International standards for genomes, transcriptomes, and metagenomes

Journal of Biomolecular Techniques

Volumn 28, Issue 1, 2017, Pages 8-18

  Mason, Christopher E ^a,b,c   Afshinnekoo, Ebrahim ^a,b,d   Tighe, Scott ^e   Wu, Shixiu ^f   Levy, Shawn ^g  

^a Department of Physiology and Biophysics ^*  (United States)

^b HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine   (United States)

^c FEIL FAMILY BRAIN AND MIND RESEARCH INSTITUTE   (United States)

^d NEW YORK MEDICAL COLLEGE   (United States)

^e UNIVERSITY OF VERMONT COLLEGE OF MEDICINE   (United States)

^f ZHEJIANG CANCER HOSPITAL   (China)

^g HUDSONALPHA INSTITUTE FOR BIOTECHNOLOGY   (United States)

Author keywords

Epigenomics; Epitranscriptomics; Genomics; Metagenomics; Transcriptomics

Indexed keywords

COMPLEMENTARY DNA; DNA; RNA; TRANSCRIPTOME;

ACCURACY; AUTOMATION; BACTERIUM; EPIGENETICS; GENOMICS; HUMAN; METAGENOME; METAGENOMICS; MICROBIOME; MOLECULAR LIBRARY; NEXT GENERATION SEQUENCING; NONHUMAN; NUCLEIC ACID ANALYSIS; POLYMERASE CHAIN REACTION; REVIEW; SEQUENCE ANALYSIS; STANDARD; TRANSCRIPTOMICS; WHOLE GENOME SEQUENCING; ANIMAL; DNA SEQUENCE; GENE EXPRESSION PROFILING; GENE LIBRARY; GENETICS; HIGH THROUGHPUT SEQUENCING; ISOLATION AND PURIFICATION; SOFTWARE; STANDARDS;

ANIMALS; DNA; GENE EXPRESSION PROFILING; GENE LIBRARY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; METAGENOME; REFERENCE STANDARDS; SEQUENCE ANALYSIS, DNA; SOFTWARE; TRANSCRIPTOME;

EID: 85018313637     PISSN: 15240215     EISSN: 19434731     Source Type: Journal    
DOI: 10.7171/jbt.17-2801-006     Document Type: Review

References (87)

