scholarly journals Identification of Aneuploidy in Dogs Screened by a SNP Microarray

2021 ◽  
Author(s):  
Lisa G Shaffer ◽  
Bradley Hopp ◽  
Marek Świtoński ◽  
Adam Zahand ◽  
Blake C Ballif
Keyword(s):  
Microarray Analysis ◽  
Copy Number ◽  
Clinical Laboratory ◽  
Snp Array ◽  
Domestic Dog ◽  
Canine Chromosome ◽  
Disease Loci ◽  
Microarray Studies ◽  
Gains And Losses ◽  
Mosaic Trisomy

Abstract Microarray analysis is an efficient approach for screening and identifying cytogenetic imbalances in humans. SNP arrays, in particular, are a powerful way to identify copy number gains and losses representing aneuploidy and aneusomy, but moreover, allow for the direct assessment of individual genotypes in known disease loci. Using these approaches, trisomies, monosomies and mosaicism of whole chromosomes have been identified in human microarray studies. For canines, this approach is not widely used in clinical laboratory diagnostic practice. In our laboratory, we have implemented the use of a propriety SNP array that represents approximately 650,000 loci across the domestic dog genome. During the validation of this microarray prior to clinical use, we identified three cases of aneuploidy after screening 2,053 dogs of various breeds including monosomy X, trisomy X and an apparent, mosaic trisomy of canine chromosome 38 (CFA 38). This study represents the first use of microarrays for copy number evaluation to identify cytogenetic anomalies in canines. As microarray analysis becomes more routine in canine genetic testing, more cases of chromosome aneuploidy are likely to be uncovered.

scholarly journals From Benign Inflammatory Dermatosis to Cutaneous Lymphoma. DNA Copy Number Imbalances in Mycosis Fungoides versus Large Plaque Parapsoriasis

Medicina ◽  
2021 ◽  
Vol 57 (5) ◽  
pp. 502
Author(s):  
Georgiana Gug ◽  
Caius Solovan
Keyword(s):  
Mycosis Fungoides ◽  
Copy Number ◽  
Snp Array ◽  
Chromosome 1 ◽  
Copy Number Alterations ◽  
Dna Copy Number ◽  
Large Plaque ◽  
Inflammatory Dermatosis ◽  
Fresh Frozen ◽  
Dna Copy Number Alterations

Background and Objectives: Mycosis fungoides (MF) and large plaque parapsoriasis (LPP) evolution provide intriguing data and are the cause of numerous debates. The diagnosis of MF and LPP is associated with confusion and imprecise definition. Copy number alterations (CNAs) may play an essential role in the genesis of cancer out of genes expression dysregulation. Objectives: Due to the heterogeneity of MF and LPP and the scarcity of the cases, there are an exceedingly small number of studies that have identified molecular changes in these pathologies. We aim to identify and compare DNA copy number alterations and gene expression changes between MF and LPP to highlight the similarities and the differences between these pathologies. Materials and Methods: The patients were prospectively selected from University Clinic of Dermatology and Venereology Timișoara, Romania. From fresh frozen skin biopsies, we extracted DNA using single nucleotide polymorphism (SNP) data. The use of SNP array for copy number profiling is a promising approach for genome-wide analysis. Results: After reviewing each group, we observed that the histograms generated for chromosome 1–22 were remarkably similar and had a lot of CNAs in common, but also significant differences were seen. Conclusions: This study took a step forward in finding out the differences and similarities between MF and LPP, for a more specific and implicitly correct approach of the case. The similarity between these two pathologies in terms of CNAs is striking, emphasizing once again the difficulty of approaching and differentiating them.

