comet: rapid and reliable hcv subtype...

http://comet.retrovirology.lu

COMET:Rapid and reliable HCV subtype predictor

(Context-based Modeling for Expeditious Typing)

Daniel StruckCRP-SANTÉ

Laboratory of Retrovirology([email protected])

Presented at the 10th EU Meeting on HIV & Hepatitis, 28 - 30 March 2012, Barcelona


Background

HCV genotype/subtype strong predictor of sustained virological response (SVR) to ribavirin/interferon and new HCV inhibitor therapies

Only one online HCV genotyping/subtyping tool based on phylogenetic analysis:

Oxford HCV Automated Subtyping Tool (Version 2.0)

COMET: Context-based modeling for classification of HIV sequences introduced in 2010 adapted to HCV subtyping



Comparison Oxford tool vs Comet:

Paired NS3-NS5B sequences (CRP dataset):

=> concordance in 182/183 cases (mismatch due to recombinant)

Subtyping full-length NS5B versus the conserved region (PR3-PR5, euHCVdb dataset)

=> 98.1% (1933/1970) match

Dataset 1 : NS3, NS5B sequences

Gene Origin n Oxford / COMET subtype

agreement

Discordance details

NS3 LANLCRP

762 99.70% 0.3% recombination events

NS5B euHCVdbCRP

2309 94.00% 2.1% COMET & Oxford WRONG

1.14% unassigned by COMET

6.6% unassigned by Oxford



COMET HCV subtyping improvements

Improvements:

Adapt recombination detection threshold to HCV

Introduce bootstrap values to assess quality of prediction



Dataset 2 : euHCVdb

The European HCV Database

min. length: 250

max length: 8500

exclude identical sequences

only seq. with provisional subtype

10223 sequences

average length: 726

79 different subtypes

dataset subtype

# %

1b 2814 27.53

1a 2609 25.52

3a 1225 11.98

4a 595 5.82

5a 361 3.53

6a 343 3.36

2a 203 1.99

2b 174 1.7

3b 149 1.46

4d 131 1.28

other (<1%) 1619 15.84Presented at the 10th EU Meeting on HIV & Hepatitis, 28 - 30 March 2012, Barcelona


Result genotype (n= 10223)

(*) genotype verified with neighbor joining tree using the LANL HCV reference sequences 2012

COMET <> euHCVdb provisional genotype

bootstrap value #

same genotype 10193 (99.7%)

different genotype unassigned 15 (0.1%)

wrong genotype for COMET (*) 100.00% 1

80% - <100% 3

<80% 9 13 (0.1%)

Oxford <> euHCVdb provisional genotype

same genotype 9403 (92%)

different genotype unassigned Check the Bootscan 4

Check the report 483

Sequence Error 272

Unassigned 61 820 (8%)



Result subtype (n=10223)

COMET <> euHCVdb provisional subtype

bootstrap (average)

# COMET training (median)

same subtype 99.58% 9613 94.03% 1-5 (2)

different subtype

unassigned / 15 0.10%

“wrong” subtype

78.43% 595 5.82% 0-1 (0)

Oxford <> euHCVdb provisional subtype

bootstrap (average)

#

same subtype 99.94% 8094 79.17%

different subtype

unassigned / 820 8.02%

only genotype 98.17% 419 4.10%

“wrong” subtype

96.19% 890 8.71%



COMET unassigned results (15)

euHCVdb COMET Recco Oxford support

1a unassigned_1;1b,1a 1b-1a Genotype 1 subtype a 95

1b unassigned_1;1b,2a 2a-1b Genotype 1 subtype b 100

2c unassigned_1;2a,2c 2a-2c Genotype 2 subtype c 100

2e unassigned_1;2q,2a 2a-2q Genotype 2 100

2k unassigned_1;1b,2a,2k 2k-1b Check the Bootscan

2k unassigned_1;1b,2a,2k 2k-1b Check the Bootscan

2e unassigned_1;2q,2a 2q-2j Genotype 2 100

3a unassigned_1;6e,6h,3a 3a-6h Check the Bootscan

2k unassigned_1;2q,2k 2k Genotype 2 subtype k 100

2k unassigned_1;2q,2k 2k Genotype 2 subtype k 100

3b unassigned_1;6e,3b,3a 3b Genotype 3 subtype b 100

3b unassigned_1;6e,3b,3a 3b Genotype 3 subtype b 100

3b unassigned_1;3b,3a 3b Genotype 3 subtype b 100

6d unassigned_1;6e,6d 6d Genotype 6 subtype d 100

6h unassigned_1;6h,6i,1a,1c,6e 6h Genotype 6 subtype h 100



Benchmark

Server setup: 2x quad core (Q1 2009, 2.93 GHz)

Analysis of the 10223 HCV sequences took 68 seconds

=> 150 sequences / second

Analysis of 500.000 sequences would take about 55 minutes



Summary

Reliable prediction of HCV subtype

Limitations due to the availability of near full length reference sequencesImprove COMET training for specific genes?

Generally it is best to compare the results of different approaches to define the subtype of a sequence (COMET: alternative to phylogenetic based Oxford tool)

High performance and scalability suitable for deep sequencing (454) analysis



Acknowledgements

CRP-Santé, Laboratory of Retrovirology

Jean-Claude Schmit

Carole Devaux

Danielle Perez Bercoff

Sandrine Ortiou



COMET website

Poster: O_15




COMET website results


comet: rapid and reliable hcv subtype...

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