scholarly journals SiCloneFit: Bayesian inference of population structure, genotype, and phylogeny of tumor clones from single-cell genome sequencing data

2019 ◽  
Vol 29 (11) ◽  
pp. 1847-1859 ◽  
Author(s):  
Hamim Zafar ◽  
Nicholas Navin ◽  
Ken Chen ◽  
Luay Nakhleh
Keyword(s):  
Population Structure ◽  
Bayesian Inference ◽  
Single Cell ◽  
Genome Sequencing ◽  
Sequencing Data ◽  
Cell Genome ◽  
Single Cell Genome

Meiotic chromatid recombination and segregation assessed with human single cell genome sequencing data

2018 ◽  
Vol 56 (3) ◽  
pp. 156-163 ◽  
Author(s):  
Jun-Yu Ma ◽  
Li-Ying Yan ◽  
Zhen-Bo Wang ◽  
Shi-Ming Luo ◽  
William S B Yeung ◽  
...  
Keyword(s):  
Single Cell ◽  
Genome Sequencing ◽  
Homologous Chromosome ◽  
Polar Body ◽  
Human Oocyte ◽  
Sequencing Data ◽  
Homologous Chromosomes ◽  
Oocyte Meiosis ◽  
Cell Genome ◽  
Single Cell Genome

BackgroundThe human oocyte transmits one set of haploid genome into female pronucleus (FPN) while discards the remaining genome into the first polar body (PB1) and the second polar body (PB2). The FPN genome carries an assembly of maternal and paternal genome that resulted from homologous recombination during the prophase of the first meiosis. However, how parental genome has been shuffled and transmitted is difficult to assess by analysing only the progeny’s genome.ObjectiveTo assess meiotic chromatid recombination and segregation in human oocytes.MethodsSingle cell genome sequencing data of PB1, PB2 and FPN that originated from the same oocyte were used to analyse the human oocyte homologous chromosome interaction and segregation. To analyse whether chromosomes were non-randomly segregated into polar bodies or pronucleus, we analysed the ratio of crossover in PB2 and FPN, and constructed a model to detect the randomness of oocyte chromosome segregation.ResultsWe found that during oocyte meiosis, in addition to homologous chromosome recombination, there was also a genome conversion phenomenon which generated a non-reciprocal genetic information transmission between homologous chromosomes. We also inferred that during meiosis, DNA breaks and repairs frequently occurred at centromere-adjacent regions. From our data we did not find obvious evidence supporting the crossover number-based or SNP-based meiotic drive in oocytes.ConclusionIn addition to the crossover-based recombination, during human oocyte meiosis, a direct genome conversion between homologous chromosomes is used in some oocytes. Our findings are helpful in understanding the specific features of meiotic chromatid recombination and segregation in human oocytes.

Characterization of Neonatal Lung Cells Through Single Cell Genome Sequencing

2019 ◽  
Author(s):  
S. Bhattacharya ◽  
J. Lillis ◽  
C. Baker ◽  
M. Guo ◽  
J.R. Myers ◽  
...  
Keyword(s):  
Single Cell ◽  
Genome Sequencing ◽  
Lung Cells ◽  
Neonatal Lung ◽  
Cell Genome ◽  
Single Cell Genome

scholarly journals An Ultrahigh-throughput Microfluidic Platform for Single-cell Genome Sequencing

10.3791/57598 ◽  
2018 ◽  
Author(s):  
Benjamin Demaree ◽  
Daniel Weisgerber ◽  
Freeman Lan ◽  
Adam R. Abate
Keyword(s):  
Single Cell ◽  
Genome Sequencing ◽  
Microfluidic Platform ◽  
Cell Genome ◽  
Single Cell Genome

scholarly journals High throughput single-cell genome sequencing gives insights into the generation and evolution of mosaic aneuploidy in Leishmania donovani

2021 ◽  
Author(s):  
Gabriel H. Negreira ◽  
Pieter Monsieurs ◽  
Hideo Imamura ◽  
Ilse Maes ◽  
Nada Kuk ◽  
...  
Keyword(s):  
Single Cell ◽  
Genome Sequencing ◽  
High Throughput ◽  
Early Stage ◽  
Population Expansion ◽  
Cellular Heterogeneity ◽  
Small Subset ◽  
Cell Genome ◽  
Mosaic Aneuploidy ◽  
Single Cell Genome

