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

xGen® Lockdown® Probes fill in drop-out regions of existing panels for more uniform coverage

 

Lincoln SE, Kobayashi Y, et al. (2015) A Systematic Comparison of Traditional and Multigene Panel Testing for Hereditary Breast and Ovarian Cancer Genes in More Than 1000 Patients. J Mol Diagn, 17(5):533–544.

Background

With multigene panels becoming more accessible and cost effective for disease research, their use in the clinic is also becoming more accepted as an alternative to traditional gene by gene analysis for diagnostic use and disease risk assessment. However, in many cases, clinical guidelines for the use of these tests have yet to be fully established and technical questions addressing analytical performance, variant interpretation concordance, and yield of various classes of findings from panel testing still need to be addressed.

In this paper the authors compare NGS-based panel testing with traditional genetic testing for assessing risk of hereditary breast and ovarian cancer (HBOC) in a large population of over 1000 patients.

Experiment

Lincoln et al. used an NGS-based gene panel covering 29 hereditary cancer genes to test 1062 patients previously indicated for HBOC risk assessment. Most of the samples had been subjected to traditional BRCA testing previously, while some had undergone other genetic tests or had high-quality reference data available. Reference samples containing known pathogenic variants were included as control specimens to measure coverage variability. 

Targeted genes were captured from whole blood genomic DNA using SureSelect® probes (Agilent). xGen® Lockdown® Probes from IDT were used to rescue drop-out regions of SureSelect probe panels, thus providing more uniform target coverage. Sequencing was performed on the Illumina MiSeq® or HiSeq® 2500 to at least 450X average coverage of 2 x 150 reads; a minimum of 50X reads was required at every targeted position.

After alignment to the reference human genome, sequence variants were called using several established of algorithms. CNVs were called using read-depth analysis, and split-read analysis was performed to identify certain structural variants that can be overlooked using read-depth analysis and indel detection. The results were then compared with existing findings from traditional testing of the samples.

Results and conclusion

The researchers observed 100% analytical concordance of gene panel data with prior corresponding tests and were able to uncover previously unidentified pathogenic variants of apparent clinical relevance in some genes. While these results are specific to the gene panel, laboratory protocols, and bioinformatics analysis used, the authors suggest that NGS panel testing can serve as a viable replacement for traditional genetic tests in appropriate circumstances and can lead to potentially actionable findings that may be otherwise missed.

Target capture reagents from IDT

xGen® Lockdown® Probes

xGen Lockdown Probes are individually synthesized, quality controlled, and normalized hybridization probes that offer:

  • Sensitive detection of SNPs, indels, CNV, LOH, and translocations
  • Available for clinical and diagnostics research
  • Use 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 Acute Myeloid Leukemia Panel
  • xGen Pan-Cancer Panel
  • xGen Inherited Diseases Panel

Discover more about xGen Lockdown Panels.


xGen Blocking Oligos

xGen Universal Blocking Oligos for single- or dual-index adapters used with common sequencing platforms improve on-target performance for multiplexed samples by reducing adapter participation in hybridization enrichment. Custom adapters can be manufactured for other barcodes or to meet the needs of customers who require specific modifications or services to improve performance in unique applications.

Discover more about xGen Blocking Oligos.


Additional reading

Read about how xGen® target capture products for NGS have been applied in other research projects:

Understanding how distal regulatory elements control gene expression—Capture-C technology 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.

Towards providing personalized medicine—considerations for reliable data—Scientists at Geneseeq Technology, Inc. share insights into how target capture can be improved for accurate clinical diagnostics by using optimized xGen Blocking Oligonucleotides and stringent hybridization conditions.

Target enrichment identifies mutations that confer fitness effects—Hybridization capture using xGen Lockdown Probes and subsequent next generation sequencing were used to track the frequency of mutations in evolving bacterial populations over a given time course and to gauge their importance based on their fitness effect.

Author: Nolan Speicher is a scientific writing intern at IDT.

© 2015 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 www.idtdna.com/trademarks.


xGen® Blocking Oligos

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

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