Open

qPCR: The Design of an Open Source,

$2200 Real-Time PCR Instrument

Networking
We integrated ethernet and WiFi
connecIvity, so the device could be accessed
over a laboratory network without requiring
a dedicated computer. We also included USB
connecIvity so a computer could be
connected when no network is available.

Web Interface
We created a user interface using HTML5/
JavaScript so the soQware could be accessed
from Mac, Windows, Linux, and tablet
devices. The machine internally runs a web
server, so no installed soQware is required.

Despite drasIc reducIon in component costs, Open

qPCR produces results comparable to exisIng Real-
Time PCR thermocyclers cosIng over 10x more. At
right is shown a 10:1 diluIon series of a lambda
phage assay (Edelman, D. and Barle*a, J. 2003.
BioTechniques). The amplicaIon proceeded with
96.8% eciency.

Standard Curve

5 point 10:1 Lambda Phage diluIon

0.7

30

Eciency = 96.8%

0.6
Well 1

25

Well 2

0.5

Well 3
Well 4

20

Well 5

0.4

Well 6
Well 7
Well 8

0.3

Ct Value

Heat Block Size

Costs increase with well count, as a larger
heat block in turn requires more pelIer
elements and power. Given our focus on
diagnosIc applicaIons, we chose to restrict
the sample count to 16, while maintaining
fast 5 C/s ramp Imes.

Processor
We uIlized the open-source Beaglebone
Black microprocessor board to control the
machine. This $45 device includes a 1 GHz
ARM processor, 4 GB ash RAM, and runs
embedded Linux.

Tech Specs

A prototype device has been created supporIng

single channel detecIon with 16 samples,
described below. This device is currently being
manufactured and expected to start shipping in
April 2015.

We are currently designing a dual channel version
which will support a SYBR/FAM channel as well as
a HEX/VIC/JOE channel. We expect the dual
channel device to ship in June 2015.

The complete design including soQware and
mechanical/electrical CAD will be released as
open source.

Real-Time PCR is the gold standard for many DNA-

based diagnosIcs, but the high cost of available
instruments have prevented more widespread
adopIon of this relaIvely mature technology. We
set out to use open source technologies to
develop a more aordable instrument that can be
used in a wider range of applicaIons, including
global health, educaIon, and industrial uses by
small and medium sized businesses.

We also aimed to create an open instrument that
can be automated via exposed APIs, and allow
third-party assay developers to integrate their
assay with the Open qPCR soQware, making it
easier for end-users to perform diagnosIcs.

Fluorescence

Results

Design Choices

Introduction

Josh Perfe*o, Steven Van Buskirk, Norberto Landicho, Kister Jimenez

Chai Biotechnologies Inc.

15

Well 9
Well 10
0.2

Well 11

10

Well 12

y = -3.4286x + 4.4511
R = 0.9929

Well 13
0.1

Well 14
Well 15

Well 16

0
0

10

15

20

25

30

35

40
0

We designed a solid-state opIcal

architecture using LEDs, photodiodes,
and dichroic lters. EliminaIng moving
mechanical parts greatly increases
reliability, which is important in the
remote areas we expect Open qPCR to
be deployed. LED light is modulated at
1 kHz to remove electrical, thermal,
and opIcal noise.

Shown at leQ is our single-channel
design. We are extending this to a
dual-channel design by placing dichroic
lters directly on top of the
photodiode die, and placing 2 dies per
well.

-6

-5

-4

-3

-2

-1

Log ConcentraIon (ug/mL)

Cycle Number

Software

Optical Architecture

-0.1

Open qPCRs soQware supports the

deniIon of arbitrary protocols,
presence/absence detecIon, relaIve
quanIcaIon, and high resoluIon melt.
Support for absolute quanIcaIon is
planned in the future.
Acknowledgements
The device exposes an API via a REST
List your informaIon ointerface
n these lw
ines.
ith a llows the Open qPCR to
be easily integrated into lab automaIon
plaiorms. The soQware also exports
data in the standardized RDML format.

All soQware is released as open source
under the Apache 2 license.

For more informaIon, visit www.chaibio.com/openqpcr