Genetic Testing

Question 1

Nomenclature for variants:
We have to specify a ___ and a ____ and indicate what the ____ to interpret is.

Answer 1

Location
Change
Reference

Question 2

____ ____ ____ 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

Answer 2

Coding sequence coordinates
c
p

Question 3

For coding or protein locations note ___ ___ is used.

Answer 3

Which transcript

Question 4

A ____ is a permanent change in DNA sequence. A ____ is a variant with a frequency in the population greater than 1%.

Answer 4

Variant
Polymorphism

Question 5

Single nucleotide variants are changes at just ___ base. They can be missense or nonsense. Insertion or deletion, resulting in ____.

Answer 5

One
Frameshift

Question 6

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.

Answer 6

Structural variant
Copy number

Question 7

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.

Answer 7

Thousands
Panels
Exome

Question 8

Exome is a ____ driven analysis. It often as sent as trio with parents sequenced also.

Answer 8

Phenotype

Question 9

Sanger sequencing looks at a _____ sequence of a few hundred base pairs out of time

Answer 9

Target

Question 10

Chromosomal microarray analysis looks for _____ ____ variants.

Answer 10

Copy number

Question 11

Methylation testing looks for DNA ____ changes.

Answer 11

Methylation

Question 12

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

Answer 12

Dideoxynucleotides
Terminating
Oligos

Question 13

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.

Answer 13

Millions
Lights up

Question 14

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

Answer 14

30

Question 15

Next generation sequencing:
For tests looking at somatic, mosaic, or cancer variation, the goal is to have ____ of reads at each spot of interest

Answer 15

Hundreds

Question 16

____ ____ 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

Answer 16

Higher coverage

Question 17

NGS overall process:

Answer 17

Question 18

_____ ____ 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.

Answer 18

Sanger sequencing
Confirmation

Question 19

Sanger sequencing is efficient and ___ effective at a small scale. Mostly ____ assessment of mixes of alleles.

Answer 19

Cost
Qualitative

Question 20

Next generation sequencing can be used for ____ or ____ assessment of ___ or ____ genes.

Answer 20

Targeted
Untargeted
Known
Unknown

Question 21

___ ___ ___ is more likely to yield variance of uncertain significance

Answer 21

Next generation sequencing

Question 22

___/___ 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.

Answer 22

CRISPR/Cas9
Cas9
Nonhomologous end joining

Question 23

____ 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.

Answer 23

PCR

Question 24

____ ____: 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.

Question 25

____ ____: RNA gel electrophoresis and blotting. RNAs move though the gel by electric current.

Answer 25

Northern blot

Question 26

____ ___: protein gel electrophoresis and blotting. Relies on antigen-antibody interactions for detection.

Answer 26

Western blot

Question 27

____/____ microarray: A patient sample genomic DNA is compared to a pool of unaffected individuals genomes. More binding means duplications. Less binding means deletions.

Answer 27

CGH/Oligonucleotide

Question 28

____ microarray: probes are paired with different alleles of SNPs represented. Genotyping of thousands of SNPs at the same time.

Answer 28

Genotyping

Question 29

When do we get genetic tests?

Answer 29

Question 30

What type of testing when?

Answer 30

Question 31

A ___ variant effects both alleles. A ___ variant has two mutations on the same allele.

Answer 31

Trans
Cis

Question 32

If a mutation arises ____ it is more suspicious and more likely be cause disease

Answer 32

De Novo

Question 33

____, including nonsense, splice, or frameshift, are strong evidence of disease causing variations

Answer 33

Nulls

Question 34

A pathogenic variant will generally not be present in ____ frequency in healthy individuals

Answer 34

High

Question 35

Anything with a frequency greater than __% in any population is strong evidence of a benign variant

Answer 35

5

Question 36

_____ is the most widely used population database. Some populations are not well represented in this database

Answer 36

gnomAD

Question 37

Variants in under sampled populations are more likely to be reported as ___ ___.

Answer 37

Uncertain significance

Question 38

Trans versus cis:
Trans is more likely to be ____ because both alleles are affected

Answer 38

Pathologic