New Regions With Molecular Alterations in a Rare Case of Insulinomatosis: Case Report With Literature Review

Insulinomatosis is characterized by monohormonality of multiple macro-tumors and micro-tumors that arise synchronously and metachronously in all regions of the pancreas, and often recurring hypoglycemia. One of the main characteristics of insulinomatosis is the presence of insulin-expressing monohormonal endocrine cell clusters that are exclusively composed of proliferating insulin-positive cells, are less than 1 mm in size, and show solid islet-like structure. It is presumed that insulinomatosis affects the entire population of β-cells. With regards to molecular genetics, this phenomenon is not related to mutation in MEN1 gene and is more similar to sporadic benign insulinomas, however, at the moment molecular genetics of this disease remains poorly investigated. NGS sequencing was performed with a panel of 409 cancer-related genes. Results of sequencing were analyzed by bioinformatic algorithms for detecting point mutations and copy number variations. DNA copy number variations were detected that harbor a large number of genes in insulinoma and fewer genes in micro-tumors. qPCR was used to confirm copy number variations at ATRX, FOXL2, IRS2 and CEBPA genes. Copy number alterations involving FOXL2, IRS2, CEBPA and ATRX genes were observed in insulinoma as well as in micro-tumors samples, suggesting that alterations of these genes may promote malignization in the β-cells population.

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Joint copy number and mutation phylogeny reconstruction from single-cell amplicon sequencing data

10.1101/2022.01.06.475205 ◽

2022 ◽

Author(s):

Etienne Sollier ◽

Jack Kuipers ◽

Niko Beerenwinkel ◽

Koichi Takahashi ◽

Katharina Jahn

Keyword(s):

Single Cell ◽

Copy Number ◽

Current Knowledge ◽

Snp Array ◽

Point Mutations ◽

Copy Number Variations ◽

Computational Method ◽

Phylogeny Reconstruction ◽

Copy Number Alterations ◽

Sequencing Data

Reconstructing the history of somatic DNA alterations that occurred in a tumour can help understand its evolution and predict its resistance to treatment. Single-cell DNA sequencing (scDNAseq) can be used to investigate clonal heterogeneity and to inform phylogeny reconstruction. However, existing phylogenetic methods for scDNAseq data are designed either for point mutations or for large copy number variations, but not for both types of events simultaneously. Here, we develop COMPASS, a computational method for inferring the joint phylogeny of mutations and copy number alterations from targeted scDNAseq data. We evaluate COMPASS on simulated data and show that it outperforms existing methods. We apply COMPASS to a large cohort of 123 patients with acute myeloid leukemia (AML) and detect copy number alterations, including subclonal ones, which are in agreement with current knowledge of AML development. We further used bulk SNP array data to orthogonally validate or findings.

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Carcinosarcoma of the prostate: case report with molecular and histological characterization

The International Journal of Biological Markers ◽

10.1177/1724600818791463 ◽

2018 ◽

Vol 33 (4) ◽

pp. 540-544 ◽

Cited By ~ 3

Author(s):

Samanta Salvi ◽

Valentina Casadio ◽

Filippo Martignano ◽

Giorgia Gurioli ◽

Maria Maddalena Tumedei ◽

...

Keyword(s):

Copy Number Variation ◽

Copy Number ◽

Copy Number Variations ◽

Molecular Characteristics ◽

Glutathione S Transferase ◽

Molecular Alterations ◽

Positive Expression ◽

Molecular Pattern ◽

Programmed Death ◽

Number Variation

Background: We report a case of prostatic carcinosarcoma, a rare variant of prostatic cancer, which is composed of a mixture of epithelial and mesenchymal components with a generally poor outcome. Aims and methods: We aim to identify molecular alterations, in particular copy number variations of AR and c -MYC genes, methylation and expression of glutathione S-transferase P1 (GSTP1), programmed death-ligand 1 (PD-L1), AR, and phosphorylated AR expression. Results: We found a distinct molecular pattern between adenocarcinoma and carcinosarcoma, which was characterized by high AR copy number variation gain; positive expression of PD-L1, AR, and phosphorylated AR; low espression of GSTP1 in epithelial component. The sarcomatoid component had a lower gain of the AR gene, and no expression of PD-L1, AR, phosphorylated AR, or GSTP1. Both components had a gain of c-MYC copy number variation. Conclusions: Our findings suggest that carcinosarcoma has specific molecular characteristics that could be indicative for early diagnosis and treatment selection.

