Application Modules for: Variant Analysis, Targeted, WES, WGS SNPs Indels Structural Variations Somatic Mutation Mining Copy Number Variation (CNV) Analysis CNV Tool MLPA-like Analysis with Batch CNV Tool Sensitive Aneuploidy Detection (SAD) Tool HLA Analysis Patient Comparison Groups Families Trios Functional Prediction Calling RNA-Seq/Transcriptome Analysis Digital Gene Expression miRNA Discovery and Quantification Assembly de novo Paired end

Benefits Instant Knowledge… Single Annotated data review screen Biologist Friendly Windows® interface… Increased Accuracy… Unique technologies increase accuracy by 4Removing sequencing errors 4Platform specific technologies Compatible with all major sequencing systems Track Manager 4Functional Prediction 4Disease Association 4Conservation Scores 4Population Frequencies Annotated results in single easy-to-navigate view… 4Automated pipeline tool speeds analysis 4Multiple integrated, exportable reports 4Analysis filters Automated Analysis Pipeline Automated format conversion tool Low-Cost Hardware...

Features Instant Knowledge  • Annotation • Easy Navigation • Exportable NextGENe’s analysis browser provides a highly interactive review of annotated analysis results in a single view. Navigation is as simple as drawing “boxes” to zoom in or out, graphics and text reports are hyperlinked to speed data review and “hot” keys ease navigation.  Example of annotated Whole Human Genome data review with NextGENe browser. Navigation is simple either using Hot Keys or by dragging mouse over screen to move across the genome or zoom in on selected areas. Text Reports are linked to browser for quick, easy...

Optimized Analysis Performance NextGENe has been optimized to perform on any Windows® 64 bit operating system from Vista through Windows 10, or Windows based server 2008R2 and forward. NextGENe also performs well on Mac® hardware when utilizing VMware, boot camp or similar boot managers along with Windows OS. NextGENe is multi-threaded, utilizing all available processors. Performance examples of alignment and variant detection on various fasta data sets. Reporting of Results and Quality Control Metrics • Customizable • Various Formats including VCF & SIFT NextGENe produces several reports, including...

Mutation Confidence Scoring • Overall mutation confidence score provided for every mutation • Any penalty score can be disabled • Quickly view the distribution of scores in a project • Filter based on the overall score or on penalty sub-scores NextGENe software includes a proprietary mutation confidence scoring system designed to make it easier to find the called mutations that are most likely to represent true variations. The overall score is the product of the coverage score and several penalty sub-scores: ● Coverage score – starts at 0 and has no upper limit, but is rarely higher than 32....

Variant Annotation Tracks and Pathogenicity Calling • Functional Prediction information SIFT, PolyPhen-2, LRT, MutationTaster, FATHMM, CADD & MutationAssessor • Disease association ClinVar & COSMIC • Conservation scores phyloP, GERP++, phastCons & SiPhy • Population frequencies 1000 Genomes and Exome Variant Server • COSMIC - Catalogue of Somatic Mutations in Cancer from Sanger Institute • dbSNP from NCBI • Custom Tracks NextGENe’s Reference and Track Manager Tool can be used to import variant databases as tracks for annotation. Information from imported tracks can be displayed and used for filtering...

Applications SNP/INDEL Detection • SNP Detection • Indel Detection (up to the read length) • Low False Positive Rate • Biologist friendly reporting • Export results in spreadsheet form or VCF format to database or LIMS system  • Scoring of Variants SNP’s and small lndels, up to the read length, can be detected in sequencing data from all sequencing technologies.Use of the Condensation® Tool elongates short reads, increasing read uniqueness probability in the genome, while polishing the data to remove chemistry and instrumental errors. NextGENe software automatically calculates a confidence score...

Analysis of Targeted Sequencing Panels NextGENe software is able to very rapidly process samples from Ion Torrent™, and Illumina platforms in order to find potentially important mutations in AmpliSeq™, HaloPlex™, Multiplicom™, NEBNext™, RainDance™, Roche GS G Type Assay and all other targeted sequencing panels. NextGENe software includes sorting and trimming tools, alignment, and mutation calling on low cost Windows PCs. NextGENe software is also able to annotate the mutations that were found using dbSNP, the dbNSFP database, the COSMIC database, or custom databases. Alignments and variant calling...

Copy Number Variation Analysis Tools CNV Tool • Two powerful CNV algorithms available • Provides confidence scores for CNV calls • Classifies regions as potential deletions, duplications, or normal copy number • Processes individual CNV changes (per exon, or per amplicon) into multi-locus calls that can be made more confidently. NextGENe includes a new Copy Number Variation (CNV) analysis tool designed to make variant calls on a case-control basis. Two powerful CNV detection algorithms are included, using proprietary technology. The “SNP-Based” method uses a global coverage normalization and...

Batch CNV Tool for MLPA-like CNV Detection The use of NGS and NextGENe software’s Batch CNV Tool for screening dramatically increases laboratory throughput while significantly reducing the cost of MLPA Analysis. NextGENe software includes a Batch CNV tool that provides a means to replace Multiplex Ligation-dependent Probe Amplification and similar techniques, typically performed by capillary electrophoresis (CE) fragment analysis, with High-Throughput or Next Generation Sequencing. HTS approach to CNV does not use the problematic steps of the traditional MLPA reaction, which are challenging to...