Post on 09-May-2015
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Early Detection ofHighly Pathogenic
Viral InfectionsIgnacio Sanchez Caballero
Wednesday, May 1, 13
Infection
Wednesday, May 1, 13
Viremia
Infection
Wednesday, May 1, 13
Viremia
Infection
Transcriptional changes
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Lassa
Marburg
17
1 2 3 4 5 6 7 8 9 10 11 120
4 6 3 6 3
15 3 3 3 3 3
Days post-exposure
Number of Samples
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Lassa Marburg
Samples taken at the same time have similar gene expression values
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Combined
Samples taken at the same time have similar gene expression values
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30
High expression
Low expression
Days post-infection
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No change
Increase in expression
Decrease in expression
30
High expression
Low expression
Days post-infection
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No change
Increase in expression
Decrease in expression
Probably random Probably significant30
High expression
Low expression
Days post-infection
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No change
Increase in expression
Decrease in expression
Probably random Probably significant30
High expression
Low expression
Days post-infection
Significant high magnitude change
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No change
Increase in expression
Decrease in expression
High expression
Low expression
Days post-infectionProbably random Probably significant
Significant high magnitude change
30
Wednesday, May 1, 13
No change
Increase in expression
Decrease in expression
High expression
Low expression
Days post-infectionProbably random Probably significant
Not significant high magnitude change
30
Wednesday, May 1, 13
No change
Increase in expression
Decrease in expression
High expression
Low expression
Days post-infectionProbably random Probably significant
Not significant high magnitude change
30
Wednesday, May 1, 13
No change
Increase in expression
Decrease in expression
High expression
Low expression
Days post-infectionProbably random Probably significant
Significant low magnitude change
30
Wednesday, May 1, 13
No change
Increase in expression
Decrease in expression
High expression
Low expression
Days post-infectionProbably random Probably significant
Significant low magnitude change
30
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A subset of probes is differentially expressed 3 days post-exposure
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A subset of probes is differentially expressed 3 days post-exposure
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Wednesday, May 1, 13
Wednesday, May 1, 13
Wednesday, May 1, 13
Lassa
Marburg
4
1 2 3 4 5 6 7 8 9 10 11 120
2
1
Days post-exposure
Number of Samples
1
Test data set
Wednesday, May 1, 13
Lassa
Marburg
4
1 2 3 4 5 6 7 8 9 10 11 120
2
1
Days post-exposure
Number of Samples
1 ✖
Test data set
Wednesday, May 1, 13
Aim 1: Early detection of highly pathogenic viral infections
Compare the early transcriptional response of Lassa and Marburg✓
Wednesday, May 1, 13
Aim 1: Early detection of highly pathogenic viral infections
Compare the early transcriptional response of Lassa and Marburg✓
Identify a set of candidate biomarker genes✓
Wednesday, May 1, 13
Validate the current set of biomarkers using qPCR
Aim 1: Early detection of highly pathogenic viral infections
Compare the early transcriptional response of Lassa and Marburg✓
Identify a set of candidate biomarker genes✓
Wednesday, May 1, 13
Validate the current set of biomarkers using qPCR
Compare the differences in using sequencing to measure gene expression
Aim 1: Early detection of highly pathogenic viral infections
Compare the early transcriptional response of Lassa and Marburg✓
Identify a set of candidate biomarker genes✓
Wednesday, May 1, 13
Validate the current set of biomarkers using qPCR
Compare the differences in using sequencing to measure gene expression
Incorporate additional viruses to the analysis
Aim 1: Early detection of highly pathogenic viral infections
Compare the early transcriptional response of Lassa and Marburg✓
Identify a set of candidate biomarker genes✓
Wednesday, May 1, 13
Aim 2: Visualization of complex biological data
Develop a software tool to easily generate interactive plots✓
Wednesday, May 1, 13
Aim 2: Visualization of complex biological data
Develop a software tool to easily generate interactive plots✓
Make generating a dynamic plot as easy as a static one
Wednesday, May 1, 13
Aim 2: Visualization of complex biological data
Develop a software tool to easily generate interactive plots✓
Make generating a dynamic plot as easy as a static one
Aim 3: Experimental training
Develop core skills in experimental virology
Wednesday, May 1, 13
Aim 2: Visualization of complex biological data
Develop a software tool to easily generate interactive plots✓
Make generating a dynamic plot as easy as a static one
Aim 3: Experimental training
Develop core skills in experimental virology
Design and carry out experiments to determine viral and host gene function
Wednesday, May 1, 13