The role of replicates for error mitigation in next-generation sequencing (original) (raw)

• O'Rawe, J. et al. Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing. Genome Med. 5, 28 (2013).
  CAS PubMed PubMed Central Google Scholar
• Kircher, M., Heyn, P. & Kelso, J. Addressing challenges in the production and analysis of Illumina sequencing data. BMC Genomics 12, 382 (2011).
  CAS PubMed PubMed Central Google Scholar
• Metzker, M. L. Sequencing technologies — the next generation. Nature Rev. Genet. 11, 31–46 (2010).
  CAS PubMed Google Scholar
• Sboner, A., Mu, X. J., Greenbaum, D., Auerbach, R. K. & Gerstein, M. B. The real cost of sequencing: higher than you think! Genome Biol. 12, 125 (2011).
  PubMed PubMed Central Google Scholar
• Ratan, A. et al. Comparison of sequencing platforms for single nucleotide variant calls in a human sample. PLoS ONE 8, e55089 (2013).
  CAS PubMed PubMed Central Google Scholar
• Peters, B. A. et al. Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells. Nature 487, 190–195 (2012).
  CAS PubMed PubMed Central Google Scholar
• Williams, C. et al. A high frequency of sequence alterations is due to formalin fixation of archival specimens. Am. J. Pathol. 155, 1467–1471 (1999).
  CAS PubMed PubMed Central Google Scholar
• Yost, S. E. et al. Identification of high-confidence somatic mutations in whole genome sequence of formalin-fixed breast cancer specimens. Nucleic Acids Res. 40, e107 (2012).
  CAS PubMed PubMed Central Google Scholar
• Akbari, M., Hansen, M. D., Halgunset, J., Skorpen, F. & Krokan, H. E. Low copy number DNA template can render polymerase chain reaction error prone in a sequence-dependent manner. J. Mol. Diagn. 7, 36–39 (2005).
  CAS PubMed PubMed Central Google Scholar
• Lawrence, M. S. et al. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature 499, 214–218 (2013).
  CAS PubMed PubMed Central Google Scholar
• Leal, S. M. Detection of genotyping errors and pseudo-SNPs via deviations from Hardy–Weinberg equilibrium. Genet. Epidemiol. 29, 204–214 (2005).
  PubMed PubMed Central Google Scholar
• Walsh, P. S., Erlich, H. A. & Higuchi, R. Preferential PCR amplification of alleles: mechanisms and solutions. PCR Methods Appl. 1, 241–250 (1992).
  CAS PubMed Google Scholar
• Hutchison, C. A. 3rd, Smith, H. O., Pfannkoch, C. & Venter, J. C. Cell-free cloning using phi29 DNA polymerase. Proc. Natl Acad. Sci. USA 102, 17332–17336 (2005).
  CAS PubMed PubMed Central Google Scholar
• Hodges, E. et al. Genome-wide in situ exon capture for selective resequencing. Nature Genet. 39, 1522–1527 (2007).
  CAS PubMed Google Scholar
• Aird, D. et al. Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biol. 12, R18 (2011).
  CAS PubMed PubMed Central Google Scholar
• Bystrykh, L. V. Generalized DNA barcode design based on Hamming codes. PLoS ONE 7, e36852 (2012).
  CAS PubMed PubMed Central Google Scholar
• Koboldt, D. C., Ding, L., Mardis, E. R. & Wilson, R. K. Challenges of sequencing human genomes. Brief Bioinform. 11, 484–498 (2010).
  CAS PubMed PubMed Central Google Scholar
• Xuan, J., Yu, Y., Qing, T., Guo, L. & Shi, L. Next-generation sequencing in the clinic: promises and challenges. Cancer Lett. 340, 284–295 (2012).
  PubMed PubMed Central Google Scholar
• Nakamura, K. et al. Sequence-specific error profile of Illumina sequencers. Nucleic Acids Res. 39, e90 (2011).
  CAS PubMed PubMed Central Google Scholar
• Fuller, C. W. et al. The challenges of sequencing by synthesis. Nature Biotech. 27, 1013–1023 (2009).
  CAS Google Scholar
• Roberts, R. J., Carneiro, M. O. & Schatz, M. C. The advantages of SMRT sequencing. Genome Biol. 14, 405 (2013).
  PubMed PubMed Central Google Scholar
• Yang, X., Chockalingam, S. P. & Aluru, S. A survey of error-correction methods for next-generation sequencing. Brief Bioinform. 14, 56–66 (2013).
  CAS PubMed Google Scholar
• Lynch, M. Rate, molecular spectrum, and consequences of human mutation. Proc. Natl Acad. Sci. USA 107, 961–968 (2010).
