Price list

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Oct 1, 2013 (4 years and 9 months ago)

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Sequencing

Prices for Genomic DNA
,

Exomes
, and Amplicons



5500x
l Sequencer

ACHRI Genomics and Bioinformatics Facility

September
, 2012



DNA Library Prices



Making a DNA library

is the first step in sample preparation

(see Fig. 1 on next
page)
.

The most common library is a fragment library
which is
used for most genomic

sequencing

as well as

exome captures with Life Technology’s TargetSeq kit

(
Agilent SureSelect exome captures

in
clude their own

library prep
)
.
Mate
-
pair libraries are only required when looking for large structural variants.
P
rices for RNA
-
based samples are listed on our separate
RNA
-
Seq price list
.
On
e library preparation is required for every
sample
. Barcode tags are included at no extra charge, but groups of four or more
barcoded
samples are
required for pooling.



Item

Cost

5500 DNA fragment library
, New England Biolabs

$120 ea.

5500
DNA fragment
library
,

Library

Builde
r System
.
Auto
mated protocol for

9

or
more libraries

$180

ea.

Life Technologies
TargetSeq h
uman exome library

(45 Mb).

Does not include
fragment library preparation.
Should

be ordered in groups
of four because four
barcoded
libraries

can be

pooled together for each exome capture (Fig. 1).

$
1,000

per capture

($250 each when in
groups of four
)

Agilent SureSelect Human All Exon V4
(51 Mb) or V4 +UTR (71 Mb)
exome.
Includes fragment library preparation and exome capture.

$530 e
a.

DNA mate
-
pair

(long
-
insert) library, 1 kb or 3 kb insert
s
, Life Technologies

$56
0

ea.


Sequencing Bead Preparation

(
emPCR)

Prices



DNA fragments
are attached to sequencing beads through
an emulsion PCR (emPCR) process. Each bead represents a single
“read” when deposited on a sequencing
slide.

Sufficient sequencing beads for the number of lanes of sequencing required must be ordered. Projects
requiring 3
-
4

or
6
-
8 lanes of sequencing are the most cost
-
effective for E80 and E120 scale
s, respectively
.

It
em

Cost

Sequencing beads (E20 scale emPCR) for one lane

$630

ea.

Sequencing beads (E80 scale emPCR) for up to four lanes

$
800

ea.

Sequencing beads (E120 scale emPCR) for up to eight lanes

$
1250 ea.


5500
xl

Sequencin
g Prices



5500
xl

sequencers have two
flowchips
, each with
six independent lanes.

Price

per lane includes sequencing reagents

and

secondary data analysis (mapping to a reference genome)
.


Forward

50 bp reads

Forward

75 bp reads

Paired
-
End

50+35 bp reads

Paired
-
End

75+35

bp
reads

Cost/lane, with no barcodes

$4
25

$5
20

$74
5

$8
20

Cost/lane, with barcodes

$4
40

$530

$76
0

$8
30

Sequence (unmapped)
*

~ 6 Gb

~ 9 Gb

~ 10 Gb

~
14

Gb

Mate
-
paired sequencing

(60+60 bp) is $800

per lane.

Exact Call

Chemistry (ECC) is
also
available as an

option if greater accuracy is required. Inquire for pricing.

*
Data mapping and the removal of PCR duplicates will reduce the amount of final sequence produced.


To calculate project costs

1.

Determine library costs from the
DNA Library Price

table.

2.

Estimate how much sequencing will be required, i.e. depth of coverage x genome size.

3.

Use the amount of sequence listed in the
Sequencing Prices

table to estimate how many lanes are
required. The cost of sequencing is the cost per lane X number of lanes.

4.

Us
e the number of sequencing lanes required to find the emPCR scale in the
Sequencing Bead
Preparation Prices

table which provides sufficient sequencing beads

5.

The project cost will be the cost of libraries plus the cost of preparing sequencing beads plus the

cost
of the sequencing lanes
.

There is no extra charge for mapping the data to a reference genome.


Figure 1.

Whole genome and exome sequencing workflows.


Example Project Costs


Library
Prep

Bead Prep

Sequencing

Total Cost

Cost per
Sample

8

samples
, 75 bp sequencing
on

1 lane

(~ 1.1
Gb each, 9 Gb total)

8
x

$120

1
x

$630

1
x

$530

$2,120

$265.00

16 samples
,
75 bp sequencing

on

3 lanes

(~

1.7
Gb each, 27 Gb total)

16
x

$180

1
x

$800

3
x

$530

$5,270

$329.38

4
Agilent SureSelect V4 Exomes
,

75+35 bp
PE sequencing on
2 lanes

(4 x ~ 7

Gb ea.)

4
x

$530

1
x

$800

2

x

$830

$
4,580

$1,
145
.
0
0

4
TargetSeq Exomes
,
75+35 bp PE sequencing
on
3 lanes

(4 x ~10 Gb ea.)

4
x
$430

1
x

$800

3
x

$830

$5,010

$1,252.50

1
sample
,
75

bp sequ
encing on
1 lane

(~ 9

Gb)

1
x

$120

1
x

$630

1
x

$
520

$1,
270

$1,27
0.00

1

sample
,
75+35

bp
PE
sequ
encing on
1 lane

(~ 14

Gb)

1
x

$120

1
x

$630

1
x

$
820

$1,
570

$1,57
0.00

1 w
hole human/mouse genome
, 75+35 bp on
3
lanes
, ~ 14X coverage (~ 42 Gb)
*

1
x

$120

1
x

$800

3
x

$820

$3,380

$3,380.00

1 whole

human/mouse genome
, 75+35 bp on
6

lanes,

~ 3
0
X coverage (~
96

GB)

*

1
x

$120

1
x

$1,250

6

x

$820

$6,290

$6,290
.00

*

-


Addition
al sequencing
may be required for some projects. Also, d
etection of large structural variants
will
require

preparation of one or more

mate
-
pair libraries
and
its

sequencing
.


For more information and assistance with project planning, please contact either



Richard T. Pon,
Facility Director
, HM 231, 403
-
220
-
4225,
rtpon@ucalgary.ca



Paul Gordon, Bioinformatics Support Specialist, HM 228, 403
-
210
-
6909,
gordonp@ucalgary.ca



Shelly Wegener, Laboratory Manager, HSC B104A, 403
-
220
-
4503,
dn
aseq@ucalgary.ca


www.research4kids.ucalgary.ca/genomics