44. Reevaluation of copy number variant (CNV) classifications in the clinical laboratory setting: challenges, insights, and experiences with a laboratory-initiated process

2021 ◽  
Vol 252-253 ◽  
pp. S15
Author(s):  
Denise I Quigley ◽  
Zoe K Lewis ◽  
Timothy Tidwell ◽  
Adam Clayton ◽  
Brandon Chandler ◽  
...  
Keyword(s):  
Copy Number ◽  
Clinical Laboratory ◽  
Copy Number Variant ◽  
Laboratory Setting

scholarly journals Transformed Canine and Murine Mesenchymal Stem Cells as a Model for Sarcoma with Complex Genomics

Cancers ◽  
2021 ◽  
Vol 13 (5) ◽  
pp. 1126
Author(s):  
Natasja Franceschini ◽  
Bas Verbruggen ◽  
Marianna A. Tryfonidou ◽  
Alwine B. Kruisselbrink ◽  
Hans Baelde ◽  
...  
Keyword(s):  
Copy Number ◽  
Point Mutations ◽  
Comparative Approach ◽  
Cell Of Origin ◽  
Mesenchymal Tumors ◽  
Spontaneous Transformation ◽  
Exon 2 ◽  
Species Analysis ◽  
Gains And Losses

Sarcomas are rare mesenchymal tumors with a broad histological spectrum, but they can be divided into two groups based on molecular pathology: sarcomas with simple or complex genomics. Tumors with complex genomics can have aneuploidy and copy number gains and losses, which hampers the detection of early, initiating events in tumorigenesis. Often, no benign precursors are known, which is why good models are essential. The mesenchymal stem cell (MSC) is the presumed cell of origin of sarcoma. In this study, MSCs of murine and canine origin are used as a model to identify driver events for sarcomas with complex genomic alterations as they transform spontaneously after long-term culture. All transformed murine but not canine MSCs formed sarcomas after subcutaneous injection in mice. Using whole genome sequencing, spontaneously transformed murine and canine MSCs displayed a complex karyotype with aneuploidy, point mutations, structural variants, inter-chromosomal translocations, and copy number gains and losses. Cross-species analysis revealed that point mutations in Tp53/Trp53 are common in transformed murine and canine MSCs. Murine MSCs with a cre-recombinase induced deletion of exon 2-10 of Trp53 transformed earlier compared to wild-type murine MSCs, confirming the contribution of loss of p53 to spontaneous transformation. Our comparative approach using transformed murine and canine MSCs points to a crucial role for p53 loss in the formation of sarcomas with complex genomics.

Screening and detection of chromosomal copy number alterations in the domestic horse using SNP‐array genotyping data

2021 ◽  
Author(s):  
Y. Pirosanto ◽  
N. Laseca ◽  
M. Valera ◽  
A. Molina ◽  
M. Moreno‐Millán ◽  
...  
Keyword(s):  
Copy Number ◽  
Snp Array ◽  
Domestic Horse ◽  
Copy Number Alterations ◽  
Chromosomal Copy Number ◽  
Chromosomal Copy

scholarly journals Comprehensive Assessment of Copy Number Alterations Uncovers Recurrent AIFM3 and DLK1 Copy Gain in Medullary Thyroid Carcinoma

Cancers ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 218
Author(s):  
Aline Neves Araujo ◽  
Cléber Pinto Camacho ◽  
Thais Biude Mendes ◽  
Susan Chow Lindsey ◽  
Lais Moraes ◽  
...  
Keyword(s):  
Thyroid Carcinoma ◽  
Medullary Thyroid Carcinoma ◽  
Copy Number ◽  
Snp Array ◽  
In Silico Analysis ◽  
Pcr Analysis ◽  
Copy Number Alterations ◽  
Medullary Thyroid ◽  
Thyroid C Cells ◽  
Ajcc Staging