1. Mason CE, Porter SG, Smith TM. Characterizing multi-omic data in systems biology. Adv Exp Med Biol 2014;799:15–38.
2. Saletore Y, Meyer K, Korlach J, Vilfan ID, Jaffrey S, Mason CE. The birth of the epitranscriptome: deciphering the function of RNA modifications. Genome Biol 2012;13:175.
3. Metzker ML. Sequencing technologies—the next generation. Nat Rev Genet 2010;11:31–46.
4. Goodwin S, McPherson JD, McCombie WR. Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet 2016;17:333–351.
5. Marioni JC, Mason CE, Mane SM, Stephens M, Gilad Y. RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 2008;18:1509–1517.
6. Brazma A, Hingamp P, Quackenbush J, et al. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet 2001;29:365–371.
7. Munro SA, Lund SP, Pine PS, et al. Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures. Nat Commun 2014;5:5125.
8. Zook JM, Catoe D, McDaniel J, et al. Extensive sequencing of seven human genomes to characterize benchmark reference materials. Sci Data 2016;3:160025.
9. Chen CY. DNA polymerases drive DNA sequencing-by-synthesis technologies: both past and present. Front Microbiol 2014;5:305.
10. MAQC Consortium. The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol 2006;24: 1151–1161.
11. SEQC/MAQC-III Consortium. A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium. Nat Biotechnol 2014;32: 903–914.
12. Xu J, Su Z, Hong H, et al. Cross-platform ultradeep transcriptomic profiling of human reference RNA samples by RNA-Seq. Sci Data 2014;1:140020.
13. Li S, Tighe SW, Nicolet CM, et al. Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study. Nat Biotechnol 2014;32:915–925.
14. Li S, Łabaj PP, Zumbo P, et al. Detecting and correcting systematic variation in large-scale RNA sequencing data. Nat Biotechnol 2014;32:888–895.
15. Gargis AS, Kalman L, Bick DP, et al. Good laboratory practice for clinical next-generation sequencing informatics pipelines. Nat Biotechnol 2015;33:689–693.
16. GEUVADIS Consortium. Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories. Nat Biotechnol 2013;31:1015–1022.
17. Risso D, Ngai J, Speed TP, Dudoit S. Normalization of RNA-seq data using factor analysis of control genes or samples. Nat Biotechnol 2014;32:896–902.
18. Benjamini Y, Speed TP. Summarizing and correcting the GC content bias in high-throughput sequencing. Nucleic Acids Res 2012;40:e72.
19. Tilgner H, Grubert F, Sharon D, Snyder MP. Defining a personal, allele-specific, and single-molecule long-read transcriptome. Proc Natl Acad Sci USA 2014;111:9869–9874.
20. Chaisson MJ, Huddleston J, Dennis MY, et al. Resolving the complexity of the human genome using single-molecule sequencing. Nature 2015;517:608–611.
21. Afshinnekoo E, Meydan C, Chowdhury S, et al. Geospatial resolution of human and bacterial diversity with city-scale metagenomics. Cell Syst 2015;1:72–87.
22. Yooseph S, Andrews-Pfannkoch C, Tenney A, et al. A metagenomic framework for the study of airborne microbial communities. PLoS One 2013;8:e81862.
23. Sinha R, Abnet CC, White O, Knight R, Huttenhower C. The microbiome quality control project: baseline study design and future directions. Genome Biol 2015;16:276.
24. Li S, Garrett-Bakelman F, Perl AE, et al. Dynamic evolution of clonal epialleles revealed by methclone. Genome Biol 2014;15: 472.
25. Li S, Garrett-Bakelman FE, Chung SS, et al. Distinct evolution and dynamics of epigenetic and genetic heterogeneity in acute myeloid leukemia. Nat Med 2016;22:792–799.
26. Meyer KD, Saletore Y, Zumbo P, Elemento O, Mason CE, Jaffrey SJ. Comprehensive analysis of mRNA methylation reveals pervasive adenosine methylation in 39 UTRs. Cell 2012; 149:1635–1646.
27. Saletore Y, Chen-Kiang S, Mason CE. Novel RNA regulatory mechanisms revealed in the epitranscriptome. RNA Biol 2013; 10;342–346.
28. Li S, Mason CE. The pivotal regulatory landscape of RNA modifications. Annu Rev Genomics Hum Genet 2014;15:127–150.
29. Garalde DR, Snell EA, Jachimowicz D, et al. Highly parallel direct RNA sequencing on an array of nanopores. bioRxiv beta Aug. 12, 2016. Available at: biorxiv.org/content/early/2016/08/ 12/068809.
30. Miyamoto M, Motooka D, Gotoh K, et al. Performance comparison of second- and third-generation sequencers using a bacterial genome with two chromosomes. BMC Genomics 2014;15: 699.
31. McIntyre AB, Rizzardi L, Yu AM, et al. Nanopore sequencing in microgravity. bioRxiv beta Dec. 10, 2015. Available at: http://biorxiv.org/content/early/2015/12/10/032342.
