Next Generation Sequencing
Support and Educational Content

Stratifying patients for targeted therapy through precision cancer medicine

Research profile: Sameek Roychowdhury, MD, PhD, Medical Oncologist at The Ohio State University Comprehensive Cancer Center – James Cancer Hospital and Solove Research Institute, where he also leads the precision-cancer medicine program. Read about the precision medicine trials his team conducts to identify individualized cancer treatments. Dr Roychowdhury also provides insights on moving from a tissue-of-origin to a pathway-based classification of cancer and the role molecular taxonomy may play.

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A solution for sample cross-talk and index hopping in multiplexed NGS

Webinar summary: Learn about the steps in NGS sample preparation that can lead to index hopping and sample crosstalk. Dr Kristina Giorda provides expert advice on how to reduce these artifacts at each point, providing cleaner, demultiplexed NGS data.

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Analyzing the exome—focus your NGS analysis with high-performance target capture

Webinar review: Targeted sequencing capture, using probe pools or panels, can increase read depth and the number of samples per run, while decreasing sequencing cost and simplifying data analysis. See how using individually synthesized, quality-checked, DNA target capture probes (xGen Lockdown Probes) covering the human exome (xGen Exome Research Panel) perform across a variety of metrics and how the xGen Exome Research Panel compares to other available exome panels.

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NGS detection of low frequency genetic variants using novel, molecular sequencing adapters

Webinar review: Watch this webinar recording to learn about unique molecular adaptors and a high-performance target capture method for NGS analysis of low frequency variants.

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NGS target capture recommendations for FFPE samples

Webinar review: Learn how it is possible to create high quality target capture libraries from formalin-fixed, paraffin-embedded samples. Dr Kristina Giorda presents an FFPE sample workflow with a concise explanation of DNA quality analysis and how quality assessment can be used to guide the amount of DNA input for NGS library preparation.

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Targeting cancer pathways: Sensitive, comprehensive detection of genomic alterations using a custom NGS panel

Citation summary: Learn how researchers use xGen Lockdown Probes to screen cancer samples for key genes related to targeted cancer therapies.

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Probe-based target enrichment improves ChIP-seq analysis of HIV and HTLV provirus

Citation summary: Learn how scientists used IDT xGen Lockdown Probes for target enrichment after ChIP enrichment to significantly increase proviral sequence reads within a human genomic background. The method was easily customizable for provirus subtypes, tolerant of mismatch, and should be adaptable for similar applications.

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ve-SEQ: An improved approach to high throughput, whole genome viral sequencing

Citation summary: Read how scientists at the University of Oxford use xGen® Lockdown® Probes in ve-SEQ, a novel method for detecting and sequencing HCV genotypes.

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Improve target capture using xGen® Lockdown® Probes and Reagents with an optimized protocol

xGen Lockdown Reagents and new hybridization capture protocol for xGen Lockdown Probes and Panels reveal the increased potential of IDT target enrichment products.

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Next generation sequencing for risk assessment in acute myeloid leukemia

Citation summary: Read how these researchers use next generation sequencing (NGS) techniques with patients diagnosed with AML to identify associations between specific mutations and disease outcome. These techniques were also used to track the elimination of leukemia-specific mutations in AML patients following chemotherapy. The IDT xGen® AML Cancer Panel v1.0 was used to target and capture 264 commonly mutated genes in AML.

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3C-MTS technology identifies distant genomic interactions made by a cancer risk locus

Citation summary: Chromosome conformation capture-based multiple target sequencing (3C-MTS) technology is used to obtain a genome-wide view of regions that physically interact with the prostate cancer risk locus 8q24. This method combines a 3C assay with multi-target capture sequencing using xGen® Lockdown® Probes (IDT).

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Gene panels vs. gene-by-gene analysis for assessing disease risk

Citation summary: Authors compared an NGS-based gene panel and traditional testing data for diagnostic use and disease risk assessment in hereditary breast and ovarian cancer. Read how xGen Lockdown Probes (IDT) were able to rescue drop-out regions of SureSelect (Agilent) probe panels.

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Get the most out of your NGS samples—expandable tumor and disease target capture panels

Learn about expandable NGS target capture panels that enrich for mutated genes implicated in tumors and genes associated with inherited diseases. Designed in collaboration with experts from the Emory Genetics Laboratory and the Cancer Genome Atlas, both panels return consistent results with high reproducibility and deep uniform coverage.

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Generate consistent, reliable exome sequencing results

Spanning 39 Mb of the human genome, the xGen® Exome Research Panel was designed to provide uniform and specific coverage of the coding regions for 19,396 genes. You can easily and cost-effectively expand this panel to include specific non-coding target regions through addition of xGen® Lockdown® Probes.

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Somatic mutations acquired in BRCA1 during embryonic development can cause early-onset breast cancer

Citation summary: See how focused sequencing using target capture probes helps identify a post-fertilization mutation in BRCA1 that may predict risk of early-onset breast cancer.

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Delivering Comprehensive Genomic Profiling for Clinical Cancer Care

Research profile: Scientists at Foundation Medicine, Inc. are leading a transformation in cancer care by helping clinicians to select appropriate treatment options for each patient, informed by a thorough understanding of the molecular changes specific to their disease. Read about the use of xGen® Lockdown® Probes in their flagship FoundationOne® Test.

