Techiques

Question 1

Peptide nucleic acid FISH

Answer 1

PNA against an organism-specific ribosomal RNA which is conjugated to a fluorophore

Question 2

PCR ESI-MS

Answer 2

PCR electronspray ionization-mass spec

Starts with PCR amplification of organism-specific 16S ribosomal RNAs - then those amplicons are submitted directly for mass spec after nucleic acid purification.

Works very well as long as organisms differ in 16S rRNA sequence.

Question 3

Steps for karyotyping

Answer 3

Isolated live cells

Culture

Treat cells with colchicine

Put cells in a hypotonic solution to cause cell swelling, spreading the chromosomes out

Fix in methanol-acetic acid buffer

Splat the cells to spread the metaphase chromosomes on a glass slide

Question 4

Traditional stain for chromosomes

Answer 4

Giemsa

The “G” in “G-banding” actually stands for Giemsa.

Question 5

Resolution of karyotype

Answer 5

3-5 megabases

ie, 3,000,000-5,000,000 bases

Question 6

Approximate human genome size

Answer 6

3 x 10^9 bases

Question 7

Why do we use a 5 micron section for FISH?

Answer 7

5 microns is approximately the size of the average cell, so you are getting roughly a monolayer

Question 8

Why are G’s a problem with NGS?

Answer 8

When you use two color encoding:
T = green
C = red
A = green + red
G = nothing

So, towards the end of the read, you will get serial “G’s”

Question 9

Confidence strand

Answer 9

A = 65
E = 101

Numbers are in ASCII code to match one character to one character

Question 10

Thread quality

Answer 10

20 = 1% error rate
30 = 1 per 1,000
40 = 1 per 10,000

Question 11

Array CHG

Answer 11

Array comparative genomic hybridization

Take red-labeled patient DNA and green-labeled control DNA, then that DNA is applied to an array of wells with probes that represent spaced on genome sequences.

Based on the relative normalized intensity in each well of the array, you can then determine whether there has been a gain or loss in the patient DNA compared to the control DNA.

It’s like FISH in reverse – the probe is in situ and the DNA is mobilized.

Question 12

Array CGH readout

Answer 12

Each well is expressed as log2(R/G), such that no difference = log2(1/1) = 0.

We define a “significant difference” as having a value greater than 0.25 or less than -0.25, but really we still wouldn’t believe a single point elevation. Rather, we would want to see a difference across a range of positions (usually at least 5) which are adjacent to one another in the chromosomal sequence.

Question 13

Resolution of aCGH

Answer 13

10’s of kbs (at its best, when wells represent 1,000 bp spacing)

Question 14

What does aCGH miss that karyotype and FISH can see?

Answer 14

Translocations and inversions

Polyploidy (3n genome rather than 2n, as in a partial hydatidiform mole)

Otherwise copy number neutral mutations

Question 15

Two flavors of uniparental disomy

Answer 15

Isodisomy: A region of a chromosome inherited from mom is lost, but is replaced by a copy of the same region from dad’s chromosome. This produces a copy number neutral karyotype, but with homozygosity within this region.

Heterodisomy: A region of a chromosome inherited from mom is lost, and is replaced by a copy of another region of dad’s DNA. This produces a copy number gain at one site and loss at another.

Question 16

When does cold ischemic time factor in to PCR amplification?

Answer 16

Even 24 hours of cold ischemic time does not affect the success rate of PCR amplification.

Question 17

When does cold ischemic time factor in to RNA quatitation?

Answer 17

Up to 12 hours out has been shown to still be effective for analysis, but less than 12 hours is generally recommended.

Question 18

As a matter of quality, the goal for ALL specimens where molecular techniques will be employed should be to have a cold ischemic time of. . .

Answer 18

. . . less than 1 hour

Question 19

Effects of formalin fixation on DNA

Answer 19

Can lead to shorter average DNA fragments and cause random cytosine deamination

Question 20

Pyrosequencing

Answer 20

Sequencing-by-synthesis method

Utilizes a series of reactions to measure the release of inorganic pyrophosphate as each nucleotide is incorporated into the DNA chain

Question 21

Melting curve analysis

Answer 21

Detection of mutations by measuring the changes in fluorescence generated by different dissociation curves between wild-type and mutated samples.

Used to detect single base pair substitutions and small indels. Can also be used to detect methylation status of a specific region.

Fast, close-ended system that is not labor intensive.

Importantly, this assay detects that a mutation is present, but now what mutation is present.

Sensitive to a VAF of around 10%.

Question 22

Methylation sequencing

Answer 22

NGS with the ability to read 5-methylcytosine

Question 23

“Generations” of NGS

Answer 23

Question 24

“Ion torrent” sequencing or “semiconductor” sequencing

Answer 24

Detects small changes in pH from H+ released by nucleotide incorporation.

The alternative to pyrosequencing for sequencing by synthesis and reading byproducts of nucleotide incorporation.

Question 25

Comparison of the major NGS platforms’ strengths and weaknesses

Answer 25