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Medical Genetics > Detection and measurement of genetic variation > Flashcards

Detection and measurement of genetic variation Flashcards

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1
Q

What is genetic variation?

A

Differences in genes resulting from mutations accumulated over time.

Genetic variation is crucial for mapping genes to specific locations on chromosomes and for genetic diagnosis.

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2
Q

What are blood groups based on?

A

Antigens located on the surfaces of erythrocytes.

Blood group systems are used to assess genetic variation.

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3
Q

Name two blood group systems with medical significance.

A
  • ABO
  • Rh
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4
Q

Who discovered the ABO antigens and when?

A

Karl Landsteiner in 1900.

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5
Q

What are the four major blood types in the ABO system?

A
  • Type A
  • Type B
  • Type AB
  • Type O
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6
Q

What determines a person’s ABO blood type?

A

The presence of A and B antigens on erythrocytes.

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7
Q

How is the ABO blood type determined in the laboratory?

A

By mixing a blood sample with solutions containing different antibodies and observing clumping.

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8
Q

What is the genetic encoding for the ABO blood group system?

A

A single gene on chromosome 9 with three primary alleles: I A, I B, and I O.

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9
Q

What is the Rh system named after?

A

The rhesus monkey.

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10
Q

What technique was developed in the 1930s to increase detectable polymorphic loci?

A

Protein electrophoresis.

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11
Q

What can a single amino acid difference in a protein cause?

A

A difference in the electrical charge of the protein.

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12
Q

What is an example of a mutation detectable by protein electrophoresis?

A

Sickle cell disease mutation.

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13
Q

What does protein electrophoresis reveal about hemoglobin?

A

It can determine if a person is an HbA homozygote, HbS homozygote, or a heterozygote.

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14
Q

What is the average number of single-base differences between human haploid DNA sequences?

A

3 to 4 million base pairs.

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15
Q

What are single nucleotide polymorphisms (SNPs)?

A

Variants at single nucleotide positions on a chromosome.

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16
Q

What is the significance of tandem repeat polymorphisms?

A

They reveal a high degree of genetic variation due to varying numbers of repeats.

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17
Q

What is the typical size of an indel?

A

Less than 50 base pairs.

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18
Q

How many indels does an average human genome contain?

A

Approximately 600,000 indels.

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19
Q

What are copy number variants (CNVs)?

A

DNA sequences larger than 500–1,000 base pairs that vary in copy number among individuals.

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20
Q

What is the role of STRs in forensic applications?

A

They are used for establishing highly specific DNA profiles.

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21
Q

How can DNA profiles be used in forensic settings?

A

To identify individuals based on genetic variation.

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22
Q

What is the probability of obtaining a matching DNA profile in criminal cases?

A

Usually very small, often around 1 in 1 trillion when using 13 or more STRs.

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23
Q

What is the significance of postconviction DNA testing?

A

It has led to the exoneration of wrongfully imprisoned individuals.

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24
Q

Fill in the blank: The ABO blood group system consists of three primary alleles: I A, I B, and ______.