  CAS PubMed PubMed Central Google Scholar
• Laurie, C. C. et al. Detectable clonal mosaicism from birth to old age and its relationship to cancer. Nature Genet. 44, 642–650 (2012).
  CAS PubMed Google Scholar
• Schmitt, M. W. et al. Detection of ultra-rare mutations by next-generation sequencing. Proc. Natl Acad. Sci. USA 109, 14508–14513 (2012).
  CAS PubMed PubMed Central Google Scholar
• Luo, C., Tsementzi, D., Kyrpides, N., Read, T. & Konstantinidis, K. T. Direct comparisons of Illumina versus Roche 454 sequencing technologies on the same microbial community DNA sample. PLoS ONE 7, e30087 (2012).
  CAS PubMed PubMed Central Google Scholar
• DePristo, M. A. et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nature Genet. 43, 491–498 (2011).
  CAS PubMed Google Scholar
• Ajay, S. S., Parker, S. C., Abaan, H. O., Fajardo, K. V. & Margulies, E. H. Accurate and comprehensive sequencing of personal genomes. Genome Res. 21, 1498–1505 (2011).
  PubMed PubMed Central Google Scholar
• Meynert, A. M., Bicknell, L. S., Hurles, M. E., Jackson, A. P. & Taylor, M. S. Quantifying single nucleotide variant detection sensitivity in exome sequencing. BMC Bioinformatics 14, 195 (2013).
  PubMed PubMed Central Google Scholar
• Leek, J. T. et al. Tackling the widespread and critical impact of batch effects in high-throughput data. Nature Rev. Genet. 11, 733–739 (2010).
  CAS PubMed Google Scholar
• Baranzini, S. E. et al. Genome, epigenome and RNA sequences of monozygotic twins discordant for multiple sclerosis. Nature 464, 1351–1356 (2010).
  CAS PubMed PubMed Central Google Scholar
• Reumers, J. et al. Optimized filtering reduces the error rate in detecting genomic variants by short-read sequencing. Nature Biotech. 30, 61–68 (2012).
  CAS Google Scholar
• Lam, H. Y. et al. Performance comparison of whole-genome sequencing platforms. Nature Biotech. 30, 78–82 (2012).
  CAS Google Scholar
• Jung, H., Bleazard, T., Lee, J. & Hong, D. Systematic investigation of cancer-associated somatic point mutations in SNP databases. Nature Biotech. 31, 787–789 (2013).
  CAS Google Scholar
• Drmanac, R. et al. Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science 327, 78–81 (2010).
  CAS PubMed Google Scholar
• Pelak, K. et al. The characterization of twenty sequenced human genomes. PLoS Genet. 6, e1001111 (2010).
  PubMed PubMed Central Google Scholar
• Li, H., Ruan, J. & Durbin, R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 18, 1851–1858 (2008).
  CAS PubMed PubMed Central Google Scholar
• Lee, W. et al. The mutation spectrum revealed by paired genome sequences from a lung cancer patient. Nature 465, 473–477 (2010).
  CAS PubMed Google Scholar
• Ball, M. P. et al. A public resource facilitating clinical use of genomes. Proc. Natl Acad. Sci. USA 109, 11920–11927 (2012).
  CAS PubMed PubMed Central Google Scholar
• Laurie, C. C. et al. Quality control and quality assurance in genotypic data for genome-wide association studies. Genet. Epidemiol. 34, 591–602 (2010).
  PubMed PubMed Central Google Scholar
• Ye, K., Schulz, M. H., Long, Q., Apweiler, R. & Ning, Z. Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics 25, 2865–2871 (2009).
  CAS PubMed PubMed Central Google Scholar
• Jurka, J. et al. Repbase Update, a database of eukaryotic repetitive elements. Cytogenet. Genome Res. 110, 462–467 (2005).
  CAS PubMed Google Scholar
• Li, H. & Durbin, R. Fast and accurate long-read alignment with Burrows–Wheeler transform. Bioinformatics 26, 589–595 (2010).
  PubMed PubMed Central Google Scholar
• Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
  PubMed PubMed Central Google Scholar
• Lindgreen, S. AdapterRemoval: easy cleaning of next-generation sequencing reads. BMC Res. Notes 5, 337 (2012).
  PubMed PubMed Central Google Scholar
• Degner, J. F. et al. Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data. Bioinformatics 25, 3207–3212 (2009).
  CAS PubMed PubMed Central Google Scholar
• McKenna, A. et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 20, 1297–1303 (2010).
  CAS PubMed PubMed Central Google Scholar
• Genovese, G. et al. Using population admixture to help complete maps of the human genome. Nature Genet. 45, 406–414 (2013).
  CAS PubMed Google Scholar
• Church, D. M. et al. Modernizing reference genome assemblies. PLoS Biol. 9, e1001091 (2011).