Medullary thyroid carcinoma (MTC) is a malignant tumor originating from thyroid C-cells that can occur either in sporadic (70–80%) or hereditary (20–30%) form. In this study we aimed to identify recurrent copy number alterations (CNA) that might be related to the pathogenesis or progression of MTC. We used Affymetrix SNP array 6.0 on MTC and paired-blood samples to identify CNA using PennCNV and Genotyping Console software. The algorithms identified recurrent copy number gains in chromosomes 15q, 10q, 14q and 22q in MTC, whereas 4q cumulated losses. Coding genes were identified within CNA regions. The quantitative PCR analysis performed in an independent series of MTCs (n = 51) confirmed focal recurrent copy number gains encompassing the DLK1 (14q32.2) and AIFM3 (22q11.21) genes. Immunohistochemistry confirmed AIFM3 and DLK1 expression in MTC cases, while no expression was found in normal thyroid tissues and few MTC samples were found with normal copy numbers. The functional relevance of CNA was also assessed by in silico analysis. CNA status correlated with protein expression (DLK1, p = 0.01), tumor size (DLK1, p = 0.04) and AJCC staging (AIFM3p = 0.01 and DLK1p = 0.05). These data provide a novel insight into MTC biology, and suggest a common CNA landscape, regardless of if it is sporadic or hereditary MTC.

17. In silico SNP array for aiding in interpretation of genomic microarray results: Application to case of mosaic trisomy 9

2021 ◽  
Vol 252-253 ◽  
pp. S6
Author(s):  
Timothy Fee ◽  
David B. Everman ◽  
Benjamin A. Hilton ◽  
Barbara DuPont
Keyword(s):  
In Silico ◽  
Snp Array ◽  
Trisomy 9 ◽  
Genomic Microarray ◽  
Mosaic Trisomy

scholarly journals Jumping translocations of 1q12 in multiple myeloma: a novel mechanism for deletion of 17p in cytogenetically defined high-risk disease

Blood ◽  
2014 ◽  
Vol 123 (16) ◽  
pp. 2504-2512 ◽  
Author(s):  
Jeffrey R. Sawyer ◽  
Erming Tian ◽  
Christoph J. Heuck ◽  
Joshua Epstein ◽  
Donald J. Johann ◽  
...  
Keyword(s):  
Multiple Myeloma ◽  
High Risk ◽  
Copy Number ◽  
High Risk Disease ◽  
Key Points ◽  
Gains And Losses

Key Points Jumping translocations of 1q12 (JT1q12) provide a mechanism for the deletion of 17p in cytogenetically defined high-risk myeloma. Sequential JT1q12s introduce unexpected copy number gains and losses in receptor chromosomes during subclonal evolution.

scholarly journals Integrative DNA copy number detection and genotyping from sequencing and array-based platforms

2017 ◽  
Author(s):  
Zilu Zhou ◽  
Weixin Wang ◽  
Li-San Wang ◽  
Nancy Ruonan Zhang
Keyword(s):  
Copy Number ◽  
Association Studies ◽  
Snp Array ◽  
Supplementary Information ◽  
Detection Accuracy ◽  
Sequencing Data ◽  
Array Data ◽  
Combining Data ◽  
Allele Specific ◽  
Cnv Detection

AbstractMotivationCopy number variations (CNVs) are gains and losses of DNA segments and have been associated with disease. Many large-scale genetic association studies are performing CNV analysis using whole exome sequencing (WES) and whole genome sequencing (WGS). In many of these studies, previous SNP-array data are available. An integrated cross-platform analysis is expected to improve resolution and accuracy, yet there is no tool for effectively combining data from sequencing and array platforms. The detection of CNVs using sequencing data alone can also be further improved by the utilization of allele-specific reads.ResultsWe propose a statistical framework, integrated Copy Number Variation detection algorithm (iCNV), which can be applied to multiple study designs: WES only, WGS only, SNP array only, or any combination of SNP and sequencing data. iCNV applies platform specific normalization, utilizes allele specific reads from sequencing and integrates matched NGS and SNP-array data by a Hidden Markov Model (HMM). We compare integrated two-platform CNV detection using iCNV to naive intersection or union of platforms and show that iCNV increases sensitivity and robustness. We also assess the accuracy of iCNV on WGS data only, and show that the utilization of allele-specific reads improve CNV detection accuracy compared to existing methods.Availabilityhttps://github.com/zhouzilu/[email protected], [email protected] informationSupplementary data are available at Bioinformatics online.

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