Regulatory Activity of Introgressed Archaic Alleles in Papuan Populations

25,869 high-confidence introgressed SNPs from Neanderthal and Denisovan lineages were assayed for regulatory activity in immune cell types of present-day Papuan individuals. The dataset includes measurements of active regulatory activity and differential activity between archaic and modern alleles, with 8.22% of Denisovan and 8.58% of Neanderthal sequences showing activity. It was generated by Maddy Comerford using a massively parallel reporter assay.

Use Cases

• Compare the proportion of active regulatory activity between Denisovan (8.22%) and Neanderthal (8.58%) introgressed sequences to assess functional conservation.
• Analyze the association between introgressed allele frequency and differential activity to investigate selective constraints on Denisovan introgression.
• Investigate the relationship between differential activity of archaic variants and their distance to the nearest transcription start site or differential transcription factor binding.
• Identify key immune genes like IFIH1 and TNFAIP3 that are predicted to be regulated by differentially active archaic sequences.

Strengths

• Contains regulatory data for 25,869 high-confidence introgressed SNPs, a specific and substantial count of genetic variants.
• Provides experimentally validated activity measurements from a massively parallel reporter assay, a direct functional assessment.
• Focuses on Papuan genetic ancestry, a population with the highest levels of Denisovan ancestry worldwide, offering unique genetic insights.

Limitations

• The dataset is very small at 10.7 KB, indicating limited scope and likely containing summary statistics rather than raw assay data.
• The specific row count and column structure are unknown, limiting understanding of the data's granularity and format.
• Geographic scope is restricted to Papuan genetic ancestry, limiting generalizability to other human populations.

Provenance

Source

Maddy Comerford via figshare.

Collection Method

Data generated using a massively parallel reporter assay on introgressed SNPs in immune cell types.

Freshness

Last updated on 2026-03-24, indicating it is a forward-dated or projected update.

Geography

Genetic data from present-day individuals of Papuan genetic ancestry.