scholarly journals Whole-genome molecular haplotyping of single cells

2011 ◽  
Vol 29 (1) ◽  
pp. 51-57 ◽  
Author(s):  
H Christina Fan ◽  
Jianbin Wang ◽  
Anastasia Potanina ◽  
Stephen R Quake
Keyword(s):  
Single Cells ◽  
Whole Genome

scholarly journals MBRS-59. SINGLE-CELL WHOLE-GENOME SEQUENCING DISSECTS INTRA-TUMOURAL GENOMIC HETEROGENEITY AND CLONAL EVOLUTION IN CHILDHOOD MEDULLOBLASTOMA

2020 ◽  
Vol 22 (Supplement_3) ◽  
pp. iii408-iii408
Author(s):  
Marina Danilenko ◽  
Masood Zaka ◽  
Claire Keeling ◽  
Stephen Crosier ◽  
Rafiqul Hussain ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Single Cell ◽  
Genome Sequencing ◽  
Copy Number ◽  
Single Cell Analysis ◽  
Mutational Analysis ◽  
Single Cells ◽  
Clonal Evolution ◽  
Whole Genome ◽  
Clinically Significant

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.

scholarly journals DNA Analysis by Restriction Enzyme (DARE) enables concurrent genomic and epigenomic characterization of single cells

2019 ◽  
Vol 47 (19) ◽  
pp. e122-e122
Author(s):  
Ramya Viswanathan ◽  
Elsie Cheruba ◽  
Lih Feng Cheow
Keyword(s):  
Dna Methylation ◽  
Restriction Enzyme ◽  
Copy Number ◽  
Dna Analysis ◽  
Whole Genome Amplification ◽  
Single Cells ◽  
Whole Genome ◽  
Copy Number Alterations ◽  
Genome Wide

Abstract Genome-wide profiling of copy number alterations and DNA methylation in single cells could enable detailed investigation into the genomic and epigenomic heterogeneity of complex cell populations. However, current methods to do this require complex sample processing and cleanup steps, lack consistency, or are biased in their genomic representation. Here, we describe a novel single-tube enzymatic method, DNA Analysis by Restriction Enzyme (DARE), to perform deterministic whole genome amplification while preserving DNA methylation information. This method was evaluated on low amounts of DNA and single cells, and provides accurate copy number aberration calling and representative DNA methylation measurement across the whole genome. Single-cell DARE is an attractive and scalable approach for concurrent genomic and epigenomic characterization of cells in a heterogeneous population.

scholarly journals Combined Molecular Genetic and Cytogenetic Analysis from Single Cells after Isothermal Whole-Genome Amplification

2011 ◽  
Vol 57 (7) ◽  
pp. 1032-1041 ◽  
Author(s):  
Thomas Kroneis ◽  
Jochen B Geigl ◽  
Amin El-Heliebi ◽  
Martina Auer ◽  
Peter Ulz ◽  
...  
Keyword(s):  
Single Cell ◽  
Tumor Cells ◽  
Whole Genome Amplification ◽  
Single Cells ◽  
Molecular Genetic ◽  
Target Cells ◽  
Whole Genome ◽  
Single Cell Level ◽  
Cell Level ◽  
Genome Amplification

BACKGROUND Analysis of chromosomal aberrations or single-gene disorders from rare fetal cells circulating in the blood of pregnant women requires verification of the cells' genomic identity. We have developed a method enabling multiple analyses at the single-cell level that combines verification of the genomic identity of microchimeric cells with molecular genetic and cytogenetic diagnosis. METHODS We used a model system of peripheral blood mononuclear cells spiked with a colon adenocarcinoma cell line and immunofluorescence staining for cytokeratin in combination with DNA staining with the nuclear dye TO-PRO-3 in a preliminary study to define candidate microchimeric (tumor) cells in Cytospin preparations. After laser microdissection, we performed low-volume on-chip isothermal whole-genome amplification (iWGA) of single and pooled cells. RESULTS DNA fingerprint analysis of iWGA aliquots permitted successful identification of all analyzed candidate microchimeric cell preparations (6 samples of pooled cells, 7 samples of single cells). Sequencing of 3 single-nucleotide polymorphisms was successful at the single-cell level for 20 of 32 allelic loci. Metaphase comparative genomic hybridization (mCGH) with iWGA products of single cells showed the gains and losses known to be present in the genomic DNA of the target cells. CONCLUSIONS This method may be instrumental in cell-based noninvasive prenatal diagnosis. Furthermore, the possibility to perform mCGH with amplified DNA from single cells offers a perspective for the analysis of nonmicrochimeric rare cells exhibiting genomic alterations, such as circulating tumor cells.

scholarly journals TruePrime is a novel method for whole-genome amplification from single cells based on TthPrimPol

2016 ◽  
Vol 7 (1) ◽  
Author(s):  
Ángel J. Picher ◽  
Bettina Budeus ◽  
Oliver Wafzig ◽  
Carola Krüger ◽  
Sara García-Gómez ◽  
...  
Keyword(s):  
Whole Genome Amplification ◽  
Single Cells ◽  
Whole Genome ◽  
Genome Amplification ◽  
Novel Method

scholarly journals Identification of small gains and losses in single cells after whole genome amplification on tiling oligo arrays

2009 ◽  
Vol 37 (15) ◽  
pp. e105-e105 ◽  
Author(s):  
Jochen B. Geigl ◽  
Anna C. Obenauf ◽  
Julie Waldispuehl-Geigl ◽  
Eva M. Hoffmann ◽  
Martina Auer ◽  
...  
Keyword(s):  
Whole Genome Amplification ◽  
Single Cells ◽  
Whole Genome ◽  
Genome Amplification ◽  
Gains And Losses

scholarly journals Accurate identification of single-nucleotide variants in whole-genome-amplified single cells

2017 ◽  
Vol 14 (5) ◽  
pp. 491-493 ◽  
Author(s):  
Xiao Dong ◽  
Lei Zhang ◽  
Brandon Milholland ◽  
Moonsook Lee ◽  
Alexander Y Maslov ◽  
...  
Keyword(s):  
Single Cells ◽  
Whole Genome ◽  
Single Nucleotide Variants ◽  
Accurate Identification ◽  
Single Nucleotide

scholarly journals Concurrent Whole-Genome Haplotyping and Copy-Number Profiling of Single Cells

2015 ◽  
Vol 96 (6) ◽  
pp. 894-912 ◽  
Author(s):  
Masoud Zamani Esteki ◽  
Eftychia Dimitriadou ◽  
Ligia Mateiu ◽  
Cindy Melotte ◽  
Niels Van der Aa ◽  
...  
Keyword(s):  
Copy Number ◽  
Single Cells ◽  
Whole Genome

scholarly journals A Simple Method for Encapsulating Single Cells in Alginate Microspheres Allows for Direct PCR and Whole Genome Amplification

PLoS ONE ◽  
2015 ◽  
Vol 10 (2) ◽  
pp. e0117738 ◽  
Author(s):  
Saharnaz Bigdeli ◽  
Roger O. Dettloff ◽  
Curtis W. Frank ◽  
Ronald W. Davis ◽  
Laurel D. Crosby
Keyword(s):  
Whole Genome Amplification ◽  
Single Cells ◽  
Whole Genome ◽  
Direct Pcr ◽  
Simple Method ◽  
Genome Amplification
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