Publisher Correction: Amplification-free single-cell whole-genome sequencing gets a makeover

Abstract Medulloblastomas harbor clinically-significant intra-tumoral heterogeneity for key biomarkers (e.g. MYC/MYCN, β-catenin). Recent studies have characterized transcriptional heterogeneity at the single-cell level, however the underlying genomic copy number and mutational architecture remains to be resolved. We therefore sought to establish the intra-tumoural genomic heterogeneity of medulloblastoma at single-cell resolution. Copy number patterns were dissected by whole-genome sequencing in 1024 single cells isolated from multiple distinct tumour regions within 16 snap-frozen medulloblastomas, representing the major molecular subgroups (WNT, SHH, Group3, Group4) and genotypes (i.e. MYC amplification, TP53 mutation). Common copy number driver and subclonal events were identified, providing clear evidence of copy number evolution in medulloblastoma development. Moreover, subclonal whole-arm and focal copy number alterations covering important genomic loci (e.g. on chr10 of SHH patients) were detected in single tumour cells, yet undetectable at the bulk-tumor level. Spatial copy number heterogeneity was also common, with differences between clonal and subclonal events detected in distinct regions of individual tumours. Mutational analysis of the cells allowed dissection of spatial and clonal heterogeneity patterns for key medulloblastoma mutations (e.g. CTNNB1, TP53, SMARCA4, PTCH1) within our cohort. Integrated copy number and mutational analysis is underway to establish their inter-relationships and relative contributions to clonal evolution during tumourigenesis. In summary, single-cell analysis has enabled the resolution of common mutational and copy number drivers, alongside sub-clonal events and distinct patterns of clonal and spatial evolution, in medulloblastoma development. We anticipate these findings will provide a critical foundation for future improved biomarker selection, and the development of targeted therapies.

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Single-cell, whole-genome sequencing of patient tumor samples

Science-Business eXchange ◽

10.1038/scibx.2012.292 ◽

2012 ◽

Vol 5 (11) ◽

pp. 292-292

Keyword(s):

Whole Genome Sequencing ◽

Single Cell ◽

Genome Sequencing ◽

Whole Genome

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PaSD-qc: Quality control for single cell whole-genome sequencing data using power spectral density estimation

10.1101/166637 ◽

2017 ◽

Cited By ~ 2

Author(s):

Maxwell A. Sherman ◽

Alison R. Barton ◽

Michael Lodato ◽

Carl Vitzthum ◽

Michael E. Coulter ◽

...

Keyword(s):

Spectral Density ◽

Whole Genome Sequencing ◽

Single Cell ◽

Power Spectral Density ◽

Genome Sequencing ◽

Dna Amplification ◽

Whole Genome Sequencing Data ◽

Whole Genome ◽

Sequencing Data ◽

Power Spectral

AbstractSingle cell whole-genome sequencing (scWGS) is providing novel insights into the nature of genetic heterogeneity in normal and diseased cells. However, scWGS introduces DNA amplification-related biases that can confound downstream analysis. Here we present a statistical method, with an accompanying package PaSD-qc (Power Spectral Density-qc), that evaluates the quality of single cell libraries. It uses a modified power spectral density to assess amplification uniformity, amplicon size distribution, autocovariance, and inter-sample consistency as well as identifies aberrantly amplified chromosomes. We demonstrate the usefulness of this tool in evaluating scWGS protocols and in selecting high-quality libraries from low-coverage data for deep sequencing.

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Single cell whole genome sequencing reveals that NFKB1 mutation affects radiotherapy sensitivity in cervical cancer

Oncotarget ◽

10.18632/oncotarget.23587 ◽

2017 ◽

Vol 9 (7) ◽

pp. 7332-7340 ◽

Cited By ~ 2

Author(s):

Dong Yang ◽

Weiyuan Zhang ◽

JunQing Liang ◽

Kexin Ma ◽

Peng Chen ◽

...

