Cost estimation - financial expenditure research on ancient finds of human remains

[ChrisR]

Cost estimation - financial expenditure for DNA research on ancient finds of human remains 
Was this discussed before (at anthrogenica)? As can't recall to have seen some real costs from finished projects. I would guess most research is publicly funded and so transparent, but I do not know where detailed expenditure costs for ancient DNA studies could be listed for (Central) Europe.

When asking a LLM-GPT this was the answer:

In general, the cost of WGS for ancient DNA can range from several hundred to several thousand dollars per sample, depending on the sequencing technology and depth of coverage used. For example, shallow coverage sequencing (1x-2x) may cost around 300-500 per sample, while deep coverage sequencing (30x-50x) may cost 1,000-3,000 or more per sample.


It is important to note that the cost of WGS for ancient DNA can be higher than for modern DNA, due to the challenges associated with extracting and preparing ancient DNA samples for sequencing. These challenges can include low DNA yield, DNA degradation, and contamination with modern DNA, all of which can impact the cost and feasibility of the project.

Additionally, the cost of data analysis and interpretation can also be a significant factor in the overall cost of ancient DNA research. This can include bioinformatic analysis of the sequencing data, as well as population genetic and statistical analysis to contextualize the results.

So could this be accurate and shallow ancient coverage not cost much more then a "normal 30x WGS"?
What might be the desirable coverage for admixture (7x?) and Y-DNA (15x?)

[teepean]

I asked ChatGPT how much would this process cost.

Code:

The sample handling and processing procedures, outlined in detail in [1], were conducted as part of the earlier published study. In brief, the steps involved anthropological analysis utilizing a CT scan generated at Lund University Hospital [5]. The DNA was extracted from the right femur of the Bishop and the left femur of the fetus. Both bones had traces of desiccated soft tissue (periosteum), which was also used in a separate DNA extraction. The procedure was undertaken at the clean ancient DNA facilities at the Archaeological Research Laboratory, Stockholm University. Samples were decontaminated via UV irradiation (254 nm) at approximately J/cm2 per side. The hard tissues (bones) were drilled with a Dremel tool at 5000 rpm, while fragments of soft tissue were removed with decontaminated forceps. Thereafter, the DNA was extracted from 93 mg (Winstrup) and 46 mg (fetus) of bone powders and from 7 mg (Winstrup) and 8 mg (fetus) of collected fragments of soft tissue covering the skeletal elements sampled.
We used our standard DNA extraction and purification protocols [11,12], followed by preparation of double-stranded DNA libraries [13] and qPCR validation. The libraries were indexed in a 3 × 50 μL PCR reaction. Finally, libraries were purified with magnetic beads (AmPure XP, Beckman Coulter, Indianapolis, IN, USA) and quantified on a bioanalyzer (Agilent TechnologiesTM, Sundbyberg, Sweden). The libraries were shotgun-sequenced both on the Illumina HiSeq X and the NovaSeq 6000 (Illumina, Inc., San Diego, CA, USA). All sequencing was performed at the SciLifeLab DNA NGI sequencing facility, Stockholm, Sweden.

Code:

To estimate the cost of the described process, we must consider several distinct components:

CT Scan: The cost varies by location, but a CT scan can range from $250 to $1,500 or more, depending on the complexity and whether it is performed in a hospital or a private clinic.

DNA Extraction and Purification: This includes the cost of chemicals, reagents, and kits used in the process. Prices can vary widely based on the quality and quantity of the reagents, but a rough estimate might be between $100 to $500 per sample.

DNA Sequencing: Costs for sequencing can vary significantly depending on the throughput, depth of coverage, and the sequencing platform used (e.g., Illumina HiSeq X or NovaSeq 6000). The prices for high-throughput sequencing can range from a few hundred dollars for low-coverage sequencing of a single genome to several thousand dollars for high-coverage sequencing. For example, high-throughput sequencing services might charge between $600 to $1,200 per gigabase of DNA, with a human genome being about 3.2 gigabases.

Ancient DNA Facilities Use: Utilizing specialized facilities for ancient DNA (aDNA) extraction and processing can add significantly to the cost. This could include clean room time, equipment use, and labor. It's challenging to estimate without specific rates, but it might range from $1,000 to several thousand dollars, depending on the extent of the work.

Materials and Miscellaneous: This includes the use of UV irradiation for decontamination, drilling of bones, collection of soft tissue, preparation of DNA libraries, qPCR validation, and purification of the libraries. Each of these steps requires specific materials, tools, and reagents, which can add up. An estimated range might be $500 to $2,000.

Labor Costs: The labor for conducting these analyses, including the work of skilled technicians and specialists, must also be considered. This can be the most variable and potentially the highest cost, depending on local wage rates and the complexity of the analysis.

Given these components, a rough estimate for the entire process per sample might range from a few thousand dollars to potentially over ten thousand dollars when considering all materials, labor, and facility use. This estimate is very rough and could vary widely based on the specific details of the procedures, the geographic location where the analyses are performed, the specific rates charged by the facilities and services used, and the level of detail and depth of sequencing and analysis required.