Protoblock - A biological standard for formalin fixed samples

Background Formalin-fixed, paraffin-embedded (FFPE) tissue is the gold standard in pathology tissue storage, representing the largest collections of patient material. Their reliable use for DNA analyses could open a trove of potential samples for research and are currently being recognised as a viable source material for bacterial analysis. There are several key features which limit bacterial-related data generation from this material: (i) DNA damage inherent to the fixing process, (ii) low bacterial biomass that increases the vulnerability to contamination and exacerbates the host DNA effects and (iii) lack of suitable DNA extraction methods, leading to data bias. The development and systematic use of reliable standards is a key priority for microbiome research. More than perhaps any other sample type, FFPE material urgently requires the development of standards to ensure the validity of results and to promote reproducibility. Results To address these limitations and concerns, we have developed the Protoblock as a biological standard for FFPE tissue-based research and method optimisation. This is a novel system designed to generate bespoke mock FFPE ‘blocks’ with a cell content that is user-defined and which undergoes the same treatment conditions as clinical FFPE tissues. The ‘Protoblock’ features a mix of formalin-fixed cells, of known number, embedded in an agar matrix which is solidified to form a defined shape that is paraffin embedded. The contents of various Protoblocks populated with mammalian and bacterial cells were verified by microscopy. The quantity and condition of DNA purified from blocks was evaluated by qPCR, 16S rRNA gene amplicon sequencing and whole genome sequencing. These analyses validated the capability of the Protoblock system to determine the extent to which each of the three stated confounding features impacts on eventual analysis of cellular DNA present in FFPE samples. Conclusion The Protoblock provides a representation of biological material after FFPE treatment. Use of this standard will greatly assist the stratification of biological variations detected into those legitimately resulting from experimental conditions, and those that are artefacts of the processed nature of the samples, thus enabling users to relate the outputs of laboratory analyses to reality.

Drafting the Dutch: Selection Biases in Dutch Conscript Records in the Second Half of the Nineteenth Century

ABSTRACTConscription records are considered to be the best sources for studying heights over cohorts. This article discusses the various steps and selection mechanisms involved in the conscription system of the Netherlands, which was more or less similar to the systems found in other European countries. Starting with a birth cohort of 4,436 boys, we run a series of regressions on the likelihood to be registered at all and to have one’s height recorded. We discuss the effects of cohort attrition through mortality and migration, and explore familial, social, and religious reasons for evading registration and (medical) examination. We find various kinds of selections, but their effects on the distribution and averages of heights are limited. Thus, heights culled from conscripts records are indeed an excellent indicator of a cohort’s biological standard of living. However, researchers focusing on social variation in height need to be aware of the unequal opportunities to evade registration and measurement.