Tuyển tập các báo cáo nghiên cứu về y học được đăng trên tạp chí y học Wertheim cung cấp cho các bạn kiến thức về ngành y đề tài: Computational challenges in the analysis of ancient DNA. | Prufer et al. Genome Biology 2010 11 R47 http 2010 11 5 R47 w Genome Biology METHOD _ Open Access Computational challenges in the analysis of ancient DNA Kay Prufer 1 Udo Stenzel1 Michael Hofreiter1 2 Svante Păăbo1 Janet Kelso1 and Richard E Green1 Abstract High-throughput sequencing technologies have opened up a new avenue for studying extinct organisms. Here we identify and quantify biases introduced by particular characteristics of ancient DNA samples. These analyses demonstrate the importance of closely related genomic sequence for correctly identifying and classifying bona fide endogenous DNA fragments. We show that more accurate genome divergence estimates from ancient DNA sequence can be attained using at least two outgroup genomes and appropriate filtering. Background Most of our understanding of how extinct species are related to living species has come from morphological analysis of fossil remains. Recovery and analysis of DNA extracted from fossil remains so called ancient DNA provide a complementary avenue for understanding evolution. Analysis of ancient DNA has been used to resolve the genetic relationships between extinct and extant species 1-5 and to deduce extinct organisms geographic ranges 6 and their phenotypic characteristics 7 8 . With the enormous throughput of next generation sequencers it has become tractable to simply shotgun sequence DNA as it is recovered from fossil bones 9-13 . Despite the fact that most of the recovered DNA is from microbes that colonized the bone after death 4 14 the sheer volume of sequence generated means that the few percent that are typically from the species of interest still constitute a sequence dataset large enough for genomescale analysis. Furthermore because ancient DNA molecules are often fragmented to very short pieces 15 ancient DNA sequencing is not limited in practice by the short read length of current sequencers. The mean ancient DNA fragment length has varied between 60 and 150 bp .