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Genetic characterization of colorectal cancer using a next generation sequencing approach to identify a specific pattern of somatic alterations in tumors arising from different anatomic sites

10.7287/peerj.preprints.1658 ◽

2016 ◽

Author(s):

Carmelo Laudanna ◽

Gianluca Santamaria ◽

Simona Migliozzi ◽

Duarte Mendes Oliveira ◽

Donatella Malanga ◽

...

Keyword(s):

Colorectal Cancer ◽

Copy Number ◽

Treatment Options ◽

Copy Number Variations ◽

Specific Pattern ◽

Surgical Approaches ◽

Anatomical Location ◽

Molecular Alterations ◽

Somatic Alterations ◽

Novel Biomarkers

Colorectal cancer (CRC) is the third leading cause of cancer-related deaths worldwide, with nearly 1.4 million new cases diagnosed in 2012. CRC results from the accumulation of multiple genetic and epigenetic aberrations. Tumor localization in the large intestine tract determines different surgical approaches and treatment options. Considering the heterogeneous nature of these tumors we hypothesized that different patterns of molecular alterations could be associated with a specific anatomical location. To identify distinct genomic alterations (e.g, copy number variations and mutations) associated to different CRC anatomical sites we sequenced 32 CRCs samples from different location (right-sided, left-sided etc.) using the Ion AmpliSeq™ Comprehensive Cancer Panel that covered the whole coding sequence of 409 tumor suppressor genes and oncogenes frequently altered in cancer. Interestingly left-sided tumors were generally more altered respect to right-sided ones. Cluster analysis of all samples allowed the identification of 21-gene core that were significantly mutated in all sample groups. As expected, KRAS and APC mutations were frequently in the tumors resected from different anatomical localizations. Unsupervised analysis of copy number variations reveals a core of 160-gene significantly altered. In addition to the expected SRC, MYC and CEBPA, we found interestingly genes in validation status. Despite missing a significant number of cases, gene panel provides a solid alternative approach to WES in order to characterize a signature of alterations correlated with CRC tumor and the identification of novel biomarkers in colorectal carcinoma that could be used as potential clinical target.

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Interactive analysis and quality assessment of single-cell copy-number variations

10.1101/011346 ◽

2014 ◽

Cited By ~ 1

Author(s):

Tyler Garvin ◽

Robert Aboukhalil ◽

Jude Kendall ◽

Timour Baslan ◽

Gurinder S. Atwal ◽

...

Keyword(s):

Quality Assessment ◽

Single Cell ◽

Open Source ◽

Visual Analytics ◽

Copy Number ◽

Phylogenetic Trees ◽

Copy Number Variations ◽

Copy Number Alterations ◽

Interactive Analysis ◽

Web Platform

We present an open-source visual-analytics web platform, Ginkgo (http://qb.cshl.edu/ginkgo), for the interactive analysis and quality assessment of single-cell copy-number alterations. Ginkgo automatically constructs copy-number profiles of individual cells from mapped reads, as well as constructing phylogenetic trees of related cells. We validate Ginkgo by reproducing the results of five major studies and examine the data characteristics of three commonly used single-cell amplification techniques to conclude DOP-PCR to be the most consistent for CNV analysis.

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Rapid detection of copy number variations and point mutations in BRCA1/2 genes using a single workflow by ion semiconductor sequencing pipeline

Oncotarget ◽

10.18632/oncotarget.26000 ◽

2018 ◽

Vol 9 (72) ◽

pp. 33648-33655 ◽

Cited By ~ 5

Author(s):

Aldo Germani ◽

Fabio Libi ◽

Stefano Maggi ◽

Gianluca Stanzani ◽

Augusto Lombardi ◽

...

