Generating barcoded libraries for multiplex high-throughput sequencing

Methods in Molecular Biology

Volumn 840, Issue , 2012, Pages 155-170

  Knapp, Michael ^a   Stiller, Mathias ^b   Meyer, Matthias ^c  

^a UNIVERSITY OF OTAGO   (New Zealand)

^b PENNSYLVANIA STATE UNIVERSITY   (United States)

^c MAX PLANCK INSTITUTE FOR EVOLUTIONARY ANTHROPOLOGY   (Germany)

Author keywords

ancient DNA; barcoding; direct multiplex sequencing; DNA capture; multiplex PCR; next generation high throughput sequencing

Indexed keywords

DNA;

ARTICLE; CHEMISTRY; DNA BARCODING; FOSSIL; GENE LIBRARY; GENETICS; HIGH THROUGHPUT SEQUENCING; METHODOLOGY; MULTIPLEX POLYMERASE CHAIN REACTION; NUCLEOTIDE SEQUENCE;

BASE SEQUENCE; DNA; DNA BARCODING, TAXONOMIC; FOSSILS; GENE LIBRARY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MULTIPLEX POLYMERASE CHAIN REACTION;

EID: 84856305295     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-516-9_19     Document Type: Article

References (13)

1. Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A 74:5463-5467
2. Knapp M, Hofreiter M (2010) Next generation sequencing of ancient DNA: requirements, strategies and perspectives. Genes 1: 227-243
3. Meyer M, Stenzel U, Hofreiter M (2008) Parallel tagged sequencing on the 454 platform. Nat Protoc 3:267-278
4. Meyer M, Kircher M (2010) Illumina sequencing library preparation for highly multiplexed target capture and sequencing. Cold Spring Harb Protoc. doi: 10.1101/pdb.prot5448
5. Margulies M, Egholm M, Altman WE et al (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376-380
6. Maricic T, Pääbo S (2009) Optimization of 454 sequencing library preparation from small amounts of DNA permits sequence determination of both DNA strands. Biotechniques 46:51-57
7. Briggs AW, Good JM, Green RE et al (2009) Targeted retrieval and analysis of five Nean dertal mtDNA genomes. Science 325:318-321
8. Meyerhans A, Vartanian JP, Wain-Hobson S (1990) DNA recombination during PCR. Nucleic Acids Res 18:1687-1691
9. Nikiforov TT, Rendle RB, Kotewicz ML, Rogers YH (1994) The use of phosphorothioate primers and exonuclease hydrolysis for the preparation of single-stranded PCR products and their detection by solid-phase hybridization. PCR Methods Appl 3:285-291
10. Craig DW, Pearson JV, Szelinger S et al (2008) Identification of genetic variants using barcoded multiplexed sequencing. Nat Methods 5:887-893
11. Meyer M, Briggs AW, Maricic T et al (2008) From micrograms to picograms: quantitative PCR reduces the material demands of highthroughput sequencing. Nucleic Acids Res 36:e5
12. Heyn P, Stenzel U, Briggs AW et al (2010) Road blocks on paleogenomes-polymerase extension profiling reveals the frequency of blocking lesions in ancient DNA. Nucleic Acids Res 38:e161
13. Stiller M, Knapp M, Stenzel U et al (2009) Direct multiplex sequencing (DMPS)-a novel method for targeted high-throughput sequencing of ancient and highly degraded DNA. Genome Res 19:1843-1848