JRA 1: PrediCtoR software tool

A novel decision-making software tool has been developed to help collections managers and Users to quantify the risks associated with destructive analysis of specimens. PrediCtoR is a web-based interface that forecast the success of PCR amplification of DNA using a predictive model of DNA decay. PrediCtoR prevents unnecessary destructive sampling. PrediCtoR is designed to predict ancient DNA survival in bone. Development is include non-vertebrate taxa into the software and to give a better understanding of rates of decay of DNA in other more contemporary collections, plus, recently excavated bone material.

Aims and objectives

  • Develop a curatorial ‘shield’, in the form of a Web-hosted software tool - PrediCtoR - which predicts the probability of successful ancient DNA recovery from archive collections in museums (predominantly focussing on fossilised and non-fossilised bone)
  • Make the tool scalable and integrate with additional databases to increase the sophistication and robustness of prediction
  • Investigate dominant factors influencing optimal DNA recovery from archive bone specimens

JRA1 will develop a novel decision-making tool to help curatorial staff, internal and external Users to quantify the risks associated with destructive analysis of organic specimens held in museums and herbaria.

Description of work

Developing the basic PrediCtoR system

The basic tool, delivered via a web-based interface, predicts the success of PCR amplification of DNA using a predictive model of DNA decay. PrediCtoR is a simple-to-use, free, non-destructive tool designed to enhance the conservation of museum and herbaria collections, by preventing unnecessary destructive sampling. It does this by predicting the success of PCR amplification based upon sample size and amplicon length

PrediCtoR normalises four of the key contributing factors to DNA (and collagen) decay, namely (i) age (ii) temperature (iii) specimen size and (iv) polymer (amplicon) length into a single parameter - thermal age (kyrs@10°C). ‘Thermal age’ normalises different samples and reports them on a common scale; in general the older the specimen the greater the projected accumulated DNA damage. The mathematics have been encoded in PHP programming language which is availavle open access.

Proof of Concept

The first part of the proof of concept was to establish that PrediCtoR successfully predicts temperatures for known sites. JRA1 compared PrediCtoR estimates of Teff with manually calculated values from actual sample sites and estimates taken directly from weather station data (n = 200). Outliers will be investigated further to establish reasons for any apparent anomalies. Two problems were obvious altitude and changing climate. JRA1 i) explored the problem of altitude, and incorporate the ICOA standard atmosphere lapse rate (of 6.4 °C km-1) into PrediCtoR and ii) produced estimates of Pleistocene temperature fluctuations. In order to achieve the latter long-term estimates of Pleistocene air temperature fluctuation (fixed to MAT estimates for the site) will be scaled using estimates of maximum depression at Last Glacial Maximum to estimate Teff for pre-Holocene samples.

The second part of the proof of concept was to use large datasets of geographically located samples with age, DNA success and amplicon length, to derive our first real estimate of the rate of decay of DNA in archive bone. This provided PrediCtoR with its first useful output, namely, the first prediction of percentage success (as a function of thermal age).

Task 1.3 Enhancement

The basic core of PrediCtoR will be extended to increase functionally. Initially this will be the implementation of a new collagen prediction algorithm, using an activation energy of 173 kJ mol-1. Collagen is another helical biopolymer, which is also prone to hydrolysis and subsequent melting, but as collagen makes up almost 50% of the total volume of bone, it is much easier to measure using non-invasive methods than DNA.

PrediCtoR normalises thermal age for amplification length and subsequently report to the User both the (a) the maximum amplicon lengths and (b) minimum sample sizes for which 25% 50% and 75% success rates are predicted. This can be computed using standard probabilistic modelling; observed fragment length patterns from non-targeted pyro-sequencing are consistent with random hydrolysis, and DNA concentration, as a general rule, directly scales with sample size. PrediCtoR aims to improve thermal age estimate by taking into account burial depth of the bone (this would invoke an exponential decay function on seasonal fluctuation) and soil type (by including a thermal diffusivity term).

The final version of the PrediCtoR Website will contain the facility to upload results of DNA extraction successes (which will also include details of PCR and ultimately sequencing success as the three elements are all part of the same result process to attain meaningful data). Equally importantly, records of failures will also be invited to enable wider understanding of the challenges and provide a platform to highlight where positive outcomes have been achieved for both User and collections managers. All potential users of museum archive specimens will be able to input information on a given specimen (including geographic location, type, size, extraction protocol, amplification protocols along with projected amplicon length and PCR amplification success.

Progress reports

The PrediCtoR site has been created and is currently being beta tested. It is available at http://thermal-age.eu/

 

Outcomes and deliverables

The PrediCtoR site has been created and is currently being beta tested. It is available at http://thermal-age.eu/

Events

There are no planned events at this stage.

How can I get involved

Each of the PrediCtoR enhancements will be made available as soon as they are developed so the tool can be accessed by researchers.

Individuals may request to upload (current and archive) comparative data on temperatures in their museum stores, which can be used to estimate the effect of storage temperature on long-term DNA viability. Data from other fossil and bone collections will be sought as part of other projects.

For more information contact synthesys@nhm.ac.uk.