In vjcitn/BiocOncoTK: Bioconductor components for general cancer genomics

library(tufte)
# invalidate cache when the tufte version changes
knitr::opts_chunk$set(tidy = FALSE, cache.extra = packageVersion('tufte'))
options(htmltools.dir.version = FALSE)
suppressPackageStartupMessages({
library(rhdf5client)
library(BiocStyle)
library(restfulSE)
library(restfulSEData)
library(ggplot2)
library(BiocOncoTK)
library(ontoProc)
library(SRAdbV2)
library(UpSetR)
library(MultiAssayExperiment)
library(htxcomp)
set.seed(1234)
})

Introduction

r newthought("Strategic thinking about computing") for cancer genomics involves a panoply of concepts evolving in an unstable technological domain.^[One snapshot of current approaches can be found at Broad's CGCA site https://www.broadinstitute.org/cancer/cancer-genome-computational-analysis] In this computable document, we lay out a series of concepts and examples around which our basic developmental strategy for cloud-oriented Bioconductor:Cancer can be understood. All demonstrations are based on Bioconductor 3.9 using R 3.6.

Basic map of the situation

We will use the term "architecture" in conjunction with the following broad categories of relevance to computing for cancer genomics.

• Conceptual architecture: How are formal ontologies^[ See the OBO Foundry Principles document (http://www.obofoundry.org/principles/fp-000-summary.html).], APIs, and concrete data tables used together efficiently to identify key biological and therapeutic processes in cancer?^[The Genomics API concept is helpfully reviewed in @Swaminathan2016.]

• Data architecture: How are cohorts, trials, experiments, samples, quantifications, and annotations best represented for efficient solutions to problems arising in computational biology of cancer? Are cloud-scale approaches to managing and interrogating "big data" effectively usable by a community of researchers with diverse interests and computational skills?

• Analysis architecture: How can advances in conceptual and data architecture help to accelerate the development of compelling new interpretations of existing and new experiments in cancer genomics?

In what follows we aim to get very concrete about the ways in which the Bioconductor:Cancer project delivers advances in these areas.

Conceptual architecture for FAIRness in cancer genomics

The FAIR (Findable, Accessible, Interoperable, Reusable) principles for scientific data stewardship are widely accepted. Ontological information science is helpful for discovery and interoperation of genomic data resources, and interfaces to genomic ontologies are a fundamental part of Bioconductor:Cancer's conceptual architecture. Using and defining APIs for component and user interaction are additional major concerns.

Ontology tools

Results of experiments and trials in human cancer produce information in many domains. Systematic synthesis of relevant information depends on harmonization of vocabularies, and more progress on adoption and verifiable compliance with best practices is needed. The ontoProc package simplifies usage of key ontologies in the Open Biological Ontologies Foundry. We consider the oncotree vocabulary produced at Sloan-Kettering.^[http://oncotree.mskcc.org/#/home?tab=news shows that this is an evolving resource, as one might expect. What we work with is a slight variation created using NCIT terms that coincide with oncotree terms, as distributed at http://purl.obolibrary.org/obo/ncit/ncit-oncotree.obo]

library(ontoProc)
otr = getOncotreeOnto()
grep("Breast", otr$name, value=TRUE)[1:4]

Code like this leads to the observation that there are r length(grep("Breast", otr$name)) terms involving Breast in the vocabulary ^[A view of relationships among 10 oncoTree terms related to "Breast". { width=70% }]. Relationships among these terms are encoded in otr. The collection of ontologies usable in this way can be gleaned from

grep("Onto", ls("package:ontoProc"), value=TRUE)

Ideally, we would use ChEBI, EFO, and Cellosaurus in integrative analyses of pharmacogenomic experiments that account for structural and functional relationships among chemical entities and genetic and functional relationships among cell types. Additional integration with clinical and molecular observations of tumors in TCGA would be fostered by adoption of conventions on genomic and clinical vocabularies. We will discuss this situation below.

APIs and microservice concepts^["Microservice architecture has taken hold in application design for a number of reasons ..., but ultimately, the fundamental driver has been the opportunity for significant increase in productivity. Gains are achieved by dividing larger, more complex applications into small, manageable projects that encapsulate common functionality. Each microservice represents a “black-box” with a well-defined application programming interface (API) bundled with its own integral resources, thus eliminating external dependencies. This encapsulation simplifies the division of labor for teams of software developers and reduces the inherent overhead of multiple developers working on the same sections of code. The narrow scope of functionality of a single microservice allows for thorough testing and optimization of each component in isolation, leading to higher reliability and performance of the overall parent application." (@Williams2016)]

It may be fruitful to construe the solutions to many problems arising in cancer genome analysis as "microservices". Numerous projects have implemented REST APIs to expose metadata and data about resources relevant to cancer genomics.
As an illustration of the basic concept, S. Davis of NCI has created the SRAdbV2 package^[https://github.com/seandavi/SRAdbV2], which provides capacity for R/Bioconductor users to survey all sequencing experiments housed in NCBI SRA. Metadata that are continuously developed at SRA are transformed for "serverless" interrogation using Elasticsearch. Thus

library(SRAdbV2)
oidx = Omicidx$new()
allhrec = oidx$search(q="sample.taxon_id: 9606")
allhrec$count()

\noindent gives the number of records involving human samples. A selection of fields that can be interrogated to acquire accession numbers for experiments of interest is

lk = allhrec$scroll()
sample(mm <- names(lk$yield()), size=5)

There are r length(mm) fields whose semantics must be known to enable effective searching^[These fields constitute a small fraction of the overall data model of the NCI Genomic Data Commons; see https://gdc.cancer.gov/developers/gdc-data-model/gdc-data-model-components.]. Some of these fields include subfields whose structure varies from experiment to experiment.

