FAQ #1: What are all of the Next-generation DNA Sequencing Technologies?

George Church (updated 6-Sep-2011, 14-Sep-2014)
    Available technologies
  1. Danaher-Dover-Polonator
  2. SbP,L,H  Fluor MA
  3. Roche-454
  4. SbPLumCT
  5. AB-SOLiD
  6. SbLFluor MA
  7. Illumina
  8. SbPFluor CA
  9. Complete Genomics Inc.
  10. SbLFluor CA
  11. Ion Torrent
  12. SbPH+ CT
  13. Pacific Bio
  14. SbPFluor CA
  15. ReadCoor - FISSEQ
  16. SbLFluor MA
  17. Intelligent Bio
  18. SbPFluor MA
    R&D phase technologies: Nanopores
  19. Nabsys
  20. SbH-PoreIon RI
  21. OxfordNanopore
  22. PoreIon UK
  23. NobleGen
  24. SbH-PoreFluor MA
  25. Genia
  26. PoreIon CA
  27. IBM-Roche
  28. PoreIon NY
  29. Electronic Biosciences
  30. SbP?Ion CA
    Other R&D phase technologies
  31. GnuBio
  32. SbL?Fluor MA
  33. Genapsys
  34. SbPH+ CA
  35. Halcyon
  36. EM Atom CA
  37. BionanoGenomics(matrix)
  38. SbHFluor PA
  39. Visigen/Starlight
  40. SbPFRET TX
  41. LightSpeed
  42. SbL,PFluor CA
  43. Genizon BioSci
  44. SbHFluor QC
  45. LaserGen
  46. SbPFluor TX
  47. ZS Genetics
  48. EMAtom NH
  49. GE Global
  50. SbPFluor NY
  51. Stratos Genomics
  52. SbX-Pore? WA
  53. Reveo
  54. STMSTM NY
  55. Base4innovation
  56. ?SERS UK
  57. Mobious Genomics
  58. SbP SPR UK
  59. Nanophotonics Biosci
  60. PoreIon CA
  61. CrackerBio
  62. SbPFluor
  63. Population Genetic Technologies
  64. SbPFluor UK
  65. Genovoxx
  66. SbPFluor Germany
    SNPs, mapping, defunct or not pursuing Sequencing?
  67. Network Biosystems
  68. ?? MA
  69. Helicos
  70. SbPFluor MA
  71. Li-cor
  72. SbPFluor NE
  73. SeiraD
  74. ?? NM
  75. AQI Sciences
  76. SbPFRET AZ
  77. USGenomics(PathoGenetix)
  78. SbHFluor MA
  79. Affymetrix
  80. SbHFluor CA
  81. Sequenom
  82. SNPMS CA
  83. Callida Genomics
  84. SbH? CA
  85. DNA Electronics
  86. SbHH+UK
    Not yet classified
  87. 10X Technologies
  88. Avantome
  89. Caerus Molecular Diagnostics
  90. Eagle Research
  91. Electron Optica
  92. Eve Biomedical
  93. Genvida
  94. Hitachi
  95. Hyseq
  96. iNanoBio
  97. Intel
  98. Lynx
  99. Manteia
  100. Moleculo
  101. NorthShore Biosciences
  102. NXP
  103. OpGen
  104. PicoSeq
  105. Pyrosequencing-Qiagen
  106. Quantapore
  107. Quantum Biosystems
  108. QuantumDx
  109. Solexa
  110. Two Pore Guys
  111. Xagros
  112. Nanofluidics
  113. Amersham-MegaBACE
  114. Agencourt
  115. SbP,H,L,X = Sequencing by Polymerase, Hybridization, Ligase, eXpansion.
    SERS = Surface Enhanced Raman Spectroscopy.
    FRET = Fluorescent Resonance Energy Transfer.
    STM = Scanning Tunneling Microscopy.
    SPR = Surface Plasmon Resonance.
    MS = Mass Spectrometry

    FAQ #2: Next Gen Sequencing Facilities Locations and Platforms?

    FAQ #3: What is the cost of human genome sequencing?

    Pushkarev et al 2009
    Year Estimated cost Technology   Ref. Machine runs     Authors Coverage
    2001 $300,000,000   Sanger (ABI)  1             ?          251    4
    2001 $100,000,000   Sanger (ABI)  2       100,000          274    5
    2007  $10,000,000   Sanger (ABI)  3       100,000           31    7
    2008   $2,000,000   Roche(454)    4           234           27    7
    2008   $1,000,000   Illumina      5            98           48   33
    2008     $500,000   Illumina      6            35           77   36
    2008     $250,000   Illumina      7            40          196   30
    2009      $48,000   Helicos   This work         4            3   28
    
    Table S1: Comparison of estimated cost and effort in published human genome sequences. The
    cost column refers to estimated consumables and the number of authors is an estimate of labor.
    
    Drmanac et al. 2010 Average Reported Estimated Reported sequencing cost per Year Reference Technology Sample Coverage consumables 40-fold depth (fold) cost coverage 2007 S4 Sanger(ABI) JCV 7 $10,000,000 $57,000,000 2008 S5 Roche(454) JDW 7 $1,000,000 $5,700,000 2008 S6 Illumina NA18507 30 $250,000 $330,000 2009 S7 Helicos SRQ 28 $48,000 $69,000 2009 this work this work NA07022 87 $8,005 $3,700 2009 this work this work NA19240 63 $3,451 $2,200 2009 this work this work NA20431 45 $1,726 $1,500
    Table S5: Historical human genome sequencing costs that have improved after these genomes (including this work) were sequenced. JDW costs may include more than consumable costs. Our costs were calculated from the amount and purchase prices of reagents (including labware and sequencing substrates) used in generating all raw reads resulting in the reported number of mapped reads.
    Nicholas Wade NY Times estimate for the 2008 JDW genome was $5.7 million and for the 2011 Gordon Moore (GEM) genome was $2 million.

    Most of the above focus on consumeable costs. The all-in costs (including labor, R&D, computing), can be estimated from the price of full human genomes in a service mode. As of Aug 2011 that is $4000 for bulk orders of 50 or more genomes from CompleteGenomics and Illumina

    As of Sep-2014 the cost (at CGI & Illumina) is estimated at $1000, bt there is not publicly announced service at that (bulk) price. Single, clinical-grade WGS can be had for $5000.