Human genetics and genomics lecture 1: Basic genetics
- DNA 13 is located in The nucleus, in structures called chromosomes. Chromosomes can
only be seen during cell division Normally they are open in order to transcribe. Genome
= 3 gigabases
DNA to protein: first transcription from DNA to RNA. This RNA is processed to mRNA, Which
can be translated into proteins by ribosomes
Proteins are also processed: post-translational modification -> diverse
- gene codes for a protein promoter, start codon, exons (coding) introns (spliced out),
stop codon and terminator sequence"
- splicing happens from pre-mRNA to mRNA.
- lots of transcription factors must bind to the regulatory sequence and the promotor in
order to start transcription by RNA polymerase
- polypeptide formation when tRNA recognizes codons and adds amino acids to each
other. Mutation doesn't have to change the amino acid, but deletion/insertion can
change the reading frame
- there are genes in both the sense and the antisense strand. which is important to keep
in mind while sequencing
when an organism Is more complex, it has more un-transcribed regions (big introns, highly
conserved regions and repetitive sequences: important in regulation) and fewer protein-coding
regions
- in humans: only 2% Of DNA is protein-coding.
Genetic variation happens through recombination (chromosomal crossing over) and
mutations (spontaneous or induced by mutagens)
- germline mutations are caused by replication errors during meiosis
- somatic mutations are caused by replication errors during mitosis
mutations can be silent or lead to gain/loss of function. Most mutations are repaired before even
having an effect, but sometimes mutations can lead to genetic part diseases.
There are 4 types of genetic diseases:
1: chromosomal abnormalities: Occurs quite often It's either numerical (loss or extra
chromosome) -> often incompatible with life. leading to spontaneous abortions. It can also be
structural (deletions, duplications, inversions, insertions or translocations).
- trisomy: 3x Chr18 = Edwards syndrome, 3* Chr21 ; Down syndrome
- XXY = KinePelter (Remale:lice male), X = Turner syndrome (male-liva female)
- Robertsonian translocation: 2 long arms of two different acrocentric chromosomes (13,
14,15,21,22) merge, short arms are lost
- translocation in meiosis leads to balanced carriers, that will cause monosomy or trisomy,
in offspring (since it gets unbalanced)
2: Monogeneie disorders: very rare, due 1/2 strong point mutations either in the coding or
non-coding part
- silent mutation: no changé in amino acid (synonymous).
- missense mutation: change in amino acid
- nonsense mutation: earlier stop codom-> no or smaller polypeptide
- frame -Shift mutation: completely different amino access
, - Splice - site mutation: new RNA Viq exon skipping. intron retention or partial intron
retention - no or altered (dysfunctional) protein
Sometimes different mutations in the same gene can lead to the same disease, mutations in
CDKN1C Lead te Beckwith-Wiedemann-
- effect of mutations based en zygosity state: homozygous = nucleotide on certain position
is same in both copies of heterozygous nucleotide on certain position is different in both
copies (I allele intact)
The effect of the mutations on the carrier depends on the inheritance pattern
- Autosomal dominant: 1 allele is defective, at least in one of the parents it happens both
in males and females: Child has 50% chance
- autosomal recessive: both alleles defective, parents often asymptomatic carriers more
common in the family, recurrence risk is 25%
- Sex-linked: either x-linked recessive, only boys, mother asymptomatic or x-linked
dominant: very rare, more in women. Child of affected mother has 50% chance, all
daughters of an affected father
Diagnosis of monogenic disorders can be hard:
- reduced penetrance in dominant inheritance leads to the healthy individual that you
would ve expected to be affected
- pleiotropy: a mutation can lead to different characteristics
- variable expression: the same mutation gives different diseases, based on the
environment, genes and allelic heterogeneity; e.g Lynen syndrome
- genetic heterogeneity different genes lead to the same disease sometimes both
present in one family.
3 Multifactorial (polygenic and environmental) disorders:
Often a combination of various mutated genes and environment It occurs relatively often, and
there are complex hereditary patterns
- examples are obesity, breast cancer, Alzheimer
Genes for complex diseases are in balance with the environment
4 Mitochondrial disorders:
caused by mutations in mitochondrial DNA that affects the function, It's inherited from the
mother and the effects are very heterogeneous due to copies
•Monogenic disorders: (single nucleotide mutations) can be found by sequencing the genome.
Candidate gene functions and genome-wide association studies (GWAS).