Keyword(s):

Cervical Cancer ◽

Whole Genome Sequencing ◽

Single Cell ◽

Genome Sequencing ◽

Whole Genome

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Single-cell whole-genome sequencing reveals the functional landscape of somatic mutations in B lymphocytes across the human lifespan

10.1101/535906 ◽

2019 ◽

Cited By ~ 3

Author(s):

Lei Zhang ◽

Xiao Dong ◽

Moonsook Lee ◽

Alexander Y. Maslov ◽

Tao Wang ◽

...

Keyword(s):

B Cell ◽

Whole Genome Sequencing ◽

Single Cell ◽

B Lymphocytes ◽

Genome Sequencing ◽

Somatic Mutations ◽

Somatic Hypermutation ◽

Whole Genome ◽

Healthy Individuals ◽

Human Lifespan

Introductory paragraphThe accumulation of mutations in somatic cells have been implicated as a cause of ageing since the 1950s1,2. Yet, attempts to establish a causal relationship between somatic mutations and ageing have been constrained by the lack of methods to directly identify mutational events in primary human tissues. Here we provide detailed, genome-wide mutation frequencies and spectra of human B lymphocytes from healthy individuals across the entire human lifespan, from newborns to centenarians, using a recently developed, highly accurate single-cell whole-genome sequencing method3. We found that the number of somatic mutations increases from <500 per cell in newborns to >3,000 per cell in centenarians. We discovered mutational hotspot regions, some of which, as expected, located at immunoglobulin genes associated with somatic hypermutation. B cell-specific mutation signatures were observed associated with development, ageing or somatic hypermutation (SHM). The SHM signature strongly correlated with the signature found in human chronic lymphocytic leukemia and malignant B-cell lymphomas4, indicating that even in B cells of healthy individuals the potential cancer-causing events are already present. We also identified multiple mutations in sequence features relevant to cellular function, i.e., transcribed genes and gene regulatory regions. Such mutations increased significantly during ageing, but only at approximately half the rate of the genome average, indicating selection against mutations that impact B cell function. This first full characterization of the landscape of somatic mutations in human B lymphocytes indicates that spontaneous somatic mutations accumulating with age can be deleterious and may contribute to both the increased risk for leukemia and the functional decline of B lymphocytes in the elderly.

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Single-cell whole-genome sequencing reveals the functional landscape of somatic mutations in B lymphocytes across the human lifespan

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1902510116 ◽

2019 ◽

Vol 116 (18) ◽

pp. 9014-9019 ◽

Cited By ~ 51

Author(s):

Lei Zhang ◽

Xiao Dong ◽

Moonsook Lee ◽

Alexander Y. Maslov ◽

Tao Wang ◽

...

Keyword(s):

B Cell ◽

Whole Genome Sequencing ◽

Single Cell ◽

B Lymphocytes ◽

Genome Sequencing ◽

Somatic Mutations ◽

Whole Genome ◽

Healthy Individuals ◽

Human Lifespan ◽

Increased Risk

Accumulation of mutations in somatic cells has been implicated as a cause of aging since the 1950s. However, attempts to establish a causal relationship between somatic mutations and aging have been constrained by the lack of methods to directly identify mutational events in primary human tissues. Here we provide genome-wide mutation frequencies and spectra of human B lymphocytes from healthy individuals across the entire human lifespan using a highly accurate single-cell whole-genome sequencing method. We found that the number of somatic mutations increases from <500 per cell in newborns to >3,000 per cell in centenarians. We discovered mutational hotspot regions, some of which, as expected, were located at Ig genes associated with somatic hypermutation (SHM). B cell–specific mutation signatures associated with development, aging, or SHM were found. The SHM signature strongly correlated with the signature found in human B cell tumors, indicating that potential cancer-causing events are already present even in B cells of healthy individuals. We also identified multiple mutations in sequence features relevant to cellular function (i.e., transcribed genes and gene regulatory regions). Such mutations increased significantly during aging, but only at approximately one-half the rate of the genome average, indicating selection against mutations that impact B cell function. This full characterization of the landscape of somatic mutations in human B lymphocytes indicates that spontaneous somatic mutations accumulating with age can be deleterious and may contribute to both the increased risk for leukemia and the functional decline of B lymphocytes in the elderly.

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