Clinical Genomics

In the Clinical Genomics team, we focus on analysis of patient-related data, including exome/genome analysis and RNA-seq, to aid in clinical research projects for diagnosis of known diseases and discovery of novel genetic disorders.

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Examples of clinical genomics methods we support:

  • Assembly and mapping of short- and long-read sequencing data.
  • Variant analysis using GATK Best Practices.
  • Rare variant filtering in probands or trios based on genetic inheritance modeling.
  • Family group or cohort analysis.
  • Transcriptome/RNA-Seq (differential gene expression, splicing, mono-allelic expression)
  • Pathways and network analyses.
  • Gene burden analysis (candidate gene hypothesis testing, gene discovery)
  • Structural variant calling from whole genome sequencing data.
  • Somatic/mosaic variant calling.
  • Linkage analysis and homozygosity mapping.

Example of tools used during data analyses

  • BWA, GATK, GEMINI, plink, EPACTS, STAR, HiSAT2, Exomiser and CADD

Clinical Genomics Team

  • Andrew Oler, Ph.D. (Group coordinator)
  • Eric Karlins, M.S.
  • Samuel Li, Ph.D.
  • Colton McNinch, Ph.D.

Selected Publications

  • Science. 2020 Oct 23;370 Autoantibodies against type I IFNs in patients with life-threatening COVID-19. Collaborator: Helen Su (LCIM)
  • Science 2020 Jul 10;369(6500):202-207. HEM1 deficiency disrupts mTORC2 and F-actin control in inherited immunodysregulatory disease. Collaborator: Michael Lenardo (LISB)
  • Blood. 2020 Dec 3;136(23):2638-2655. Extended clinical and immunological phenotype and transplant outcome in CD27 and CD70 deficiency. Collaborator: Helen Su (LCIM) and Michael Lenardo (LISB)
  • J Clin Invest. 2020 Apr 1;130(4):1669-1682. Distinct interferon signatures and cytokine patterns define additional systemic autoinflammatory diseases. Collaborator: Raphaela Goldbach-Mansky.
Related tools developed by BCBB


Genomic Research Integration System (GRIS). In order to access GRIS you should connect to the NIH network using your NIH credentials.