Ancient DNA studies: Common limitations and Genotyping

Anastasia V. Poznyak ¹*, Nikolay A. Orekhov ², Tatiana Ivanovna Kovyanova ^1,3, Irina Alexandrovna Starodubtseva ⁴, Natalia V. Elizova ², Vasily N. Sukhorukov ³, Alexander N. Orekhov ³

Mapping human genes transformed genomic research, revealing human evolution, disease susceptibility, and ethical challenges in ancient DNA studies.

Abstract

Ancient DNA (aDNA) studies have revolutionized research on human origins and genetic diversity, providing insights into evolutionary history and disease susceptibility. This review article explores common limitations and genotyping techniques in aDNA research. The Human Genome Project (HGP) laid the foundation for genomic studies, enabling the sequencing of millions of modern and prehistoric human genomes. Advancements in technology and bioinformatics have facilitated the analysis of aDNA, revealing interbreeding events and ancient genetic variants shaping modern traits and health conditions. Laboratory work with aDNA involves complex processes to extract and sequence degraded samples, often obtained from skeletal remains. Techniques such as hybridization capture and high-throughput sequencing enhance data quality and analysis efficiency. Post-mortem DNA damage, including fragmentations and nucleotide conversions, poses challenges in authenticating aDNA sequences. Strategies like uracil-DNA glycosylase treatment help mitigate damage and improve data reliability. Ancient DNA genotyping methods, such as pseudohaploid and probabilistic genotyping, cater to varying data quality levels and analysis requirements. Genotype accuracy, affected by low coverage and post-mortem damage, poses challenges in differentiating heterozygous and homozygous loci. Ethical considerations in aDNA research highlight the importance of respecting individual and cultural rights, preserving cultural heritage, and addressing social implications of genetic findings. Transparency, accountability, and collaboration with descendant communities are essential for conducting ethically sound aDNA research.

Keywords: Human Genome Project (HGP), Ancient DNA (aDNA), Genomic Sequencing, Bioinformatics, Ethical Considerations

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