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Jean Fan | ISMB 2018 1
Integrated
genetic and
transcriptional
analysis at the
single-cell level
Jean Fan
NCI F99/K00 Fello...
Jean Fan | ISMB 2018 2
Introduction
Heterogeneity exists within individual patients
(intra-tumoral heterogeneity)
Jean Fan | ISMB 2018 3
Valent P, Bonnet D, D...
Intra-tumoral heterogeneity presents challenges to
current treatment standards
4
Subclonal proportions change over time!
I...
Intra-tumoral heterogeneity presents challenges to
current treatment standards
5
Subclonal frequencies change over time!
I...
Single cell measurements and analysis is needed to
understand varying levels of heterogeneity
6
Scenario 1
(co-occurring)
...
Single cell measurements and analysis is needed to
understand varying levels of heterogeneity
7
Single cell measurements
r...
Single cell measurements and analysis is needed to
understand varying levels of heterogeneity
8Jean Fan | ISMB 2018
Transc...
Jean Fan | ISMB 2018 9
Connecting Genetic and Transcriptional
Heterogeneity at the Single-Cell Level
How to simultaneously assess transcriptional and
genetic heterogeneity at the single cell level?
10Jean Fan | ISMB 2018
1....
How to simultaneously assess transcriptional and
genetic heterogeneity at the single cell level?
11Jean Fan | ISMB 2018
1....
Idea: If we can infer (some) genetic information from
scRNA-seq, then we can directly connect genetic and
transcriptional ...
High mono-allelic detection and sparse coverage
limits ability to confidently infer point mutations in
scRNA-seq data
Jean...
Joint analysis on multiple SNPs such as within CNVs
enables genotypic classification of cells
Jean Fan | ISMB 2018 14
HoneyBADGER identifies and assesses the status of
CNVs in single cells using scRNA-seq data
HMM-integrated Bayesian
Approa...
HoneyBADGER identifies and assesses the status of
CNVs in single cells using scRNA-seq data
Jean Fan | ISMB 2018 16
1-2) Single cells are clustered and pooled based on
smoothed minor allele fractions
Jean Fan | ISMB 2018 17
3) HMM model identifies regions affected by CNVs
and LOHs
Jean Fan | ISMB 2018 18
4-5) Bayesian model assesses posterior probability of
each CNV in each cell
Jean Fan | ISMB 2018 19
6-7) Cells are split into branches and algorithm is
recursively applied to each branch
Jean Fan | ISMB 2018 20
HoneyBADGER separates tumor from normal cells,
consistent with bulk tumor purity estimates
Sample MM16 MM16-R
Purity 81-95...
Jean Fan | ISMB 2018 22
HoneyBADGER separates tumor from normal cells,
consistent with bulk tumor purity estimates
Jean Fan | ISMB 2018 23
HoneyBADGER separates tumor from normal cells,
consistent with bulk tumor purity estimates
Confirm CNVs by WES and FISH
Jean Fan | ISMB 2018 24
HoneyBADGER separates MM from normal cells
based on identified CNVs using 3’ scRNA-seq data
Jean Fan | ISMB 2018 25
HoneyBADGER separates MM from normal cells
based on identified CNVs using 3’ scRNA-seq data
Jean Fan | ISMB 2018 26
HoneyBADGER separates MM from normal cells
based on identified CNVs using 3’ scRNA-seq data
Jean Fan | ISMB 2018 27
HoneyBADGER separates MM from normal cells
based on identified CNVs using 3’ scRNA-seq data
Jean Fan | ISMB 2018 28
HoneyBADGER applied to progressive MM provides
insights into subclonal expansion
Jean Fan | ISMB 2018 29
MM34 (bone marrow...
HoneyBADGER applied to progressive MM provides
insights into subclonal expansion
Jean Fan | ISMB 2018 30
Bulk WES
scRNA-se...
HoneyBADGER identifies CNVs in MM34A
Jean Fan | ISMB 2018 31
HoneyBADGER identifies CNVs in MM34A
Jean Fan | ISMB 2018 32
HoneyBADGER identifies CNVs in MM34A
Jean Fan | ISMB 2018 33
scRNA-seq data used by HoneyBADGER directly lends
itself to transcriptomic comparison of subclones
Jean Fan | ISMB 2018 34
scRNA-seq data used by HoneyBADGER directly lends
itself to transcriptomic comparison of subclones
GO:0007049 cell cycle
J...
scRNA-seq data used by HoneyBADGER directly lends
itself to transcriptomic comparison of subclones
Jean Fan | ISMB 2018 36...
