Research

Master’s Thesis Research

Master’s thesis: Assessing the effect of long-term storage on ancient DNA (aDNA) samples

Ancient DNA research has revolutionized our understanding of human evolution and palaeogenomics through direct genetic evidence. However, aDNA is an inherently degraded molecule, which complicates its handling and analysis. While sample preservation is critical for obtaining high-quality results, the effects of long-term storage on aDNA remain insufficiently explored.

Methods:This project investigated the impact of long-term storage by reprocessing bone powders, extracts, and indexed libraries originally prepared eight years earlier from 12 individuals. Using standardized protocols consistent with those applied in 2015, DNA degradation was assessed through DNA extraction, library preparation, indexing PCR, and Illumina sequencing (NextSeq and NovaSeq), followed by bioinformatic and statistical analyses in R and SPSS. After data filtering, 11 individuals were included in the final analysis.

Results: Extract samples showed significantly higher cytosine-to-thymine and guanine-to-adenine deamination, indicating increased degradation over time. In contrast, bone powder and indexed library samples exhibited lower deamination rates, suggesting better preservation. Additionally, mean fragment length and the proportion of unique reads increased significantly across all sample types, likely reflecting improvements in sequencing technologies (MiSeq vs. NovaSeq/NextSeq).

This study provides insights into aDNA degradation mechanisms and highlights the importance of optimized storage conditions, including stable temperature, to preserve DNA quality and improve long-term sample usability in paleogenomic research.

As a laboratory technician in the Pinhasi aDNA Lab I contributed for over 2 years to the "Harvard’s Atlas of Humanity Project" by processing large volumes of samples (bones) for subsequent DNA extraction, to build an extensive aDNA database.

Bioinformatics Projects

LongTermStorageaDNA pipeline

Development of a reproducible bioinformatics pipeline for processing ancient DNA sequencing data.
Current modules available: First module: aDNAPrePro (v1.1), to preprocess aDNA data, was released in March 2026 and
the second module RunAmber (v1.0), to run the Python program AMBER and assess fragmentation, was released in April 2026.

Computational Skills

Programming: R, Bash (advanced), Python (basic)

aDNA & NGS: Cutadapt, BWA, SAMtools, MapDamage, TKGWV2, READ, Calico, AMBER, PLINK

Phylogenetics: MEGA, BEAST2 (basic)

Statistics: R, SPSS (advanced), PCA

Metagenomics: MEGAHIT, MetaWRAP, Kraken2 (basic)

Population genetics: ADMIXTOOLS, ADMIXTURE, KING, PONG

HPC: Linux clusters (LiSC) (advanced), SLURM, nf-core/eager

Affiliations

International Society for Biomolecular Archaeology (ISBA)

Austrian Association of Molecular Life Sciences and Biotechnology (ÖGMBT)

Conference Poster Presentation (upcoming in June 2026):

ICP 2026 (Stockholm)
Raimo, A., et al. Abstract based on master’s thesis “The effect of long-term storage on ancient DNA samples”; accepted for poster presentation.