© Forensic Science Service Ltd. 2010. All rights reserved. New DNA developments better, faster and cheaper Martin Bill, R&D Forensic Science Service Ltd.

© Forensic Science Service Ltd. 2010. All rights reserved.

New DNA developmentsbetter, faster and cheaper

Martin Bill, R&DForensic Science Service Ltd

SPSA / SIPR conference14th & 15th September


Agenda

1. Better – new multiplexes2. Faster – Custody suite DNA testing3. Cheaper – DNA INSIGHT


Better – new multiplexes

Assessing the performance of the new miniSTR chemistries


ENFSI RequirementRobust multiplexes, inc. Mini STRs• Fifteen STR loci

– Ten SGM Plus® loci, FGA, TH01, VWA, D3S1358, D8S1179, D18S51, D21S11, D2S1338, D16S539, D19S433

– Additional 5 loci D1S1656, D2S441, D10S1248, D12S391, D22S1045

– Amelogenin

• ENFSI DNAWG December 2009– Expansion of ESS to include additional 5

loci.


Strategic multiplexes

• Two different approaches– Make SGM Plus ® Markers “Standard”– Make SGM Plus ® Markers “Mini”

Resp

onse

Size /bp


Strategic multiplexing

• Choice of PowerPlex® multiplexes• ESX-16 & ESX-17 – Standard size

“SGMPlus®” loci• ESI-16 & ESI-17 – “Mini” SGMPlus® loci• Optimised for 500pg DNA and 30

cycles

• Applied Biosystems NGM• BioType Mentype® ESSplex


ESX

D2

S1

33

8

D1

6S5

39

D1

S1

65

6

D1

0S1

24

8

D1

9S4

33

D2

S4

41

D1

2S3

91

D2

2S1

04

5

vW

A

D8

S1

17

9

FGA

SE3

3

Am

el

D3

S1

35

8

D1

8S5

1

D2

1S1

1

TH

01


ESI

Am

el

D3

S1

35

8

D1

9S4

33

D2

S1

33

8

D2

2S1

04

5

D1

6S5

39

D1

8S5

1

D1

S1

65

6

D1

0S1

24

8

D2

S4

41

D8

S1

17

9

FGA

SE3

3

vW

A

D2

1S1

1

D1

2S3

91

TH

01


Evaluation of Performance

SensitivityInhibitorsDegraded samplesConcordance


Sensitivity


Sensitivity


Sensitivity

DNA Template (pg)

1 locus

10 loci


Working Range


Inhibitors

Humic AcidIndigoHaematin


Humic Acid

Humic Acid

0

20

40

60

80

100

120

0 10ng/ul 20ng/ul 120ng/ul 240ng/ul

% p

rofil

e

SGM+

Humic Acid

0

20

40

60

80

100

120


% p

rofi

le SGM+

MiniFiler

Humic Acid

0

20

40

60

80

100

120


% p

rofi

le SGM+

MiniFiler

ESX-16

Humic Acid

0

20

40

60

80

100

120


% p

rofi

le

SGM+

MiniFiler

ESX 16

ESI-16


Indigo

Indigo

0

20

40

60

80

100

120

0uM 75uM 150uM 300uM 600uM 1200uM

% p

rofi

le

SGM+

Indigo

0

20

40

60

80

100

120

0uM 75uM 150uM 300uM 600uM 1200uM

% p

rofi

le

SGM+

MiniFiler

Indigo

0

20

40

60

80

100

120

0uM 75uM 150uM 300uM 600uM 1200uM

% p

rofi

le SGM+

MiniFiler

ESX-16

Indigo

0

20

40

60

80

100

120

0uM 75uM 150uM 300uM 600uM 1200uM

% p

rofi

le

SGM+

MiniFiler

ESX -16

ESI-16


Haematin

Haematin

0

20

40

60

80

100

120

0 30uM 60uM 120uM 240uM 360uM 480uM 600uM

% p

rofi

le

SGM+

Haematin

0

20

40

60

80

100

120

0 30uM 60uM 120uM 240uM 360uM 480uM 600uM

% p

rofi

le

SGM+

MiniFiler

Haematin

0

20

40

60

80

100

120

0 30uM 60uM 120uM 240uM 360uM 480uM 600uM

% p

rofil

e

SGM+

MiniFiler

ESX-16

ESI-16


Degraded DNA

ESX vs ESI vs SGMPlus®


Analysis of degraded DNA

• SGMPlus® with degraded DNA


Degraded DNA

• ESX-16 with degraded DNA


Degraded DNA • ESI-16 with degraded DNA


Degraded DNA

Sample ESX ESI SGM+

16 loci

11 loci

16 loci

11 loci 11 loci

Degraded 56% 38% 63% 86% 33%

FSS UV1 38% 27% 34% 50% 0%

FSS UV2 16% 9% 28% 41% ND

ENZ 10’ 65% 64% 65% 86% 59%

ENZ 15’ 42% 36% 58% 77% 36%

UV sem ND ND 100% 100% 76%


Degradation

Amp of SGMPlus® Loci with degraded DNA

0

20

40

60

80

100

120

Deg FSS UV1 FSS UV2 Enz 10 Enz 15 Control

Sample

% p

rofi

le SGM+

ESX-16

ESI-16


Concordance

NISTFSS


NIST Concordance with Identifiler®

1461 samples • ESX-16

– 4 loci discordant – 99.98% concordance

• ESI-16– 3 loci discordant – 99.98% concordant


FSS Concordance with SGMPlus®

Number of loci

compared

Number of concordant

loci

Concordance (%)

ESX 16 3500 3498 99.94

ESI 16 3500 3499 99.97

Non-concordant alleles currently being sequenced

~1 in 200 profiles non-concordant


Summary

• Promega ES multiplexes– Sensitive– Robust to inhibitors– ESI “SGMPlus” loci very robust with

degraded DNA– High level of concordance with NIST

samples


Next steps:

• For new multiplexes meeting the ENFSI requirement:– Gain acceptance to NDNAD – Concordance

• (ESX vs ESI vs SGMPlus® vs NGM vs ESSplex)

– Frequency databases– Check for independence (product rule)


Development of a forensically integrated DNA analysis system.

