Scientists are always coming up with new and creative methods in the dynamic field of genetic research of DNA analysis to learn more about our prehistoric past. The development of a technique to measure chromosome counts in ancient genomes with previously unheard-of precision is one such breakthrough. This progress has yielded some amazing findings, such as the identification of the first person to have mosaic Turner syndrome in prehistory. Let’s investigate the most recent methods advancing our knowledge of human history as we dive into the fascinating field of ancient genome DNA analysis.
Precision in Chromosome Counting:
Recent Developments in Ancient DNA Analysis:
Researchers from the Max Planck Institute for Evolutionary Anthropology and Harvard University have introduced ancIBD, a tool designed to extract Identical by Descent (IBD) segments from genomes of humans who lived hundreds, thousands, or even tens of thousands of years ago. This tool promises to provide crucial information about genetic relationships and population dynamics in ancient societies.
Uracil DNA Glycosylase (UDG) Treatment:
A major innovation in ancient DNA library preparation, UDG treatment significantly reduces the impact of postmortem cytosine deamination on ancient DNA molecules. This advancement enhances the accuracy and reliability of genetic data obtained from ancient specimens.
Ancient Tooth Tartar:
Christina Warinner and her team have harnessed the power of ancient tooth tartar to successfully reconstruct the genomes of microorganisms dating back up to 100,000 years. This novel approach offers a unique window into the microbial communities that coexisted with our ancestors.
Cheaper Techniques and New Methods:
The development of cost-effective techniques and novel methods has made damaged DNA legible to commercial sequencers, fueling a boom in ancient DNA analysis. These advancements are democratizing access to genetic information from ancient specimens and revolutionizing the study of human history.
Imputation: A Game-Changer in Ancient DNA Analysis:
Genotype calling in ancient genomes is often hindered by low depth of coverage due to postmortem DNA degradation and microbial colonization. To address this challenge, researchers have turned to genotype imputation, a method that enhances accuracy for low-coverage genomes. A recent study, re-sequencing an ancient trio and imputing 43 ancient genomes, revealed comparable accuracy between ancient and modern DNA imputation. This suggests that imputation is a reliable method, even at depths as low as 0.5x, and can significantly improve ancient DNA studies for most populations.
The field of ancient genome DNA analysis is experiencing a renaissance, driven by cutting-edge techniques that offer unprecedented insights into our ancestral past. From precise chromosome counting to novel tools like ancIBD and UDG treatment, researchers are rewriting the narrative of human evolution. As we unlock the secrets encoded in ancient DNA, the journey into our past becomes clearer, shedding light on the intricate tapestry of human history.
Marchini J, Howie B. Genotype imputation for genome-wide association studies. Nat. Rev. Genet. 2010;11:499–511. doi: 10.1038/nrg2796. [PubMed] [CrossRef] [Google Scholar]
Howie BN, Donnelly P, Marchini J. A flexible and accurate genotype imputation method for the next generation of genome-wide association studies. PLoS Genet. 2009;5:e1000529. doi: 10.1371/journal.pgen.1000529. [PMC free article] [PubMed] [CrossRef] [Google Scholar]
Browning BL, Browning SR. Genotype imputation with millions of reference samples. Am. J. Hum. Genet. 2016;98:116–126. doi: 10.1016/j.ajhg.2015.11.020. [PMC free article] [PubMed] [CrossRef] [Google Scholar]
Spiliopoulou A, Colombo M, Orchard P, Agakov F, McKeigue P. GeneImp: Fast imputation to large reference panels using genotype likelihoods from ultralow coverage sequencing. Genetics. 2017;206:91–104. doi: 10.1534/genetics.117.200063. [PMC free article] [PubMed] [CrossRef] [Google Scholar]
Rubinacci S, Ribeiro DM, Hofmeister RJ, Delaneau O. Efficient phasing and imputation of low-coverage sequencing data using large reference panels. Nat. Genet. 2021;53:120–126. doi: 10.1038/s41588-020-00756-0. [PubMed] [CrossRef] [Google Scholar]