32. Castro-Wallace SL, Chiu CY, John KK, et al. Nanopore DNA sequencing and genome assembly on the International Space Station. bioRxiv beta Sept. 27, 2016. Available at: http://biorxiv.org/content/early/2016/09/27/077651.
33. Lever MA, Torti A, Eickenbusch P, Michaud AB, Šantl-Temkiv T, Jørgensen BB. A modular method for the extraction of DNA and RNA, and the separation of DNA pools from diverse environmental sample types. Front Microbiol 2015;6: 476.
34. Fisher Scientific. Thermo Scientific™ ART™ Non-Filtered Extended-Length Wide-Bore Genomic pipette Tips. Available at: https://www.fishersci.com/shop/products/thermo-scientific-art-non-filtered-extended-length-wide-bore-genomic-pipette-tips-3/p-3206875.
35. Pan X, Durrett RE, Zhu H, et al. Two methods for full-length RNA sequencing for low quantities of cells and single cells. Proc Natl Acad Sci USA 2013;110:594–599.
36. Oxford Nanopore Technologies. VolTRAX™: rapid,programma-ble, portable, disposable sample processor. https://nanoporetech. com/publications/2016/05/26/voltrax-rapid-programmable-portable-disposable-sample-processor.
37. Zumbo P, Mason CE. Methods for RNA isolation, characterization, and sequencing. In: Genome Analysis: Current Procedures and Applications. Poole, UK: Caister Academic, 2014:Chapt. 2.
38. Adey A, Shendure J. Ultra-low-input, tagmentation-based whole-genome bisulfite sequencing. Genome Res 2012;22:1139–1143.
39. Tatsumi K, Nishimura O, Itomi K, Tanegashima C, Kuraku S. Optimization and cost-saving in tagmentation-based mate-pair library preparation and sequencing. Biotechniques 2015;58:253–257.
40. Dunham JP, Friesen ML. A cost-effective method for high-throughput construction of Illumina sequencing libraries. Cold Spring Harb Protoc 2013;2013:820–834.
41. Cantara WA, Crain PF, Rozenski J, et al. The RNA Modification Database, RNAMDB: 2011 update. Nucleic Acids Res 2011;39:D195–D201.
42. Ayub M, Hardwick SW, Luisi BF, Bayley H. Nanopore-based 42. Ayub M, Hardwick SW, Luisi BF, Bayley H. Nanopore-based identification of individual nucleotides for direct RNA sequencing. Nano Lett 2013;13:6144–6150.
43. Ozsolak F, Platt AR, Jones DR, et al. Direct RNA sequencing. Nature 2009;461:814–818.
44. Meyer KD, Saletore Y, Zumbo P, Elemento O, Mason CE, Jaffrey SJ. Comprehensive analysis of mRNA methylation reveals pervasive adenosine methylation in 39 UTRs. Cell 2012; 149:1635–1646.
45. Dominissini D, Moshitch-Moshkovitz S, Schwartz S, et al. Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq. Nature 2012;485:201–206.
46. Linder B, Grozhik AV, Olarerin-George AO, Meydan C, Mason CE, Jaffrey SR. Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome. Nat Methods 2015;12:767–772.
47. Landan G, Cohen NM, Mukamel Z, et al. Epigenetic polymorphism and the stochastic formation of differentially methylated regions in normal and cancerous tissues. Nat Genet 2012;44:1207–1214.
48. Vilfan ID, Tsai YC, Clark TA, et al. Analysis of RNA base modification and structural rearrangement by single-molecule real-time detection of reverse transcription. J Nanobiotechnology 2013;11:8.
49. Dominissini D. Genomics and proteomics. Roadmap to the epitranscriptome. Science 2014;346:1192.
50. Cancer Genome Atlas Research Network. Identification of a CpG island methylator phenotype that defines a distinct subgroup of glioma. Cancer Cell 2010;17:510–522.
51. Landau DA, Tausch E, Taylor-Weiner AN, et al. Mutations driving CLL and their evolution in progression and relapse. Nature 2015;526:525–530.
52. Pan H, Jiang Y, Boi M, et al. Epigenomic evolution in diffuse large B-cell lymphomas. Nat Commun 2016;6:6921.
53. Vembar SS, Seetin M, Lambert C, et al. Complete telomere-to-telomere de novo assembly of the Plasmodium falciparum genome through long-read (.11 kb), single molecule, real-time sequencing. DNA Res 2016;23:339–351.
54. Kurylo CM, Alexander N, Dass RA, et al. Genome sequence and analysis of Escherichia coli MRE600, a colicinogenic, nonmotile strain that lacks RNase I and the type I methyltransferase, EcoKI. Genome Biol Evol 2016;8:742–752.
55. Feng Z, Fang G, Korlach J, et al. Detecting DNA modifications from SMRT sequencing data by modeling sequence context dependence of polymerase kinetic. PLOS Comput Biol 2013;9: e1002935.
56. Genest PA, Baugh L, Taipale A, et al. Defining the sequence requirements for the positioning of base J in DNA using SMRT sequencing. Nucleic Acids Res 2015;43:2102–2115.
57. Simpson JT, Workman R, Zuzarte PC, David M, Jonathan L, Timp WD. Detecting DNA methylation using the Oxford Nanopore Technologies MinION sequencer. bioRxiv beta April 4, 2016. Available at: http://biorxiv.org/content/early/2016/04/04/047142.