Keyword(s):

Rapid Detection ◽

Copy Number ◽

Point Mutations ◽

Copy Number Variations ◽

Semiconductor Sequencing

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Comprehensive Genomic Analysis Reveals the Prognostic Role of LRRK2 Copy-Number Variations in Human Malignancies

Genes ◽

10.3390/genes11080846 ◽

2020 ◽

Vol 11 (8) ◽

pp. 846

Author(s):

Gianluca Lopez ◽

Giulia Lazzeri ◽

Alessandra Rappa ◽

Giuseppe Isimbaldi ◽

Fulvia Milena Cribiù ◽

...

Keyword(s):

Copy Number ◽

Prognostic Significance ◽

Point Mutations ◽

Genomic Analysis ◽

Genetic Alterations ◽

Copy Number Variations ◽

Cancer Development ◽

Future Research ◽

Gene Deletions ◽

Significant Difference

Genetic alterations of leucine-rich repeat kinase 2 (LRRK2), one of the most important contributors to familial Parkinson’s disease (PD), have been hypothesized to play a role in cancer development due to demographical and preclinical data. Here, we sought to define the prevalence and prognostic significance of LRRK2 somatic mutations across all types of human malignancies by querying the publicly available online genomic database cBioPortal. Ninety-six different studies with 14,041 cases were included in the analysis, and 761/14,041 (5.4%) showed genetic alterations in LRRK2. Among these, 585 (76.9%) were point mutations, indels or fusions, 168 (22.1%) were copy number variations (CNVs), and 8 (1.0%) showed both types of alterations. One case showed the somatic mutation R1441C. A significant difference in terms of overall survival (OS) was noted between cases harboring somatic LRRK2 whole deletions, amplifications, and CNV-unaltered cases (median OS: 20.09, 57.40, and 106.57 months, respectively; p = 0.0008). These results suggest that both LRRK2 amplifications and whole gene deletions could play a role in cancer development, paving the way for future research in terms of potential treatment with LRRK2 small molecule inhibitors for LRRK2-amplified cases.

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Large copy number variations in combination with point mutations in the TYMP and SCO2 genes found in two patients with mitochondrial disorders

European Journal of Human Genetics ◽

10.1038/ejhg.2013.148 ◽

2013 ◽

Vol 22 (3) ◽

pp. 431-434 ◽

Cited By ~ 7

Author(s):

Alžběta Vondráčková ◽

Kateřina Veselá ◽

Hana Kratochvílová ◽

Vendula Kučerová Vidrová ◽

Kamila Vinšová ◽

...

Keyword(s):

Copy Number ◽

Point Mutations ◽

Mitochondrial Disorders ◽

Copy Number Variations

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Hereditary breast and ovarian cancer: assessment of point mutations and copy number variations in Brazilian patients

BMC Medical Genetics ◽

10.1186/1471-2350-15-55 ◽

2014 ◽

Vol 15 (1) ◽

Cited By ~ 33

Author(s):

Felipe C Silva ◽

Bianca CG Lisboa ◽

Marcia CP Figueiredo ◽

Giovana T Torrezan ◽

Érika MM Santos ◽

...

Keyword(s):

Ovarian Cancer ◽

Copy Number ◽

Point Mutations ◽

Copy Number Variations ◽

Breast And Ovarian Cancer

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Detecting copy number alterations in RNA-Seq using SuperFreq

10.1101/2020.05.31.126888 ◽

2020 ◽

Author(s):

Christoffer Flensburg ◽

Alicia Oshlack ◽

Ian J. Majewski

Keyword(s):

