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

xGen® Lockdown® Probes capture prostate cancer risk locus 8q24 and its physical contacts throughout the genome

Du M, Yuan T, et al. (2015) Prostate cancer risk locus at 8q24 as a regulatory hub by physical interactions with multiple genomic loci across the genome. Hum Mol Genet, 24 (1):154–166.

Background

Genetic variants of the 8q24 locus have been shown to increase the risk of prostate cancer (PC) because of their potential to influence distant target genes. Technical barriers in the past have limited studies of 8q24 to its interactions with 2 known proto-oncogenes, MYC and PVT1, which are both found intra-chromosomally on chromosome 8. Technological advances, however, now allow a region of interest to undergo a high-resolution survey where interaction frequencies with other loci across the entire genome can be seen. In this paper, the authors report on use of genome-wide capture technology to further understand the role of 8q24 in PC risk.

Experiment

Du et al. used chromosome conformation capture-based multiple target sequencing (3C-MTS) technology to obtain a genome-wide view of regions that physically interact with the 8q24 risk locus. The method, which combines a 3C assay with multi-target capture sequencing, was applied to 6 distinct cell lines, including 3 prostate-derived lines that were known to be cancerous. DNA from each line was cross-linked, digested, and ligated to create a 3C library, and xGen® Lockdown® Probes (IDT) and qPCR were used to target and quantify specific regions of DNA upstream and downstream of EcoRI sites.

Results and Conclusion

In all 6 cell lines, multiple gene regions were seen to interact with the 8q24 risk locus, including both intra-chromosomal and inter-chromosomal regions. In particular, the MYC locus commonly interacted with the 8q24 locus, which supports previous genetic research on factors influencing PC risk. Another common interacting region was 3q13, which contains the protein-coding CD96 gene. Interestingly, the 3 cancerous cell lines revealed much higher interaction frequencies with 3q13 when compared to the non-malignant lines. Other frequent interactions with the 8q24 locus include known members of β-catenin and Wnt signaling pathways. These findings support the 8q24 locus as a regulatory hub that is highly involved in cell proliferation mechanisms, and validate 3C-MTS technology as a powerful tool for surveying genome-wide interactions between loci.

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

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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.

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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.


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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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