Linked-Read Sequencing Advances Understanding of Cancers

A new study* from the University of Connecticut Medical School, Jackson Labs, and collaborators demonstrate the utility of using emulsion based linked-read sequencing (10X Genomics) for cancer research. Published in January’s Otology & Neurotology studies patients with Neurofibromatosis Type 2 (NF2) – a disease that manifests as benign brain tumors in the sheath of the cranial nerve VIII, typically causing hearing loss. The researchers compared DNA from five patients with fast-growing tumors with DNA from five patients slow-growing tumors and DNA from matching blood samples.

Using whole genome linked-read sequencing, results identified several large deletions (ranging from 5 to 650kb) in the NF2 locus correlating to the severity of the disease phenotype. The study reveals other correlating structural variants in a number of genes including FBXW7 (implicated in tumorigenesis in many other cancers) and TSPAN (implicated in esophogeal cancer). Interestingly, 4 of 5 of the high-growth tumor patients showed deletion in the VEGF-C locus. Citing a number of studies and trials of the anti-VEGF drug bevacizumab, which targets VEGF-A, the authors believe that the VEGC-C result supports previous findings that suggest that it could be predictive of treatment response.

From a methods standpoint, linked-read sequencing requires only 1 ng of DNA input and produces haplotype phasing information. For this study, our PippinHT was used to filter away smaller DNA fragments (using the >40kb High Pass protocol) to maximize the efficiency of the linked-reads for long range SV analysis. With a 1 ng input requirement, there is ample recovery in the PippinHT – users simply quantify the sample with a Qubit fluorometric assay, and dilute the sample accordingly. Concentration or buffer exchange is not necessary. On a side note, our SageHLS platform has the capability to provide very large targeted genomic regions, a great application for linked-reads given the low input requirement (read a preprint about this here).

*Linked-read Sequencing Analysis Reveals Tumor-specific Genome Variation Landscapes in Neurofibromatiosis Type 2 (NF2) Patients
Roberts, Daniel S. et al., Ontology & Neurotology: February 2019 – Volume 40 – Issue 2 – p e150-e159
doi: 10.1097/MAO.0000000000002096

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