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.
____ ____: RNA gel electrophoresis and blotting. RNAs move though the gel by electric current.
Northern blot
____ ___: protein gel electrophoresis and blotting. Relies on antigen-antibody interactions for detection.
Western blot
____/____ microarray: A patient sample genomic DNA is compared to a pool of unaffected individuals genomes. More binding means duplications. Less binding means deletions.
CGH/Oligonucleotide
____ microarray: probes are paired with different alleles of SNPs represented. Genotyping of thousands of SNPs at the same time.
Genotyping
When do we get genetic tests?
What type of testing when?
A ___ variant effects both alleles. A ___ variant has two mutations on the same allele.
Trans
Cis
If a mutation arises ____ it is more suspicious and more likely be cause disease
De Novo
____, including nonsense, splice, or frameshift, are strong evidence of disease causing variations
Nulls
A pathogenic variant will generally not be present in ____ frequency in healthy individuals
High
Anything with a frequency greater than __% in any population is strong evidence of a benign variant
5
_____ is the most widely used population database. Some populations are not well represented in this database
gnomAD
Variants in under sampled populations are more likely to be reported as ___ ___.
Uncertain significance
Trans versus cis:
Trans is more likely to be ____ because both alleles are affected
Pathologic
