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

Target capture with xGen® Lockdown® Probes

Friedman E, Efrat N, et al. (2015) Low-level constitutional mosaicism of a de novo BRCA1 gene mutation. Br J Cancer, 112 (4):765–768.

Background

Traditionally, sequencing for cancer management has been performed to achieve one of two objectives: (a) to detect heterozygous germline mutations to predict risk of disease or (b) to identify somatic mutations that may define therapeutic targets. Clinicians assess heterozygous germline mutations in BRCA1 and BRCA2 genes to predict breast and/or ovarian cancer risk and recommend early detection programs or risk-reducing surgery. Detection of somatic mutations in DNA from tumor tissue is used to identify therapeutic targets and determine appropriate treatment.

Experiment

Friedman et al. investigated the possibility of a third objective for cancer sequencing—identification of somatic mutations acquired in early embryonic development that predispose one to disease, but which are not detected by traditional sequencing methods. The authors performed targeted sequencing of specific genes in DNA isolated from the blood or breast tissue of a woman diagnosed with triple-negative, high-grade, invasive unilateral breast cancer at age 43 years. The genes were captured using SureSelect® probes (Agilent) or xGen® Lockdown® Probes from IDT.

Results and conclusion

Sequencing data revealed a pathogenic BRCA1 mutation in ~5% of reads from DNA extracted from blood, a buccal swab, and the histopathologically normal breast sample. However, the same mutation was detected in 47% of reads from DNA extracted from the tumor tissue. These findings were indicative of constitutional mosaicism for this mutation. The researchers also identified a common BRCA1 SNP in the patient’s DNA, but not the mother’s. Upon further analysis of sequencing reads that spanned the positions of both mutations, the authors discovered that the pathogenic mutation did not always occur with the SNP. From this latter observation, the authors deduced the pathogenic mutation was on the paternally inherited allele, but acquired after fertilization.

Target capture reagents from IDT

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

  • Complete, uniform capture of the target space
  • 4-hour hybridization time
  • Sensitive detection of SNV, indels, CNV, LOH, and translocations
  • 21 CFR Part 820 manufacture for clinical and diagnostics research
  • Availability as stocked or custom panels
  • Quick delivery

Discover more about xGen Lockdown Probes.

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

Discover more about xGen Lockdown Panels.

xGen Blocking Oligos

xGen Universal Blocking Oligos for single- or dual-index adapters of 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—Hybrid capture using xGen Lockdown Probes and 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.

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Author: Nicola Brookman-Amissah, PhD, is a senior scientific writer 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

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