Upgrade to Pro — share decks privately, control downloads, hide ads and more …

SACNAS 2016

SACNAS 2016

Using data science to study human brain genomic measurements

Leonardo Collado-Torres

October 15, 2016
Tweet

More Decks by Leonardo Collado-Torres

Other Decks in Science

Transcript

  1. Using Data Science to Study
    Human Brain Genomic Measurements
    Leonardo Collado-Torres
    @fellgernon

    View Slide

  2. Mo#va#ng problem: iden#fy and validate
    regions of the genome that change expression
    during brain development

    View Slide

  3. Research theme
    - annota#on-agnos#c
    - reproducible analyses
    - easily accessible data
    - sta#s#cal tools for the genomics community

    View Slide

  4. RNA-seq
    reads
    Genome
    (DNA)
    RNA transcripts
    (many possible
    variants)
    Measuring gene expression: RNA-seq
    Adapted from @jtleek

    View Slide

  5. Genome
    (DNA)
    Mapped reads
    Adapted from @jtleek
    Common analysis pipelines:
    • Feature coun#ng (gene or exon level)
    • Transcript assembly

    View Slide

  6. Challenges in counting
    hBp://www-huber.embl.de/users/anders/HTSeq/doc/count.html

    View Slide

  7. Annotation variation
    Frazee et al, Biostatistics, 2014

    View Slide

  8. Project size is increasing






































    2009
    (11)
    2010
    (46)
    2011
    (121)
    2012
    (235)
    2013
    (408)
    2014
    (625)
    2015
    (548)
    2016
    (18)
    7
    8
    9
    10
    11
    12
    Project size in base−pairs over the years
    log10 base−pairs per project
    hBps://jhubiosta#s#cs.shinyapps.io/recount/

    View Slide

  9. Genome
    (DNA)
    Mapped reads
    Adapted from @jtleek

    View Slide

  10. DER finder approach
    •  Find con#guous base pairs with
    Differen#al Expression signal à DE
    Regions or DERs
    •  Find nearest annotated feature

    View Slide

  11. coverage
    vector
    2 6 0 11 6
    Genome
    (DNA)
    Read coverage
    Adapted from @jtleek

    View Slide

  12. View Slide

  13. View Slide

  14. Identifying brain development DERs
    Fetal Infant
    Child Teen
    Adult 50+
    6 / group, N = 36
    Discovery data
    Null:
    Alt:
    Models
    Initial results
    Jaffe et al, Nat. Neuroscience, 2015
    50,650 DERs replicated
    63,135 DERs
    Final results

    View Slide

  15. Jaffe et al, Nat. Neuroscience, 2015

    View Slide

  16. Widespread differential expression of novel
    transcriptional activity
    Jaffe et al, Nat. Neuroscience, 2015

    View Slide

  17. Age-associated DERs lack regional specificity
    in the human brain
    BrainSpan data
    Jaffe et al, Nat. Neuroscience, 2015

    View Slide

  18. Propor#on of Cells
    Expression changes across development may
    represent a changing neuronal phenotype
    Jaffe et al, Nat. Neuroscience, 2015
    Estimation method: Houseman et al, BMC Bioinformatics, 2012

    View Slide

  19. Chromatin immunoprecipitation seq.
    http://assets.illumina.com/content/dam/illumina-marketing/images/techniques/large/web-graphic-chipseq-workflow-large.jpg

    View Slide

  20. Common ChIP-seq analysis pipeline
    Sample 1
    Sample 2
    ...
    Sample N
    1
    call peaks
    call peaks
    call peaks
    U
    11
    U
    12
    U
    1N
    Number of
    unique peaks
    Merge unique
    peaks
    Total peaks:
    U
    merged
    ≤ U
    1
    + U
    2
    Determine differentially
    bound peaks
    between groups 1 & 2
    Total tests: U
    merged
    1
    Total: U
    1
    Sample 1
    Sample 2
    ...
    Sample N
    2
    call peaks
    call peaks
    call peaks
    U
    21
    U
    22
    U
    2N
    Number of
    unique peaks
    2
    Total: U
    2
    Group 1
    Group 2
    (A)
    (A)
    (B)
    (C)

