Clinical Genomics at BCBB

Bioinformatics and Computational Biosciences Branch's (BCBB) Clinical Genomics team focuses 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.

Examples of clinical genomics methods we support:

  • Assembly and mapping of short- and long-read sequencing data
  • Variant analysis using standard 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

Publications

Collaborator: Steven M. Holland (LCIM), Michail Lionakis (LMI). Immunogenetics associated with severe coccidioidomycosis. JCI Insight. 2022 Nov 22;7(22):e159491.

Collaborator: Steven M. Holland (LCIM), Luigi D. Notarangelo. Clinical exome sequencing of 1000 families with complex immune phenotypes: Toward comprehensive genomic evaluations. J Allergy Clin Immunol. 2022 Oct;150(4):947-954. doi: 10.1016/j.jaci.2022.06.009.

Collaborator: Zhiyong Lu (NCBI). PhenoRerank: A re-ranking model for phenotypic concept recognition pre-trained on human phenotype ontology. Biomed Inform. 2022 May;129:104059. doi: 10.1016/j.jbi.2022.104059.

Collaborator: Michael Lenardo (LISB). Congenital iRHOM2 deficiency causes ADAM17 dysfunction and environmentally directed immunodysregulatory disease. Nat Immunol. 2022 Jan;23(1):75-85. doi: 10.1038/s41590-021-01093-y.

Collaborator: Steven M. Holland (LCIM). Genome-wide association study in patients with pulmonary Mycobacterium avium complex disease. Eur Respir J. 2021 Aug 12;58(2):1902269. doi: 10.1183/13993003.02269-2019.

Collaborator: Helen Su (LCIM). Autoantibodies against type I IFNs in patients with life-threatening COVID-19. Science. 2020 Oct 23;370

Collaborator: Michael Lenardo (LISB). HEM1 deficiency disrupts mTORC2 and F-actin control in inherited immunodysregulatory disease. Science. 2020 Jul 10;369(6500):202-207.

Collaborator: Helen Su (LCIM) and Michael Lenardo (LISB). Extended clinical and immunological phenotype and transplant outcome in CD27 and CD70 deficiency. Blood. 2020 Dec 3;136(23):2638-2655.

Collaborator: Raphaela Goldbach-Mansky. Distinct interferon signatures and cytokine patterns define additional systemic autoinflammatory diseases. J Clin Invest. 2020 Apr 1;130(4):1669-1682.

Research Team

Team Lead

Andrew J. Oler, Ph.D.

Contact: andrew.oler@nih.gov

Education:

Ph.D., 2011, University of Utah, Salt Lake City, UT

Languages Spoken: French

Andrew Oler uses computational methods to understand and explain the genetics of rare immunological disorders and infectious disease susceptibilities. He also assists in the development of the Genomic Research Integration System (GRIS), a tool for integrating patient genotype and phenotype information and for prioritizing variants based on Mendelian inheritance models.

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Team Members

Joanne Berghout, Ph.D.

(Contractor)

Contact: joanne.berghout@nih.gov

Education:

Ph.D., 2014, McGill University, Montreal, QC

BSc, 2003, Carleton University, Ottawa, ON

Joanne Berghout is a geneticist with 15+ years’ experience exploring the role of variation in human disease, especially rare disorders and differential responses to infection. She is excited by genetics and bioinformatics entering its translational era. She’s a member of BCBB’s clinical genomics team, with previous roles as a computational geneticist at Pfizer, research faculty at University of...

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Zeeshan Fazal, Ph.D.

(Contractor)

Contact: zeeshan.fazal@nih.gov

Education:

Ph.D., 2017, University of Illinois at Urbana-Champaign, IL

MS., 2012, University of Illinois at Urbana-Champaign, IL

Languages Spoken: Urdu

Zeeshan is working with researchers on clinical genomics projects to discover rare variants in rare diseases. He delivers high-value genomic discoveries and has a strong knowledge of molecular biology, genetics, genomics and immunology (focused on clinical genomics), single and bulk RNA-seq, Chip-seq, DNA methylation, developing workflows for Biomarker identification, as well as bioinformatics...

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Biju Issac, Ph.D.

(Contractor)

Contact: biju.issac@nih.gov

Education:

Ph.D. 2005 Jawaharlal Nehru University, New Delhi, India

Languages Spoken: Hindi, Malayalam

Biju Issac is a Bioinformatics with 15+ years of research experience on gene expression in various tumor and other tissue models. He is a transcriptomics specialist within the Science Support Section of BCBB providing analytical and training support to NIAID researchers involving transcriptomics projects. He has broad knowledge in bioinformatics involving bulk RNA-Seq, sc/sn-RNA-Seq, spatial...

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Eric Karlins, M.S.

(Contractor)

Contact: karlinser@mail.nih.gov

Education:

M.S. in Computer Science, 2024 (expected), Georgia Tech, Atlanta, GA

M.S. in Biotechnology, 2002, Johns Hopkins University, Baltimore, MD

B.S. in Biology, 1998, The College of William and Mary, Williamsburg, VA

Eric has been a Computational Genomics Specialist with Bioinformatics and Computational Bioscience Branch (BCBB) since 2018, and he’s worked at the NIH since 2000. He works performing bioinformatics analysis for genomics projects ranging from Whole Genome Sequencing to Genome Wide Association Study. He also helps with data engineering projects for the Genomic Research Integration System (GRIS)...

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Colton M. McNinch, Ph.D.

(Contractor)

Contact: colton.mcninch@nih.gov

Education:

B.S., 2014, Southwestern College, Winfield, KS

Ph.D, 2020, Iowa State University, Ames, IA

Colton McNinch is a transcriptomics specialist within the Science Support Section of Bioinformatics and Computational Bioscience Branch (BCBB). He provides analytical and training support to NIAID researchers on projects involving RNA-Sequencing data (e.g. Bulk RNA-Seq, scRNA-Seq, and spatial transcriptomics). He was trained as a molecular biologist and currently leverages that expertise in his...

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Adam X. Miranda

(Contractor)

Contact: For contact information, search the NIH Enterprise Directory.

Education:

Ph.D., Cancer Biology 2024
Vanderbilt University, Nashville, TN


B.S., Genetics 2017
North Carolina State University, Raleigh, NC

Adam is a transcriptomics specialist within BCBB. He has experience with not only transcriptional analyses but a number of different epigenetic assays including ChIP-seq, ATAC-seq, and HiC. His experience as a bench scientist is an asset to his communication skills and understanding of experimental design. He also enjoys making creative and insightful graphical representations of his findings.

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