Improved molecular karyotyping in glioblastoma

Ian E Burbulis; Margaret B Wierman; Matt Wolpert; Mark Haakenson; Maria-Beatriz Lopes; David Schiff; James Hicks; Justin Loe; Aakrosh Ratan; Michael J McConnell

doi:10.1016/j.mrfmmm.2018.06.002

Improved molecular karyotyping in glioblastoma

Mutat Res. 2018 Sep:811:16-26. doi: 10.1016/j.mrfmmm.2018.06.002. Epub 2018 Jul 8.

Authors

Affiliations

¹ Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, VA, United States; Escuela de Medicina, Universidad San Sebastian, Puerto Montt, Chile.
² Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, VA, United States.
³ Department of Pathology, University of Virginia, School of Medicine, Charlottesville, VA, United States.
⁴ Department of Neurology, University of Virginia, School of Medicine, Charlottesville, VA, United States.
⁵ Michelson Center, University of Southern California, Los Angeles, CA, United States; Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States.
⁶ Full Genomes Corp, Inc., Rockville, MD, United States.
⁷ Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, VA, United States; Center for Public Health Genomics, University of Virginia, School of Medicine, Charlottesville, VA, United States.
⁸ Department of Biochemistry and Molecular Genetics, University of Virginia, School of Medicine, Charlottesville, VA, United States; Department of Neuroscience, University of Virginia, School of Medicine, Charlottesville, VA, United States; Center for Public Health Genomics, University of Virginia, School of Medicine, Charlottesville, VA, United States; Center for Brain Immunology and Glia, University of Virginia, School of Medicine, Charlottesville, VA, United States. Electronic address: mjm2zv@virginia.edu.

PMID: 30055482
DOI: 10.1016/j.mrfmmm.2018.06.002

Abstract

Uneven replication creates artifacts during whole genome amplification (WGA) that confound molecular karyotype assignment in single cells. Here, we present an improved WGA recipe that increased coverage and detection of copy number variants (CNVs) in single cells. We examined serial resections of glioblastoma (GBM) tumor from the same patient and found low-abundance clones containing CNVs in clinically relevant loci that were not observable using bulk DNA sequencing. We discovered extensive genomic variability in this class of tumor and provide a practical approach for investigating somatic mosaicism.

Keywords: Copy number variation; Glioblastoma; Molecular karyotype; Single cell; Tumor evolution; Whole genome sequencing.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

DNA Copy Number Variations
Glioblastoma / genetics*
Humans
Karyotyping / methods*
Sequence Analysis, DNA
Single-Cell Analysis
Whole Genome Sequencing

Abstract

Publication types

MeSH terms

Grants and funding