Ultrasensitive Multiparameter Phenotyping of Rare Cells Using an Integrated Digital‐Molecular‐Counting Microfluidic Well Plate

Small ◽  
2021 ◽  
pp. 2101743
Author(s):  
Shiuan‐Haur Su ◽  
Yujing Song ◽  
Michael W. Newstead ◽  
Tao Cai ◽  
MengXi Wu ◽  
...  
Keyword(s):  
Rare Cells

scholarly journals Red panda: a novel method for detecting variants in single-cell RNA sequencing

BMC Genomics ◽  
2020 ◽  
Vol 21 (S11) ◽  
Author(s):  
Adam Cornish ◽  
Shrabasti Roychoudhury ◽  
Krishna Sarma ◽  
Suravi Pramanik ◽  
Kishor Bhakat ◽  
...  
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Articular Chondrocytes ◽  
Genetic Diseases ◽  
Simulated Data ◽  
Single Nucleotide ◽  
Single Cell Rna Sequencing ◽  
Red Panda ◽  
Novel Method ◽  
Rare Cells

Abstract Background Single-cell sequencing enables us to better understand genetic diseases, such as cancer or autoimmune disorders, which are often affected by changes in rare cells. Currently, no existing software is aimed at identifying single nucleotide variations or micro (1-50 bp) insertions and deletions in single-cell RNA sequencing (scRNA-seq) data. Generating high-quality variant data is vital to the study of the aforementioned diseases, among others. Results In this study, we report the design and implementation of Red Panda, a novel method to accurately identify variants in scRNA-seq data. Variants were called on scRNA-seq data from human articular chondrocytes, mouse embryonic fibroblasts (MEFs), and simulated data stemming from the MEF alignments. Red Panda had the highest Positive Predictive Value at 45.0%, while other tools—FreeBayes, GATK HaplotypeCaller, GATK UnifiedGenotyper, Monovar, and Platypus—ranged from 5.8–41.53%. From the simulated data, Red Panda had the highest sensitivity at 72.44%. Conclusions We show that our method provides a novel and improved mechanism to identify variants in scRNA-seq as compared to currently existing software. However, methods for identification of genomic variants using scRNA-seq data can be still improved.

scholarly journals Ultrasensitive Clinical Enumeration of Rare Cells ex Vivo Using a Micro-Hall Detector

2012 ◽  
Vol 4 (141) ◽  
pp. 141ra92-141ra92 ◽  
Author(s):  
D. Issadore ◽  
J. Chung ◽  
H. Shao ◽  
M. Liong ◽  
A. A. Ghazani ◽  
...  
Keyword(s):  
Ex Vivo ◽  
Rare Cells

Raman spectroscopy-based label-free cell identification using wavelet transform and support vector machine

RSC Advances ◽  
2016 ◽  
Vol 6 (55) ◽  
pp. 50027-50033 ◽  
Author(s):  
S. Bakhtiaridoost ◽  
H. Habibiyan ◽  
S. Muhammadnejad ◽  
M. Haddadi ◽  
H. Ghafoorifard ◽  
...  
Keyword(s):  
Support Vector Machine ◽  
Raman Spectroscopy ◽  
Wavelet Transform ◽  
Raman Spectra ◽  
Free Cell ◽  
Support Vector ◽  
Label Free ◽  
Cell Identification ◽  
Rare Cells

Wavelet transform and SVM applied to Raman spectra makes a powerful and accurate tool for identification of rare cells such as CTCs.

scholarly journals Reversible Immunoaffinity Interface Enables Dynamic Manipulation of Trapping Force for Accumulated Capture and Efficient Release of Circulating Rare Cells

2021 ◽  
pp. 2102070
Author(s):  
Xiaofeng Chen ◽  
Hongming Ding ◽  
Dongdong Zhang ◽  
Kaifeng Zhao ◽  
Jiafeng Gao ◽  
...  
Keyword(s):  
Trapping Force ◽  
Rare Cells ◽  
Dynamic Manipulation

High-grade Urothelial Carcinoma with Malignant Melanocytic Differentiation

2021 ◽  
pp. 106689692110004
Author(s):  
Hongzhi Xu ◽  
Elizabeth M. Genega ◽  
Liyan Zhuang ◽  
Ming Zhou
Keyword(s):  
Urothelial Carcinoma ◽  
Bladder Wall ◽  
Minor Component ◽  
Asian Woman ◽  
High Grade ◽  
Therapeutic Implications ◽  
Divergent Differentiation ◽  
Rare Cells ◽  
A Minor ◽  
Melanocytic Differentiation

Urothelial carcinoma usually shows divergent differentiation and variant histology with squamous and glandular morphology being most common. In this report, we present a case of divergent malignant melanocytic differentiation in a high-grade urothelial carcinoma. A 98-year-old East Asian woman with an anterior bladder wall mass underwent resection, which revealed a high-grade poorly differentiated tumor. A minor component of high-grade papillary urothelial carcinoma and carcinoma in situ is also present. The majority of the tumor cells are morphologically and immunohistochemically consistent with melanoma, a minority of cells are positive for urothelial markers, and rare cells coexpress both melanocytic and urothelial markers. Cells that express melanocytic markers or urothelial markers are intimately admixed together. Taken together, a diagnosis of high-grade urothelial carcinoma with malignant melanocytic differentiation was rendered. This is the first report in the literature of malignant melanocytic differentiation in a high-grade urothelial carcinoma, a finding that may have important diagnostic and therapeutic implications.

