yayoi Takahashi ◽  
Makoto Eizuka ◽  
Ryo Sugimoto ◽  
Yasuko Fujita ◽  
...  
Keyword(s):  
Copy Number ◽  
Molecular Profiling ◽  
Colorectal Cancers ◽  
Copy Number Alterations ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Somatic Copy Number Alterations

scholarly journals Genome-Wide Somatic Copy Number Alterations in Low-Grade PanINs and IPMNs from Individuals with a Family History of Pancreatic Cancer

2012 ◽  
Vol 18 (16) ◽  
pp. 4303-4312 ◽  
Author(s):  
Seung-Mo Hong ◽  
Audrey Vincent ◽  
Mitsuro Kanda ◽  
Julie Leclerc ◽  
Noriyuki Omura ◽  
...  
Keyword(s):  
Pancreatic Cancer ◽  
Family History ◽  
Copy Number ◽  
Low Grade ◽  
Copy Number Alterations ◽  
Genome Wide ◽  
History Of ◽  
Somatic Copy Number Alterations

Genome-Wide Analysis of Copy Number Alterations/LOH/Allelic Imbalances in Non-Hodgkin Lymphoma Using Ultrahigh-Density SNP-Genotyping Microarrays with the Robust CNAG Algorithms.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 420-420
Author(s):  
Kumi Nakazaki ◽  
Yasuhito Nannya ◽  
Masashi Sanada ◽  
Go Yamamoto ◽  
Chiaki Aoyama ◽  
...  
Keyword(s):  
Copy Number ◽  
B Cell Lymphoma ◽  
Genetic Alterations ◽  
Snp Genotyping ◽  
High Grade ◽  
Copy Number Alterations ◽  
Copy Number Analysis ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Allele Specific

Abstract Non-Hodgkin lymphomas (NHL) are hematopoietic malignancies originated from diversity of peripheral lymphoid organs. During the past two decades, there have been significant advances in the pathogenesis of NHL including identification of a number of genes associated with the disease-specific translocations and other genetic alterations. In view of cytogenetics, however, NHL frequently shows complex chromosomal abnormalities involving copy number alterations as well as other unbalanced translocations, many of which have not been unveiled at the molecular levels. Affymetrix® 100K/500K mapping arrays were originally developed for large-scale SNP typing required for genome-wide association studies, but the quantitative nature of the whole-genome amplification and hybridization used in these platforms also makes them powerful tools for genome-wide analysis of cancer genomes with use of uniformly distributed 116,204/520,000 SNP-specific probes. Moreover the use of SNP specific probes enables allele-specific copy number analysis that is totally impossible with other platforms. Here we developed the robust algorithms (Copy number analyzer for Affymetrix® GeneChip®; CNAG) for high-quality processing of 100K/500K data and analyzed a total of 72 NHL samples (61 primary samples including 34 diffuse large B-cell lymphoma, 18 follicular lymphoma and 11 cell lines including 3 adult T cell leukemia/ lymphoma) for genome-wide copy number alterations, LOH, and allelic imbalances at the resolutions of 23.6/5.4 kb. In 100K analysis, 34 homozygous deletions and 42 high-grade amplifications and other numerous copy number alternations and/or LOH, were identified together with possible gene targets as for some regions. 500K analysis disclosed even more subtle changes. Common overlapping alternations included deletions in 1p31.1 and 9p21.3, and 19p13.32 and high-grade amplifications in 3p14.2–p14.1,7q21.13–q21.3, and 20q11.21. Of particular importance is, however, the finding of otherwise undetected copy number neutral LOHs, which are revealed only by allele-specific copy-number analysis. In fact the copy number neutral LOHs represented a novel type of genetic abnormality in NHL because they were very frequent and found in more than 87% (20/23) of NHL cases examined with allele-specific copy number analysis, making a stark contrast to ALL, in which these abnormalities were rare. They typically involved chromosomal ends, indicating somatic recombinations are the potential mechanism of generating these abnormalities. Notably, there was a clear predisposition of the copy number neutral LOH to specific chromosomal loci including 1p, 1q, 6p, 9p, 17q, and 19p suggesting existence of relevant genes to NHL pathogenesis within these common regions. In conclusion, Affymetrix® SNP-genotyping microarrays and our CNAG algorithms provide a powerful platform of dissecting NHL genomes and could facilitate identification of the novel molecular mechanisms for lymphomagenesis.

