PI: Andrew Jaffe Team: • Staff Scientist: Emily Burke • Postdocs: Carrie Wright, Amanda Price • Grad students: Matt Nguyen, Brianna Barry • Research Associate: Anandita Rajpurohit • Research Assistant: Nick Eagles, Stephen Semick* • Role details: like a postdoc (major role in some projects) with some support projects • https://www.libd.org/careers/ & you can always email Andrew [email protected] for job inquiries * Now at University of Maryland in med school
biorxiv.org/content/early/2018/10/30/445437 • DNAm and gene DE in Alzheimer’s disease biorxiv.org/content/early/2018/09/29/430603 • DNAm on WGBS across development & cell types biorxiv.org/content/early/2018/09/29/428391 • RNA-seq DE in Schizophrenia disorder & 2 brain regions biorxiv.org/content/early/2018/09/26/426213 • RNA-seq from stem cells biorxiv.org/content/early/2018/07/31/380758 Peer reviewed: • RNA-seq smoking during pregnancy doi.org/10.1038/s41380-018-0223-1 • RNA-seq DE in Schizophrenia disorder on DLPFC doi.org/10.1038/s41593-018-0197-y • Histamine signaling in autism spectrum disorder doi.org/10.1038/tp.2017.87
to - develop methods to process and analyze data from recount2 - use recount2 to address specific biological questions This project involves the Hansen, Leek, Langmead and Battle labs at JHU Contact: Kasper D. Hansen ([email protected] | www.hansenlab.org)
N=9,962 TCGA N=11,284 SRA N=49,848 samples expression estimates gene exon junctions ERs Answer meaningful questions about human biology and expression slide adapted from Shannon Ellis
male 1240 Male 141 Total 3640 Even when information is provided, it’s not always clear… sra_meta$S ex “1 Male, 2 Female”, “2 Male, 1 Female”, “3 Female”, “DK”, “male and female” “Male (note: ….)”, “missing”, “mixed”, “mixture”, “N/A”, “Not available”, “not applicable”, “not collected”, “not determined”, “pooled male and female”, “U”, “unknown”, “Unknown” slide adapted from Shannon Ellis
samples in recount gene, exon, exon-exon junction and expressed region RNA-Seq data SRA Sequence Read Archive N=49,848 TCGA The Cancer Genome Atlas N=11,284 GTEx Genotype Tissue Expression Project N=9,662 slide adapted from Shannon Ellis
samples in recount gene, exon, exon-exon junction and expressed region RNA-Seq data SRA Sequence Read Archive N=49,848 GTEx Genotype Tissue Expression Project N=9,662 divide samples build and optimize phenotype predictor training set test accuracy of predictor test set TCGA The Cancer Genome Atlas N=11,284 slide adapted from Shannon Ellis
samples in recount gene, exon, exon-exon junction and expressed region RNA-Seq data SRA Sequence Read Archive N=49,848 GTEx Genotype Tissue Expression Project N=9,662 divide samples build and optimize phenotype predictor training set test accuracy of predictor predict phenotypes across samples in TCGA test set TCGA The Cancer Genome Atlas N=11,284 slide adapted from Shannon Ellis
samples in recount gene, exon, exon-exon junction and expressed region RNA-Seq data SRA Sequence Read Archive N=49,848 GTEx Genotype Tissue Expression Project N=9,662 divide samples build and optimize phenotype predictor training set predict phenotypes across SRA samples test accuracy of predictor predict phenotypes across samples in TCGA test set TCGA The Cancer Genome Atlas N=11,284 slide adapted from Shannon Ellis
from >60 projects from the SRA, out of which 3,214 (72.5%) samples have expression data available from recount2 (Collado-Torres et al. 2017c). recount-brain supports powerful search and filter capabilities by tissue phenotype, including spanning 3,600 neurological controls with 2,900 from SRP025982 (SEQC/MAQC-III Consortium 2014); 15 neurological diseases and information on brain tumor subtype, grade, and stage; 3 levels of detailed anatomic tissue site information; 5 developmental stages (Fetus, Infant, Child, Adolescent, Adult); demographic data (age, sex, race); and technical sequencing information (RIN, PMI, sequencing layout, library source, etc.). • 62 SRA studies • 4,431 rows by 48 columns Ashkaun Razmara, in prep.
Black Hispanic White Tissue Site 1 Cerebral cortex Hippocampus Brainstem Cerebellum Tissue Site 2 Frontal lobe Temporal lobe Midbrain Basal ganglia Tissue Site 3 Dorsolateral prefrontal cortex Superior temporal gyrus Substantia nigra Caudate Hemisphere Left Right Brodmann Area 1-52 Disease Status Disease Neurological control Disease Brain tumor Alzheimer’s disease Parkinson’s disease Bipolar disorder Tumor Type Glioblastoma Astrocytoma Oligodendroglioma Ependymoma Clinical Stage 1 Grade I Grade II Grade III Grade IV Clinical Stage 2 Primary Secondary Recurrent Viability Postmortem Biopsy Preparation Frozen Thawed Ashkaun Razmara, in prep.
(around April 2018) https://docs.google.com/presentation/d/1FgUZZU6pW91J7zH0OqrEgxfnV1Py_ZGL3ZKHfbOZskY/edit#slide=id.g2f831fd4ae_0_306 * Dustin J. Sokolowski from Michael D. Wilson’s lab is using recount2 * Dustin joins the project and merges recount-brain with GTEx and TCGA Ashkaun Razmara, in prep. recount_brain_v2 The SRA samples in recount-brain are complemented by 1,409 GTEx (GTEx Consortium 2015) and 707 TCGA (Brennan et al. 2013; Cancer Genome Atlas Research Network et al. 2015) samples covering 13 healthy regions of the brain and 2 tumor types, respectively. In total, there are 6,547 samples with metadata in recount-brain with 5,330 (81.4%) present in recount2
#biodata18 * Potential for contributing recount-brain to SRAdbV2 github.com/seandavi/SRAdbV2 * Currently working with him to make this happen * Might map some columns to ontologies Ashkaun Razmara, in prep. What about maintaining/growing it?
benefited a bit from being slow: Dustin + Sean’s input have improved recount-brain * Full draft has been checked by authors, got LIBD’s permission to post on bioRxiv * How valuable is this resource? - other curated metadata projects include expression (here expression is already in recount2) * Advice from LW: pre-print, grow user base interest, then submit to a journal quoting usage numbers Ashkaun Razmara, in prep. Lieber Institute for Brain Development
T. Leek University of Toronto Dustin J. Sokolowski Michael D. Wilson NIH Sean Davis LIBD Andrew E. Jaffe Funding NIH R01 GM105705 NIH 1R21MH109956 NIH R01 GM121459 CIHR, NSERC Ontario Ministry of Research IDIES SciServer Hosting recount2 github.com/LieberInstitute/recount-brain