, Human genetics and genomics lecture 2: techniques for genetic analysis
Mutations can be detected Through genetic analysis. There are different techniques, each with
its pros and cons
for larger chromosomal abnormalities: karyotyping, FISH, SNP array
- karyotyping: ranking of microscopically photographed chromosomes during mitosis
based on length, centromere location and banding pattern
- can only be done in live cells: prenatal or postnatal material, bone marrow, lymphomas
or tumours are often used
- Colchine can stop at a particular part in mitosis, cells are lysed.
- numerical or large structural abnormalities of 5 -10 Mb (resolution 550 basepairs)
* Benefits: visualisation chromosomes, balanced deviations shown, cheap
* Cons: low resolution (solution = FISH), live celLs needed (solution = SNP)
- FISH: fluorescence in situ hybridization, the principle is detection by presence or
absence of a certain region by using fluorescently labelled probes that bind these
regions. Multicolour FISH colours au chromosomes
* Benefits: defection microdeletions structural and numerical deviations
* Cons: limited resolution (1 Mb, solution: SNP), only known translocations.
- SNP array: Single nucleotide polymorphisms are present a lot, they are just random
variations. Beads and Fluorescent nucleotides bind to the SNPs, after which Fluorescent
signals can be plotted. The piot can show deletions, duplications and insertions
* Benefits- high resolution (a lot of measuring points), homozygosity mapping
*Cons unable to see translocation (dosage still hetero or homozygous)
For smaller abnormalities (single nucleotide): Sanger sequencing
- First PCR for amplification of short DNA fragments using heat to separate strands and
DNA polymerase to make copies. One fragment at the time can be sequenced: primers
are added, together with normal and fluorescently labelled nucleotides Lead to a Lot of
differently, sized Fragments that can be separated using gel electrophoresis
- shorter fragments travel faster: sequence can be read.
can also be done automatically: double wave = heterozygous mutation
If the mutation is then identified, Further research is done: function of the gene, the effect of the
mutation on the function of the gene etc. This is done using functional Studies: qRT-PcR
(RNA expresSiOn), in vitro studies and knock out mice
- qRT-PCR is a gene expression analysis: Fluorescent probes bind to DNA (after it was
formed by reverse transcriptase from RNA) - When the DNA is expressed, there is
fluorescence. High Fluorescence = high expression
Gene expression analysis can also be done for the whole genome.
- DNA 13 is located in The nucleus, in structures called chromosomes. Chromosomes can
only be seen during cell division Normally they are open in order to transcribe. Genome
= 3 gigabases
DNA to protein: first transcription from DNA to RNA. This RNA is processed to mRNA, Which
can be translated into proteins by ribosomes
Proteins are also processed: post-translational modification -> diverse
- gene codes for a protein promoter, start codon, exons (coding) introns (spliced out),
stop codon and terminator sequence"
- splicing happens from pre-mRNA to mRNA.
- lots of transcription factors must bind to the regulatory sequence and the promotor in
order to start transcription by RNA polymerase
- polypeptide formation when tRNA recognizes codons and adds amino acids to each
other. Mutation doesn't have to change the amino acid, but deletion/insertion can
change the reading frame
- there are genes in both the sense and the antisense strand. which is important to keep
in mind while sequencing
when an organism Is more complex, it has more un-transcribed regions (big introns, highly
conserved regions and repetitive sequences: important in regulation) and fewer protein-coding
regions
- in humans: only 2% Of DNA is protein-coding.
Genetic variation happens through recombination (chromosomal crossing over) and
mutations (spontaneous or induced by mutagens)
- germline mutations are caused by replication errors during meiosis
- somatic mutations are caused by replication errors during mitosis
mutations can be silent or lead to gain/loss of function. Most mutations are repaired before even
having an effect, but sometimes mutations can lead to genetic part diseases.
There are 4 types of genetic diseases:
1: chromosomal abnormalities: Occurs quite often It's either numerical (loss or extra
chromosome) -> often incompatible with life. leading to spontaneous abortions. It can also be
structural (deletions, duplications, inversions, insertions or translocations).
- trisomy: 3x Chr18 = Edwards syndrome, 3* Chr21 ; Down syndrome
- XXY = KinePelter (Remale:lice male), X = Turner syndrome (male-liva female)
- Robertsonian translocation: 2 long arms of two different acrocentric chromosomes (13,
14,15,21,22) merge, short arms are lost
- translocation in meiosis leads to balanced carriers, that will cause monosomy or trisomy,
in offspring (since it gets unbalanced)
2: Monogeneie disorders: very rare, due 1/2 strong point mutations either in the coding or
non-coding part
- silent mutation: no changé in amino acid (synonymous).
