COM.on C.A.4:e15/96-100   Online published on Jul.16, 2010.
doi:10.4236/coca.2010.41015
REVIEW
 Eliminating and Assessing Contamination during Ancient DNA Analyses

YUAN Yuan

MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433 China

ABSTRACT: Ancient DNA is recovered from post mortem materials, such as archaeological or historical specimens. Because samples tend to be sparse and highly damaged, ancient DNA is vulnerable to different sources of contamination during the process of manipulation. Thus, the authenticity of the DNA sequences retrieved is crucial to ancient DNA research. Recent advances in high-throughput DNA sequencing have made amplifying low-content ancient DNA molecules possible. However, contaminant DNA is amplified greatly in the mean time, which makes eliminating and assessing contamination more difficult. Authentication based on PCR reactions is also effective in high-throughput DNA sequencing; more approaches for high-throughput DNA sequencing have been developed, such as length distribution, nucleotide misincorporation patterning, nucleotide frequency at and around the ends of DNA fragments, and correlation of coverage with GC content. The level of contamination in the sample can, to some extent, be observed at the heterozygote. Overall, a wide range of methods are necessary to judge whether or not the retrieved DNA is usable.

Key words: ancient DNA; contamination; high-throughput sequencing

Recieved: Jun.28, 2010   Accepted: Jul.14, 2010  Corresponding: yuanyuan.fudan@gmail.com

《现代人类学通讯》第四卷e15篇 第96-100页  2010年7月16日网上发行

专题综述

控制古DNA污染的方法

袁媛

复旦大学 生命科学学院 现代人类学教育部重点实验室，上海，200433

摘要：控制污染是古DNA研究的难题之一。当前，高通量测序提高了古DNA检测灵敏度的同时使污染分子大量扩增，这使控制和检测古DNA污染更加重要。先前的古DNA行业标准基于PCR反应，所以对现行的古DNA研究仍适用。现在针对高通量测序，古DNA研究又发展了新的减少和检测污染的手段。目前，证明古DNA可靠性的方法，主要有检测片段长度、DNA的错配模式、片段末端5'和3'的碱基频率、测序覆盖率与GC含量的相关性。而对于样本的检测前污染，染色体的杂合态分析可以一定程度上判断污染状况。在现阶段的研究条件下，多方面的证据的支持更有利于判定所得的古DNA序列是否可靠。

关键词：古DNA；污染；高通量测序

 

收稿日期： 2010年6月28日  修回日期： 2010年7月14日 联系人：袁媛 yuanyuan.fudan@gmail.com
全文链接 Full text: [PDF]

参考文献 References

1.Willerslev E, Cooper A (2005) Ancient DNA. Proc Biol Sci 272: 3-16.
2.Green RE, Briggs AW, Krause J, Prüfer K, Burbano HA, Siebauer M, Lachmann M, Pääbo S (2009) The Neandertal genome and ancient DNA Authenticity. EMBO J 28: 2494-2502.
3.Handt O, Krings M, Ward RH, Pääbo S (1996) The retrieval of ancient human DNA equences. Am J Hum Genet 59: 368-376.
4.Cooper A, Lalueza-Fox C, Anderson S, Rambaut A, Austin J, Ward R (2001) Complete mitochondrial genome sequences of two extinct moas clarify ratite evolution. Nature 409: 704-707.
5.Li H, Huang Y, Mustavich LF, Zhang F, Tan JZ, Wang LE, Qian J, Gao MH, Jin L (2007) Y chromosomes of prehistoric people along the Yangtze River. Hum Genet 122: 383-388
6.Cooper A, Poinar HN (2000) Ancient DNA: do it right or not at all. Science 289:1139.
7.Willerslev E, Hansen AJ, Poinar HN (2004) Isolation of nucleic acids and cultures from ice and permafrost. Trends Ecol Evol 19:141-147.
8.Briggs AW, Good JM, Green RE, Krause J, Maricic T, Stenzel U, Pääbo S (2009) Primer Extension Capture: Targeted Sequence Retrieval from Heavily Degraded DNA Sources. J Vis Exp 31:1573.
9.Krause J, Fu Q, Good JM, Viola B, Shunkov MV, Derevianko AP, Pääbo S (2010) The complete mitochondrial DNA genome of an unknown hominin from southern Siberia. Nature 464:894-897.
10.Krause J, Fu Q, Good JM, Viola B, Shunkov MV, Derevianko AP, Pääbo S (2010) A Complete mtDNA Genome of an Early Modern Human from Kostenki, Russia. Curr Biol 20:231-236.
11.Handt O, Höss M, Krings M, Pääbo S (1994) Ancient DNA: methodological challenges. Experientia 50:524-529.
12.Serre D, Hofreiter M, Pääbo S (2004) Mutations induced by ancient DNA extracts? Mol Biol Evol 21:1463-1467.
13.Briggs AW, Good JM, Green RE, Krause J, Maricic T, Stenzel U, Lalueza-Fox C, Rudan P, Brajkovic D, Kucan Z, Gusic I, Schmitz R, Doronichev VB, Golovanova LV, de la Rasilla M, Fortea J, Rosas A, Pääbo S (2009) Targeted retrieval and analysis of five Neandertal mtDNA genomes. Science 325:318-321.