Genetic Testing Flashcards
Nomenclature for variants:
We have to specify a ___ and a ____ and indicate what the ____ to interpret is.
Location
Change
Reference
____ ____ ____ is the most common way to represent variance in clinical applications
___: counts in coding sequence from the first A of the start ATG as 1
__: numbers the amino acids with the first with methionine as 1
Coding sequence coordinates
c
p
For coding or protein locations note ___ ___ is used.
Which transcript
A ____ is a permanent change in DNA sequence. A ____ is a variant with a frequency in the population greater than 1%.
Variant
Polymorphism
Single nucleotide variants are changes at just ___ base. They can be missense or nonsense. Insertion or deletion, resulting in ____.
One
Frameshift
Insertion or deletion’s that are greater than 50 base pairs is called a ___ ___. Larger deletions are insertions above 1000 base pairs are sometimes called ___ ___ variants.
Structural variant
Copy number
Next generation sequencing (NGS) looks at ____ of sequences. They have ___ that look at sequences of lists of genes. And ____ which looks at coding regions and edges of introns/exons.
Thousands
Panels
Exome
Exome is a ____ driven analysis. It often as sent as trio with parents sequenced also.
Phenotype
Sanger sequencing looks at a _____ sequence of a few hundred base pairs out of time
Target
Chromosomal microarray analysis looks for _____ ____ variants.
Copy number
Methylation testing looks for DNA ____ changes.
Methylation
In Sanger,
_____ (ddNTPs) have a removal of a hydroxyl group from the ribose, and another base cannot be added to the chain, therefore ____ the sequence. This leads to a mix of sizes of DNA ____ matching the template sequence, but of varying lengths
Dideoxynucleotides
Terminating
Oligos
Next generation sequencing relies on making copies of ____ of small fragments of the template DNA. Each base ____ ___ when added, and a camera takes a picture of each addition. Each spot corresponds to a specific piece of template. This results in millions of short reads of sequence from the template all being sequenced at once.
Millions
Lights up
Next generation sequencing:
For tests looking at heterozygous or homozygous and alien type of variance the goal is to have at least ____ reads of each spot of interest
30
Next generation sequencing:
For tests looking at somatic, mosaic, or cancer variation, the goal is to have ____ of reads at each spot of interest
Hundreds
____ ____ means more reads at a given spot. It means higher accuracy calling bases and greater ability to call variants that are present at a low allele fraction
Higher coverage
NGS overall process:
_____ ____ is good for a targeted assessment of a known region or a series of known regions. It is often used as a ____ for variants found on NGS.
Sanger sequencing
Confirmation
Sanger sequencing is efficient and ___ effective at a small scale. Mostly ____ assessment of mixes of alleles.
Cost
Qualitative
Next generation sequencing can be used for ____ or ____ assessment of ___ or ____ genes.
Targeted
Untargeted
Known
Unknown
___ ___ ___ is more likely to yield variance of uncertain significance
Next generation sequencing
___/___ allows for precise gene editing. It is derived from bacteria. It includes a ____ endonuclease that cuts DNA as a double strand break in a known location based on target sequence. _____ ____ ____ of the breaks leads to a deletion.
CRISPR/Cas9
Cas9
Nonhomologous end joining
____ makes many copies of a sequence between two primer sequences. DNA template is denatured by heat. Primers bind. DNA is denatured again. Primers bind again and start copying. Multiple cycles.
PCR
____ ____: DNA is cut into smaller pieces by enzymes and separated on a gel by electrophoresis. Blot the separated DNA from gel to a membrane. Hybridize the membrane with labeled probe.
