CLC Main Workbench

CLC Main Workbench provides integrated analysis for detecting and annotating single nucleotide polymorphisms (SNPs), small insertions and deletions (indels), and genomic rearrangements from high-throughput cDNA and other sequencing data using de novo and reference-based assembly.

Key Features:

• High-Throughput Transcriptome Sequencing: Processes high-throughput cDNA sequencing data (e.g., 120 Mb from the HCC1954 breast cancer cell line) to analyze transcriptomes and detect events such as gene fusions and truncations.
• Genomic Rearrangement Detection: Identifies complex genomic alterations and rearrangements, including events involving oncogenes such as MRE11 and NSD1.
• Annotation Capabilities: Annotates detected genetic variations and links them to known biological functions and pathways.
• Application in Cancer Research: Applied to identify novel genomic alterations in breast cancer cell lines to support studies of tumorigenesis.

Scientific Applications:

• Cancer Genomics: Detection and annotation of SNPs and indels relevant to cancer diagnosis, characterization, and treatment research.
• Genomic Rearrangement Studies: Investigation of genomic rearrangements in disease contexts to provide insights into gene function and disease mechanisms.

Methodology:

Performs de novo assembly and reference-based assembly of sequencing data and analyzes high-throughput cDNA/transcriptome sequences to detect and annotate SNPs, indels, and genomic rearrangements.