DNA Sequencing

Question 1

DNA Sequence Information

Answer 1

The order of nucleotides in the DNA molecule

Question 2

Maxam-Gilbert Sequencing

Answer 2

A chemical sequencing method based on controlled breakage of DNA.

Question 3

Sanger Sequencing

Answer 3

A modification of the DNA replication process. Dideoxy chain termination sequencing.

Question 4

Dideoxy Chain Termination Method

Answer 4

Sanger Method. A method using dideoxynucleotides to determine the order or sequence of nucleotides in a nucleic acid.

Question 5

Internal Labeling

Answer 5

Incorporation of radioactive nucleotides in chain termination sequencing for visualization of the sequencing ladder.

Question 6

ddNTP

Answer 6

Dideoxynucleotide. Causes the new DNA chain to terminate due to the lack of the hydroxyl group found on the 3’ ribose carbon.

Question 7

M13 Universal Primer

Answer 7

A sequencing primer that could be used for all sequences cloned into the M13 RF plasmid.

Question 8

Dye Blobs

Answer 8

Bright flashes of fluorescence caused by failure to clean the sequencing ladder properly.

Question 9

Dye Primer

Answer 9

Covalent attachment of fluorescent molecules to a sequencing primer.

Question 10

Dye Terminator

Answer 10

Covalent attachment of fluorescent molecules to dideoxynucleotides.

Question 11

Electropherogram

Answer 11

Results from capillary electrophoresis where fluorescent signals are recorded as graphical peaks.

Question 12

Dye Blobs

Answer 12

Artifactual peak pattern caused by risidual unincorporated labeled dideoxynucleotides in a sequencing reaction. Bright flashes of fluorescence.

Question 13

Pyrosequencing

Answer 13

A method designed to determine a DNA sequence without having to make a sequencing ladder. Based on the release of pyrophosphates during DNA replication.

Question 14

Pyrogram

Answer 14

The results from a pyrosequencing reaction that consist of peaks of luminescence associated with the addition of the complementary nucleotide from a pyrosequencer.

Question 15

Bisulfite DNA Sequencing

Answer 15

Methylation-specific sequencing. Chain termination sequencing designed to detect methylated cytosine nucleotides. DNA has been treated with sodium bisulfite.

Question 16

Polonies

Answer 16

Collection of products of fragments that hybridized to the immobilized probes that were amplified by branch PCR.

Question 17

Indexing

Answer 17

Bar coding. Adaptors that contain short sequences, 6-8 bases, that will identify the sample, allowing multiple samples to be sequenced together.

Question 18

Bioinformatics

Answer 18

The merger of biology with information technology.

Question 19

in silico

Answer 19

By computer

Question 20

Annotation

Answer 20

Classification of sequence variants based on their biological and/or clinical significance.

Question 21

Consensus Sequences

Answer 21

A family of sequences.

Question 22

Filtering

Answer 22

Selection of variants found in a sequence based on variant features such as variant frequency, coverage, exon, or intron location, germline/somatic status, or other properties.

Question 23

Bioinformatics

Answer 23

The merger of biology with information technology.

Question 24

in silico

Answer 24

Analysis performed by computer

Question 25

M13

Answer 25

A single-stranded DNA bacteriophage used in early procedures to make single-stranded templates for sequence analysis.

Question 26

Consensus Sequences

Answer 26

A family of sequences representing different variations in a population but with similar motifs in nucleotide order.

Question 27

BLAST

Answer 27

The Basic Local Alignment Search Tool. A system for homology searches. Compares nucleotide or protein sequences to find regions of similarity between them.

Question 28

Homology

Answer 28

Having the same.

Question 29

Sequencing by Synthesis

Answer 29

Involves taking a single strand of the DNA to be sequenced and then synthesizing its complementary strand enzymatically, one base at a time.

Question 30

Reversible Terminator Sequencing

Answer 30

A sequencing approach that relies on solid-phase amplification of DNA templates immobilized to a solid surface (usually a flow cells) separated across it to generate clusters on the order of millions.

Question 31

Bridge Amplification

Answer 31

A double stranded DNA is denatured so that each strand can separately attach to an oligonucleotide sequence anchored to the flow cell. One will be the reverse strand; the other, the forward.

Question 32

Flow Cell

Answer 32

An Illumina flow cell is a hollow glass slide with one or more channels (“lanes”), coated with oligonucleotides which are complementary to the sequencing adapters so that single-stranded, adapter-ligated DNA fragments can attach through hybridization.