Jane Houldswortha, Ekaterina Bogdanovaa, Tatyana Sidorenkob, Zinnia Maib, Avisek Parajulib, Meenakshi Mehrotraa, Brett Baskovicha
aIcahn School of Medicine At Mount Sinai, New York, NY, United States; bMount Sinai Health System, New York, NY, United States
Molecular testing to detect clonal T-cell populations is commonly applied to dermatologic specimens to support cutaneous T-cell lymphoma diagnosis. With clinical implementation of TRG and TRB clonality by NGS using Lymphotrack (Invivoscribe) sequenced on the Miseq (Illumina), increased specimen numbers have been submitted for testing. For 66 specimens (50 patients) received to date, high insufficiency rates were found for TRG (30%) and TRB (56%). Thus, to improve testing efficiency and effect better specimen triage, we examined tissue features, DNA size by fragment analysis, library concentration, reads and overall call. Nine specimens either had inadequate DNA for library preparation or amplified fragments <300bp in size. Another 9 supported 300bp fragment amplification, 11 400bp, and 37 600bp which yielded acceptable reads for interpretation (>50,000) for TRG (33%, 82%, 78%) and TRB (0%, 45%, 54%) respectively. This was not unexpected given the larger size of the TRB amplicon compared to TRG. For the latter 48 specimens, estimated biopsy lymphocyte content was available for 34, and exhibited a weak correlation with TRG and TRB library concentrations (R2=0.26, 0.29). Only 64% of punch biopsies (9/14) but 85% (29/34) of shave biopsies achieved acceptable reads, and 40% and 66% respectively for TRB. For all specimens, 50% of punch biopsies were deemed insufficient and 19% of shave biopsies. Thus biopsy type, ability to support 400bp amplification, and amplicon size impacted the overall diagnostic yield of TCR clonality testing by NGS on dermatologic specimens. Diagnostic advantages of TCR clonality assessed by NGS will be discussed for specific cases.