- missense mutation: change in amino acid
- nonsense mutation: earlier stop codom-> no or smaller polypeptide
- frame -Shift mutation: completely different amino access
, - Splice - site mutation: new RNA Viq exon skipping. intron retention or partial intron
retention - no or altered (dysfunctional) protein
Sometimes different mutations in the same gene can lead to the same disease, mutations in
CDKN1C Lead te Beckwith-Wiedemann-
- effect of mutations based en zygosity state: homozygous = nucleotide on certain position
is same in both copies of heterozygous nucleotide on certain position is different in both
copies (I allele intact)
The effect of the mutations on the carrier depends on the inheritance pattern
- Autosomal dominant: 1 allele is defective, at least in one of the parents it happens both
in males and females: Child has 50% chance
- autosomal recessive: both alleles defective, parents often asymptomatic carriers more
common in the family, recurrence risk is 25%
- Sex-linked: either x-linked recessive, only boys, mother asymptomatic or x-linked
dominant: very rare, more in women. Child of affected mother has 50% chance, all
daughters of an affected father
Diagnosis of monogenic disorders can be hard:
- reduced penetrance in dominant inheritance leads to the healthy individual that you
would ve expected to be affected
- pleiotropy: a mutation can lead to different characteristics
- variable expression: the same mutation gives different diseases, based on the
environment, genes and allelic heterogeneity; e.g Lynen syndrome
- genetic heterogeneity different genes lead to the same disease sometimes both
present in one family.
3 Multifactorial (polygenic and environmental) disorders:
Often a combination of various mutated genes and environment It occurs relatively often, and
there are complex hereditary patterns
- examples are obesity, breast cancer, Alzheimer
Genes for complex diseases are in balance with the environment
4 Mitochondrial disorders:
caused by mutations in mitochondrial DNA that affects the function, It's inherited from the
mother and the effects are very heterogeneous due to copies
•Monogenic disorders: (single nucleotide mutations) can be found by sequencing the genome.
Candidate gene functions and genome-wide association studies (GWAS).
, Human genetics and genomics lecture 2: techniques for genetic analysis
Mutations can be detected Through genetic analysis. There are different techniques, each with
its pros and cons
for larger chromosomal abnormalities: karyotyping, FISH, SNP array
- karyotyping: ranking of microscopically photographed chromosomes during mitosis
based on length, centromere location and banding pattern
- can only be done in live cells: prenatal or postnatal material, bone marrow, lymphomas
or tumours are often used
- Colchine can stop at a particular part in mitosis, cells are lysed.
- numerical or large structural abnormalities of 5 -10 Mb (resolution 550 basepairs)
* Benefits: visualisation chromosomes, balanced deviations shown, cheap
* Cons: low resolution (solution = FISH), live celLs needed (solution = SNP)
- FISH: fluorescence in situ hybridization, the principle is detection by presence or
absence of a certain region by using fluorescently labelled probes that bind these
regions. Multicolour FISH colours au chromosomes
* Benefits: defection microdeletions structural and numerical deviations
* Cons: limited resolution (1 Mb, solution: SNP), only known translocations.
- SNP array: Single nucleotide polymorphisms are present a lot, they are just random
variations. Beads and Fluorescent nucleotides bind to the SNPs, after which Fluorescent
signals can be plotted. The piot can show deletions, duplications and insertions
* Benefits- high resolution (a lot of measuring points), homozygosity mapping
*Cons unable to see translocation (dosage still hetero or homozygous)
For smaller abnormalities (single nucleotide): Sanger sequencing
- First PCR for amplification of short DNA fragments using heat to separate strands and
DNA polymerase to make copies. One fragment at the time can be sequenced: primers
are added, together with normal and fluorescently labelled nucleotides Lead to a Lot of
differently, sized Fragments that can be separated using gel electrophoresis
- shorter fragments travel faster: sequence can be read.
can also be done automatically: double wave = heterozygous mutation
If the mutation is then identified, Further research is done: function of the gene, the effect of the
mutation on the function of the gene etc. This is done using functional Studies: qRT-PcR
(RNA expresSiOn), in vitro studies and knock out mice
- qRT-PCR is a gene expression analysis: Fluorescent probes bind to DNA (after it was
formed by reverse transcriptase from RNA) - When the DNA is expressed, there is
fluorescence. High Fluorescence = high expression
Gene expression analysis can also be done for the whole genome.
