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Nxclinical software

Manufactured by BioDiscovery
Sourced in United States

NxClinical software is a bioinformatics tool designed for the analysis and interpretation of genomic data. The software provides a platform for processing, visualizing, and reporting on genetic variants and associated clinical information.

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4 protocols using nxclinical software

1

Genomic Analysis of CLL/SLL-DLBCL Transformation

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We performed a retrospective analysis of all patients at our institution with confirmed CLL/SLL between 01/01/2010 and 02/14/2019. Patients with CLL/SLL were then evaluated for RT by reviewing clinical documentation and pathologic data in the electronic medical record. We collected baseline demographic, clinical, laboratory, pathology, and outcomes data on patients with CLL/SLL and subsequent DLBCL and who had CMA performed on both the CLL/SLL and DLBCL samples. One patient did exhibit transformation to Hodgkin Lymphoma; however, CMA data was not available on both samples thus was excluded.
CMA was performed using the Infinium HD Human Omni1 BeadChip or the CytoSNP-850 K v1.1 BeadChip Array (Illumina, Inc., San Diego, CA) on genomic DNA extracted from peripheral blood/marrow and fresh or formalin fixed paraffin-embedded (FFPE) lymph node samples. Copy number and genotype data were analyzed using NxClinical software (BioDiscovery, El Segundo, CA). Aberrations that were in 100% of cells and were present in public databases of germline variants were considered constitutional and not included in analysis; whereas, aberrations found in less than 100% of cells were considered clonal changes. Genome build hg19 (February 2009) was used for probe locations and data interpretation.
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2

Identifying Tumor-Driving Chromosomal Aberrations

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For neuroblastoma tumors, chromosomal regions with aberrations in copy numbers were identified through SNP array. SNP array copy number profiling and analysis of regions of homozygosity were performed according to standard procedures using the CytoSNP-850 K BeadChip (Illumina, San Diego, CA). Visualizations of SNP array results and data analysis were performed using NxClinical software (BioDiscovery, Los Angeles, CA), using Human genome build February 2009 GRCh37/hg1. Chromosomal aberrations that are known to be tumor driving or associated with high- risk disease were preferentially selected for TLA/TLC breakpoint identification (e.g. chromosome 1p, 1q, 2p (including MYCN locus), 3p, 11q, 17q) (4 (link)). The fusion partners of FOXO1 in the fusion-positive alveolar rhabdomyosarcomas were validated through RT-qPCR on tumor organoid models (tumoroids) grown from primary tumor material, as described previously (28 (link)). In the Ewing sarcoma sample, the fusion between EWSR1 and FLI1 was validated through RT-qPCR on the tumoroid with primers located on EWSR1 exon 8 (AGGAGAGAACCGGAGCATGA) and FLI1 exon 5 (CCCTGAGGTAACTGAGGTGTG).
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3

Copy Number Variation Analysis

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CNV data analysis was performed using the NxClinical software (BioDiscovery, California, USA), which calls copy number changes by comparing the number of reads of an experimental sample to an internal reference library. The data were normalized and the log 2 ratio Test/Reference was calculated. Following the same principle of microarray analysis, the theoretically expected log2 ratio value, when there are no changes in copy number, corresponds to zero (test/reference = 1). To identify CNVs, we used the SNP-FASST2 segmentation algorithm, based on the Hidden Markov Model, with a sensitivity threshold of 1.0 E-6. A genomic segment was considered duplicated or deleted when the log 2 ratio of a given region encompassing at least three targets was above 0.3 or below - 0.3, respectively 14, (link)17, 18 . Detected CNVs were classi ed according to their potential clinical impact as Pathogenic (P), Likely Pathogenic (LP), Variants of Uncertain Signi cance (VUS), Likely Benign (LB) and Benign (B), according to the European guidelines for constitutional cytogenomics analysis, American College of Medical Genetics (ACMG) and Clinical Genome Resource (ClinGen) guidelines 19, 20 . The common variants (LB/B) were not reported in this study.
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4

Genetic Investigation of Congenital Muscular Dystrophy

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The family is of Kurdish ethnic origin. The asymptomatic parents are second degree cousins.
A maternal aunt is also affected. Detailed clinical, electrophysiological, imaging and pathological examinations were performed.
After obtaining informed consent, genomic DNA from patients and their parents was extracted from blood. Molecular-genetic testing with Next Generation Sequencing (NGS) using a congenital muscular dystrophy (CMD) panel was done using the TruSight One Sequencing Kit (Illumina, Inc). The library was sequenced on a MiSeq (Illumina, Inc.) with 2x150bp reads.
Coverage was 98.48% >20x for the targeted panel where only coding exons were selected. Bioinformatic pipeline and analysis was performed using SophiaDDM (Sophia Genetics SA).
Variant classification and interpretation were done according to the ACMG guidelines [3] .
CNV analysis of the NGS data was performed using the NxClinical software (BioDiscovery, Inc.). Exon 36 of the COL6A3 was amplified and sequenced. SYBR Green I was used as intercalating dye and the PCR products were run on the LightCycler 480 (F. Hoffmann-La Roche Ltd). Array-CGH was run with Microchip Agilent 180K according to manufacturer instructions and analysed using Agilent CytoGenomics v3.0 software (Agilent Technologies, Inc.).
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