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 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

MP28-19 GENOME-WIDE ANALYSIS OF COPY NUMBER ALTERATIONS IN RENAL-PELVIC AND URETERAL CANCERS

2014 ◽  
Vol 191 (4S) ◽  
Author(s):  
Shigekatsu Maekawa ◽  
Taketo Kawai ◽  
Yusuke Sato ◽  
Toru Nakagawa ◽  
Haruki Kume ◽  
...  
Keyword(s):  
Copy Number ◽  
Copy Number Alterations ◽  
Genome Wide Analysis ◽  
Genome Wide

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

scholarly journals Concordance of copy number alterations using a common analytic pipeline for genome-wide analysis of Illumina and Affymetrix genotyping data: a report from the Children's Oncology Group

2015 ◽  
Vol 208 (7-8) ◽  
pp. 408-413 ◽  
Author(s):  
Marijana Vujkovic ◽  
Edward F. Attiyeh ◽  
Rhonda E. Ries ◽  
Michelle Horn ◽  
Elizabeth K. Goodman ◽  
...  
Keyword(s):  
Copy Number ◽  
Copy Number Alterations ◽  
Oncology Group ◽  
Genome Wide Analysis ◽  
Genome Wide

435 GENOME-WIDE ANALYSIS OF COPY NUMBER ALTERATIONS AND GENE MUTATIONS IN RENAL CELL CARCINOMA

2012 ◽  
Vol 187 (4S) ◽  
Author(s):  
Yusuke Sato ◽  
Shigektsu Maekawa ◽  
Aiko Sato ◽  
Yasunobu Nagata ◽  
Kenichi Yoshida ◽  
...  
Keyword(s):  
Renal Cell Carcinoma ◽  
Cell Carcinoma ◽  
Renal Cell ◽  
Copy Number ◽  
Gene Mutations ◽  
Copy Number Alterations ◽  
Genome Wide Analysis ◽  
Genome Wide

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.

Genome-Wide Analysis of Copy Number Analysis of Myelodysplastic Syndromes Using High-Density SNP-Genotyping Microarrays.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 3420-3420
Author(s):  
Masashi Sanada ◽  
Yasuhito Nannya ◽  
Kumi Nakazaki ◽  
Go Yamamoto ◽  
Lili Wang ◽  
...  
Keyword(s):  
Myelodysplastic Syndromes ◽  
Copy Number ◽  
Large Scale ◽  
Target Genes ◽  
Chromosomal Abnormalities ◽  
High Density ◽  
Copy Number Alterations ◽  
Genome Wide Analysis ◽  
Conventional Cytogenetic Analysis ◽  
Genome Wide

Abstract Myelodysplastic syndromes (MDS) are clonal disorders of hematopoietic progenitors characterized by impaired blood cell production due to ineffective hematopoiesis and high propensity to acute myeloid leukemias. One of the prominent features of MDS is the high frequency of unbalanced chromosomal abnormalities that result in genetic imbalances and copy number alterations. Although the chromosomal segments involved in these abnormalities are thought to contain relevant genes to the pathogenesis of MDS, conventional analyses including FISH have failed to identify critical regions small enough to pinpoint their target genes. Affymetrix® GeneChip® 100K/500K mapping arrays were originally developed for large-scale genotyping of more than 100,000/500,000 SNPs in two separate arrays, but the quantitative nature of the preparative whole-genome amplification and array hybridization thereafter also allows for accurate copy number estimate of the genome using these platforms at the resolutions of 21.3 kb and 5.4 kb with 116,204 and 520,000 oligonucleotide probes, respectively. Here we developed robust algorithms (CNAG) for copy number detection using 100K and/or 500K arrays and analyzed 88 MDS samples on these platforms in order to identify relevant genes for development of MDS. With these huge numbers of uniformly distributed SNP probes, numerous copy number alterations were sensitively detected in cases with MDS with more numbers of abnormalities found in advanced diseases (RAEB and RAEB-t). In addition to large-scale alterations of various chromosomal segments previously reported in these syndromes, a number of small cryptic chromosomal abnormalities were identified that would escape conventional cytogenetic analysis or array CGH analysis. Minimum overlapping deletions in 5q, 7q, 12p, 13q, and 20q were precisely defined, although no pinpoint homozygous deletions were detected within these regions. A common 20q deletion spans a 400 kb segment harboring five transcriptomes and the common 12p deletion defines a 1.3 Mb region that contains the ETV6 gene. Other common overlapping abnormalities include deletions in 21q22, 17q13, and gains of 11q25. Genome-wide analysis of copy number changes using high-density oligonucleotide arrays provides valuable information about genetic abnormalities in MDS.

Sign in / Sign up

Export Citation Format

Share Document