Copy Number ◽

Point Mutations ◽

Variant Calling ◽

Read Depth ◽

The Cancer Genome Atlas ◽

Nucleotide Polymorphisms ◽

Rna Seq ◽

Copy Number Alterations ◽

Cancer Genome Atlas ◽

High Level

AbstractCalling copy number alterations (CNAs) from RNA-Seq is challenging, because differences in gene expression mean that read depth across genes varies by several orders of magnitude and there is a paucity of informative single nucleotide polymorphisms (SNPs). We previously developed SuperFreq to analyse exome data of tumours by combining variant calling and copy number estimation in an integrated pipeline. Here we have used the SuperFreq framework for the analysis of RNA sequencing (RNA-Seq) data, which allows for the detection of absolute and allele sensitive CNAs. SuperFreq uses an error-propagation framework to combine and maximise the information available in the read depth and B-allele frequencies of SNPs (BAFs) to make CNA calls on RNA-seq data. We used data from The Cancer Genome Atlas (TCGA) to evaluate the CNA called from RNA-Seq with those generated from SNP-arrays. When ploidy estimates were consistent, we found excellent agreement with CNAs called from DNA of over 98% of the genome for acute myeloid leukaemia (TCGA-AML, n=116) and 87% for colorectal cancer (TCGA-CRC, n=377), which has a much higher CNA burden. As expected, the sensitivity of CNA calling from RNA-Seq was dependent on gene density. Nonetheless, using RNA-Seq SuperFreq detected 78% of CNA calls covering 100 or more genes with a precision of 94%. Recall dropped markedly for focal events, but this also depended on the signal intensity. For example, in the CRC cohort SuperFreq identified 100% (7/7) of cases with high-level amplification of ERBB2, where the copy number was typically >20, but identified only 6% (1/17) of cases with moderate amplification of IGF2, typically 4 or 5 copies over a smaller region (median 5 flanking genes for IGF2, compared to 20 for ERBB2). We were able to reproduce the relationship between mutational load and CNA profile in CRC using RNA-Seq alone. SuperFreq offers an integrated platform for identification of CNAs and point mutations from RNA-seq in cancer transcriptomes.The software is implemented in R and is available through GitHub: https://github.com/ChristofferFlensburg/SuperFreq.

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Analytical and Clinical Validation of an Amplicon-based Next Generation Sequencing Assay for Ultrasensitive Detection of Circulating Tumor DNA

10.1101/2021.08.03.21261575 ◽

2021 ◽

Author(s):

Jonathan Poh ◽

Kao Chin Ngeow ◽

Michelle Pek ◽

Kian-Hin Tan ◽

Jing Shan Lim ◽

...

Keyword(s):

Next Generation Sequencing ◽

Copy Number ◽

Point Mutations ◽

Circulating Tumor Dna ◽

Clinical Validation ◽

Gene Fusions ◽

Copy Number Alterations ◽

Next Generation ◽

Tumor Dna ◽

Generation Sequencing

Next-generation sequencing of circulating tumor DNA presents a promising approach to cancer diagnostics, complementing conventional tissue-based diagnostic testing by enabling minimally invasive serial testing and broad genomic coverage through a simple blood draw to maximize therapeutic benefit to patients. LiquidHALLMARK® is an amplicon-based next-generation sequencing assay developed for the genomic profiling of plasma-derived cell-free DNA. The comprehensive 80-gene panel profiles point mutations, insertions/deletions, copy number alterations, and gene fusions, and further detects oncogenic viruses (EBV and HBV) and microsatellite instability. Here, the analytical and clinical validation of the assay is reported. Analytical validation using reference genetic materials demonstrated a sensitivity of 99.38% for point mutations and 95.83% for insertions/deletions at 0.1% variant allele frequency (VAF), and a sensitivity of 91.67% for gene fusions at 0.5% VAF, with high specificity even at 0.1% VAF (99.11% per-base). The limit of detection for copy number alterations, EBV, HBV, and microsatellite instability were also empirically determined. Orthogonal comparison of EGFR variant calls made by LiquidHALLMARK and a reference allele-specific PCR method for 355 lung cancer specimens revealed an overall concordance of 93.80%, while external validation with cobas® EGFR Mutation Test v2 for 50 lung cancer specimens demonstrated an overall concordance of 84.00%, with a 100% concordance rate for EGFR variants above 0.4% VAF. Clinical application of LiquidHALLMARK in 1,592 consecutive patients demonstrated a high detection rate (74.8% alteration-positive in cancer samples) and broad actionability (50.0% of cancer samples harboring alterations with biological evidence for actionability). Among ctDNA-positive lung cancers, 72.5% harbored at least one biomarker with a guideline-approved drug indication. These results establish the high sensitivity, specificity, accuracy, and precision of the LiquidHALLMARK assay and supports its clinical application for blood-based genomic testing.

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