Alternatively characterize transcriptional
heterogeneity and assess correspondence with
genetic heterogeneity
Jean Fan | I...
Alternatively characterize transcriptional
heterogeneity and assess correspondence with
genetic heterogeneity
Jean Fan | I...
Alternatively characterize transcriptional
heterogeneity and assess correspondence with
genetic heterogeneity
Jean Fan | I...
Jean Fan | ISMB 2018 40
Software and Tutorials Available at jef.works/HoneyBADGER
Summary
◦ Point mutation detection from scRNA-seq is difficult due
to mono-allelic detection
◦ HoneyBADGER uses allele inf...
Thanks and happy to take questions!
Zhuang Lab
Xiaowei Zhuang
Jeff Moffitt
Stephen Eichorn
Guiping Wang
Kharchenko Lab
Pet...
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Integrated genetic and transcriptional analysis at the single-cell level Slide 1 Integrated genetic and transcriptional analysis at the single-cell level Slide 2 Integrated genetic and transcriptional analysis at the single-cell level Slide 3 Integrated genetic and transcriptional analysis at the single-cell level Slide 4 Integrated genetic and transcriptional analysis at the single-cell level Slide 5 Integrated genetic and transcriptional analysis at the single-cell level Slide 6 Integrated genetic and transcriptional analysis at the single-cell level Slide 7 Integrated genetic and transcriptional analysis at the single-cell level Slide 8 Integrated genetic and transcriptional analysis at the single-cell level Slide 9 Integrated genetic and transcriptional analysis at the single-cell level Slide 10 Integrated genetic and transcriptional analysis at the single-cell level Slide 11 Integrated genetic and transcriptional analysis at the single-cell level Slide 12 Integrated genetic and transcriptional analysis at the single-cell level Slide 13 Integrated genetic and transcriptional analysis at the single-cell level Slide 14 Integrated genetic and transcriptional analysis at the single-cell level Slide 15 Integrated genetic and transcriptional analysis at the single-cell level Slide 16 Integrated genetic and transcriptional analysis at the single-cell level Slide 17 Integrated genetic and transcriptional analysis at the single-cell level Slide 18 Integrated genetic and transcriptional analysis at the single-cell level Slide 19 Integrated genetic and transcriptional analysis at the single-cell level Slide 20 Integrated genetic and transcriptional analysis at the single-cell level Slide 21 Integrated genetic and transcriptional analysis at the single-cell level Slide 22 Integrated genetic and transcriptional analysis at the single-cell level Slide 23 Integrated genetic and transcriptional analysis at the single-cell level Slide 24 Integrated genetic and transcriptional analysis at the single-cell level Slide 25 Integrated genetic and transcriptional analysis at the single-cell level Slide 26 Integrated genetic and transcriptional analysis at the single-cell level Slide 27 Integrated genetic and transcriptional analysis at the single-cell level Slide 28 Integrated genetic and transcriptional analysis at the single-cell level Slide 29 Integrated genetic and transcriptional analysis at the single-cell level Slide 30 Integrated genetic and transcriptional analysis at the single-cell level Slide 31 Integrated genetic and transcriptional analysis at the single-cell level Slide 32 Integrated genetic and transcriptional analysis at the single-cell level Slide 33 Integrated genetic and transcriptional analysis at the single-cell level Slide 34 Integrated genetic and transcriptional analysis at the single-cell level Slide 35 Integrated genetic and transcriptional analysis at the single-cell level Slide 36 Integrated genetic and transcriptional analysis at the single-cell level Slide 37 Integrated genetic and transcriptional analysis at the single-cell level Slide 38 Integrated genetic and transcriptional analysis at the single-cell level Slide 39 Integrated genetic and transcriptional analysis at the single-cell level Slide 40 Integrated genetic and transcriptional analysis at the single-cell level Slide 41 Integrated genetic and transcriptional analysis at the single-cell level Slide 42
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Integrated genetic and transcriptional analysis at the single-cell level. Jean Fan. NCI F99/K00 Fellow. Zhuang Lab. Harvard University.

