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Archive for the ‘cancer-general’ Category


Reporter: Danielle Smolyar, Research Assistant 3 – Text Analysis for 2.0 LPBI Group’s TNS #1 – 2020/2021 Academic Internship in Medical Test Analysis (MTA) 

Reporting on a Study published on July 6, 2021 by  Oregon Health & Science University

Recently, researchers have found many ways to manipulate and alter gene activity in specific cells. As a result of seeing this alteration, it has caused much development and progress in understanding cancer, brain function, and immunity.

IMAGE SOURCE: 3D-model of DNA. Credit: Michael Ströck/Wikimedia/ GNU Free Documentation Lic

Tissues and Organs are composed of cells that look the same but have different roles. For example, single-cell analysis allows us to research and test the cells within an organ or cancerous tumor. However, the single-cell study has its boundaries and limits in trying a more significant number of cells. This result is not an accurate data and analysis of the cells.

Andrew Adey, Ph.D., the senior author of a paper in Nature Biotechnology, https://www.nature.com/articles/s41587-021-00962-z

Mulqueen, R. M., Pokholok, D., O’Connell, B. L., Thornton, C. A., Zhang, F., O’Roak, B. J., Link, J., Yardımcı, G. G., Sears, R. C., Steemers, F. J., & Adey, A. C. (2021, July 5). High-content single-cell combinatorial indexing. Nature News. https://www.nature.com/articles/s41587-021-00962-z

states that the new method gives us the ability to have a ten-fold improvement in the amount of DNA produced from a single DNA sequence. A DNA sequence is composed of units which are called bases. The sequence puts the bases in chronological order for it to code correctly. 

To understand cancer better, single-cell studies are a crucial factor in doing so. Different cells catch on to other mutations in the DNA sequence in a cancerous tumor, which ultimately alters the DNA sequence. This results in tumor cells with new alterations, which could eventually spread to the rest of the body. 

Adey and his team provided evidence that the method they had created can show DNA alterations that have come from cells present in tumor samples from patients with pancreatic cancer. Adey stated,

quote “For example, you can potentially identify rare cell subtypes within a tumor that are resistant to therapy.” 

Abey and his team have been working with OHSU Knight Cancer Institute, and with them, they are testing a single-cell method to see if patients’ tumors have changed by doing chemo or drug therapy. 

This new method allows itself to create DNA libraries and fragments of DNA that helps analyze the different genes and mutations within the sequence. This method uses something called an enzymatic reaction that attaches primers to the end of each DNA fragment.  For the cells to be analyzed, each primer must be present on both ends of the fragment. 

As a result of this new method, all library fragments present must-have primers on both ends of the fragments. At the same time, it improves efficiency by reducing its sequencing  price overall, that these adapters can be used instead of the regular custom workflows. 

SOURCE

Original article:

Mulqueen, R.M., Pokholok, D., O’Connell, B.L. et al. High-content single-cell combinatorial indexing. Nat Biotechnol (2021). https://doi.org/10.1038/s41587-021-00962-z

Research categories – Cell biology, cancer-general, research, DNA Fragment TAGS- DNA, sequencing, cell fragments, single-cell

Other related articles published on this Open Access Online Scientific Journal include the following: 

Series B: Frontiers in Genomics Research

Series Content Consultant:

Larry H. Bernstein, MD, FCAP, Emeritus CSO, LPBI Group

Volume Content Consultant:

Prof. Marcus W. Feldman

BURNET C. AND MILDRED FINLEY WOHLFORD PROFESSOR IN THE SCHOOL OF HUMANITIES AND SCIENCES

Stanford University, Co-Director, Center for Computational, Evolutionary and Human Genetics (2012 – Present)

Latest in Genomics Methodologies for Therapeutics:

Gene Editing, NGS & BioInformatics,

Simulations and the Genome Ontology

2019

Volume Two

https://www.amazon.com/dp/B08385KF87

 

Part 4: Single Cell Genomics

Introduction to Part 4: Single Cell Genomics – Voice of Aviva Lev-Ari & Stephen Williams


4.1 The Science

4.1.1   Single-cell biology

Special | 05 July 2017

https://www.nature.com/collections/gbljnzchgg

4.1.2   The race to map the human body — one cell at a time, A host of detailed cell atlases could revolutionize understanding of cancer and other diseases

https://www.nature.com/news/the-race-to-map-the-human-body-one-cell-at-a-time-1.21508

4.1.3   Single-cell Genomics: Directions in Computational and Systems Biology – Contributions of Prof. Aviv Regev @Broad Institute of MIT and Harvard, Cochair, the Human Cell Atlas Organizing Committee with Sarah Teichmann of the Wellcome Trust Sanger Institute

