Next Generation Sequencing

• Agilent and Illumina Whole exome capture
• Adaptive Biotechnologies ImmunoSEQ TCR/BCR receptor sequencing
• VISA Retroviral integration site analysis
• 16S rRNA sequencing
• CRISPR-Cas9 high-throughput screening and validation

DNA Assay/Mutation Detection

• Qiagen Pyromark genome wide CpG methylation
• Target_MethylSeq promoter/enhancer methylation analysis for specific genes
• MiLaboratory DNA based TCRseq
• iRepertoire DNA based TCRseq
• SNP or mutation detection
• DNA extraction and QC
• Avida cell free DNA/circulating tumor DNA assay for liquid biopsy

RNA Assay/Gene Expression

• Takara RNA based TCRseq
• sgRNA Seq for genome-wide or targeted screening

Oxford Nanopore, Direct Protein Sequencing

The Next-Gen Sequencing Group, in collaboration with other proteomics labs within CCR, such as the Protein Characterization Laboratory, is highly interested in acquiring and developing new emerging technology from Oxford Nanopore Technologies. This innovative technology enables the reading of amino acid sequences for specific proteins by detecting changes in ionic current as the amino acids pass through a nanopore.

Single-cell Spatial Proteomic

The Pixelgen single-cell spatial proteomic technology using for cell surface protein-protein interaction and colocalization studies. This technology uses barcoded antibodies to bind multiple proteins and ligate the neighboring barcodes together to detect protein colocalization. We can collaborate with the CCR Protein Characterization Laboratory (PCL) within the LBR to validate this technology.

Illumina Direct Base Modification & Comprehensive WGS

One of the new applications Illumina is developing is the 5-base genome, which will enable both genetic variant and methylation detection in a single whole genome assay. This approach allows for direct interrogation of methylation without the cumbersome bisulfite conversion process. Another innovative product from Illumina is the comprehensive Whole Genome Sequencing (WGS) solution, designed to perform library preparation directly on the flow cell. This product provides comprehensive insights, including single nucleotide variants, structural variants, phasing, and repeat expansions. By eliminating traditional library preparation steps, this technology reduces labor, shortens turnaround times, and minimizes variability and failure points.

Chromatin Conformation Capture, Pore-C

Pore-C is an end-to-end workflow that combines 3C with long nanopore sequencing reads, offering contact information that enables existing assemblies to be scaffolded with high contiguity. Unlike traditional 3C methods, which typically detect pairwise interactions between two genomic loci, Pore-C generates higher-order contact information from multiple loci. The method is amplification-free, allowing access to GC-rich and repetitive genomic regions. Additionally, epigenetic modifications are preserved in the long nanopore reads and can be characterized alongside the nucleotide sequence.