scholarly journals Somatic mutations and copy number variations in breast cancers with heterogeneous HER2 amplification

2020 ◽  
Vol 14 (4) ◽  
pp. 671-685 ◽  
Author(s):  
Mieke R. Van Bockstal ◽  
Marie Colombe Agahozo ◽  
Ronald van Marion ◽  
Peggy N. Atmodimedjo ◽  
Hein F. B. M. Sleddens ◽  
...  
Keyword(s):  
Copy Number ◽  
Somatic Mutations ◽  
Copy Number Variations ◽  
Breast Cancers ◽  
Her2 Amplification

scholarly journals 25P Breast cancers with heterogeneous HER2 amplification show a diverse distribution of ‘driver’ and ‘passenger’ somatic mutations and copy number variations

2020 ◽  
Vol 31 ◽  
pp. S25
Author(s):  
M.R. Van Bockstal ◽  
M.C. Agahozo ◽  
R. van Marion ◽  
P.N. Atmodimedjo ◽  
H.F.B.M. Sleddens ◽  
...  
Keyword(s):  
Copy Number ◽  
Somatic Mutations ◽  
Copy Number Variations ◽  
Breast Cancers ◽  
Her2 Amplification

scholarly journals HiCancer: accurate and complete cancer genome phasing with Hi-C reads

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Weihua Pan ◽  
Desheng Gong ◽  
Da Sun ◽  
Haohui Luo
Keyword(s):  
Copy Number ◽  
Somatic Mutations ◽  
Copy Number Variations ◽  
Cancer Genome ◽  
Structural Variations ◽  
Genome Map ◽  
Linkage Information ◽  
Suboptimal Solution ◽  
Allelic Copy Number ◽  
Very High

AbstractDue to the high complexity of cancer genome, it is too difficult to generate complete cancer genome map which contains the sequence of every DNA molecule until now. Nevertheless, phasing each chromosome in cancer genome into two haplotypes according to germline mutations provides a suboptimal solution to understand cancer genome. However, phasing cancer genome is also a challenging problem, due to the limit in experimental and computational technologies. Hi-C data is widely used in phasing in recent years due to its long-range linkage information and provides an opportunity for solving the problem of phasing cancer genome. The existing Hi-C based phasing methods can not be applied to cancer genome directly, because the somatic mutations in cancer genome such as somatic SNPs, copy number variations and structural variations greatly reduce the correctness and completeness. Here, we propose a new Hi-C based pipeline for phasing cancer genome called HiCancer. HiCancer solves different kinds of somatic mutations and variations, and take advantage of allelic copy number imbalance and linkage disequilibrium to improve the correctness and completeness of phasing. According to our experiments in K562 and KBM-7 cell lines, HiCancer is able to generate very high-quality chromosome-level haplotypes for cancer genome with only Hi-C data.

scholarly journals Genomic alterations caused by HPV integration in a cohort of Chinese endocervical adenocarcinomas

2021 ◽  
Author(s):  
Wenhui Li ◽  
Wanjun Lei ◽  
Xiaopei Chao ◽  
Xiaochen Song ◽  
Yalan Bi ◽  
...  
Keyword(s):  
Copy Number ◽  
Somatic Mutations ◽  
Hpv Infection ◽  
Copy Number Variations ◽  
Cervical Adenocarcinoma ◽  
Structural Variations ◽  
Driver Genes ◽  
Genetic Changes ◽  
Genomic Changes ◽  
Whole Exome

