Copy number Varia/on in Human Health and Disease
Varia%on in the human genome
- Human genome
- 22 chromosomes
“The” sequence of the Human Genome
- We are not iden4cal, so no one has the ‘the’ sequence of the human genome
- What can explain the differences between people?
Single Nucleo%de Polymorphism (SNP)
- On average 1 SNP / 700bp
- Long thought to be the major source of human varia4on
- We differ from each other in terms of SNPs
o SNPs = differences in base paires one predefined posi4ons in the genome
- The varia4on is more of less constant in Europe/Asia/America, in Africa the varia4on
is much higher
Down syndrome - trisomy 21
- One extra chromosome 21
- There is also trisomy 18 -> don’t live very long
- All the other trisomies are lethal
Prader-Willi syndrome
- Obese
- Small hands
- Small feet
- Intellect disabled
- Dele4on of chromosome 15 -> cause of the prader willi syndrome
FISH
- Fluorescent in situ hybdridisa4on (FISH)
- You denature DNA
- You make of the deleted piece a probe -> label it (fluorescent label)
- That piece of DNA will search for the complementary DNA -> probe signal on the
chromosome
- Take another probe -> look at the other chromosome
- You need to repeat this, probe per probe
- Very difficult to upscale this
Principle of array-CGH
- Probes were brought on an array
- The whole genome is brought into small vectors
- You label the DNA green and you compare that with a control (healthy individual)
o You combine
§ Dele4on -> only one of the two chromosomes 15 -> less green and more
red (two copies of the reference DNA)
§ No change -> yellow
- In one array you can analyze the whole genome
- There is a laser that reads the intensity and it makes a log ra4o
o Around zero -> reference
o Nega4ve -> dele4on
, o Posi4ve -> duplica4on
- Schema4c representa4on: why not exactly zero -> because it is a biological
experiment
o Noise
o Not every probe has the same quality
- What would you do next ?
CNV in the control popula%on
- Only if you compare with a control you can conclude certain things)
- At some of the posi4ons you see a lot of duplica4ons and dele4ons -> hotspot in the
genome
- Also dele4ons and duplica4on at random posi4ons
à There seems to be a varia4on in the human genome (SNPs + CNV)
Defini%on
DNA copy number variants, defined as stretches of DNA larger than 1 kb that display copy
number differences in the normal popula4on
CNV is a subtype of structural varia%on
- Three groups:
o Gain:
§ Inser4on
§ Duplica4on
o Loss:
§ Dele4on
• Replacement:
§ Inversion
§ Transloca4on
How frequent are CNVs
- Ini4al maps showed > 10% of genome to be copy number variant
- 4% of the genome more realis4c es4mates
Mechanisms of rearrangements
- HR
o For example crossover during meiosis
o Different rearrangement/combina4on
Varia%on in the human genome
- Human genome
- 22 chromosomes
“The” sequence of the Human Genome
- We are not iden4cal, so no one has the ‘the’ sequence of the human genome
- What can explain the differences between people?
Single Nucleo%de Polymorphism (SNP)
- On average 1 SNP / 700bp
- Long thought to be the major source of human varia4on
- We differ from each other in terms of SNPs
o SNPs = differences in base paires one predefined posi4ons in the genome
- The varia4on is more of less constant in Europe/Asia/America, in Africa the varia4on
is much higher
Down syndrome - trisomy 21
- One extra chromosome 21
- There is also trisomy 18 -> don’t live very long
- All the other trisomies are lethal
Prader-Willi syndrome
- Obese
- Small hands
- Small feet
- Intellect disabled
- Dele4on of chromosome 15 -> cause of the prader willi syndrome
FISH
- Fluorescent in situ hybdridisa4on (FISH)
- You denature DNA
- You make of the deleted piece a probe -> label it (fluorescent label)
- That piece of DNA will search for the complementary DNA -> probe signal on the
chromosome
- Take another probe -> look at the other chromosome
- You need to repeat this, probe per probe
- Very difficult to upscale this
Principle of array-CGH
- Probes were brought on an array
- The whole genome is brought into small vectors
- You label the DNA green and you compare that with a control (healthy individual)
o You combine
§ Dele4on -> only one of the two chromosomes 15 -> less green and more
red (two copies of the reference DNA)
§ No change -> yellow
- In one array you can analyze the whole genome
- There is a laser that reads the intensity and it makes a log ra4o
o Around zero -> reference
o Nega4ve -> dele4on
, o Posi4ve -> duplica4on
- Schema4c representa4on: why not exactly zero -> because it is a biological
experiment
o Noise
o Not every probe has the same quality
- What would you do next ?
CNV in the control popula%on
- Only if you compare with a control you can conclude certain things)
- At some of the posi4ons you see a lot of duplica4ons and dele4ons -> hotspot in the
genome
- Also dele4ons and duplica4on at random posi4ons
à There seems to be a varia4on in the human genome (SNPs + CNV)
Defini%on
DNA copy number variants, defined as stretches of DNA larger than 1 kb that display copy
number differences in the normal popula4on
CNV is a subtype of structural varia%on
- Three groups:
o Gain:
§ Inser4on
§ Duplica4on
o Loss:
§ Dele4on
• Replacement:
§ Inversion
§ Transloca4on
How frequent are CNVs
- Ini4al maps showed > 10% of genome to be copy number variant
- 4% of the genome more realis4c es4mates
Mechanisms of rearrangements
- HR
o For example crossover during meiosis
o Different rearrangement/combina4on
