Quantification of human DNA from century-old archived FFPE samples for retrospective genomic studies

Background Formalin-fixed, paraffin-embedded (FFPE) tissue archives are an invaluable resource for genomic research, offering the potential to link genomic data to long-term clinical outcomes. Their utility has however been limited by the degradation caused by fixation and long-term storage, particularly for samples archived for many decades. Methods This study evaluates a cohort of 79 FFPE tissue blocks collected and archived in 1973 from the Strasbourg Pathological Tissue Archive (SPTA), and a cohort of 51 FFPE tissue blocks from the Geneva Brain Bank (GBB), collected between 1928 and 1971. DNA was quantified using a forensic-grade quantitative PCR (qPCR) assay (QIAGEN Investigator Quantiplex Pro Kit on a Rotor-Gene Q) to precisely measure human DNA concentration, assess degradation, and detect PCR inhibition. We present a “discovery” approach, with sampling and extraction techniques dictated by the material constraints of each archive, with a common quantification method. Results A high proportion of the samples yielded human DNA fragments of 80 bp and 95 bp and very few fragments of 205 bp. All organ samples treated with Bouin’s solution ( n = 12) gave poor results, but among samples fixed in formalin ( n = 117), 58.1% showed over 0.25ng/µL of 80 bp human DNA fragments and 37.6% over 1ng/µL. Conclusions This work indicates that automated extraction methods optimized for FFPE allow for the recovery of usable material even in century-old, archived samples with inconsistent conditions of conservation. Our data also suggests that, in this dataset, variation in DNA recovery was more strongly associated with fixation conditions than with duration of storage, although further controlled analyses are needed to parse these influences. Crucially, given the fragmented nature of the material recovered (an expected result), future analyses of this material will have to be conducted using next-generation sequencing (NGS) technologies and approaches that rely on short fragments.