Concordance between single-nucleotide polymorphism–based genomic instability assays and a next-generation sequencing–based homologous recombination deficiency test

Background: We evaluated the performance of single-nucleotide polymorphism (SNP) genotyping arrays OncoScan (Thermo Fisher Scientific, San Diego, CA) and Infinium CytoSNP-850K (CytoSNP; Illumina, Waltham, MA) for assessing homologous recombination deficiency (HRD) genomic instability. Methods: DNA (...

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Veröffentlicht in:BMC cancer Jg. 22; H. 1; S. 1310 - 9
Hauptverfasser: Cristescu, Razvan, Liu, Xiao Qiao, Arreaza, Gladys, Chen, Cai, Albright, Andrew, Qiu, Ping, Marton, Matthew J.
Format: Journal Article
Sprache:Englisch
Veröffentlicht: London BioMed Central 14.12.2022
BioMed Central Ltd
Springer Nature B.V
BMC
Schlagworte:
Algorithms
Analysis
Biological markers
Biomarkers
Biomedical and Life Sciences
Biomedicine
BRCA
Cancer Research
Care and treatment
Chromosomal instability syndromes
Clinical trials
Copy number
Copy number variations
Diagnosis
DNA Copy Number Variations
FDA approval
Gene polymorphism
Genetic aspects
Genomic Instability
Genotyping
Health Promotion and Disease Prevention
Heterozygosity
High-Throughput Nucleotide Sequencing
Homologous Recombination
Homologous recombination deficiency
Humans
International organizations
Large-scale state transition
Loss of Heterozygosity
Medical prognosis
Medicine/Public Health
Mutation
Next-generation sequencing
Oncology
Ovarian cancer
Patients
Polymorphism
Polymorphism, Single Nucleotide
Prevention
Risk factors
Segmentation
Single nucleotide polymorphisms
Single-nucleotide polymorphism
Surgical Oncology
Telomeric-allelic imbalance number
Tumors
Vascular endothelial growth factor
China
United States > US
Telomeric-allelic imbalance number
BRCA
Homologous recombination deficiency
Loss of heterozygosity
Large-scale state transition
ISSN:1471-2407, 1471-2407
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Zusammenfassung:Background: We evaluated the performance of single-nucleotide polymorphism (SNP) genotyping arrays OncoScan (Thermo Fisher Scientific, San Diego, CA) and Infinium CytoSNP-850K (CytoSNP; Illumina, Waltham, MA) for assessing homologous recombination deficiency (HRD) genomic instability. Methods: DNA (pretreatment samples) across 20 tumor types was evaluated with OncoScan, CytoSNP, and the clinically validated HRD test. Copy number variation (CNV) and loss of heterozygosity (LOH) analyses were performed with ASCATv2.5.1. Aggregate HRD genomic metrics included LOH, telomeric-allelic imbalance number (TAI), and large-scale state transition (LST). Associations between BRCA mutation ( BRCA m) status and the clinically validated HRD test metric (dichotomized at a clinical cut-off) were evaluated using area under the receiver operating characteristic (AUROC); Spearman ρ was calculated for continuous metrics. CNV segmentation and HRD genomic metrics were calculated ( n  = 120, n  = 106, and n  = 126 for OncoScan, CytoSNP and clinically validated HRD test, respectively). Results: When assessed by SNP arrays, the genomic metric demonstrated good association with BRCA m (AUROC of HRD: OncoScan, 0.87; CytoSNP, 0.75) and the clinically validated test (cut-off, 42; AUROC of HRD: OncoScan, 0.92; CytoSNP, 0.91). The genomic metrics demonstrated good correlation with the clinically validated aggregate HRD test metric (ρ: OncoScan, 0.82; CytoSNP, 0.81) and for each component (ρ: OncoScan, 0.68 [LOH], 0.76 [TAI], and 0.78 [LST]; CytoSNP, 0.59 [LOH], 0.77 [TAI], and 0.82 [LST]). HRD assessed by SNP genotyping arrays and the clinically validated test showed good correlation. Conclusion: OncoScan and CytoSNP may potentially identify most HRD-positive tumors with appropriate clinically relevant cut-offs.
Bibliographie:ObjectType-Article-1
SourceType-Scholarly Journals-1
ObjectType-Feature-2
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ISSN:1471-2407
1471-2407
DOI:10.1186/s12885-022-10197-z