Linear amplification for deep sequencing

Linear amplification for deep sequencing (LADS) is an amplification method that produces representative libraries for Illumina next-generation sequencing within 2 d. The method relies on attaching two different sequencing adapters to blunt-end repaired and A-tailed DNA fragments, wherein one of the adapters is extended with the sequence for the T7 RNA polymerase promoter. Ligated and size-selected DNA fragments are transcribed in vitro with high RNA yields. Subsequent cDNA synthesis is initiated from a primer complementary to the first adapter, ensuring that the library will only contain full-length fragments with two distinct adapters. Contrary to the severely biased representation of AT- or GC-rich fragments in standard PCR-amplified libraries, the sequence coverage in T7-amplified libraries is indistinguishable from that of nonamplified libraries. Moreover, in contrast to amplification-free methods, LADS can generate sequencing libraries from a few nanograms of DNA, which is essential for all applications in which the starting material is limited.

[1]  A. Hyman,et al.  Quantitative Interaction Proteomics and Genome-wide Profiling of Epigenetic Histone Marks and Their Readers , 2010, Cell.

[2]  Nicholas T Ingolia,et al.  Genome-wide translational profiling by ribosome footprinting. , 2010, Methods in enzymology.

[3]  M. Gerstein,et al.  RNA-Seq: a revolutionary tool for transcriptomics , 2009, Nature Reviews Genetics.

[4]  Mariël Brok,et al.  Improved genome-wide localization by ChIP-chip using double-round T7 RNA polymerase-based amplification , 2008, Nucleic acids research.

[5]  S. Linnarsson.  Recent advances in DNA sequencing methods - general principles of sample preparation. , 2010, Experimental cell research.

[6]  H. Stunnenberg,et al.  H2A.Z Demarcates Intergenic Regions of the Plasmodium falciparum Epigenome That Are Dynamically Marked by H3K9ac and H3K4me3 , 2010, PLoS pathogens.

[7]  Nancy F. Hansen,et al.  Accurate Whole Human Genome Sequencing using Reversible Terminator Chemistry , 2008, Nature.

[8]  A. Fire,et al.  Rolling replication of short DNA circles. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[9]  Richard Durbin,et al.  A large genome center's improvements to the Illumina sequencing system , 2008, Nature Methods.

[10]  Matthias Platzer,et al.  Sequence and analysis of chromosome 2 of Dictyostelium discoideum , 2002, Nature.

[11]  Natalie Jäger,et al.  Genome-wide mapping of DNA methylation: a quantitative technology comparison , 2010, Nature Biotechnology.

[12]  S. Schreiber,et al.  Development and validation of a T7 based linear amplification for genomic DNA , 2003, BMC Genomics.

[13]  B. Turner,et al.  Immunoprecipitation of native chromatin: NChIP. , 2003, Methods.

[14]  B. Barrell,et al.  Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence , 1998, Nature.

[15]  Gabor T. Marth,et al.  Whole-genome sequencing and variant discovery in C. elegans , 2008, Nature Methods.

[16]  R. A. Atherton,et al.  Whole genome sequencing of enriched chloroplast DNA using the Illumina GAII platform , 2010, Plant Methods.

[17]  S. Turner,et al.  Real-Time DNA Sequencing from Single Polymerase Molecules , 2009, Science.

[18]  B. Williams,et al.  Mapping and quantifying mammalian transcriptomes by RNA-Seq , 2008, Nature Methods.

[19]  S. Ranade,et al.  Stem cell transcriptome profiling via massive-scale mRNA sequencing , 2008, Nature Methods.

[20]  H. Stunnenberg,et al.  A hierarchy of H3K4me3 and H3K27me3 acquisition in spatial gene regulation in Xenopus embryos. , 2009, Developmental cell.

[21]  Catalin C. Barbacioru,et al.  RNA-Seq analysis to capture the transcriptome landscape of a single cell , 2010, Nature Protocols.

[22]  Lira Mamanova,et al.  FRT-seq: Amplification-free, strand-specific, transcriptome sequencing , 2010, Nature Methods.

[23]  Jonathan E. Allen,et al.  Genome sequence of the human malaria parasite Plasmodium falciparum , 2002, Nature.

[24]  P. Park.  ChIP–seq: advantages and challenges of a maturing technology , 2009, Nature Reviews Genetics.

[25]  A. Regev,et al.  Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA , 2010, Nature Methods.

[26]  U. Stenzel,et al.  Parallel tagged sequencing on the 454 platform , 2008, Nature Protocols.

[27]  M. Metzker.  Sequencing technologies — the next generation , 2010, Nature Reviews Genetics.

[28]  Blaise T. F. Alako,et al.  Dynamic histone H3 epigenome marking during the intraerythrocytic cycle of Plasmodium falciparum , 2009, Proceedings of the National Academy of Sciences.

[29]  Juliane C. Dohm,et al.  Substantial biases in ultra-short read data sets from high-throughput DNA sequencing , 2008, Nucleic acids research.

[30]  S. Kingsmore,et al.  Comprehensive human genome amplification using multiple displacement amplification , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[31]  Richard I. Gumport,et al.  Transcription termination by bacteriophage T7 RNA polymerase at rho-independent terminators. , 1990, The Journal of biological chemistry.

[32]  P. Krieg,et al.  Improved synthesis of full-length RNA probe at reduced incubation temperatures. , 1990, Nucleic acids research.

[33]  Leighton J. Core,et al.  Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters , 2008, Science.

[34]  Jingde Zhu,et al.  Whole-genome DNA methylation profiling using MethylCap-seq. , 2010, Methods.

[35]  Z. Ning,et al.  Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of GC-biased genomes , 2009, Nature Methods.

[36]  Ryan E. Mills,et al.  Complete Sequence and Comparative Analysis of the Genome of Herpes B Virus (Cercopithecine Herpesvirus 1) from a Rhesus Monkey , 2003, Journal of Virology.

[37]  Ronghua Chen,et al.  Digital transcriptome profiling using selective hexamer priming for cDNA synthesis , 2009, Nature Methods.

[38]  Jürg Bähler,et al.  Defining transcribed regions using RNA-seq , 2010, Nature Protocols.

[39]  Dongyu Liu,et al.  Rolling Circle DNA Synthesis: Small Circular Oligonucleotides as Efficient Templates for DNA Polymerases. , 1996, Journal of the American Chemical Society.