Annotation error of a common beta degrees -thalassemia mutation (619 bp-deletion) has implications for molecular diagnosis.

摘要

We report a series of patients in whom diagnosis of the 619 bp-deletion Indian betadeg-thalassemia mutation was confounded by a systematic annotation error in the public domain. The index patient is a healthy 27-year old Asian Indian woman with known beta-thalassemia trait who had molecular genetic testing performed for preconception planning. Complete beta-globin gene sequencing and gap-PCR for the 619 bp-deletion were initially negative, which prompted further investigation. Redesigning the 3' gap-PCR primer to a more distal location in the beta-globin gene uncovered the 619 bp-deletion. Sequencing across the deletion revealed the breakpoints to be shifted 132 bp 3' of the breakpoints reported in dbSNP (rs63751625) and the globin server (http://globin.bx.psu.edu), databases that had been used to design the original 3' gap-PCR primer (online Supporting Information Fig. 1). Sequencing of five additional unrelated patients with the 619 bp-deletion, and careful literature review [1,2], provide strong evidence that the breakpoint provided in the dbSNP and globin server annotation is incorrect. The correct annotation for the 619 bp-deletion in HGVS nomenclature using reference sequence NM_000518.4 is c.316-149_*342delinsAAGTAGA (deletion of nucleotides 1,197-1,816 relative to the start of transcription). This report highlights the need for caution in the use of public databases during assay development, and the importance of alternative verification methods.