Sheathless acoustic based flow cell sorter for enrichment of rare cells

2021 ◽  
Author(s):  
Ce Wang ◽  
Yuting Ma ◽  
Zhiguo Pei ◽  
Feifei Song ◽  
Jinfeng Zhong ◽  
...  
Keyword(s):  
Flow Cell ◽  
Cell Sorter ◽  
Rare Cells

scholarly journals Discovery of rare cells from voluminous single cell expression data

2018 ◽  
Vol 9 (1) ◽  
Author(s):  
Aashi Jindal ◽  
Prashant Gupta ◽  
Jayadeva ◽  
Debarka Sengupta
Keyword(s):  
Single Cell ◽  
Expression Data ◽  
Rare Cells ◽  
Cell Expression

scholarly journals Definitive Hematopoietic Stem Cells Minimally Contribute to Embryonic Hematopoiesis

2021 ◽  
Author(s):  
Bianca A Ulloa ◽  
Samima S Habbsa ◽  
Kathryn S Potts ◽  
Alana Lewis ◽  
Mia McKinstry ◽  
...  
Keyword(s):  
Stem Cells ◽  
Hematopoietic Stem Cells ◽  
De Novo ◽  
Marker Gene ◽  
Lineage Tracing ◽  
Hematopoietic Stem ◽  
Functional Potential ◽  
Injury Model ◽  
Rare Cells

Hematopoietic stem cells (HSCs) are rare cells that arise in the embryo and sustain adult hematopoiesis. Although the functional potential of nascent HSCs is detectable by transplantation, their native contribution during development is unknown, in part due to the overlapping genesis and marker gene expression with other embryonic blood progenitors. Using single cell transcriptomics, we defined gene signatures that distinguish nascent HSCs from embryonic blood progenitors. Applying a new lineage tracing approach, we selectively tracked HSC output in situ and discovered significantly delayed lymphomyeloid contribution. Using a novel inducible HSC injury model, we demonstrated a negligible impact on larval lymphomyelopoiesis following HSC depletion. HSCs are not merely dormant at this developmental stage as they showed robust regeneration after injury. Combined, our findings illuminate that nascent HSCs self-renew but display differentiation latency, while HSC-independent embryonic progenitors sustain developmental hematopoiesis. Understanding the differences among embryonic HSC and progenitor populations will guide improved de novo generation and expansion of functional HSCs.

scholarly journals The SCL/TAL-1 gene is expressed in progenitors of both the hematopoietic and vascular systems during embryogenesis

Blood ◽  
1994 ◽  
Vol 83 (5) ◽  
pp. 1200-1208 ◽  
Author(s):  
AR Kallianpur ◽  
JE Jordan ◽  
SJ Brandt
Keyword(s):  
T Cell ◽  
Neural Development ◽  
Fetal Liver ◽  
Chromosomal Rearrangements ◽  
Chromosomal Translocation ◽  
Cell Types ◽  
Hematopoietic Differentiation ◽  
Helix Loop Helix ◽  
Adult Mice ◽  
Rare Cells

Activation of the SCL (or TAL-1) gene as a result of chromosomal translocation or deletion is a frequent molecular lesion in acute T- cell leukemia. By virtue of its membership in the basic helix-loop- helix family of transcription factors, the SCL gene is a candidate to regulate events in hematopoietic differentiation. We have used polyclonal antibody raised against a bacterial expressed malE-SCL fusion protein to characterize SCL protein expression in postimplantation embryos and in neonatal and adult mice. SCL protein was detected at day 7.5 post coitum at both embryonic and extraembryonic sites, approximately 24 hours before the formation of recognizable hematopoietic elements. Expression then localized to blood islands of the yolk sac followed by localization to fetal liver and spleen, paralleling the hematopoietic activity of these tissues during development. SCL protein was detected in erythroblasts in fetal and adult spleen, myeloid cells and megakaryocytes in spleen and bone marrow, mast cells in skin, and in rare cells in fetal and adult thymus. In addition, SCL protein was noted in endothelial progenitors in blood islands and in endothelial cells and angioblasts in a number of organs at times coincident with their vascularization. SCL expression was also observed in other nonhematopoietic cell types in the developing skeletal and nervous systems. These results show that SCL expression is one of the earliest markers of mammalian hematopoietic development and are compatible with a role for this transcription factor in terminal differentiation of the erythroid and megakaryocytic lineages. SCL expression by cells in the thymus suggests that the gene may be active at some stage of T-cell differentiation and may be relevant to its involvement by chromosomal rearrangements in T- lymphoid leukemias. Finally, expression of the gene in developing brain, cartilage, and vascular endothelium indicates SCL may have actions in neural development, osteogenesis, and vasculogenesis, as well as in hematopoietic differentiation.

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