  CAS PubMed PubMed Central Google Scholar
• Pruitt, K. D., Tatusova, T. & Maglott, D. R. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 35, D61–D65 (2007).
  CAS PubMed Google Scholar
• Rusk, N. One genome, two haplotypes. Nature Methods 8, 107 (2011).
  CAS PubMed Google Scholar
• Fan, H. C., Wang, J., Potanina, A. & Quake, S. R. Whole-genome molecular haplotyping of single cells. Nature Biotech. 29, 51–57 (2011).
  CAS Google Scholar
• Kitzman, J. O. et al. Haplotype-resolved genome sequencing of a Gujarati Indian individual. Nature Biotech. 29, 59–63 (2011).
  CAS Google Scholar
• Browning, S. R. & Browning, B. L. Haplotype phasing: existing methods and new developments. Nature Rev. Genet. 12, 703–714 (2011).
  CAS PubMed Google Scholar
• Bansal, V. & Bafna, V. HapCUT: an efficient and accurate algorithm for the haplotype assembly problem. Bioinformatics 24, i153–i159 (2008).
  PubMed Google Scholar
• Chen, R. et al. Personal omics profiling reveals dynamic molecular and medical phenotypes. Cell 148, 1293–1307 (2012).
  CAS PubMed PubMed Central Google Scholar
• Roach, J. C. et al. Analysis of genetic inheritance in a family quartet by whole-genome sequencing. Science 328, 636–639 (2010).
  CAS PubMed PubMed Central Google Scholar
• Lupski, J. R. et al. Whole-genome sequencing in a patient with Charcot-Marie-Tooth neuropathy. N. Engl. J. Med. 362, 1181–1191 (2010).
  CAS PubMed PubMed Central Google Scholar
• Chapman, S. J. & Hill, A. V. Human genetic susceptibility to infectious disease. Nature Rev. Genet. 13, 175–188 (2012).
  CAS PubMed Google Scholar
• Ott, J., Kamatani, Y. & Lathrop, M. Family-based designs for genome-wide association studies. Nature Rev. Genet. 12, 465–474 (2011).
  CAS PubMed Google Scholar
• Gibson, G. Rare and common variants: twenty arguments. Nature Rev. Genet. 13, 135–145 (2011).
  Google Scholar
• Wang, K., Li, M. & Hakonarson, H. Analysing biological pathways in genome-wide association studies. Nature Rev. Genet. 11, 843–854 (2010).
  CAS PubMed Google Scholar
• Schloissnig, S. et al. Genomic variation landscape of the human gut microbiome. Nature 493, 45–50 (2013).
  PubMed Google Scholar
• Robins, W. P., Faruque, S. M. & Mekalanos, J. J. Coupling mutagenesis and parallel deep sequencing to probe essential residues in a genome or gene. Proc. Natl Acad. Sci. USA 110, E848–857 (2013).
  CAS PubMed PubMed Central Google Scholar
• Conrad, T. M., Lewis, N. E. & Palsson, B. O. Microbial laboratory evolution in the era of genome-scale science. Mol. Syst. Biol. 7, 509 (2011).
  PubMed PubMed Central Google Scholar
• Shendure, J. et al. Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309, 1728–1732 (2005).
  CAS PubMed Google Scholar
• Barrick, J. E. & Lenski, R. E. Genome dynamics during experimental evolution. Nature Rev. Genet. 14, 827–839 (2013).
  CAS PubMed Google Scholar
• Xu, X. et al. The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line. Nature Biotech. 29, 735–741 (2011).
  CAS Google Scholar
• Lewis, N. E. et al. Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome. Nature Biotech. 31, 759–765 (2013).
  CAS Google Scholar
• Brinkrolf, K. et al. Chinese hamster genome sequenced from sorted chromosomes. Nature Biotech. 31, 694–695 (2013).
  CAS Google Scholar
• Becker, J. et al. Unraveling the Chinese hamster ovary cell line transcriptome by next-generation sequencing. J. Biotechnol. 156, 227–235 (2011).
  CAS PubMed Google Scholar
• Kildegaard, H. F., Baycin-Hizal, D., Lewis, N. E. & Betenbaugh, M. J. The emerging CHO systems biology era: harnessing the 'omics revolution for biotechnology. Curr. Opin. Biotechnol. 24, 1102–1107 (2013).
  PubMed Google Scholar
• Furey, T. S. ChIP-seq and beyond: new and improved methodologies to detect and characterize protein–DNA interactions. Nature Rev. Genet. 13, 840–852 (2012).
  CAS PubMed Google Scholar
• Meaburn, E. & Schulz, R. Next generation sequencing in epigenetics: insights and challenges. Semin. Cell Dev. Biol. 23, 192–199 (2012).
  CAS PubMed Google Scholar
• Ley, T. J. et al. DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature 456, 66–72 (2008).