    View Slide

  21. View Slide

  22. Brain ChIP-seq data
    EpiMap project

    View Slide

  23. Variation mostly explained


























































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































    ● ●


























































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































































    0 20 40 60 80 100
    Percentage variance explained
    Brain
    region
    C
    ell type
    Age
    at death
    H
    em
    isphere
    PM
    I
    pH
    Sex
    H
    eight
    BM
    I
    C
    hrom
    atin
    am
    ount
    M
    apped
    reads
    Individual
    Flow
    cell batch
    Library
    batch
    R
    esidual variation
    All Regions
    H3K4me3 data: all regions with binding signal

    View Slide

  24. Differentially bound regions
    0 16 64 128 256 512
    A:N−:− A:N+:− A:N−:+ A:N+:+ D:N−:− D:N+:− D:N−:+ D:N+:+
    Coverage
    PRB2, 0 bp from tss: overlaps 5'

    +
    Genes
    11652500 11653000 11653500 11654000 11654500

    Tx
    chr12

    View Slide

  25. Collado-Torres et al, F1000Research, 2015
    regionReport
    chr start end strand p-value
    chr1 1000 2000 + 0.9
    chr2 5000 8000 - 0.001
    chr3 2468 2668 + 0.051
    . . . . .
    . . . . .
    . . . . .
    chrX 6000 6300 + 0.009
    chrX 6500 6800 - 0.5
    Genomic workflow:
    identify regions
    renderReport
    (A) default (B) custom
    (C) derfinderReport
    (D) DESeq2Report (E) edgeReport
    Create HTML/PDF
    report

    View Slide

  26. Collado-Torres et al, F1000Research, 2015
    regionReport

    View Slide

  27. Collado-Torres et al, F1000Research, 2015
    Interactive HTML reports
    (A)
    (B) Clickable buttons:
    show/hide code

    View Slide

  28. Collado-Torres et al, F1000Research, 2015
    Interactive HTML reports
    (A)
    (B)

    View Slide

  29. •  Resource with data from 2,040 projects
    •  Aligned with
    •  Total RNA-seq samples:
    49,657 + 9,662 = 59,319
    hBps://jhubiosta#s#cs.shinyapps.io/recount/

    View Slide

  30. recount: via the web
    hBps://jhubiosta#s#cs.shinyapps.io/recount/

    View Slide

  31. View Slide

  32. Mo#va#ng problem: iden#fy and validate
    regions of the genome that change expression
    during brain development
    1. derfinder permits discovery of novel expressed
    & differen#ally bound regions
    2.  we iden#fied & validated gene expression
    changes in the developing brain
    3.  we have developed tools for reproducible
    shareable repor#ng
    4.  these tools can be easily be used to process
    2,040 projects via recount

    View Slide

  33. Acknowledgements
    Advisors
    Jeffrey Leek
    Andrew Jaffe
    Collaborators
    Alyssa Frazee
    Abhinav Nellore
    Michael Love
    Ben Langmead
    Rafael Irizarry
    EpiMap project
    Funding
    NIH
    LIBD
    JHU-Biostats
    CONACyT México
    Conference Support
    Harvard Health Policy Data Science Lab, SACNAS 2016

    View Slide

  34. References + software + code: @fellgernon
    •  Collado-Torres, et al. Nucleic Acids Research (2016) doi: 10.1093/nar/gkw852
    –  http://bioconductor.org/packages/derfinder
    –  http://leekgroup.github.io/derSupplement/
    •  Collado-Torres, et al. F1000Research (2015) doi:10.12688/f1000research.6379.1
    -  http://www.bioconductor.org/packages/regionReport
    -  http://leekgroup.github.io/regionReportSupp/
    •  Collado-Torres and Nellore, et al. bioRxiv (2016) doi: 10.1101/068478
    –  http://bioconductor.org/packages/recount
    –  https://jhubiostatistics.shinyapps.io/recount
    •  Nellore, Collado-Torres, et al. Bioinformatics (2016) doi:10.1093/bioinformatics/btw575
    -  rail.bio
    • Nellore, …, Collado-Torres, et al. bioRxiv (2016) doi:10.1101/038224
    - intropolis.rail.bio
    •  Jaffe, Shin, Collado-Torres, et al. Nat. Neurosci. (2015) doi:10.1038/nn.3898
    –  https://github.com/lcolladotor/libd_n36
    –  https://github.com/leekgroup/enrichedRanges

    View Slide