scholarly journals Non-invasive detection of genome-wide somatic copy number alterations by liquid biopsies

2015 ◽  
Vol 10 (3) ◽  
pp. 494-502 ◽  
Author(s):  
Ellen Heitzer ◽  
Peter Ulz ◽  
Jochen B. Geigl ◽  
Michael R. Speicher
Keyword(s):  
Copy Number ◽  
Copy Number Alterations ◽  
Liquid Biopsies ◽  
Non Invasive ◽  
Genome Wide ◽  
Somatic Copy Number Alterations

scholarly journals Association of Cell-Free DNA Tumor Fraction and Somatic Copy Number Alterations With Survival in Metastatic Triple-Negative Breast Cancer

2018 ◽  
Vol 36 (6) ◽  
pp. 543-553 ◽  
Author(s):  
Daniel G. Stover ◽  
Heather A. Parsons ◽  
Gavin Ha ◽  
Samuel S. Freeman ◽  
William T. Barry ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Triple Negative Breast Cancer ◽  
Copy Number ◽  
Triple Negative ◽  
Copy Number Alterations ◽  
Cell Free Dna ◽  
Primary Tumors ◽  
Free Dna ◽  
Genome Wide ◽  
Somatic Copy Number Alterations

Purpose Cell-free DNA (cfDNA) offers the potential for minimally invasive genome-wide profiling of tumor alterations without tumor biopsy and may be associated with patient prognosis. Triple-negative breast cancer (TNBC) is characterized by few mutations but extensive somatic copy number alterations (SCNAs), yet little is known regarding SCNAs in metastatic TNBC. We sought to evaluate SCNAs in metastatic TNBC exclusively via cfDNA and determine if cfDNA tumor fraction is associated with overall survival in metastatic TNBC. Patients and Methods In this retrospective cohort study, we identified 164 patients with biopsy-proven metastatic TNBC at a single tertiary care institution who received prior chemotherapy in the (neo)adjuvant or metastatic setting. We performed low-coverage genome-wide sequencing of cfDNA from plasma. Results Without prior knowledge of tumor mutations, we determined tumor fraction of cfDNA for 96.3% of patients and SCNAs for 63.9% of patients. Copy number profiles and percent genome altered were remarkably similar between metastatic and primary TNBCs. Certain SCNAs were more frequent in metastatic TNBCs relative to paired primary tumors and primary TNBCs in publicly available data sets The Cancer Genome Atlas and METABRIC, including chromosomal gains in drivers NOTCH2, AKT2, and AKT3. Prespecified cfDNA tumor fraction threshold of ≥ 10% was associated with significantly worse metastatic survival (median, 6.4 v 15.9 months) and remained significant independent of clinicopathologic factors (hazard ratio, 2.14; 95% CI, 1.4 to 3.8; P < .001). Conclusion We present the largest genomic characterization of metastatic TNBC to our knowledge, exclusively from cfDNA. Evaluation of cfDNA tumor fraction was feasible for nearly all patients, and tumor fraction ≥ 10% is associated with significantly worse survival in this large metastatic TNBC cohort. Specific SCNAs are enriched and prognostic in metastatic TNBC, with implications for metastasis, resistance, and novel therapeutic approaches.

scholarly journals Genome-wide analysis of somatic copy number alterations and chromosomal breakages in osteosarcoma

2017 ◽  
Vol 141 (4) ◽  
pp. 816-828 ◽  
Author(s):  
Jan Smida ◽  
Hongen Xu ◽  
Yanping Zhang ◽  
Daniel Baumhoer ◽  
Sebastian Ribi ◽  
...  
Keyword(s):  
Copy Number ◽  
Copy Number Alterations ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Somatic Copy Number Alterations
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