CRIS

CRIS reconstructs complete immunoglobulin heavy chain variable, diversity, and joining (IGHV-D-J) sequences from RNA-seq data to analyze B-cell receptor repertoires and determine somatic hypermutation (SHM) status.

Key Features:

• IGHV-D-J Sequence Reconstruction: Reconstructs complete IGHV-D-J sequences from RNA-seq datasets for B-cell receptor analysis.
• Somatic Hypermutation (SHM) Analysis: Determines SHM status of IGHV genes by aligning reconstructed sequences to reference Ig sequences and enumerating mutations.
• High Concordance with Clinical Data: Demonstrated high concordance with clinical classifications of SHM status across multiple independent patient cohorts.
• De Novo Assembly Approach: Employs de novo assembly of immunoglobulin transcripts to utilize entire IGHV gene segments rather than partial segment inference.
• Resource Efficiency: Leverages RNA-seq as a higher-throughput alternative to targeted Sanger sequencing for IGHV-D-J analysis.

Scientific Applications:

• Prognostic Marker Analysis: Evaluating IGHV mutation status as a prognostic marker in B-cell malignancies such as chronic lymphocytic leukemia.
• B-cell Receptor Repertoire Studies: Investigating the diversity and evolution of B-cell receptors from RNA-seq data.

Methodology:

Extracts RNA-seq reads aligned to immunoglobulin gene loci, performs de novo assembly of Ig transcripts to generate contigs, aligns contigs to reference Ig sequences, and enumerates and classifies somatic hypermutations within IGHV genes.