A

I O

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25
True or False: Protein electrophoresis can detect silent substitutions.
False
26
What is the maximum number of different DNA profiles that can be generated?
1 trillion ## Footnote This is achievable under well-controlled laboratory conditions with sufficient loci.
27
How can DNA profiles benefit innocent individuals?
By exonerating suspects when a match is not obtained ## Footnote Postconviction DNA testing has led to the release of hundreds wrongly imprisoned.
28
What can panels of SNPs predict about an individual?
* Genetic ancestry * Eye color * Hair color ## Footnote These predictions are made with a fair degree of accuracy.
29
What information can methylation profiles provide?
Estimate age within several years
30
How can a DNA sample alone help identify a perpetrator?
By matching it with stored DNA profiles in national databases
31
True or False: DNA profiles can only identify guilty parties.
False ## Footnote They can also exonerate innocent suspects.
32
What are indels in the context of DNA?
Insertions or deletions of segments of DNA smaller than 50 bp
33
Define copy number variants (CNVs).
Differences in the numbers of larger repeated segments of DNA (>500 bp)
34
What is the role of restriction enzymes in DNA analysis?
They cleave human DNA at specific sequences, producing restriction fragments.
35
What is a Southern blot?
A method to transfer DNA fragments from a gel to a solid membrane for visualization.
36
What is the function of probes in Southern blotting?
To hybridize with complementary single-stranded DNA fragments for visualization.
37
What is recombinant DNA technology?
Laboratory alteration of genes, including the creation of clones.
38
What is a plasmid?
A small, circular, self-replicating piece of DNA that resides in bacteria.
39
Fill in the blank: The sequence recognized by the restriction enzyme EcoRI is _______.
GAATTC
40
What is the primary purpose of the polymerase chain reaction (PCR)?
To replicate a short, specific DNA sequence quickly and efficiently.
41
List the four components required for PCR.
* Two primers * DNA polymerase * Free DNA nucleotides * Genomic DNA ## Footnote Primers are usually 15 to 20 bases long.
42
What happens to DNA during the denaturing step of PCR?
It is heated to approximately 95°C, causing it to become single-stranded.
43
How does the number of DNA copies change with each cycle of PCR?
It doubles with each cycle (e.g., 2, 4, 8, 16, etc.)
44
What is the significance of sticky ends in recombinant DNA technology?
They allow human DNA and plasmid DNA to anneal and recombine.
45
What is the typical temperature range for primer hybridization in PCR?
Approximately 35°C to 65°C
46
What does autoradiography reveal in the context of Southern blotting?
The positions of specific DNA fragments on the blot.
47
What is the role of the restriction enzyme MstII in sickle cell diagnosis?
It cleaves DNA at specific sites, which can differ based on mutations.
48
What is the banding pattern for sickle cell homozygotes in an autoradiogram?
A single 1.3-kb band ## Footnote Normal homozygotes show a single 1.1-kb band, and heterozygotes show both bands.
49
What is the process of the polymerase chain reaction (PCR)?
Heating to denature DNA, cooling to anneal primers, and extending DNA strands with DNA polymerase ## Footnote PCR amplifies DNA by cycling through these steps.
50
What are the advantages of PCR?
* Can use extremely small quantities of DNA * Faster than older techniques * Produces large quantities of pure DNA ## Footnote PCR can analyze DNA from sources like blood stains or hair.
51
What are some disadvantages of PCR?
* Requires identification of flanking DNA sequences * Susceptible to contamination * Difficult to apply to sequences longer than a few kilobases ## Footnote Alternative techniques like Southern blotting may be needed for larger deletions.
52
What is the dideoxy method of DNA sequencing?
A method that uses chain-terminating dideoxynucleotides to determine DNA sequences ## Footnote Invented by Frederick Sanger, it results in fragments that can be separated and analyzed.
53
How does the dideoxy sequencing method work?
Incorporates labeled primers and dideoxynucleotides into DNA, terminating the chain at specific bases ## Footnote The resulting fragments are separated by electrophoresis for sequence analysis.
54
What is the key advantage of high-throughput DNA sequencing?
Enables rapid sequencing of entire genomes at low cost ## Footnote Also known as next-generation sequencing.
55
What is the role of adapters in high-throughput DNA sequencing?
Join to the ends of genomic DNA fragments and serve as primers for PCR amplification ## Footnote This allows for the visualization of clusters of identical DNA fragments.
56
What is the typical read length for third-generation DNA sequencing methods?
Greater than 10 kb ## Footnote This allows for better analysis of large or repetitive structural variants.
57
What is RNA sequencing (RNAseq)?
A method to assess mRNA transcript levels and quantify gene expression ## Footnote It provides insights into when and where genes are expressed.
58
What does the term 'methylome' refer to?
The genome-wide pattern of DNA methylation ## Footnote It is important for evaluating patterns of gene regulation.
59
What is the purpose of Southern blotting?
Detection of insertions, deletions, and rearrangements in DNA ## Footnote It involves digestion with restriction enzymes and gel electrophoresis.
60
What is the function of allele-specific oligonucleotide (ASO) hybridization?
Detection of alleles with known base compositions ## Footnote It preferentially hybridizes labeled probes to test DNA.
61
How does mass spectrometry contribute to mutation detection?
Detects physical mass of DNA strands ## Footnote It can differentiate between sense and antisense strands.
62
What is the purpose of labeled probes in DNA testing?
Detection of small insertions or deletions, point mutations ## Footnote Labeled probes are used to identify mismatches in DNA sequences.
63
What does allele-specific oligonucleotide (ASO) hybridization detect?
Detection of alleles of known composition ## Footnote ASO hybridization relies on uniquely complementary base composition.
64
What is multiplex ligation-dependent probe amplification (MLPA) used for?
Detection of deletions and duplications of exons or whole genes ## Footnote MLPA involves the ligation of DNA fragments after probe hybridization.
65
How does mass spectrometry contribute to DNA analysis?
Detection of small insertions or deletions, point mutations ## Footnote Mass spectrometry measures the physical mass of DNA strands.
66
What is the function of DNA microarray hybridization?
Detection of SNPs, CNVs, expression differences ## Footnote It involves hybridizing test DNA to arrays of oligonucleotides.
67
What does protein truncation analysis detect?
Detection of frameshift, splice-site, or nonsense mutations that truncate the protein product ## Footnote It uses cDNA made from test DNA and resolves products by SDS-PAGE.
68
What has high-throughput DNA sequencing enabled?
Sequencing of thousands of human genomes ## Footnote This technology has significantly reduced time and cost for genome sequencing.
69
What is the difference between second-generation and third-generation sequencing?
Second-generation uses massively parallel processing; third-generation targets single DNA molecules ## Footnote Third-generation sequencing avoids amplification bias and provides longer reads.
70
What is the role of DNA microarrays in detecting DNA variation?
Affordable means of detecting DNA variation ## Footnote They can analyze millions of SNPs and identify known mutations.
71
How can DNA microarrays be used for gene expression analysis?
Determine which genes are being expressed in a tissue sample ## Footnote mRNA is converted to cDNA and hybridized with oligonucleotides on the microarray.
72
True or False: DNA microarrays can detect previously unidentified mutations.
False ## Footnote Microarrays typically test for known mutations incorporated in oligonucleotide probes.
73
What is a key advantage of using DNA microarrays?
Extraordinary speed, miniaturization, and accuracy of mutation analysis ## Footnote They are gradually being supplanted by RNA sequencing.
74
Fill in the blank: High-throughput DNA sequencing can now complete a human genome in _______ at a cost of one to several thousand dollars.
several hours
75
What is the significance of direct sequencing of DNA?
Used increasingly as the definitive method of identifying and verifying mutations ## Footnote It provides a precise identification of specific mutations.
76
What does the hybridization pattern in DNA microarrays indicate?
Which genes are expressed in the tissue sample ## Footnote The pattern is analyzed by a computer to determine expression levels.

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