Institute of Molecular Design Sequencing Center

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Institute of Molecular Design Sequencing Center

• University of Houston
• College of Natural Sciences and Mathematics

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Website Draft

• Institute for Molecular Design Sequencing Center

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Results

• Results for control (phiX) for (Installation run)
  run_1

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Results

• Results for control (phiX) for run_2 run_8

04/16/2008 Run 8 / Lane 1 Since the control
undergoes a different dilution protocol than the
samples, it is likely that the low number of
clusters generated (2000) is due to the loading
of 0.5 pM instead of the necessary 2 pM for the
control.
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Run Troubleshooting Report
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Run 2 Lane 1 (Control - phiX) / Lanes 2 8
(Small RNA)
Might be due to the fact that the 3 hundred tiles
are in three rows of 1 hundred
Proportion of nucleotide calls for the tiles
within lanes
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Typical behavior of the solexa quality of the
nucleotide calls per cycle (5 first tiles)
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Typical behavior of the proportion of nucleotide
calls per cycle (5 first tiles)
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Remaining Reads
Poly-As
Poly-As And Linkers
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Remaining Reads
Possible linkers found in reads (only part of
linkers appeared in reads)
Poly-As found in reads
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Quality Control

• Using statistical properties of reads to catch
  problems in sequencing experiments
• Statistical properties
• of reads per lane/tile
• of A,T,G,C, and unknowns per lane/tile/cycle
• Quality of A,T,G,C per lane/tile/cycle
• Overrepresented poly-nucleotides

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Mapping

• Mapping finding possible locations on a
  reference sequence where a read could have come
  from
• Features
• Mapping read to multiple locations
• Exhaustively checking up-to all possible 2
  changes (insertion, deletion, substitution) of
  read
• Fast (mapping of 1.8 bp ref-seq with 80 coverage
  up to 1-change can be done in less than an hour)
• MGAS_summary.xls

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• We can map short subsequences on the
  reference genome(s) and identify all types of
  genomic variation
• SNPs,
• short insertions and deletions,
• long deletions and duplications

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What We Can Do....

• DNA Sequencing
• Any sample prepared using Illumina Genomic DNA
  adapters
• Includes sequencing of samples prepared according
  to Illumina ChIP-Seq protocols

• Small RNA Sequencing
• Any cDNA sample prepared using Illumina Small RNA
  adapters
• mRNA Sequencing
• Any cDNA sample prepared using Illumina
  DGE-Nlalll or DGE-Dpnll adapters

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What Is Needed From Users...

• 5 µL prepared sample
• Can submit 10 nM stock if sample is quantified by
  a dsDNA specific assay
• Can submit concentrated cDNA for the center to
  quantify using the PicoGreen Assay prior to
  Cluster Generation
• First time Users should plan for 2-3 lanes per
  sample, as optimal loading concentration is quite
  User dependent

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Time Frame of Run?

• Cluster Generation (1 day)
• 1 PhiX Control Lane
• 7 User Sample Lanes
• All 7 User lanes must be filled for the run to
  occur, but they need not be from the same User
  nor need they be the same sample type
• Sequencing (3.5 days)
• Analysis Pipeline (2 days)

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Cost of a Run
The additional Hyb Manifold is necessary in order
to utilize the PhiX Control for QC monitoring.
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Cost of a Run Personnel Depreciation
The additional Hyb Manifold is necessary in order
to utilize the PhiX Control for QC monitoring.

• Personnel costs are based on an annual salary of
  65,000/yr with full benefits, and the center
  performing an estimated 50 runs/year
• - Depreciation costs are based on the annual
  expense from the State mandated 10 year schedule
  divided by 50 runs/year

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Cost of a Run Potential Cost Recovery
The additional Hyb Manifold is necessary in order
to utilize the PhiX Control for QC monitoring.
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Pricing - Sequencing
Price per Run
Price per Lane
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Costs Future Service Under Consideration
Pricing Determination
- Pricing is calculated as the (supply cost x
number of samples) personnel cost - Personnel
costs are based on the assumption of 65K/year
full benefits