IMMUNOGLOBULIN HEAVY VARIABLE GENES AND ALLELES: NEW ENTITIES, NEW NAMES AND IMPLICATIONS FOR RESEARCH AND PROGNOSTICATION IN CLL

ABSSUB-5252

Background: The development of novel sequencing technologies has led to a far more accurate view of the human genome. Indeed, recent findings have altered our notions regarding the configuration of immunoglobulin (IG) gene loci and the actual number of gene alleles, as described by the International ImMunoGeneTics information system (IMGT), the global reference in Immunogenetics and Immunoinformatics. Overall, 34 changes were incorporated in the latest version (3.3.0 reference directory release: 201408-4) of the IMGT/V-QUEST tool. Twenty of these changes concerned the identification and addition of new germline immunoglobulin heavy variable (IGHV) gene alleles (19 Functional and 1 Open Reading Frame), whereas the remaining 14 were due to the assignment of new allele names to the existing nomenclature system (13/14 Functional, 1 Open Reading Frame).

Aims: In CLL, the mutational status of the clonotypic rearranged IGHV gene is strongly associated with patient outcome. Correct determination of this parameter strictly depends on the comparison of the nucleotide sequence of the clonotypic rearranged IGHV gene with that of the closest germline counterpart. Consequently, changes in the reference directories could, in principle, affect the correct interpretation of the IGHV mutational status in CLL which is the focus of the present study.

Methods: In order to explore this issue, we analyzed 8337 IGHV-IGHD-IGHJ rearrangement sequences from CLL patients from our database with the IMGT/HighV-QUEST tool using two different versions of the IMGT/V-QUEST: version 3.2.32 (2 December 2013) versus version: 3.3.0 (20 February 2014) and compared the tool outputs.

Results: Differences due to change of the IGHV gene allele name were identified in 405 sequences (4.8%). In 291/405 (71.9%) of these cases, the germline identity (GI) remained the same, since the difference concerned only the renamed gene allele. In the remaining 114 (28.1%) cases, differences were also identified in % GI since a novel IGHV gene allele was recognized. Focusing on the IGHV mutational status and in keeping with previous reports, we subdivided our sequences into four different subgroups: truly unmutated (100% GI), minimally mutated (99-99.9% GI), borderline mutated (98-98.9% GI) and mutated (<98% GI). Overall, a change in the mutational status category was identified in 50 (0.6%) sequences, though never one that entailed crossing the 98% GI cut-off value used for prognostication in CLL. In more detail, 2 sequences moved from the mutated to the borderline mutated subgroup; 15 from the borderline mutated to either the truly unmutated (4/15) or the minimally mutated (11/15) subgroup; and 33 from the minimally mutated to the truly unmutated subgroup. Understandably, cases that were reported as truly unmutated from the previous IMGT/HighV-QUEST tool version were not affected. All 4 sequences that moved from the borderline mutated to the truly unmutated group were previously assigned to IGHV3-43*01 and are now assigned to the newly reported  IGHV3-43D*01.

Summary/Conclusion: In conclusion, the recent addition of new germline IGHV gene alleles led to a number of changes concerning both IGHV gene nomenclature and germline sequence composition affecting the alignment output of the IMGT/HighV-QUEST tool. Given the prognostic value of somatic hypermutation status in CLL, both physicians and researchers should be alerted and re-evaluate sequence data, especially for those IGHV-IGHD-IGHJ gene rearrangements that up to date were considered as borderline mutated, where caution is warranted.

Keywords: None

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