The authors demonstrate that sample cross talk due to combinatorial indexes can be corrected by using unique adapters containing unique molecular identifiers (UMIs). Their results suggest that such adapters are critical to reducing false positive rates in sensitive applications, such as somatic variant discovery. The adapter design presented in this article uses dual matched indexes. xGen Dual Index UMI Adapters—Tech Access incorporate an updated design, using dual unique indexes based on Illumina’s best practice guidelines.
xGen Lockdown Probes and Blocking Oligos were used to generate a custom gene panel that targeted 382 cancer-relevant genes in multiple cancer types. The panel provided target enrichment across 605 circulating tumor (ctDNA) samples.
xGen Lockdown Probes were used to rescue drop-out regions of SureSelect® probe panels (Agilent), giving more uniform target coverage. The probes were able to target 29 genes from whole blood genomic DNA, isolated from over 1000 patients.
Next generation sequencing was used to accurately detect constitutional mosaicism in an individual diagnosed with early onset, high-grade breast cancer. xGen Lockdown Probes were used to target multiple genes of interest, including <em>BRCA1</em>, in DNA isolated from the individual’s blood.
xGen Lockdown Probes were designed to target and capture segments of DNA at the 8q24 locus, a chromosomal region known for being involved in prostate cancer susceptibility.
xGen Lockdown Probes were used to target regions of the genome containing commonly mutated genes. The probes allowed the authors to achieve sequencing with more specificity and depth, which greatly improved the efficiency and cost of data collection.
Scientists at the University of Oxford used xGen Lockdown Probes in a new, high-throughput method for detecting and sequencing HCV genotypes.
Target-capture using xGen Lockdown Probes was combined with throughput RNA sequencing to provide high resolution detection of known gene fusions. The targeted gene fusions were known to be associated with several childhood sarcomas.
xGen Lockdown Probes were used to target an entire coding region, exon-intron boundaries, and segments of DNA containing known pathogenic variants in BRCA1 and BRCA2 genes.
The authors explain how next generation sequencing has advanced mitochondrial genetics research. They note how IDT’s xGen Lockdown Probes can be used to accomplish solution phase capture of mtDNA.