It is useful to contrast this approach to the predecessor package, SRAdb, which was based on a 35GB SQLite database, updated semiannually, that was installed on each user's system. SRAdbV2 is based on a chain of transformations from NCBI's XML metadata compendium, harvested every other week, leading to a service that responds to detailed queries in the Lucene query idiom. The stability and local nature of the SRAdb approach is traded for a potentially more volatile resource that is very light weight and universally accessible.

The REST API underlying the SRAdbV2 service is documented at https://api-omicidx.cancerdatasci.org/sra/1.0/ui/.

Data architecture

We consider two cloud-scale solutions for multiomic data in cancer: Google BigQuery, as employed in the ISB CGC project, extended from TCGA to the Pancancer Atlas, and the HDF Scalable Data Service. Our approach emphasizes hybridized data interfaces: certain data such as focused annotation and sample attributes can be resident in memory, while voluminous quantifications are managed remotely and queried only when needed.

Lazy MultiAssayExperiments with BigQuery back end

The SummarizedExperiment class unifies genomic quantifications with metadata about samples, assay features, and experimental protocol. This has been generalized for multi-assay experiments (where tissue from a given sample is characterized along various molecular dimensions). We used the buildPancanSE function of the BiocOncoTK package, and the MultiAssayExperiment construction API to develop blcaMAE, the Pancancer Atlas data on RNA-seq, miRNA-seq, and Illumina Infinium methylation results for both tumor and normal tissues derived from the TCGA Bladder Cancer cohort.

load("blcaMAE.rda")
assay(experiments(blcaMAE)$meth_n)@seed@seed@filepath@bqconn@quiet = TRUE

blcaMAE

The relative frequencies of multiomic and tumor:normal pair availability are shown below.

upsetSamples(blcaMAE)

Quantifications are accessed as needed through the DelayedArray protocol:

suppressMessages(assay(experiments(blcaMAE)$meth_n["rs939290",]))

Lazy SummarizedExperiments over HDF Scalable Data Service

HDF5 is widely used for array-structured quantification sets in genomics. The HDF Scalable Data Service (HSDS) leverages the HDF data model for efficient design of hierarchical organizations of numerical arrays and their metadata, deployed in an S3 object store, exposed through a REST API. Query resolution is multiplexed.

In this example, we acquire a lazy but richly annotated HSDS-resident image of the BigRNA compendium assembled by Sean Davis of NCI (http://bigrna.cancerdatasci.org/). This is a collection of all RNA-seq studies of human-derived samples, uniformly preprocessed and quantified to gene models of GENCODE version 27.
We present it to the user as a SummarizedExperiment, and construct a query to filter the content of the compendium based on transcript location.

library(htxcomp) # github.com/vjcitn/htxcomp
htxg = loadHtxcomp()
dim(htxg)
subsetByOverlaps(htxg, GRanges("chr1", IRanges(1e6,2e6)))

\noindent Notice the number of samples, 181134. Selection of experiments of interest is accomplished using SRAdbV2 to obtain accession codes, say \texttt{KP}, and then working with \texttt{htxg[,kp]}.

Thanks to John Readey of the HDF Group, HSDS images of the RNA-seq archives from GTEx, Tabula Muris, HapMap, and two single-cell RNA-seq experiments in glioblastoma are available for public use via the HDF Kita Lab. The Bioconductor restfulSE package can also be used to work with these datasets.

Analysis architecture

We now demonstrate some virtues of the hybrid data architecture consisting of numerical data in a remote bigdata back end, and annotation and query support provided by R/Bioconductor.

Multitumor, multigene survey of association of gene expression with microsatellite instability

Figure 5C^[Code segment for boxplot panel. {width=60%}] of @Bailey2018 indicates that microsatellite instability (MSI) is associated with different expression signatures of immune cell infiltration for adenocarcinomas of colon (COAD) and stomach (STAD), and uterine corpus endometrial carcinoma (UCEC).
The MSI scores developed using MSIsensor are found in Table S5 of @Ding2018. To reproduce aspects of this finding using the BigQuery Pancancer-atlas back end, we a) authenticate to the BigQuery platform, b) select tumor types and assay for \texttt{SummarizedExperiment} construction, c) bind Ding et al.'s MSI values d) acquire and transform the expression values of interest, and e) form the stratified boxplots. The basic findings of Bailey et al. are replicated.

\newpage

Comparing cell-type-specific expression distributions after immunopanning in GBM samples

As a prelude to single-cell RNA-sequencing of glioblastoma (GBM) tumors from four patients, @Darmanis2017 used immunopanning to increase the proportion of non-neoplastic cells that constitute the "migrating front" of progression of glioblastoma. Antibody to CD45 was used to capture microglial cells. Using the code to the right^[ Code segment to create density traces. {width=65%} ], we compare the distribution of CD45 expression among the classes of cells as labeled in the metadata of GSE84465, the NCBI GEO archive from which the quantifications were derived.

library(rhdf5client)
library(SummarizedExperiment)
library(BiocOncoTK)
library(ggplot2)
cdar = BiocOncoTK::darmGBMcls
ind = match("PTPRC", rowData(cdar)$symbol)
var = gsub("selection: ", "", 
       cdar$characteristics_ch1.8)
vals = log10(assay(cdar[ind,])+1)
ddd = data.frame(log10norm=vals, pan=var)
ggplot(ddd, aes(x=log10norm, colour=pan)) + 
  geom_density() + ylim(0,1) + 
  xlab("log10 CD45+1")

Funding support

This work was supported by NCI U01 CA214846, V. Carey, PI, NCI U24 CA180996, M. Morgan PI. Work of Sean Davis was supported by the NCI Center for Cancer Research.

vjcitn/BiocOncoTK documentation built on Feb. 14, 2023, 11:56 p.m.