Evaluation of the Affymetrix CytoScan<sup>®</sup>Dx Assay for developmental delay

Webb, Bryn D.; Scharf, Rebecca J.; Spear, Emily; Edelmann, Lisa; Stroustrup, Annemarie

doi:10.1586/14737159.2015.975213

Cited by 11 publications

(14 citation statements)

References 13 publications

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“…We first used an independent set of CNV calls generated by a non-NGS-based technology as the truth set. We performed Affymetrix CytoScan Array, which incorporates 2.68 million genomic markers to detect genome-wide chromosomal abnormalities [28, 29] and categorized each bin into amplification, deletion, or marginal as we did for NGS-based callers. Overall, array calls were more similar to CNVkit and Segmentum (Figure 5A).…”

Section: Resultsmentioning

confidence: 99%

Comprehensive Assessment of Somatic Copy Number Variation Calling Using Next-Generation Sequencing Data

Chen

Seifuddin

Nguyen

et al. 2021

Preprint

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Copy number variation (CNV) is a common type of mutation that often drives cancer progression. With advances in next-generation sequencing (NGS), CNVs can be detected in a detailed manner via newly developed computational tools but quality of such CNV calls has not been carefully evaluated. We analyzed CNV calls reported by 6 cutting-edge callers for 91 samples which were derived from the same cancer cell line, prepared and sequenced by varying the following factors: type of tissue sample (Fresh vs. Formalin Fixed Paraffin Embedded (FFPE)), library DNA amount, tumor purity, sequencing platform (Whole-Genome Sequencing (WGS) versus Whole-Exome Sequencing (WES)), and sequencing coverage. We found that callers greatly determined the pattern of CNV calls. Calling quality was drastically impaired by low purity (<50%) and became variable when WES, FFPE, and medium purity (50%-75%) were applied. Effects of low DNA amount and low coverage were relatively minor. Our analysis demonstrates the limitation of benchmarking somatic CNV callers when the real ground truth is not available. Our comprehensive analysis has further characterized each caller with respect to confounding factors and examined the consistency of CNV calls, thereby providing guidelines for conducting somatic CNV analysis.

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Section: Resultsmentioning

confidence: 99%

Comprehensive Assessment of Somatic Copy Number Variation Calling Using Next-Generation Sequencing Data

Chen

Seifuddin

Nguyen

et al. 2021

Preprint

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“…A discrete copy number value is determined from the relative intensity data and is displayed. Genotype information for the SNP markers is visualized with the Allele Track [20] .…”

Section: Methodsmentioning

confidence: 99%

Complex Chromosomal Rearrangements in B-Cell Lymphoma: Evidence of Chromoanagenesis? A Case Report

et al. 2016

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Genomic instability is a well-known hallmark of cancer. Recent genome sequencing studies have led to the identification of novel phenomena called chromothripsis and chromoanasynthesis in which complex genomic rearrangements are thought to be derived from a single catastrophic event rather than by several incremental steps. A new term chromoanagenesis or chromosomal rebirth was coined recently to group these two one-step catastrophic events together. These phenomena suggest an evolutionary modality for cancer cells to circumvent individual mutational events with one simultaneous shattering of chromosomes resulting in the random reassembling of segmented genetic material to form complex derivative chromosomes. We report a case of possible chromoanagenesis in a patient with diffuse large B-cell lymphoma. Chromosome analysis from the biopsy showed a complex karyotype with multiple numerical and structural rearrangements including a translocation of chromosomes 3 and 7 involving the BCL6 gene region, with the derivative chromosome further rearranging with chromosomes 14, 7, and 22 with involvement of the IGH gene region. Fluorescence in situ hybridization studies confirmed these findings. Chromosomal microarray studies showed multiple complex copy number variations including a chromosome 12 abnormality, the complexity of which appears to suggest the phenomenon of chromoanagenesis. Our case further illustrates that lymphomagenesis can be complex and may arise from a catastrophic event resulting in multiple complex chromosome rearrangements.

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“…A discrete copy number value is determined from the relative intensity data and is displayed. Genotype information for the SNP markers is visualized with the Allele Track [ 7 ].…”

Section: Single Nucleotide Polymorphism (Snp) Oligonucleotide Microarraymentioning

confidence: 99%

Copy neutral absence of heterozygosity on chromosome 15 distal long arm: A surrogate marker for Prader–Willi/Angelman syndromes?

et al. 2021

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Background Copy-neutral absence of heterozygosity (CN-AOH) observed on a single chromosome or part of a chromosome may be indicative of uniparental disomy (UPD) and may require additional testing when such chromosomes or chromosome regions are known to harbor imprinted genes. Case presentation Here we report 2 cases of neonates that presented to clinic with hypotonia, poor oral skills including inability to feed by mouth, weak cry, no response to noxious stimulation and vertical plantar creases (case 1) and hypotonia and respiratory distress (case 2). A preliminary chromosome analysis showed normal karyotypes in both cases while the high-resolution single nucleotide polymorphism (SNP) microarray showed copy neutral absence of heterozygosity involving chromosome 15 distal long arm. In case 1, the CN-AOH involved a 28.7 Mb block from genomic coordinates 73703619_102429049. In case 2, the CN-AOH involved a 15.3 Mb block from genomic coordinates 54729197_70057534. In both cases, methylation-specific PCR did not detect an unmethylated allele for the SNRPN gene suggesting either a deletion of paternal allele or maternal UPD for chromosome 15. Since microarray analysis did not show any copy number alterations on chromosome 15, a microdeletion was ruled out. Conclusions Based on our cases, we suggest that CN-AOH on chromosome 15, even if it does not involve the critical region of 15q12q13, should warrant additional studies for diagnosis of Prader–Willi/Angelman syndromes.

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Evaluation of the Affymetrix CytoScan^®Dx Assay for developmental delay

Cited by 11 publications

References 13 publications

Comprehensive Assessment of Somatic Copy Number Variation Calling Using Next-Generation Sequencing Data

Comprehensive Assessment of Somatic Copy Number Variation Calling Using Next-Generation Sequencing Data

Complex Chromosomal Rearrangements in B-Cell Lymphoma: Evidence of Chromoanagenesis? A Case Report

Copy neutral absence of heterozygosity on chromosome 15 distal long arm: A surrogate marker for Prader–Willi/Angelman syndromes?

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Evaluation of the Affymetrix CytoScan®Dx Assay for developmental delay

Cited by 11 publications

References 13 publications

Comprehensive Assessment of Somatic Copy Number Variation Calling Using Next-Generation Sequencing Data

Comprehensive Assessment of Somatic Copy Number Variation Calling Using Next-Generation Sequencing Data

Complex Chromosomal Rearrangements in B-Cell Lymphoma: Evidence of Chromoanagenesis? A Case Report

Copy neutral absence of heterozygosity on chromosome 15 distal long arm: A surrogate marker for Prader–Willi/Angelman syndromes?

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Evaluation of the Affymetrix CytoScan^®Dx Assay for developmental delay