13 software found
BioDiscovery, A Bionano Genomics Company Software
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CNVs from NGS
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BioDiscovery - Copy Number and AOH Detection from NGS
High-quality detection of CNV from NGS data has been a challenge for many years. BioDiscovery has perfected algorithms for the detection of CNV and AOH from almost all NGS ...
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BioDiscovery - Algorithms Software for CNV and AOH Detection
BioDiscovery has developed two algorithms for the detection of CNV and AOH events from NGS using its decades-long expertise in the area. One algorithm, the “Self-reference” algorithm, can be used for all WGS data regardless of sequencing depth. The second is the “Multi-Scale Reference” (MSR) algorithm that is applicable to all NGS data (WGS, WES, and Gene panels). The MSR algorithm is able to create “virtual” bins with ...
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BioDiscovery - Whole Exome Sequencing Tools
Getting CNV calls from Whole Exome Sequencing has been one of the most challenging efforts in the community. There have been numerous algorithms proposed but they suffer either from poor sensitivity or too many false-positive calls. The MSR algorithm has been able to offer the best balance of these competing measures, detecting small true-positives without generating many false-positives. The image below shows a small 12Kb deletion overlapping part of ...
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BioDiscovery - Whole Genome Sequencing Tools
As described in Chaubey et al., Journal of Molecular Diagnostics, vol. 22, No. 6 June 2020, they used 10x WGS and validated that the NxClinical algorithm detected all CNVs and AOH that were found by high-resolution SNP arrays. Figure 2. shows a small exonic deletion detected using 10x WGS with the MSR algorithm. With higher depth NGS, smaller CNVs can be detected and integrated with sequence variants to provide a holistic view of the sample. In Figure 3., ...
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BioDiscovery - Gene Panels
The MSR algorithm can be applied to any gene panel from single gene (e.g. DMD test) to large panels having thousands of gene. The image below is from the Illumina TruSightTM Oncology 500 (TSO500) panel showing a somatic cancer profile. The cytogenetic complexity of the tumor sample is clearly evident with a large copy number gain of 8p and loss of a large section of 13q. Aberrations associated with genomic scarring, such as Loss of Heterozygosity (LOH), ...
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BioDiscovery - Shallow Sequencing
The MSR algorithm can also be applied to detect CNVs from shallow sequencing, including very low-level mosaic events seen in NIPS or ctDNA samples. The image below shows a sample with trisomy 21 detected using 1x WGS. CNVs are an important contributor to disease and are required for accurate diagnosis. For clinical sequencing to be fully accepted as a replacement for microarrays and other widely used techniques, it must provide high-quality CNV ...
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Genomic Scar Scoring
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Bionano NxClinical - Automated Genomic Scar Analysis for HRD with Software
Bionano's NxClinicalTM Software is the leading copy number variation (CNV) analysis software solution for cytogenetics and molecular laboratories. The latest software (v6.2) release adds three measures of genomic instability for homologous recombination repair deficiency (HRD) in solid tumors: Loss of heterozygosity (LOH). Telomeric Allelic Imbalance (TAI). Large-Scale State ...
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ACMG Scoreboard
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BioDiscovery - Version ACMG - Scoreboard Software
The most recent version of NxClinical, the leading copy number variation (CNV) analysis software for clinical cytogenetics and molecular labs, now includes an integrated ACMG guidelines scoreboard ...
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Automated Pre-Classification Software
In addition to using the scoreboard as a stand-alone guideline, this new feature can also be coupled with NxClinical's popular automated variant pre-classification decision tree to pre-classify events. This allows analysts to quickly sort through the events on the table and prioritize for ...
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One-Click UPD
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BioDiscovery - Investigate Further Software
The probe track view in NxClinical shows greater detail related to the supporting probes involved in this heteroUPD15 example. Enlarge the image to the right to reveal the heteroUPD15 visualized on both the top chromosome view (represented by the pink horizontal line) and the BAF plot for parental informative SNPs ...
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BioDiscovery - Quickly Visualize Software
Within the karyogram view, vertical bars are drawn within the AOH affected chromosome(s) to indicate parent-of-origin (pink=maternal; blue=paternal), and the same color indicators are displayed in the zygosity track. The image to the left displays a maternal inheritance represented by the pink probes on the BAF ...
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Others
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BioDiscovery - User-friendly and Powerful Statistical Tools for Nexus Copy Number
Arming researchers with advanced genomic data analysis and visualization tools. Easy-to-use software provides cutting-edge statistical tools to advance scientific ...
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BioDiscovery NxClinical - Comprehensive and Up-to-date Solution for Cytogenetics and Molecular Genetics
The most comprehensive and up-to-date solution for cytogenetics and molecular genetics in one system for analysis and interpretation of all genomic variants from microarray and NGS ...