Abstract
The field of ancient genomics has undergone a true revolution during the last decade. Input material, time requirements and processing costs have first limited the number of specimens amenable to genome sequencing. However, the discovery that archaeological material such as petrosal bones can show increased ancient DNA preservation rates, combined with advances in sequencing technologies, molecular methods for the recovery of degraded DNA fragments and bioinformatics, has vastly expanded the range of samples compatible with genome-wide investigation. Experimental procedures for DNA extraction, genomic library preparation and target enrichment have become more streamlined, and now also include automation. These procedures have considerably reduced the amount of work necessary for data generation, effectively adapting the processing capacity of individual laboratories to the increasing numbers of analyzable samples. Handling vast amounts of samples, however, comes with logistical challenges. Laboratory capacities, equipment, and people need to be efficiently coordinated, and the progress of each sample through the different experimental stages needs to be fully traceable, especially as archaeological remains of animals or plants are often provided and/or handled by many different collaborators. Here we present CASCADE, a laboratory information management system (LIMS) dealing with the specificities of ancient DNA sample processing and tracking, applicable by large and small laboratories alike, and scalable to large projects involving the analysis of thousands of samples and more. By giving an account of the specimen’s progress at any given analytical step, CASCADE not only optimizes the collaborative experience, including real-time information sharing with third parties, but also improves the efficacy of data generation and traceability in-house.
Highlights
The first draft of the human genome was released in 2001, following 20 years of extensive collaborative efforts among large research centers across the world (Lander et al, 2001; Venter et al, 2001)
A commonly used repair method is the incubation of ancient DNA (aDNA) extracts with an enzymatic mixture consisting of Uracil DNA glycosylase and Endonuclease VIII (USER treatment, New England Biolabs), which can eliminate most or even all those cytosines that have been deaminated post-mortem (Rohland et al, 2015), and which represent the most common aDNA damage (Briggs et al, 2007)
By integrating laboratory information management system (LIMS) features tailored to the experimental procedures underlying aDNA analyses, CASCADE provides the first solution toward this objective, and empowers experimental work and collaborative sharing through the possibility of automatic queries providing real-time information about ongoing progress and results
Summary
The first draft of the human genome was released in 2001, following 20 years of extensive collaborative efforts among large research centers across the world (Lander et al, 2001; Venter et al, 2001). Specific types of osseous material, such as petrosal bones (Pinhasi et al, 2015) and tooth cementum (Damgaard et al, 2015), have been found to show better DNA preservation rates than previously explored sources, and to be generally less prone to contamination by environmental microbes. These developments have lowered the sequencing efforts needed to retrieve significant coverage of the focal genome and have reduced the time required for and costs incurred by ancient genome characterization. The survey of genome-wide variation among humans in Iberia carried out by Olalde and colleagues included 271 individual specimens spanning the last ∼5,000 years (Olalde et al, 2019), while the study from Damgaard et al (2018) released no fewer than 137 genome sequences of ancient humans from across the Eurasian steppes and spanning the last 4,000 years
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