Leishmania, a unicellular eukaryotic parasite, is a unique model for aneuploidy and cellular heterogeneity, along with their potential role in adaptation to environmental stresses. Somy variation within clonal populations was previously explored in a small subset of chromosomes using fluorescence hybridization methods. This phenomenon, termed mosaic aneuploidy (MA) might have important evolutionary and functional implications, but remains under-explored due to technological limitations. Here, we applied and validated a high throughput single-cell genome sequencing method to study for the first time the extent and dynamics of whole karyotype heterogeneity in two Leishmania clonal populations representing different stages of MA evolution in vitro. We found that drastic changes in karyotypes quickly emerge in a population stemming from an almost euploid founder cell. This possibly involves polyploidization/hybridization at an early stage of population expansion, followed by assorted ploidy reduction. During further stages of expansion, MA increases by moderate and gradual karyotypic alterations. MA usually affected a defined subset of chromosomes, of which some display enrichment in snoRNA genes which could represent an adaptative benefit to the amplification of these chromosomes. Our data provide the first complete characterization of MA in Leishmania and pave the way for further functional studies.

scholarly journals Analysis of single-cell genome sequences of bacteria and archaea

2017 ◽  
Vol 1 (3) ◽  
pp. 249-255 ◽  
Author(s):  
Robert M. Bowers ◽  
Devin F.R. Doud ◽  
Tanja Woyke
Keyword(s):  
Single Cell ◽  
Genome Sequencing ◽  
Genome Analysis ◽  
Sequence Data ◽  
Bacterial Cells ◽  
Genome Sequences ◽  
Genetic Makeup ◽  
Cell Genome ◽  
Uncultured Microorganisms ◽  
Single Cell Genome

Single-cell genome sequencing of individual archaeal and bacterial cells is a vital approach to decipher the genetic makeup of uncultured microorganisms. With this review, we describe single-cell genome analysis with a focus on the unique properties of single-cell sequence data and with emphasis on quality assessment and assurance.

scholarly journals Clonal Decomposition and DNA Replication States Defined by Scaled Single-Cell Genome Sequencing

Cell ◽  
2019 ◽  
Vol 179 (5) ◽  
pp. 1207-1221.e22 ◽  
Author(s):  
Emma Laks ◽  
Andrew McPherson ◽  
Hans Zahn ◽  
Daniel Lai ◽  
Adi Steif ◽  
...  
Keyword(s):  
Dna Replication ◽  
Single Cell ◽  
Genome Sequencing ◽  
Cell Genome ◽  
Single Cell Genome

scholarly journals Construction of thousands of single cell genome sequencing libraries using combinatorial indexing

2016 ◽  
Author(s):  
Sarah A. Vitak ◽  
Kristof A. Torkenczy ◽  
Jimi L. Rosenkrantz ◽  
Andrew J. Fields ◽  
Lena Christiansen ◽  
...  
Keyword(s):  
Single Cell ◽  
Genome Sequencing ◽  
Copy Number ◽  
Low Cost ◽  
Single Cells ◽  
Copy Number Variant ◽  
Tumor Evolution ◽  
Somatic Variation ◽  
Cell Genome ◽  
Single Cell Genome

AbstractSingle cell genome sequencing has proven to be a valuable tool for the detection of somatic variation, particularly in the context of tumor evolution and neuronal heterogeneity. Current technologies suffer from high per-cell library construction costs which restrict the number of cells that can be assessed, thus imposing limitations on the ability to quantitatively measure genomic heterogeneity within a tissue. Here, we present Single cell Combinatorial Indexed Sequencing (SCI-seq) as a means of simultaneously generating thousands of low-pass single cell libraries for the purpose of somatic copy number variant detection. In total, we constructed libraries for 16,698 single cells from a combination of cultured cell lines, frontal cortex tissue from Macaca mulatta, and two human adenocarcinomas. This novel technology provides the opportunity for low-cost, deep characterization of somatic copy number variation in single cells, providing a foundational knowledge across both healthy and diseased tissues.

Sign in / Sign up

Export Citation Format

Share Document