Tag Archives: NGS

Illumina Launches TruSight™ Tumor Content Set

By Business Wirevia The Motley Fool

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Illumina Launches TruSight™ Tumor Content Set

Enables Somatic Variant Detection in Solid Tumors Using Next-Generation Sequencing (NGS)

SAN DIEGO–(BUSINESS WIRE)– Illumina, Inc. (NAS: ILMN) today announced the next product in its TruSight line of content sets, TruSight Tumor, for NGS-based somatic variant detection in solid tumors. TruSight Tumor provides optimized amplicon-based library preparation of 26 oncogenes and tumor suppressor genes selected for their involvement in common solid tumors, including lung, colon, melanoma, gastric, and ovarian cancer.

TruSight Tumor also offers a comprehensive NGS-based tumor profiling solution that provides a broader and more cost-effective view of tumor heterogeneity compared to genotyping-based methods. Researchers can simultaneously detect somatic changes in multiple genes across the tumor genome, as referenced in industry guidelines, as well as emerging biomarkers implicated in pharmaceutical clinical trials. Designed for use with formalin-fixed paraffin-embedded (FFPE) samples, TruSight Tumor enables high levels of sensitivity for minor allele detection (below 5%), with limited DNA input requirements.

“TruSight Tumor is designed to run on Illumina’s industry-leading sequencing platforms and enables clinical researchers to understand the molecular heterogeneity of FFPE tumor samples,” said Matt Posard, Senior Vice President and General Manager of Illumina’s Translational and Consumer Genomics business. “This technology has the potential to expand candidates for targeted therapies who may otherwise be missed with single variant or single gene approaches.”

“Tumor characterization using next-generation sequencing enables clinical research laboratories to gain a deeper understanding of underlying biology. In order to detect clinically relevant variants, it is important to look beyond single genes or hotspot mutations while achieving very low levels of sensitivity,” said Dr. Robert Daber, Technical Director of Clinical Genomics, Center for Personalized Diagnostics, Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania.

TruSight Tumor is the first content set designed for somatic variant detection on the Illumina MiSeq® platform. As a portfolio, TruSight content sets are designed for high performance targeted sequencing to meet the specific needs of the clinical research laboratory by providing high analytical sensitivity and specificity. They offer exceptional performance in the capture and sequencing of targeted genomic regions, and are selected through collaborations with experts from leading institutions.

TruSight content sets are for research use only and not intended for diagnostic use. TruSight Tumor is now available for order with shipment expected in Q2’13. For more information, visit www.illumina.com/TruSightTumor.

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Source: FULL ARTICLE at DailyFinance

Delete lines in a file

By sonia102

Hi

This is a sample of my data file.

##field PH01000000 1 4869017
#PH01000000G0240
WWW278545G0240 P.he_model_v1.0 erine 119238 121805 . – . ID=PH01000000G0240;Description=”zinc finger, C3HC4 type domain containing protein, expressed”
WWW278545G0240 P.he_model_v1.0 RA 119238 121805 . – . ID=PH01000000G0240.mRNA;Parent=PH01000000G0240
WWW278545G0240 P.he_model_v1.0 NGS 120721 121773 . – . ID=PH01000000G0240.CDS;Parent=PH01000000G0240

#PH01000000G0250
WWW278545G0250 P.he_model_v1.0 erine 125260 126544 . – . ID=PH01000000G0250;Description=”FERONIA receptor-like kinase, putative, expressed”
WWW278545G0250 P.he_model_v1.0 RA 125260 126544 . – . ID=PH01000000G0250.mRNA;Parent=PH01000000G0250
WWW278545G0250 P.he_model_v1.0 NGS 125971 126544 . – . ID=PH01000000G0250.CDS;Parent=PH01000000G0250

#PH01000000G0290
WWW278545G0290 P.he_model_v1.0 erine 151334 153926 . + . ID=PH01000000G0290;Description=”DUF581 domain containing protein, expressed”
WWW278545G0290 P.he_model_v1.0 RA 151334 153926 . + . ID=PH01000000G0290.mRNA;Parent=PH01000000G0290

I want to use some basic vi command or any comand to delete all those lines whose third column entry is RA or NGS.

I want to retain only those lines whos 3rd column is erine.

Is this possible?

Thanks

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Source: FULL ARTICLE at The UNIX and Linux Forums

The first goat genome sets a good example for facilitating de novo assembly of large genomes

In a collaborative study published online today in Nature Biotechnology, researchers from Kunming Institute of Zoology, Chinese Academy of Sciences, BGI, and other institutes, have completed the first genome sequence of domestic goat by a robust approach integrated with next-generation sequencing (NGS) and whole-genome mapping (WGM) technologies. The goat genome is the first reference genome for small ruminant animals and may help to advance the understanding of distinct ruminants’ genomic features from non-ruminant species. This work also yields a valuable experience for facilitating the de novo assemblies of large, complex genomes in the future.
Source: Phys.org