6. Bonus lesson: glossary and links.

Great that you have mastered this course. Our experts added some bonus material, if you are interested to deepen your knowledge further.
Read on and visit the links below to find out more about Genomics Technologies.

Bonus material

Testing techniques not covered in this course….

Fluorescentie In-Situ Hybridisatie test (FISH):
A molecular genetic technique that uses probes with fluorescent molecules to detect complementary DNA or RNA strands. The absence or presence of these DNA sequences is detected using fluorescence microscopy.

Chromogene In-Situ Hybridisatie test (CISH)
CISH is similar to FISH, but the labeling is done with biotin or digoxigenin, allowing (cheaper) bright-field microscopes to be used for detection.

Nanopore sequencing
A third-generation approach used in the sequencing of biopolymers- specifically, polynucleotides in the form of DNA or RNA. Using nanopore sequencing, a single molecule of DNA or RNA can be sequenced without the need for PCR amplification or chemical labeling of the sample.

Links to bonus course material.

Bonus puzzle

This puzzle is published in the GCHQ Puzzle Book (2016), EAN: 9780718185541

“New directions in genetic research have led to the feasibility of cloning almost any genome. Recreate the sequence of 80 base pairs from which each of these strands of nucleotides have each degraded. You may wish to carefully examine the twelve strands in their present orientations before recreating the sequence (bearing in mind common conventions such as A=1 etc. ).

Reveal the next creature to benefit from the advances of tomorrow, today!”

For your convenience you may find a representation of the DNA fragments in the next image.

Please be advised there are two layers in this puzzle. Our preferred layer is recreate the 80 base pair sequence!
Good luck finding your own solution. This puzzle nicely shows the complexity of completing the whole genome, and the advantages of using modernday’s computers.


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.

AdaptorsAdaptors Single-stranded or double-stranded synthetic oligonucleotides that can be ligated to the ends of other DNA or RNA molecules
Bridge amplificationA polymerase chain reaction (PCR) technique that embeds DNA on an oligo-decorated solid surface for cloning
Copy number variation (CNV)Variation in the number of copies of a particular gene compared to a reference standard
DNA sequencingDNA sequencing Determining the sequential order of nucleotides in DNA
DNA fragmentationSeparating or breaking DNA strands into pieces
ExomeIncludes the coding region within the genome and does not include the introns or non-coding regions
Fusion geneA hybrid gene formed from partial or complete sequences of 2 previously separate genes
Incidental findingsVariants identified that are not directly relevant to the diagnostic question
Insertion deletionInsertion or deletion of nucleotide base(s) into the genome of an organism
MicrotomeThe tool used to cut very, very thin slices of (f.i.) the biopsy tissue, preparing it for microscopic use.
Quantitative PCRAn extremely sensitive PCR-based laboratory technique that allows the accurate measurement of the amount of specific nucleic acids in a sample
PCRA technique in which segments of DNA can be amplified, generating thousands to millions of copies of a particular DNA sequence
Polyacrylamide gel electrophoresisA technique used to separate biological molecules, usually proteins or nucleic acids, based on their molecular weight
ProbeA probe is a single strand of DNA or RNA that is complementary to a nucleotide sequence that is subject to research.
Reference sequenceThis is a consensus sequence of the DNA bases of an organism. The NGS sample is compared to the reference sequence to look for alterations
Single nucleotide variant (SNV) and single nucleotide polymorphism (SNP)Variation of a single nucleotide of a particular gene between individuals (SNV). If this variant is present with some degree of frequency in a population, it referred to as a single-nucleotide polymorphism (SNP)
VariantAlteration of a DNA sequence as compared to the reference sequence that may or may not be associated with a disease state.
Variant callingThe process by which variants are identified from sequence data
Whole exome sequencing (WES)The process of determining the DNA sequence of all the coding exons of a genome
Whole genome sequencing (WGS)The process of determining the complete DNA sequence of a genome

Links to sources of video’s and images:

  • Course page, 1.1. Image of COVID-19 Real-time PCR Assay: attogene.com
  • 1.2. Image of location of DNA: https://en.wikipedia.org/wiki/DNA
  • 2.0. Image of James Watson: The Atlantic
  • 2.0 Pencil sketch of DNA double helix: Wikipedia
  • 2.1 Image of DNA, genes, and proteins: https://www.researchgate.net/figure/
  • 3.1. Video IHC: Youtube, BiogGenex Laboratories
  • 3.1 Video ICC: St. Johns Laboratory
  • 3.2 Image of thermocycler: PCRmax.com
  • 3.3 Video Overview of qPCR: New England Biolabs Inc.
  • 3.4 Video NGS: Youtube, Medical Sciences Animations
  • 3.4 Video NGS Animation: Youtube, Dr. double B
  • 3.4 Image NGS and breast cancer: biomedcentral.com
  • 3.5 Image Overnight shipping system: fishersci.com
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