This study demonstrates incorporation of multi-omics analyses with Stereo-Seq results to achieve unmatched characterization of the complex tumor immune microenvironment. Corroboration of spatial gene expression with previous findings, as well as strong similarity between sections within a sample demonstrate accuracy and precision of results. Novel marker genes within tumor subtypes may reveal new therapeutic targets.

This study evaluates the performance of two Celemics library preparation kits and two target enrichment panels on the Complete Genomics DNBSEQ-G400 sequencing platform. Complete Genomics offers a full lineup of sequencers powered by its proprietary DNBSEQ™ technology. DNBSEQ utilizes Rolling Circle Replication (RCR) instead of traditional PCR amplification, resulting in highly accurate sequencing data with no clonal errors, index hopping, and low duplication rates.

The DNBSEQ-G400 provides high sequencing quality (>93% Q30), is fully compatible with the PIPseeker analysis pipeline, and offers comparable or better sequencing results than the NextSeq 2000. Additionally, the generation of PIPseq sequencing data with the DNBSEQ-G400 system costs an estimated $0.11 per cell, making affordability an advantage of this scRNA-seq workflow. This work shows that coupling PIPseq and DNBSEQ technologies offers scientists an alternative scRNA-seq workflow that is both efficient and cost-effective for smaller validation studies or comprehensive, large-scale projects.

In this application note, we highlight the compatibility of Takara Bio’s SMART-Seq Human TCR (with UMIs) and the SMART-Seq Human BCR (with UMIs) with the DNBSEQ-G99 sequencing platform by Complete Genomics. Both kits adopt SMART technology and a 5’-RACE-based approach to capture full-length information from V(D)J variable regions of TCRs and BCRs, making them ideal tools for analyzing TCR and BCR repertoire diversity from bulk samples, including total RNA or purified cells. Unique molecular identifiers (UMIs) are incorporated to facilitate PCR error correction and clonotype quantification during data analysis.

Acquiring genomic phasing information has been challenging and costly, requiring specialized long-read sequencing technology. However, with the DNBSEQ Complete WGS (cWGS) solution, researchers can now generate highly accurate data while reducing costs. The solution combines the output of WGS data generated through a PCR-free method with the DNBSEQ Complete WGS Kit which labels long DNA fragments, essentially reconstructing the long fragment DNA.

This study demonstrates that Olink Explore HT is highly compatible with the DNBSEQ-T7 Genetic Sequencer, and the resulting data is comparable with Illumina NextSeq. The libraries generated from the Explore HT kit were first circularized by the MGIEasy Olink Circularization Set to enable compatibility with the DNBSEQ sequencing platforms. The circularized libraries were then sequenced on the DNBSEQ-T7 with App-D sequencing primer spiked into the PE100 sequencing cartridge. Comparative results between Complete Genomics actual data and Illumina NextSeq demonstrate that the Olink Explore HT kit is perfectly compatible with the DNBSEQ-T7.

The results of this study demonstrated that the newly trained DNAscope model for the Complete Genomics DNBSEQ platform, along with the combined improvements in the underlying sequencing chemistry resulted in high variant calling accuracy. The elimination of PCR amplification during both library prep and sequencing array prep greatly reduced errors introduced prior to sequencing. The retrained DNAscope model improves DNAscope’s accuracy with DNBSEQ reads, allowing DNAscope to more accurately model systematic error patterns andenabling more accurate discrimination of false positive and false negative variant calls. The overall variant calling accuracy is improved from the previously published accuracy, as are the integrated sequencing and analysis solutions.

Pillar Biosciences oncoReveal assays, when sequenced on the DNBSEQ-G99, are accurate and reliable, as demonstrated by higher Q30, mapping rate, and on-target rates. They also produce variant calling frequencies concordant with the Illumina NextSeq 550.

The objective of this immune profiling study is to assess the compatibility of Takara Bio’s SMARTer Human TCR α/β Profiling Kit v2 and the SMART-Seq Human BCR (with UMI) Profiling Kit with the Complete Genomics DNBSEQ-G400 sequencing platform. Both Takara kits adopt SMART technology and a 5’-RACE-based approach to capture full-length information from V(D)J variable regions of TCRs and BCRs, making them ideal tools for analyzing TCR and BCR repertoire diversity from bulk samples, including total RNA or purified cells.