title: Calibrating genomic and allelic coverage bias in single-cell sequencing.
abstract: Artifacts introduced in whole-genome amplification (WGA) make it difficult to derive accurate genomic information from single-cell genomes and require different analytical strategies from bulk genome analysis. Here, we describe statistical methods to quantitatively assess the amplification bias resulting from whole-genome amplification of single-cell genomic DNA. Analysis of single-cell DNA libraries generated by different technologies revealed universal features of the genome coverage bias predominantly generated at the amplicon level (1-10 kb). The magnitude of coverage bias can be accurately calibrated from low-pass sequencing (∼0.1 × ) to predict the depth-of-coverage yield of single-cell DNA libraries sequenced at arbitrary depths. We further provide a benchmark comparison of single-cell libraries generated by multi-strand displacement amplification (MDA) and multiple annealing and looping-based amplification cycles (MALBAC). Finally, we develop statistical models to calibrate allelic bias in single-cell whole-genome amplification and demonstrate a census-based strategy for efficient and accurate variant detection from low-input biopsy samples.
authors: Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.|Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.
authors: Cheng-Zhong
authors: CZ
authors: Zhang
authors: Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.|Department of Chemical Engineering Cambridge, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.|Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
authors: Viktor A
authors: VA
authors: Adalsteinsson
authors: Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.|Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.
authors: Joshua
authors: J
authors: Francis
authors: Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.|Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors: Hauke
authors: H
authors: Cornils
authors: Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.
authors: Joonil
authors: J
authors: Jung
authors: Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.
authors: Cecile
authors: C
authors: Maire
authors: Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.|Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA.|Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA.|Department of Pathology, Boston Children's Hospital, Boston, Massachusetts 02115, USA.|Center for Molecular Oncologic Pathology, Dana Farber Cancer Institute, Boston, Massachusetts 02115, USA.
authors: Keith L
authors: KL
authors: Ligon
authors: Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA.|Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.|Department of Pathology, Harvard Medical School, Boston, Massachusetts 02115, USA.|Center for Cancer Genome Discovery, Dana Farber Cancer Institute, Boston, Massachusetts 02215, USA.
authors: Matthew
authors: http://orcid.org/0000-0002-9133-8108
authors: M
authors: Meyerson
authors: Cancer Program, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.|Department of Chemical Engineering Cambridge, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.|Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
authors: J Christopher
authors: JC
authors: Love
mesh_terms: D000483:Alleles; D015982:Bias; D002138:Calibration; D002460:Cell Line; D015723:Gene Library; D015894:Genome, Human; D023281:Genomics / Q000379:methods*; D006801:Humans; D021141:Nucleic Acid Amplification Techniques; D016133:Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D059010:Single-Cell Analysis / Q000379:methods*; D013223:Statistics as Topic