Methods and compositions relating to detection of recombination and rearrangement events

A method for high throughput, repertoire sequencing-based detection of Ig repertoire sequences in a cell, the method comprising the steps of:

• a) enriching a sample for a lymphocyte;
• b) extracting genomic DNA and/or mRNA from the lymphocyte;
• c) producing:
• a single-stranded PCR product from genomic DNA by Linear Amplification Mediated (LAM)-PCR with at least one primary locus-specific primer;
• and/or
• cDNA from mRNA by reverse-transcription with at least one primary locus-specific primer;
• d) producing a ligated DNA and/or cDNA product by ligating the single-stranded PCR product or cDNA produced in step (c) to a double-stranded adaptor, wherein the double-stranded adaptor comprises:
• a distal portion of known DNA sequence that can be used to design PCR primers for a nested PCR amplification;
• a proximal portion of random nucleotides;
• and
• a 3′ overhang;
• e) producing a nested PCR product by performing a nested-PCR with an adaptor-specific primer and at least one secondary locus-specific primer using the ligated product of step (d), thereby amplifying the nucleic acid sequence comprising the Ig repertoire sequence, wherein the Ig repertoire comprises V(D)J recombination events and/or somatic hypermutations (SMH);
• f) producing a sequenced nested PCR product by sequencing the nested PCR product;
• and
• g) aligning the sequenced nested PCR product against a reference sequence or antigen receptor database.