Next Generation Sequencing
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NGS target capture recommendations for FFPE samples

Understanding the impact of DNA quality

Cancer biopsies are commonly preserved as formalin-fixed, paraffin-embedded (FFPE) samples. This type of fixation preserves the tissue structures important for histological analysis of cells used in cancer diagnosis. The same samples are also invaluable for understanding the underlying genetic mechanisms that give rise to cancers. However, this preservation method causes crosslinking of macromolecules like DNA and proteins, and fragmentation of molecular bonds. This poses unique challenges for sequencing DNA from FFPE tissue samples.

In the webinar, Target capture of DNA from FFPE samples—recommendations for generating robust sequencing data, Dr Kristina Giorda discusses the FFPE sample workflow for NGS. She follows this with a concise explanation of DNA quality analysis and explains how quality assessment can be used to guide the amount of DNA input for NGS library preparation. Finally, using the xGen® Acute Myeloid Leukemia Cancer Panel, Dr Giorda demonstrates that you can create high quality capture libraries from FFPE samples, although library quality is heavily dependent on the initial DNA quality.

Product focus: Target capture reagents

xGen® Lockdown® Probes—target capture probe pools for NGS

xGen Lockdown Probes are pools of individually synthesized, quality controlled, and normalized hybridization probes. Use them to generate custom capture panels for targeted sequencing to enhance the performance of existing panels. xGen Predesigned Gene Capture Probe Pools are available for any human RefSeq coding gene. Select from predesigned and custom probes that offer:

  • Sensitive detection of SNPs, indels, CNV, LOH, and translocations
  • GMP compliance for clinical and diagnostics research
  • Flexibility to augment existing panels or create completely custom panels
  • Quick delivery

Discover more about xGen Lockdown Probes.

xGen Lockdown Panels

xGen Lockdown Panels are preconfigured, validated, and stocked pools of xGen Lockdown Probes for targeted next generation sequencing of defined gene families:

  • xGen Exome Research Panel
  • xGen Acute Myeloid Leukemia Panel
  • xGen Pan-Cancer Panel
  • xGen Inherited Diseases Panel
  • xGen Human ID Research Panel
  • xGen Human mtDNA Research Panel

Discover more about xGen Lockdown Panels.

xGen Lockdown Reagents—hybridization and wash kit

xGen Lockdown Reagents have been optimized to deliver deep, even coverage of targets captured using xGen Lockdown Probes and Panels. Achieve uniform coverage with hybridization and wash buffers that are optimized for target enrichment using xGen Lockdown Probes and Panels. A short, 4-hour hybridization protocol generates results quickly.

Discover more about xGen Lockdown Reagents.

xGen Blocking Oligos

xGen Blocking Oligos prevent adapter cross hybridization and minimize off-target capture, increasing specificity during targeted sequencing. Universal Blocking Oligos—TS Mix are designed for use with Illumina barcoded adapters. This ready-to-use mix effectively blocks dual- or single-index adapters to significantly improve on-target performance.

Discover more about xGen Blocking Oligos.

Related reading

These peer reviewed publications show how your colleagues are successfully using IDT NGS tools and reagents in their sequencing research:

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.

Probe-based target enrichment improves ChIP-seq analysis of HIV and HTLV provirus—Citation summary: Read 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.

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.

Review other DECODED Online newsletter articles on NGS applications.

You can also browse our DECODED Online newsletter for additional application reviews, lab tips, and citation summaries to facilitate your research.

Author: Hans Packer, PhD, is a scientific writer at IDT.

© 2017 Integrated DNA Technologies. All rights reserved. Trademarks contained herein are the property of Integrated DNA Technologies, Inc. or their respective owners. For specific trademark and licensing information, see

xGen® Blocking Oligos

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

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