Somatic Copy-Number Alterations
Thin and thick primary cutaneous melanomas reveal distinct patterns of somatic copy number alterations
... Cutaneous melanoma is one of the most aggressive type of skin tumor. Early stage melanoma can be often cured by surgery; therefore current management guidelines dictate a different approach for thin (<1mm) versus ...
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Somatic copy number alterations detected by ultra-deep targeted sequencing predict prognosis in oral cavity squamous cell carcinoma
... of copy number amplifications and deletions, ...total number of samples classified as harboring CNAs in the targeted ...the number of SNVs reported by the Torrent Variant Caller, we noticed ...
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Imprint of parity and age at first pregnancy on the genomic landscape of subsequent breast cancer
... of somatic mutations, somatic copy number alterations, transcriptomic profiles, and tumor immune microenvironment by assessing tumor-infiltrating lymphocytes (TILs) levels of subsequent ...
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Evidence-based genomic diagnosis characterized chromosomal and cryptic imbalances in 30 elderly patients with myelodysplastic syndrome and acute myeloid leukemia
... genomic alterations in patients with MDS and AML ...detecting somatic chromo- somal and segmental copy number alterations (CNAs), we have performed aCGH analysis on 30 MDS and AML cases ...
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Review Article Copy number alterations in colorectal cancer
... acquire somatic CNAs, namely, the amplification of oncogenes or deletion of tumor suppressor genes ...various somatic CNA- affected tumor-associated genes have been identified across human cancers (solid, ...
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A genomic case study of desmoplastic small round cell tumor: comprehensive analysis reveals insights into potential therapeutic targets and development of a monitoring tool for a rare and aggressive disease
... protein alterations including 12 somatic and 14 germline events (11 germline compound heterozygous mutations and 3 rare homozygous polymorphisms) affecting genes predominantly involved in mesenchymal cell ...
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High-resolution analysis of copy number alterations and associated expression changes in ovarian tumors
... As somatic DNA copy number alterations (CNAs) can indicate the presence of genes involved in tumorigen- esis, studies of DNA instability in ovarian cancers could potentially lead to ...
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PubMedCentral-PMC5777758.pdf
... substantial number of individuals never responded to ...identify somatic point mutations, insertions/deletions, and copy number alterations (CNAs) associated with resistance to ...
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Pan-Cancer Analysis Reveals Differential Susceptibility of Bidirectional Gene Promoters to DNA Methylation, Somatic Mutations, and Copy Number Alterations
... CpG islands. The size of the points indicates the relative sample size and 95% confidence intervals are shown.. intersecting regions of copy number alteration are lower for the 657 C/C b[r] ...
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Genomic alterations in abnormal neutrophils isolated from adult patients with systemic lupus erythematosus
... genomic copy number variants from somatic alterations ...genome-wide alterations, they lack the necessary degree of fine specificity required for an associated functional ana- ...a ...
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Difference of molecular alterations in HER2-positive and HER2-negative gastric cancers by whole-genome sequencing analysis
... average number of somatic SNVs and mutation spectrum were similar between HER2+ and HER2– ...For somatic SV, number of intrachromosomal translocation ...(1/10). Copy number gain ...
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Two classes of intrahepatic cholangiocarcinoma defined by relative abundance of mutations and copy number alterations
... identify somatic mutations, it can be also used to call CNAs ...substantial number of somatic ...recurrent somatic mutations on KRAS, TP53 and APC do not appear to be specifically enriched in ...
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Importance of rare gene copy number alterations for personalized tumor characterization and survival analysis
... gene copy numbers for the 15,942 genes con- sidered in the CCLE cancer cell line data ...gene-specific copy number log-ratios for each tumor patient, we mapped the tumor-specific aCGH segments to the ...
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Somatic mutation and gain of copy number of PIK3CA in human breast cancer
... of copy number of the ...of copy number of PIK3CA, suggesting that somatic mutations are a major contributory factor in the PIK3CA signaling path- ...of copy number of ...
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Landscape of somatic allelic imbalances and copy number alterations in HER2 amplified breast cancer
... HER2 copy number (CN) estimates compared to remaining samples from respective data set (Figure S1, Additional file ...genomic alterations was performed as described ([27] and Additional file ...
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A method to reduce ancestry related germline false positives in tumor only somatic variant calling
... of copy number and clonal heterogeneity Since somatic variants will only occur in tumor cells, but germline variants will occur in all cells, we can leverage differences in allele frequencies to ...
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Appraising the relevance of DNA copy number loss and gain in prostate cancer using whole genome DNA sequence data
... recurrent somatic copy num- ber alteration (SCNA) in human ...of alterations of lincRNA sequences was illustrated by the identification of a novel mutational hotspot at the KCCAT42, FENDRR, CAT1886 ...
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Copy number alterations detected by whole-exome and whole-genome sequencing of esophageal adenocarcinoma
... the copy number ...the copy num- ber ratios, and the positions with nonzero coefficients were considered as change ...lute copy numbers if the ploidy information is ...
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Genome-wide copy number alterations in subtypes of invasive breast cancers in young white and African American women.
... Copy number gain at 10p has been reported to be a distinguishing CNA for TN/basal tumors compared to other breast cancer subtypes [32 ...a copy number gain in the region of 10p spanning ...
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Interpretation of Mutations, Expression, Copy Number in Somatic Breast Cancer: Implications for Metastasis and Chemotherapy
... Comparative genomic hybridization (CGH) was developed for use on solid tumours in 1992, and was initially performed genome wide using metaphase chromosomes (41). The technique involves differentially labeling normal and ...
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