SCANGEN - ISMB 2018

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Integrated genetic and transcriptional analysis at the single-cell level

  1. 1. Jean Fan | ISMB 2018 1 Integrated genetic and transcriptional analysis at the single-cell level Jean Fan NCI F99/K00 Fellow Zhuang Lab Harvard University
  2. 2. Jean Fan | ISMB 2018 2 Introduction
  3. 3. Heterogeneity exists within individual patients (intra-tumoral heterogeneity) Jean Fan | ISMB 2018 3 Valent P, Bonnet D, De maria R, et al. Cancer stem cell definitions and terminology: the devil is in the details. Nat Rev Cancer. 2012;12(11):767-75.
  4. 4. Intra-tumoral heterogeneity presents challenges to current treatment standards 4 Subclonal proportions change over time! Indicative of an active evolutionary process! Jean Fan | ISMB 2018
  5. 5. Intra-tumoral heterogeneity presents challenges to current treatment standards 5 Subclonal frequencies change over time! Indicative of an active evolutionary process! Jean Fan | ISMB 2018
  6. 6. Single cell measurements and analysis is needed to understand varying levels of heterogeneity 6 Scenario 1 (co-occurring) Scenario 2 (mutually exclusive) or Jean Fan | ISMB 2018
  7. 7. Single cell measurements and analysis is needed to understand varying levels of heterogeneity 7 Single cell measurements reveal mutual exclusivity of subclonal mutations! cells Jean Fan | ISMB 2018 Scenario 1 (co-occurring) Scenario 2 (mutually exclusive) or
  8. 8. Single cell measurements and analysis is needed to understand varying levels of heterogeneity 8Jean Fan | ISMB 2018 Transcriptional Differences?
  9. 9. Jean Fan | ISMB 2018 9 Connecting Genetic and Transcriptional Heterogeneity at the Single-Cell Level
  10. 10. How to simultaneously assess transcriptional and genetic heterogeneity at the single cell level? 10Jean Fan | ISMB 2018 1. Technology Development Approach (Targeted RT-QPCR) 2. Computational Methods Approach (HoneyBADGER)
  11. 11. How to simultaneously assess transcriptional and genetic heterogeneity at the single cell level? 11Jean Fan | ISMB 2018 1. Technology Development Approach (Targeted RT-QPCR) 2. Computational Methods Approach (HoneyBADGER) bit.ly/GR_WangFan
  12. 12. Idea: If we can infer (some) genetic information from scRNA-seq, then we can directly connect genetic and transcriptional heterogeneity in single cells 12Jean Fan | ISMB 2018 scRNA-seq genetics
  13. 13. High mono-allelic detection and sparse coverage limits ability to confidently infer point mutations in scRNA-seq data Jean Fan | ISMB 2018 13
  14. 14. Joint analysis on multiple SNPs such as within CNVs enables genotypic classification of cells Jean Fan | ISMB 2018 14
  15. 15. HoneyBADGER identifies and assesses the status of CNVs in single cells using scRNA-seq data HMM-integrated Bayesian Approach to CNV Detection from single cell RNA-seq (HoneyBADGER) Jean Fan | ISMB 2018 15 Soo Lee Peter Park Woong-Yang ParkHae-Ock Lee jef.works/HoneyBADGER Just accepted! August 2018
  16. 16. HoneyBADGER identifies and assesses the status of CNVs in single cells using scRNA-seq data Jean Fan | ISMB 2018 16
  17. 17. 1-2) Single cells are clustered and pooled based on smoothed minor allele fractions Jean Fan | ISMB 2018 17
  18. 18. 3) HMM model identifies regions affected by CNVs and LOHs Jean Fan | ISMB 2018 18
  19. 19. 4-5) Bayesian model assesses posterior probability of each CNV in each cell Jean Fan | ISMB 2018 19
  20. 20. 6-7) Cells are split into branches and algorithm is recursively applied to each branch Jean Fan | ISMB 2018 20
  21. 21. HoneyBADGER separates tumor from normal cells, consistent with bulk tumor purity estimates Sample MM16 MM16-R Purity 81-95% 4.5-20% Ncells 23 21 Jean Fan | ISMB 2018 21
  22. 22. Jean Fan | ISMB 2018 22 HoneyBADGER separates tumor from normal cells, consistent with bulk tumor purity estimates
