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.
Nxclinical software
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.
4 protocols using nxclinical software
Genomic Analysis of CLL/SLL-DLBCL Transformation
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.
Identifying Tumor-Driving Chromosomal Aberrations
Copy Number Variation Analysis
Genetic Investigation of Congenital Muscular Dystrophy
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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