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Agilent Technologies Launches New Platform for Analyzing Cell-Free DNA

Agilent Technologies
9 Mar 2016
Alex Waite
Editorial Assistant

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Agilent Technologies Inc. has introduced OneSight, a new software platform designed to help researchers visualize and analyze chromosomal aneuploidies in cell-free DNA sequencing data.

Agilent unveiled its new bioinformatics product at the annual meeting of the American College of Medical Genetics and Genomics in Tampa, Florida.

“The study of cell-free DNA is a very active area of research, and we expect growth in applications such as analysis of liquid biopsies and cell-free fetal DNA,” said Herman Verrelst, Agilent vice president and general manager of the company’s Genomics Solutions Division and Clinical Applications Division. “With OneSight, researchers will be able to gain a deeper understanding of their sequencing data and apply that to a wide range of applications, from the early detection of cancer to screening for fetal abnormalities.”

Verrelst noted that OneSight offers genetics laboratories a cost-effective way to perform high-quality, cell-free DNA analysis in-house (which used to require an often-prohibitive investment).

The software platform is independent of NGS sequencing technology. With an established NGS infrastructure in place, OneSight effectively allows labs to set up an end-to-end cfDNA analysis pipeline. Through the new platform’s unique visualization tools and statistical parameters, scientists can now minimize the impact of recurrent technical variations and assess the presence of confounding biological factors such as segmental aberrations and genome-wide chromosomal instability.

The new software was developed with expertise from a company Agilent acquired last year, Cartagenia, known for its software solutions for variant assessment and reporting of clinical genomics data.

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GeneSpring NGS Software

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Agilent’s GeneSpring NGS software suite includes data analysis workflows for Methyl-Seq, RNA-Seq, DNA-Seq, Chip-Seq and Small RNA-Seq data. GeneSpring NGS provides SureSelect customers with an easy to use QC, visualization and reporting tool for Methyl-Seq, RNA-Seq and DNA-Seq applications. GeneSpring NGS also allows the detection of transcriptomic changes like splice variants and gene fusions, or identify structural variation from whole genome or target enriched samples. Small RNA-Seq allows for the measurement of expression levels of known small RNA genes, mature miRNA and the detection of novel genes. GeneSpring provides comprehensive visualization, data management, and genomic annotations all in one place. GeneSpring NGS support SureSelect sequencing applications for Methyl-Seq, DNA-Seq, RNA-Seq as well as whole genome application for Methyl-Seq, DNA-Seq, RNA-Seq, ChIP-Seq and Small RNA-Seq with a special emphasis on read, mapping, and library quality control: • Import of aligned read sequences from Illumina, ABI and 454 (Roche) sequencing platforms • Import of aligned NGS data in SAM, BAM, and vendor formats like Illumina's ELAND format (in either compressed or uncompressed forms). • Support for Single End, Paired End and Mate Pair library types • Interactive QC module for whole genome and SureSelect target enrichment QA/QC • Automated sample QC report generation Methyl-Seq analysis features include: • Enhanced Quality Control Manager for SureSelect • SureSelect Target Region QC • Enhanced Genome Browser and Visualizations • Bisulfite Conversion Error Rate Computation • Methylation Detection Algorithm • Lollipop Plot • Differentially Methylated Cytosines Algorithm • Differentially Methylated Regions Analysis Algorithm • Intra Sample Analysis • Methylation Effect Analysis • Translate Target Regions to Genes • Pathway Analysis DNA-Seq analysis features include: • Enhanced Quality Control Manager for SureSelect • SureSelect Target Region Filtering • Enhanced Genome Browser and Visualizations • SNP Detection through built-in Bayesian SNP calling algorithm (MAQ) • Differential SNP Analysis • Effects of SNPs on transcripts • Structural Variation (SV) Detection through built-in PEMer and k-BIC algorithms • Translate Target Regions to Genes • Pathway Analysis RNA-Seq analysis features include: • Enhanced Quality Control Manager for SureSelect • SureSelect Target Region Filtering • Enhanced Genome Browser and Visualizations • Differential Expression Analysis • T-Test • Anova • Identification of differential splice variant by Expectation-Maximization (EM) • Gene Fusion Analysis • Identification of novel exons and splice junctions • Quantification with Novel Detection Report • RPKM Filtering • Pooled Analysis • Z-test • Audic-Claverie test • Clustering • PCA • Pathway Analysis Small RNA-Seq analysis features include: • Enhanced Quality Control Manager • Enhanced Genome Browser and Visualizations • Quantification • Expression Analysis • TargetScan, TarBase, PicTar, PITA and microRNA.org databases available for targeted genes and miRNA identification • Validation of Mature RNA Annotation • Pathway Analysis

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