Faster - Custody suite DNA testing


Introduction

• What is the aim?• What have we accomplished• What will we achieve in the future


Suspect Arrest

DNA sample taken

Submission process

Submission process

DNA lab

Profile interp

DNA loaded to NDNAD

Current Process

Suspect Released

6-7 h

Match


Requirement

• Environment– deployment

• Operator– Skill – Training

• Outcome– DNA profile loaded

to the NDNAD– Match reported in

Real Time

• Robust• Simple User

Interface• Automated

– Chemistry– Analysis– Database search

• 2h turn round• Evidential quality

Eliminate submission by processing at POC


What we’ve accomplished

4h process


How does it work?

• Chambers • Channels • Pumps • Valves• Vents• ECB


PCR Chamber

Direct to

µCE

Elute

Waste

V

VV

V

V

V

V V

V

VV

Wash

Magnet

ArchiveDenature


Micro Capillary Electrophoresis

• 140-mm glass chip

• PVP/HEC polymer 200 V/cm

• Detection by LIF λex 491 nm


Profile from fully integrated run


Ladders

TH01


What we will achieve in the future

• Single cartridge– Plastic CE

• Reduce time to <2h Sample to match

• Multiple samples– Maintain sample integrity

• Casework samples

• Integrated lysis vial


Review

• Simple set up • Self contained cartridge • Minimised opportunity for

contamination; batch control• Full 16-plex DNA profiles with no

manual intervention• Identified requirement for further

work (in progress)• Software/database solutions

essential for benefit realisation


Improved DNA interpretation

Cheaper – FSS DNA INSIGHT & DNAboost


24

26

16

20

How does DNA interpretation work and why is it suboptimal?

DNA is visualised as a signal referred to as an EPG.

The role of the scientist is to translate the signal into a simple set of paired numbers that define the DNA profile. These numbers are then compared between profiles in a case (suspect to crimestain) or through the National DNA Database.

Issue 1: Complex data are impossible to convert into a simple set of paired numbers. ?

Issue 2: A high proportion of reporting officer interpretation work is performed manually.


Where does DNAboost fit into all this?

DNAboost, in part, addresses Issue 1: “Complex data are impossible to convert into a simple set of paired numbers” by a simple improvement to the database design.

15 17 15 18 17 18 15 15 17 17 18 18

Issue 2: “A high proportion of reporting officer interpretation work is performed manually” remains largely unimproved and has opportunities for improvements in efficiency, response time, effectiveness and quality.

DNAboost was always intended to be a development milestone towards improved coding, searching and matching.

DNAboost improves the search and match rate for DNA intelligence and demonstrates that improved encoding of data is a key way of improving performance.


How could DNA interpretation be further improved?The current approach always discards useful information that may be required for case assessment, intelligence or troubleshooting.

DBNational DNA Database or interp process

18, 16, 11

Lost information.

Next GenerationInterpretation

The answer is to develop a new interpretation approach that always retains and uses all the useful information. This requires ‘whole EPG interpretation’.

Improved capacity& cost effectiveness

Needs manual, paper review later in the process.

Use all the information in a new continuous model

3 pieces of informatio

n.

~80,000 pieces of

information.

Manual ‘best guess’


Design and deployment of the new interpretation model

Analyst Reporting Officer

Interprets batches of DNA data to confirm validity.

– Software-based.– Partially automated.– Rule-based &

objective

Unprocessed digital data Valid digital

data

Valid paper data Expertopinion

Interprets cases of DNA data to form opinion.

– Paper-based.– (Very) manual.– Guideline-based and

artisan(?)


Analyst Reporting Officer

– Software to interpret DNA data

Settings server

FSS DNA

INSIGHT

FSS DNA

INSIGHT

APB

Data server

– Server to regularise and disseminate DNA data

– Server to control settings and administration

– Science, publication, validation, process, training and support

FSS DNA INSIGHT design


Increased capacity


Good examples of forensic science getting better, faster and cheaper…

… in reality they all add value in a number of areas


Better, faster, cheaper

• The new chemistries may increase timeliness through higher first pass success rates with a reduced requirement for specialist methods like LCN

• Custody suite testing may reduce total forensic supply chain costs.

• DNA INSIGHT may increase success rates through the improved interpretation models.


Thanks for listening

Martin Bill, R&DForensic Science Service Ltd

SPSA / SIPR conference14th & 15th September

© Forensic Science Service Ltd. 2010. All rights reserved. New DNA developments better, faster and cheaper Martin Bill, R&D Forensic Science Service Ltd.

Documents

rd forensic science

degraded dna slide

sensitivity slide

indigo slide

range slide

degradation slide

future slide

samples concordance