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Advantages of high quality, probe-based gene capture panels

Target enrichment by hybrid capture lets you focus your genomic analysis on specific regions of interest, increasing depth of coverage of targeted sequences and improving the detection of rare genomic events. You can create custom human gene capture panels quickly and cost-effectively using IDT preconfigured pools of probes targeting the coding sequences (CDS) of human protein-coding genes, or with predesigned disease or exome panels.

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Understanding How Distal Regulatory Elements Control Gene Expression

Research profile: Based on Chromosomal Conformational Capture technology, Capture-C, a method developed by the Hughes laboratory (Oxford University, United Kingdom), allows researchers to isolate distal regulatory elements that interact with specific promoters in 3 dimensional space. By combining Capture-C with target capture using IDT xGen® Lockdown® Probes, and next generation sequencing, the researchers can interrogate the regulatory landscapes of hundreds of genes in a single experiment.

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Augmenting pathology data with molecular profiling for improved cancer treatment

Research profile: Foundation Medicine uses a unique approach to targeted next-generation sequencing to generate molecular information that will better inform cancer categorization and treatment decisions. Review this summary and view the presentation given at the 2014 Association for Molecular Pathology Annual Meeting (AMP) by Dr Geoff Otto (Foundation Medicine).

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Get just the targets you need in NGS capture panels

There are several disadvantages to purchasing fixed target capture panels or having custom panels manufactured. A solution is to create your own custom NGS target capture panels from stocked human gene probe pools.

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Improving uniform coverage of targeted sequences for NGS

Learn about the challenges researchers face for obtaining uniform coverage of NGS data and how IDT xGen® Lockdown® Probes are uniquely positioned to facilitate uniform sequence coverage.

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NGS Target Capture Custom Panels—Determining Probe Number and Cost

The experimental design options that will determine the number (and cost) of probes required for an NGS target capture panel.

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Towards providing personalized medicine—considerations for reliable NGS data

Research profile: Read how scientists at Geneseeq Technology, Inc. improved their target capture methods to increase accuracy in clinical diagnostics by using optimized blocking oligos and stringent hybridization conditions.

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How important are those NGS metrics?

Of the many metrics used in evaluating target capture data for NGS applications, read about which ones our researchers consider important for evaluating performance of target enrichment panels.

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Targeted sequencing for acute myeloid leukemia

Use this NGS target enrichment panel, composed of >11,500 xGen Lockdown® Probes, to sequence more than 260 genes associated with the acute myeloid leukemia (AML) disease pathway.

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Target enrichment facilitates focused next generation sequencing

Understand the rationale and benefits of enriching subsets of the genome (target enrichment by hybrid capture) prior to sequencing. Use this strategy for genotyping, identifying splice variants and indels, and profiling genomic recombination events as well as viral and transposon integration sites.

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Insertion site detection and targeted RNA capture using NGS

Research profile: See how scientists at Cofactor Genomics use in-solution hybridization to focus on regions of interest for next generation sequencing. Use xGen Lockdown Probes to determine number of inserts per genome and their location.

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Target enrichment identifies mutations that confer fitness effects

Research profile: Learn how target enrichment using xGen® Lockdown® Probes and NGS were used to track the frequency of mutations in evolving bacterial populations. The research team gauge mutational importance based on their fitness effect.

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Next generation sequencing in the clinic: A perspective from Dr Elaine Mardis

Research profile: Dr Elaine Mardis shares her views on the current uses of NGS, the challenges that NGS technologies face, and what can be expected in the future.

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Genomic Target Selection Using Individually Synthesized Capture Probes

Research profile: Foundation Medicine, Inc describes development of its cancer diagnostic genomic test for solid tumors, with the goal to provide a fully informative profile that helps physicians make personalized therapy decisions for patients with cancer. It has been optimized for FFPE samples and small specimens and interrogates over 182 cancer-related genes plus 37 introns from 14 genes frequently rearranged in cancer. Their research shows how IDT Biotinylated Ultramer™ Oligonucleotides perform better than array-synthesized probes during target capture for next generation sequencing with this panel.

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xGen® Blocking Oligos

Adapter blocking oligos increase the number of on-target reads by preventing non-specific binding during hybridization.

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Related Articles

Target Enrichment Facilitates Focused Next Generation Sequencing

The rationale and benefits of enriching subsets of the genome (target enrichment by hybrid capture) prior to sequencing.

Read more ≫

Improving Uniform Coverage of Targeted Sequences for NGS

The challenges faced in obtaining uniform coverage of NGS data and how IDT xGen® Lockdown® Probes are uniquely positioned to facilitate uniform sequence coverage.

Read more ≫

Towards Providing Personalized Medicine—Considerations for Reliable NGS Data

Geneseeq Technology, Inc. demonstrates how they improved their target capture methods to increase accuracy in clinical diagnostics by using optimized blocking oligos and stringent hybridization conditions.

Read more ≫

Delivering Comprehensive Genomic Profiling for Clinical Cancer Care Using Targeted Sequencing

Read how scientists at Foundation Medicine, Inc use hybrid selection in their FoundationOne® Test to help clinicians select patient specific treatment options.

Read more ≫

Insertion Site Detection and Targeted RNA Capture Using Next Generation Sequencing

Scientists at Cofactor Genomics use in-solution hybridization to focus on regions of interest for next generation sequencing.

Read more ≫