Curator: Aviva Lev-Ari, PhD, RN

4.1.4   Cellular Genetics

https://www.sanger.ac.uk/science/programmes/cellular-genetics

4.1.5   Cellular Genomics

https://www.garvan.org.au/research/cellular-genomics

4.1.6   SINGLE CELL GENOMICS 2019 – sometimes the sum of the parts is greater than the whole, September 24-26, 2019, Djurönäset, Stockholm, Sweden http://www.weizmann.ac.il/conferences/SCG2019/single-cell-genomics-2019

Reporter: Aviva Lev-Ari, PhD, RN

4.1.7   Norwich Single-Cell Symposium 2019, Earlham Institute, single-cell genomics technologies and their application in microbial, plant, animal and human health and disease, October 16-17, 2019, 10AM-5PM

Reporter: Aviva Lev-Ari, PhD, RN

4.1.8   Newly Found Functions of B Cell

Reporter and Curator: Dr. Sudipta Saha, Ph.D.

4.1.9 RESEARCH HIGHLIGHTS: HUMAN CELL ATLAS

https://www.broadinstitute.org/research-highlights-human-cell-atlas

4.2 Technologies and Methodologies

4.2.1   How to build a human cell atlas – Aviv Regev is a maven of hard-core biological analyses. Now she is part of an effort to map every cell in the human body.

Anna Nowogrodzki, 05 July 2017, Article tools

https://www.nature.com/news/how-to-build-a-human-cell-atlas-1.22239

4.2.2   Featuring Computational and Systems Biology Program at Memorial Sloan Kettering Cancer Center, Sloan Kettering Institute (SKI), The Dana Pe’er Lab

Reporter: Aviva Lev-Ari, PhD, RN

4.2.3   Genomic Diagnostics: Three Techniques to Perform Single Cell Gene Expression and Genome Sequencing Single Molecule DNA Sequencing

Curator: Aviva Lev-Ari, PhD, RN

4.2.4   Three Technology Leaders in Single Cell Sequencing: 10X Genomics, Illumina and MissionBio

Reporter: Aviva Lev-Ari, PhD, RN

4.2.5   scPopCorn: A New Computational Method for Subpopulation Detection and their Comparative Analysis Across Single-Cell Experiments

Reporter and Curator: Dr. Sudipta Saha, Ph.D.

4.2.6   Nano-guided cell networks: new methods to detect intracellular signaling and implications

Curator: Stephen J. Williams, PhD

4.3 Clinical Aspects

4.3.1 Using single cell sequencing data to model the evolutionary history of a tumor.

Kim KI, Simon R.

BMC Bioinformatics. 2014 Jan 24;15:27. doi: 10.1186/1471-2105-15-27.

PMID:

4.3.2   eProceedings 2019 Koch Institute Symposium – 18th Annual Cancer Research Symposium – Machine Learning and Cancer, June 14, 2019, 8:00 AM-5:00 PM ET MIT Kresge Auditorium, 48 Massachusetts Ave, Cambridge, MA

Real Time Press Coverage: Aviva Lev-Ari, PhD, RN

4.3.3   The Impact of Heterogeneity on Single-Cell Sequencing

Samantha L. Goldman1,2, Matthew MacKay1,2, Ebrahim Afshinnekoo1,2,3, Ari M. Melnick4, Shuxiu Wu5,6 and Christopher E. Mason1,2,3,7*

https://www.frontiersin.org/articles/10.3389/fgene.2019.00008/full

4.3.4   Single-cell approaches to immune profiling

https://www.nature.com/articles/d41586-018-05214-w

4.3.5   Single-cell sequencing made simple. Data from thousands of single cells can be tricky to analyse, but software advances are making it easier.

by Jeffrey M. Perkel

https://www.nature.com/news/single-cell-sequencing-made-simple-1.22233

4.3.6  Single-cell RNA-seq helps in finding intra-tumoral heterogeneity in pancreatic cancer

Reporter and Curator: Dr. Sudipta Saha, Ph.D.

4.3.7 Cancer Genomics: Multiomic Analysis of Single Cells and Tumor Heterogeneity

Curator: Stephen J. Williams, PhD

4.4 Business and Legal

4.4.1   iBioChips integrate diagnostic assays and cellular engineering into miniaturized chips that achieve cutting-edge sensitivity and high-throughput. We have resolved traditional biotech challenges with innovative biochip approaches

https://ibiochips.com/?gclid=Cj0KCQjwuLPnBRDjARIsACDzGL0wb6u79VHHkftodfApMYs-oxI-5cOZIBUaELdmd2wDOIk3W0OQg2caAqMyEALw_wcB

4.4.2   Targeted Single-Cell Solutions for High Impact Applications – Mission Bio’s Tapestri® Platform is the only technology that provides single-cell targeted DNA sequencing at single-base resolution.

Part 4: Summary – Single Cell Genomics – Voice of Stephen Williams

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