58. Rand AC, Jain M, Eizenga J, et al. Cytosine variant calling with high-throughput Nanopore sequencing. bioRxiv beta April 4, 2016. Available at: http://biorxiv.org/content/early/2016/04/04/047134.
59. Stranges PB, Palla M, Kalachikov S, et al. Design and characterization of a nanopore-coupled polymerase for single-molecule DNA sequencing by synthesis on an electrode array. Proc Natl Acad Sci USA 2016;113:E6749–E6756.
60. Madoui MA, Engelen S, Cruaud C, et al. Genome assembly using Nanopore-guided long and error-free DNA reads. BMC Genomics 2015;16:327.
61. Kaper F, Swamy S, Klotzle B, et al. Whole-genome haplotyping by dilution, amplification, and sequencing. Proc Natl Acad Sci USA 2013;110:5552–5557.
62. Kuleshov V, Xie D, Chen R, et al. Whole-genome haplotyping using long reads and statistical methods. Nat Biotechnol 2014; 32:261–266.
63. Amini S, Pushkarev D, Christiansen L, et al. Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing. Nat Genet 2014;46:1343–1349.
64. Peters BA, Kermani BG, Sparks AB, et al. Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells. Nature 2012;487:190–195.
65. Peters BA, Liu J, Drmanac R.. Co-barcoded sequence reads from long DNA fragments: a cost-effective solution for “perfect genome” sequencing. Front Genet 2015;5:466.
66. Lieberman-Aiden E, van Berkum NL, Williams L, et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 2009;326: 289–293.
67. Putnam NH, O’Connell BL, Stites JC, et al. Chromosome-scale shotgun assembly using an in vitro method for long-range linkage. Genome Res 2016;26;342–350.
68. Burton JN, Liachko I, Dunham MJ, Shendure J. Species-level deconvolution of metagenome assemblies with Hi-C-based contact probability maps. G3 (Bethesda) 2014;4: 1339–1346.
69. Clarke J, Wu HC, Jayasinghe L, Patel A, Reid S, Bayley H. Continuous base identification for single-molecule nanopore DNA sequencing. Nat Nanotechnol 2009;4:265–270.
70. Arguel MJ, LeBrigand K, Paquet A, et al. A cost effective 59 selective single cell transcriptome profiling approach with improved UMI design. Nucleic Acids Res 2016 [Epub ahead of print]. doi:10.1093/nar/gkw1242
71. Macosko EZ, Basu A, Satija R, et al. Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets. Cell 2015;161:1202–1214.
72. Klein AM, Mazutis L, Akartuna I, et al. Droplet barcoding for single-cell transcriptomics applied to embryonic stem cells. Cell 2015;161:1187–1201.
73. Coombe L, Warren RL, Jackman SD, et al. Assembly of the complete Sitka spruce chloroplast genome using 10X Geno-mics’ GemCode sequencing data. PLoS One 2016;11: e0163059.
74. Macaulay IC, Haerty W, Kumar P, et al. G&T-seq: parallel sequencing of single-cell genomes and transcriptomes. Nat Methods 2015;12:519–522.
75. Hou Y, Guo H, Cao C, et al. Single-cell triple omics sequencing reveals genetic, epigenetic, and transcriptomic heterogeneity in hepatocellular carcinomas. Cell Res 2016;26: 304–319.
76. Chin CS, Sorenson J, Harris JB, et al. The origin of the Haitian cholera outbreak strain. N Engl J Med 2011;364:33–42.
77. Rasko DA, Webster DR, Sahl JW, et al. Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany. N Engl J Med 2011;365:709–717.
78. Bashir A, Klammer AA, Robins WP, et al. A hybrid approach for the automated finishing of bacterial genomes. Nat Biotechnol 2012;30:701–707.
79. Lan Y, Rosen G, Hershberg R. Marker genes that are less conserved in their sequences are useful for predicting genome-wide similarity levels between closely related prokaryotic strains. Microbiome 2016;4:18.
80. Mao DP, Zhou Q, Chen CY, Quan ZX. Coverage evaluation of universal bacterial primers using the metagenomic datasets. BMC Microbiol 2012;12:66.
81. Erlich Y. A vision for ubiquitous sequencing. Genome Res 2015; 25:1411–1416.
82. Zaaijer S; Columbia University Ubiquitous Genomics 2015 class, Erlich Y. Using mobile sequencers in an academic classroom. eLife 2016;5:e14258.
83. MetaSUB International Consortium. The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report. Microbiome 2016;4:24.
84. Salter SJ, Cox MJ, Turek EM, et al. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol 2014;12:87.
85. Smith CC, Wang Q, Chin CS, et al. Validation of ITD mutations in FLT3 as a therapeutic target in human acute myeloid leukaemia. Nature 2012;485:260–263.
86. Li S, Garrett-Bakelman FE, Akalin A, et al. An optimized algorithm for detecting and annotating regional differential methylation. BMC Bioinformatics 2013;14 (Suppl 5):S10.
87. Rosenfeld J, Mason CE, Smith T. Limitations of the human genome reference. PLoS One 2012;7:e40294.