Bonus lesson: Precision Oncology Glossary and links.

Glossary:

Key terms help you in understanding clinical encounters and are provided for reference in a glossary that covers the specific vocabulary relevant to the clinical linkage.
Below are the key terms from this clinical linkage, listed alphabetically.
A complete glossary of all terms can be found under the ‘references’ heading on the home page.

Copy Number Variants (CNVs) Variation in the number of copies of a particular gene compared to a reference standard.
Drivers Mutations in oncogenes rendering them constitutively active, central control points for the progression of malignancies.
FusionsFusions exist where genetic information is brought together in the wrong place. The presence of certain chromosomal aberrations and their resulting fusion genes is commonly used within cancer diagnostics in order to set a precise diagnosis. Gene 1 and gene 2 of two chromosomes join incorrectly, resulting in a fusion protein.
Genetics Genetics is a branch of biology concerned with the study of genes, genetic variation, and heredity in organisms.
Gene panel A test that analyzes multiple genes at once. The scope of a panel refers to the number of genes to be tested.
Genome The genome is the total genetic information of humans.
GenomicsThe study and understanding of the genome.
IndelsShort for insertions or deletions, describe the relative gain or loss of a segment of one or more nucleotides in a genomic sequence. It is a genetic alteration, where chunks of genetic information during DNA replication have been added or deleted in a cell.
Liquid biopsy A test done on a sample of blood to look for cancer cells from a tumor that are circulating in the blood or for pieces of DNA from tumor cells that are in the blood. A liquid biopsy may be used to help find cancer at an early stage. It may also be used to help plan treatment or to find out how well treatment is working or if cancer has come back. Being able to take multiple samples of blood over time may also help doctors understand what kind of molecular changes are taking place in a tumor.
Mutations Mutations play an important role in the development of cancer. They cause a cell to make (or not make) proteins that affect how the cell grows and divides into new cells.
Next Generation Sequencing (NGS)Next Generation Sequencing (NGS) technology is a massively parallel sequencing technology, with the aid of computer technologies, to identify complex DNA sequences.
Nucleotide A nucleotide is the basic building block of DNA and RNA, there four types, A’s, T’s, G’s, and C’s.
Precision Oncology Precision genomics or precision oncology is defined as the molecular profiling of tumors to identify targetable alterations.
Proteins Proteins are large and complex molecules, made up of thousands of smaller units, amino acids. They are required for the structure, function, and regulation of the body’s tissues and organs.
Read depthAlso known as sequencing depth, describes the number of times that a given nucleotide in the genome has been read in an experiment. These are individually read and then bioinformatically overlapped or “tiled” to generate longer contiguous sequences making up the meaningful end data.
RNARibonucleic acid (RNA) is a polymeric molecule, essential in various biological roles in coding, decoding, regulation, and expression of genes. RNA and DNA are nucleic acids. The nitrogenous bases in RNA are adenine (A), guanine (G), cytosine (C), and uracil (U), which replaces thymine (T) in DNA.
Single Nucleotide Variant (SNVs) A variation in a single nucleotide without any limitations of frequency and may arise in somatic cells. A somatic single-nucleotide variation (e.g., caused by cancer) may also be called a single-nucleotide alteration.
Single Nucleotide Polymorphism (SNPs) An SNV which occurs in at least 1-2% of the population.
Suppressors Natural tumor pathogenesis control, can cause cancer progression when inactivated through mutation or allele loss.
VariantAn alteration in a DNA nucleotide sequence. The term variant is used more and more in place of the term mutation, meaning an alteration that may be benign, pathogenic, or of unknown significance.
Whole Exome Sequencing (WES) The method of sequencing all of the protein-coding regions of genes in a genome (the exome). Exons constitute about 1% of the human genome, and can therefore be sequenced at a lower cost than Whole-Genome Sequencing (WGS).
Whole Genome Sequencing (WGS)The process of determining the complete DNA sequence of a genome.
Whole Transcriptome Sequencing (WTS)This creates a view of the complete complement of transcripts in a specific cell, like mRNA and all non-coding RNAs. This method is useful when healthy and disease states are compared.

Links to extra material:

Links to sources of video’s and images:

  • Course page: Video The promise of Precision Oncology. Source Youtube; Novartis Oncology.
  • 1: Video Precision medicine. Copyright Henry Ford TV.
  • 1.1: Video Precision medicine. Copyright Henry Ford TV.
  • 1.2: Video How Precision Oncology is making strides in the fight against cancer. By Micron/greatbigstory.com.
  • 2.3: several images; source Wikipedia.
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