Gene and Genome (With explanations from Van Camp)
The course is presented by Prof. Van Camp, Prof. Van Hul and Prof. Kooy The style leans in to genetics
from 3rd Ba. It taught using slides is based on a book for every professional, differs a bit if you have
additional needs to learn from the book.
Oral: (this is only for Prof Van Camp, appr. 2 oral questions)
1. Genetically defective search dwarfism, mental retardation, facial deformities
2. How can you avoid a smear?
3. You can find a number of patients with an autosomal recessive disease a variety of homozygous
and heterozygous frameshift mutations compound. What is probably the disease mechanism,
and which strategy would follow in order to construct an in vitro and in vivo model for the study
of gene function.
4. You are doing your master thesis in a genetic lab. You have to develop a PCR reaction point for a
particular gene fragment. However, you get a large number of bands instead of one beautiful
band on your gel. How could this be? What can you do?
5. A patient with a bone disease wants molecular verification. There are 2 known disease-causing
genes each with 3 exons. Does anything change when the patient also has another illness?
6. There’s a new protein discovered which induces cell death, also in yeast. It’s from the same
family as another protein, which makes pores in the cell wall when its N-terminal segment is
cleaved. Make an interesting hypothesis.
Written (appr. 4 questions for the written part)
1. Enter principle and application of the yeast-two-hybrid technology
2. What types of genomic changes have occurred during the evolution that may help to establish
evolutionary trees?
3. What mechanisms underlying the formation of CNVs? Explain briefly each mechanism
4. Explain two ways how you can perform using real time PCR SNP genotyping
5. What does a eukaryotic vector need (so what’s not needed if you want to clone in bacteria)?
Also give elements which can help with later purification.
, 6. Pyrosequencing and how it’s implemented in the 454 technology?
7. Difference in organisation between nuclear and ribosomal genome?
8. DNase I footprinting?
9. ChIPon-chip applications +
10. Para Logs and ortho logos + how they arise
11. Advantages and disadvantages of various detection mechanisms CNVs (techniques not in detail)
12. Renaturation kinetics
Example questions
1. Genotyping of a single base variant on 500 samples: Which techniques would you use
(advantages and disadvantages)? Remark: It’s for a small company, which has limited access
to expansive techniques.
(1) PCR for allele specific PCR
(2) Sanger sequencing
(3) Dot blot hybridization
(alternatives not seen in class) Taqman, Real-Time PCR
2. 10 patients with a very rare genetic disease (all parents are healthy, = homozygous): How to
discover the mutation?
Next generation sequencing
(1) Genome (and after compare the results)
(2) Panel of candidate genes (= less certain, only for presence in blood, could be just a guess so
not the best option)
(3) RNA (//)
(4) Exome sequencing (cDNA) = best option
3. Unrelated patients with a neurological disease, a deletion was detected through micro-array
CGH: By which mechanisms did this mutation happen?
Non-Allelic Homologous Recombination (NAHR) (causes exchange between distant alleles) with
a deletion
<> Allelic Homologous Recombination (occurs during DNA-repair and cell division, happens often
and is not dangerous)
=> NAHR does not work for repetitive sequences (breaking point where the deletion happened
lies in the repetitive sequences)
The course is presented by Prof. Van Camp, Prof. Van Hul and Prof. Kooy The style leans in to genetics
from 3rd Ba. It taught using slides is based on a book for every professional, differs a bit if you have
additional needs to learn from the book.
Oral: (this is only for Prof Van Camp, appr. 2 oral questions)
1. Genetically defective search dwarfism, mental retardation, facial deformities
2. How can you avoid a smear?
3. You can find a number of patients with an autosomal recessive disease a variety of homozygous
and heterozygous frameshift mutations compound. What is probably the disease mechanism,
and which strategy would follow in order to construct an in vitro and in vivo model for the study
of gene function.
4. You are doing your master thesis in a genetic lab. You have to develop a PCR reaction point for a
particular gene fragment. However, you get a large number of bands instead of one beautiful
band on your gel. How could this be? What can you do?
5. A patient with a bone disease wants molecular verification. There are 2 known disease-causing
genes each with 3 exons. Does anything change when the patient also has another illness?
6. There’s a new protein discovered which induces cell death, also in yeast. It’s from the same
family as another protein, which makes pores in the cell wall when its N-terminal segment is
cleaved. Make an interesting hypothesis.
Written (appr. 4 questions for the written part)
1. Enter principle and application of the yeast-two-hybrid technology
2. What types of genomic changes have occurred during the evolution that may help to establish
evolutionary trees?
3. What mechanisms underlying the formation of CNVs? Explain briefly each mechanism
4. Explain two ways how you can perform using real time PCR SNP genotyping
5. What does a eukaryotic vector need (so what’s not needed if you want to clone in bacteria)?
Also give elements which can help with later purification.
, 6. Pyrosequencing and how it’s implemented in the 454 technology?
7. Difference in organisation between nuclear and ribosomal genome?
8. DNase I footprinting?
9. ChIPon-chip applications +
10. Para Logs and ortho logos + how they arise
11. Advantages and disadvantages of various detection mechanisms CNVs (techniques not in detail)
12. Renaturation kinetics
Example questions
1. Genotyping of a single base variant on 500 samples: Which techniques would you use
(advantages and disadvantages)? Remark: It’s for a small company, which has limited access
to expansive techniques.
(1) PCR for allele specific PCR
(2) Sanger sequencing
(3) Dot blot hybridization
(alternatives not seen in class) Taqman, Real-Time PCR
2. 10 patients with a very rare genetic disease (all parents are healthy, = homozygous): How to
discover the mutation?
Next generation sequencing
(1) Genome (and after compare the results)
(2) Panel of candidate genes (= less certain, only for presence in blood, could be just a guess so
not the best option)
(3) RNA (//)
(4) Exome sequencing (cDNA) = best option
3. Unrelated patients with a neurological disease, a deletion was detected through micro-array
CGH: By which mechanisms did this mutation happen?
Non-Allelic Homologous Recombination (NAHR) (causes exchange between distant alleles) with
a deletion
<> Allelic Homologous Recombination (occurs during DNA-repair and cell division, happens often
and is not dangerous)
=> NAHR does not work for repetitive sequences (breaking point where the deletion happened
lies in the repetitive sequences)