AbstractThe association between human papillomavirus (HPV) integration and relevant genomic changes in uterine cervical adenocarcinoma is poorly understood. This study is to depict the genomic mutational landscape in a cohort of 20 patients. HPV+ and HPV− groups were defined as patients with and without HPV integration in the host genome. The genetic changes between these two groups were described and compared by whole-genome sequencing (WGS) and whole-exome sequencing (WES). WGS identified 2916 copy number variations and 743 structural variations. WES identified 6113 somatic mutations, with a mutational burden of 2.4 mutations/Mb. Six genes were predicted as driver genes: PIK3CA, KRAS, TRAPPC12, NDN, GOLGA6L4 and BAIAP3. PIK3CA, NDN, GOLGA6L4, and BAIAP3 were recognized as significantly mutated genes (SMGs). HPV was detected in 95% (19/20) of patients with cervical adenocarcinoma, 7 of whom (36.8%) had HPV integration (HPV+ group). In total, 1036 genes with somatic mutations were confirmed in the HPV+ group, while 289 genes with somatic mutations were confirmed in the group without HPV integration (HPV− group); only 2.1% were shared between the two groups. In the HPV+ group, GOLGA6L4 and BAIAP3 were confirmed as SMGs, while PIK3CA, NDN, KRAS, FUT1, and GOLGA6L64 were identified in the HPV− group. ZDHHC3, PKD1P1, and TGIF2 showed copy number amplifications after HPV integration. In addition, the HPV+ group had significantly more neoantigens. HPV integration rather than HPV infection results in different genomic changes in cervical adenocarcinoma.

Abstract 95: Somatic mutations and copy number variations in cancer-associated genes in 695 ovarian cancer patients

2016 ◽  
Author(s):  
Elizabeth H. Stover ◽  
Brooke Howitt ◽  
Neal I. Lindeman ◽  
Levi A. Garraway ◽  
Ursula A. Matulonis
Keyword(s):  
Ovarian Cancer ◽  
Cancer Patients ◽  
Copy Number ◽  
Somatic Mutations ◽  
Copy Number Variations

scholarly journals Gliosarcoma Is Driven by Alterations in PI3K/Akt, RAS/MAPK Pathways and Characterized by Collagen Gene Expression Signature

Cancers ◽  
2019 ◽  
Vol 11 (3) ◽  
pp. 284 ◽  
Author(s):  
Bartosz Wojtas ◽  
Bartlomiej Gielniewski ◽  
Kamil Wojnicki ◽  
Marta Maleszewska ◽  
Shamba Mondal ◽  
...  
Keyword(s):  
Gene Expression ◽  
Copy Number ◽  
Somatic Mutations ◽  
Complex Analysis ◽  
Expression Patterns ◽  
Gene Expression Signature ◽  
Genetic Alterations ◽  
Copy Number Variations ◽  
Gene Expression Patterns ◽  
Sequencing Analysis

Gliosarcoma is a very rare brain tumor reported to be a variant of glioblastoma (GBM), IDH-wildtype. While differences in molecular and histological features between gliosarcoma and GBM were reported, detailed information on the genetic background of this tumor is lacking. We intend to fill in this knowledge gap by the complex analysis of somatic mutations, indels, copy number variations, translocations and gene expression patterns in gliosarcomas. Using next generation sequencing, we determined somatic mutations, copy number variations (CNVs) and translocations in 10 gliosarcomas. Six tumors have been further subjected to RNA sequencing analysis and gene expression patterns have been compared to those of GBMs. We demonstrate that gliosarcoma bears somatic alterations in gene coding for PI3K/Akt (PTEN, PI3K) and RAS/MAPK (NF1, BRAF) signaling pathways that are crucial for tumor growth. Interestingly, the frequency of PTEN alterations in gliosarcomas was much higher than in GBMs. Aberrations of PTEN were the most frequent and occurred in 70% of samples. We identified genes differentially expressed in gliosarcoma compared to GBM (including collagen signature) and confirmed a difference in the protein level by immunohistochemistry. We found several novel translocations (including translocations in the RABGEF1 gene) creating potentially unfavorable combinations. Collected results on genetic alterations and transcriptomic profiles offer new insights into gliosarcoma pathobiology, highlight differences in gliosarcoma and GBM genetic backgrounds and point out to distinct molecular cues for targeted treatment.

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