  CAS PubMed PubMed Central Google Scholar
• Rios, J., Stein, E., Shendure, J., Hobbs, H. H. & Cohen, J. C. Identification by whole-genome resequencing of gene defect responsible for severe hypercholesterolemia. Hum. Mol. Genet. 19, 4313–4318 (2010).
  CAS PubMed PubMed Central Google Scholar
• Schneeberger, K. et al. SHOREmap: simultaneous mapping and mutation identification by deep sequencing. Nature Methods 6, 550–551 (2009).
  CAS PubMed Google Scholar
• Cooper, G. M. & Shendure, J. Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data. Nature Rev. Genet. 12, 628–640 (2011).
  CAS PubMed Google Scholar
• Gonzalez-Perez, A. et al. Computational approaches to identify functional genetic variants in cancer genomes. Nature Methods 10, 723–729 (2013).
  CAS PubMed PubMed Central Google Scholar
• Reva, B., Antipin, Y. & Sander, C. Predicting the functional impact of protein mutations: application to cancer genomics. Nucleic Acids Res. 39, e118 (2011).
  CAS PubMed PubMed Central Google Scholar
• Lewis, N. E. & Abdel-Haleem, A. M. The evolution of genome-scale models of cancer metabolism. Front. Physiol. 4, 237 (2013).
  PubMed PubMed Central Google Scholar
• Ala-Korpela, M., Kangas, A. J. & Inouye, M. Genome-wide association studies and systems biology: together at last. Trends Genet. 27, 493–498 (2011).
  CAS PubMed Google Scholar
• Moreau, Y. & Tranchevent, L. C. Computational tools for prioritizing candidate genes: boosting disease gene discovery. Nature Rev. Genet. 13, 523–536 (2012).
  CAS PubMed Google Scholar
• Zamft, B. M. et al. Measuring cation dependent DNA polymerase fidelity landscapes by deep sequencing. PLoS ONE 7, e43876 (2012).
  CAS PubMed PubMed Central Google Scholar
• Drukier, A. et al. New dark matter detectors using DNA for nanometer tracking. arXiv 1206.6809 (2012).
• Hubisz, M. J., Lin, M. F., Kellis, M. & Siepel, A. Error and error mitigation in low-coverage genome assemblies. PLoS ONE 6, e17034 (2011).
  CAS PubMed PubMed Central Google Scholar
• Macabeo-Ong, M. et al. Effect of duration of fixation on quantitative reverse transcription polymerase chain reaction analyses. Mod. Pathol. 15, 979–987 (2002).
  PubMed Google Scholar
• Kerick, M. et al. Targeted high throughput sequencing in clinical cancer settings: formaldehyde fixed-paraffin embedded (FFPE) tumor tissues, input amount and tumor heterogeneity. BMC Med. Genom. 4, 68 (2011).
  CAS Google Scholar
• Lin, M. T. et al. Quantifying the relative amount of mouse and human DNA in cancer xenografts using species-specific variation in gene length. Biotechniques 48, 211–218 (2010).
  CAS PubMed PubMed Central Google Scholar
• Innis, M. A., Gelfand, D. H., Sninsky, J. J. & White, T. J. PCR protocols: a guide to methods and applications (Academic press, 1990).
  Google Scholar
• Wojdacz, T. K., Hansen, L. L. & Dobrovic, A. A new approach to primer design for the control of PCR bias in methylation studies. BMC Res. Notes 1, 54 (2008).
  PubMed PubMed Central Google Scholar
• Kanagawa, T. Bias and artifacts in multitemplate polymerase chain reactions (PCR). J. Biosci. Bioeng. 96, 317–323 (2003).
  CAS PubMed Google Scholar
• Nagalakshmi, U. et al. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320, 1344–1349 (2008).
  CAS PubMed PubMed Central Google Scholar
• Pont-Kingdon, G. et al. Design and analytical validation of clinical DNA sequencing assays. Arch. Pathol. Lab Med. 136, 41–46 (2012).
  CAS PubMed Google Scholar
• Gogol-Doring, A. & Chen, W. An overview of the analysis of next generation sequencing data. Methods Mol. Biol. 802, 249–257 (2012).
  CAS PubMed Google Scholar
• Whiteford, N. et al. Swift: primary data analysis for the Illumina Solexa sequencing platform. Bioinformatics 25, 2194–2199 (2009).
  CAS PubMed PubMed Central Google Scholar
• Loman, N. J. et al. Performance comparison of benchtop high-throughput sequencing platforms. Nature Biotech. 30, 434–439 (2012).
  CAS Google Scholar
• Huse, S. M., Huber, J. A., Morrison, H. G., Sogin, M. L. & Welch, D. M. Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol. 8, R143 (2007).
  PubMed PubMed Central Google Scholar