  23. 23. Jean Fan | ISMB 2018 23 HoneyBADGER separates tumor from normal cells, consistent with bulk tumor purity estimates
  24. 24. Confirm CNVs by WES and FISH Jean Fan | ISMB 2018 24
  25. 25. HoneyBADGER separates MM from normal cells based on identified CNVs using 3’ scRNA-seq data Jean Fan | ISMB 2018 25
  26. 26. HoneyBADGER separates MM from normal cells based on identified CNVs using 3’ scRNA-seq data Jean Fan | ISMB 2018 26
  27. 27. HoneyBADGER separates MM from normal cells based on identified CNVs using 3’ scRNA-seq data Jean Fan | ISMB 2018 27
  28. 28. HoneyBADGER separates MM from normal cells based on identified CNVs using 3’ scRNA-seq data Jean Fan | ISMB 2018 28
  29. 29. HoneyBADGER applied to progressive MM provides insights into subclonal expansion Jean Fan | ISMB 2018 29 MM34 (bone marrow) MM34A (ascites) Bulk WES
  30. 30. HoneyBADGER applied to progressive MM provides insights into subclonal expansion Jean Fan | ISMB 2018 30 Bulk WES scRNA-seqMM34 (bone marrow) MM34A (ascites)
  31. 31. HoneyBADGER identifies CNVs in MM34A Jean Fan | ISMB 2018 31
  32. 32. HoneyBADGER identifies CNVs in MM34A Jean Fan | ISMB 2018 32
  33. 33. HoneyBADGER identifies CNVs in MM34A Jean Fan | ISMB 2018 33
  34. 34. scRNA-seq data used by HoneyBADGER directly lends itself to transcriptomic comparison of subclones Jean Fan | ISMB 2018 34
  35. 35. scRNA-seq data used by HoneyBADGER directly lends itself to transcriptomic comparison of subclones GO:0007049 cell cycle Jean Fan | ISMB 2018 35
  36. 36. scRNA-seq data used by HoneyBADGER directly lends itself to transcriptomic comparison of subclones Jean Fan | ISMB 2018 36 GO:0002376 immune system processes
  37. 37. Alternatively characterize transcriptional heterogeneity and assess correspondence with genetic heterogeneity Jean Fan | ISMB 2018 37 bit.ly/NATURE_Fan
  38. 38. Alternatively characterize transcriptional heterogeneity and assess correspondence with genetic heterogeneity Jean Fan | ISMB 2018 38
  39. 39. Alternatively characterize transcriptional heterogeneity and assess correspondence with genetic heterogeneity Jean Fan | ISMB 2018 39 HoneyBADGER infers CNV from single-cell RNA-seq data to simultaneously assess gene expression and CNV status from same single cell
  40. 40. Jean Fan | ISMB 2018 40 Software and Tutorials Available at jef.works/HoneyBADGER
  41. 41. Summary ◦ Point mutation detection from scRNA-seq is difficult due to mono-allelic detection ◦ HoneyBADGER uses allele information across many SNPs to identify and infer the probability of CNVs and LOHs ◦ Inferring CNVs and LOHs from scRNA-seq allows direct comparison of genetic heterogeneity with transcriptional heterogeneity ◦ Integrative approaches at the single-cell level are needed to connect transcriptional and genetic heterogeneity in the context of a single patient / common microenvironment Jean Fan | ISMB 2018 41
  42. 42. Thanks and happy to take questions! Zhuang Lab Xiaowei Zhuang Jeff Moffitt Stephen Eichorn Guiping Wang Kharchenko Lab Peter Kharchenko Joseph Herman Nikolas Barkas Ruslan Soldatov Wu Lab Catherine Wu Lili Wang Ken Livak Shuqiang Li Jean Fan | ISMB 2018 42 Zhang Lab Kun Zhang Blue Lake Brandon Sos Song Chen Chun Lab Jerold Chun Gwen Kaeser Many others CZ Zhang Angela Brooks Alexander Misharin Rohan Verman Find me online! Web: http://JEF.works Github: JEFworks Twitter: @JEFworks jeanfan@fas.harvard.edu Park Lab Peter Park Soo Lee Semin Lee SGI Woong-yang Park Hae-Ock Lee Walsh Lab Chris Walsh Xiaochang Zhang Dulac Lab Catherine Dulac Eric Vaughn Mentors Collaborators Funding
  • alabarga

    Oct. 30, 2018

Integrated genetic and transcriptional analysis at the single-cell level. Jean Fan. NCI F99/K00 Fellow. Zhuang Lab. Harvard University. SCANGEN - ISMB 2018

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