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Services

The BTI Bioinformatics Core offers a range of computational and analytical support for projects involving genomic, transcriptomic, and clinical data. See Working with the Core for how to initiate a collaboration.

Data Transfers & Management

  • Data transfer from external or internal sites
  • Data deposition to repositories (GEO, dbGaP, PRIDE)
  • Data storage — creation and management of AWS buckets or L Drive shares
  • Data Access Agreement support (dbGAP, EGA, CBTN, PNOC expertise)
  • Globus/IT/ServiceNow general support (e.g. - AD group setup, L drive, Box, Slack)

Data Ingest

  • Manifest generation, bioassay ID and internal identifier generation, data file warehouse ingest
  • Data merge across datasets/sources

Sequencing Data Harmonization (Defaults listed below)

For additional customization of workflows, additional fees may apply.

PDX preprocessing

  • Quality control assessment
  • Xenome classification of human and mouse reads

Normal DNA

  • Quality control assessment
  • Sentieon alignment, single sample genotyping (GATK HaplotypeCaller) with gnomAD v3.1.1 and 4.1 annotation
  • Normal CNV calls (CNVnator, MantaSV, SVaba) with AnnotSV annotation
  • Normal SV calls (MantaSV, SVaba) with AnnotSV annotation
  • Pathogenicity assessment (ClinVar, InterVar, AutoPVS1, AutoGVP)

Tumor DNA (WGS, WXS, Panel from T/N pairs)

  • Quality control assessment
  • Sentieon alignment, somatic SNV calls (Lancet, VarDict, Strelka2, Mutect2), and consensus SNV calls with VEP v105 annotation
  • CNV (ControlFREEC, CNVkit) and SV (MantaSV) calls (WGS and WXS only) with AnnotSV annotation

Tumor only DNA (WGS, WXS, Panel)

  • Quality control assessment
  • Sentieon alignment, somatic SNV calls (Mutect2) using PON with VEP v105 annotation
  • CNV (ControlFREEC, CNVkit) and SV (MantaSV) calls (WGS and WXS only) with AnnotSV annotation

Quality control (sample identity/relatedness checks)

  • NGSCheckMate or
  • Somalier Relate

Short-read RNA (tumor or normal)

  • Quality control assessment (RNASeCQ, STAR)
  • STAR two-pass alignment (GENCODE v39 annotation)
  • Gene counts and TPM (RSEM)
  • Isoform counts and TPM (RSEM)
  • Isoform abundance (Kallisto)
  • Fusion detection (STAR-Fusion, Arriba Fusion)
  • Splice events (rMATS turbo)
  • Flash-Seq supported

miRNA-Seq

  • novel miRNA target prediction (miRanda, GENCODE v39)

Long-read RNA (PacBio Kinnex)

  • Quality control assessment
  • Alignment
  • Gene and isoform expression

Single cell or nucleus whole transcriptome

  • Quality control assessment
  • Alignment and filtering (ALSF CCDL workflow, alevin-fry)
  • Gene expression
  • Cell type annotation

10X Flex Gene Expression

  • Custom probe design
  • Quality control assessment
  • Alignment and filtering (STAR alignment with Cell Ranger)
  • Gene expression
  • Cell type annotation

Methylation

  • CNS tumor classification via NIH Methylscape (CNS tumors only; subject to API limits)
  • Preprocessing — m-values, beta values, CNVs
  • Probe annotation

Neoantigen Discovery (paired RNA-Seq and DDA proteomics)

  • Translation of DNA SNVs and/or RNA fusions/splice events into peptides
  • Peptide identification with custom FASTA (FragPipe)
  • Peptide ranking

Kids First DNA long-read (PacBio, ONT)

  • Available on request

LOH assessment

  • AlleleCouNT for paired germline/tumor samples

Software Development / Engineering

  • New workflow development (GitHub, local, EC2)
  • New workflow development (CWL, EC2)

Manuscript Contributions

  • Poster review — collaborative, not charged
  • Figure compilation — collaborative, not charged
  • Manuscript writing and review — collaborative, not charged
  • Public code releases — final run script, repo readiness, GitHub release, Zenodo DOI

Bioinformatics Consultation

  • Experimental design
  • Grant review and cost estimation
  • Grant writing
  • Clinical trial readiness (typically a 6+ month engagement)

Custom Projects

  • Custom engineering (e.g. FreezerPro API extract, transform, and ingest to REDCap, Dashboard or App design and creation)
  • Custom scientific analyses (e.g. understanding the effects of CAR-T treatment on the tumor microenvironment using paired miRNA-Seq and RNA-Seq across species)

Administration & Infrastructure

  • Scheduling, project management, and PI coordination
  • Project meetings
  • CAVATICA API support
  • Data file warehouse
  • Automations
  • Bug fixes and upgrades

Workflows in Development

The following workflows are newer or still under active development. Availability and turnaround may vary — check with the Core when scoping a project that needs one of these.

  • Methylation CNV segmentation and annotation
  • Visium spatial transcriptomics
  • TIRTL-seq
  • Ribo-seq + RNA-seq
  • Kinnex long-read RNA-Seq
  • IsoLaser for isoform-level analysis of long-read RNA-Seq
  • VarRNA for RNA variant calling