SAMENVATTING 2
Genes & Genomes
BMW20605 2019-2020
Marieke Roos
,2
Week 4. Gene mapping: linkage, de novo mapping and
homozygosity mapping
H17. Mapping and identifying genes for monogenic disorders
17.1 Positional cloning
Positional cloning: Identify the disease genes by first mapping them to a
precise chromosomal location
To minimize the amount of Sanger sequencing
Linkage analysis
Determine the distance between two loci
o Test if the marker is close to the disease mutation
Recombination fraction
• Recombination: During meiotic cell division
During prophase of meiosis I
Individual chromatids exchange segments at crossovers
• Recombination fraction: The proportion of
gametes that are recombinant for two loci:
𝑛𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝑟𝑒𝑐𝑜𝑚𝑏𝑖𝑛𝑎𝑛𝑡𝑠
𝑛𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝑛𝑜𝑛𝑟𝑒𝑐𝑜𝑚𝑏𝑖𝑛𝑎𝑛𝑡𝑠
• The recombination fraction between two loci is a
measure of their distance on the chromosome
• When two loci are on different chromosomes,
50% will be recombinant
Linked loci Unlinked loci
Markers on the same chromosome Markers are on different chromosomes
Both markers on the same arm Markers are on different arms
Recombination fraction 𝜃 < 50% Recombination fraction 𝜃 = 50%
Marker
A suitable genetic marker would have the following characteristics:
o It should show a clean patterns of Mendelian inheritance, so that the
genotype can always be inferred from the phenotype
o It should be easily available
o The locus should be highly polymorphic
o Markers should be spread at known chromosomal locations across the entire
genome
If there is no recombination, the marker is linked
, 3
Rules
• The person which is used to set the hypothesis doesn’t count
• Affected people from out of the family doesn’t count
LOD score
• Calculate the likelihood of the pedigree, on the alternative assumptions that
the loci are linked or not linked
• Odds: The ratio of Linked/Unlinked
• LOD score: Logarithm of the odds
𝑝𝑟𝑜𝑏𝑎𝑏𝑖𝑙𝑖𝑡𝑦 𝑜𝑓 𝑓𝑖𝑛𝑑𝑖𝑛𝑔 𝑥 𝑅 𝑎𝑛𝑑 𝑦 𝑁𝑅 𝑖𝑓 𝜃 = 𝜃 ∗
𝑂𝑑𝑑𝑠 =
𝑝𝑟𝑜𝑏𝑎𝑏𝑖𝑙𝑖𝑡𝑦 𝑜𝑓 𝑓𝑖𝑛𝑑𝑖𝑛𝑔 𝑥 𝑅 𝑎𝑛𝑑 𝑦 𝑁𝑅 𝑖𝑓 𝜃 = 0.5
𝐿𝑂𝐷 = log(𝑜𝑑𝑑𝑠)
Linkage Nonrecombinants: (1 − 𝜃) 𝜃 " ∗ (1 − 𝜃)#
Linkage Recombinants: 𝜃 𝐿𝑂𝐷 = log F H
0.5"$#
No linkage: 0.5"$#
The most likely recombination fraction is the one with the highest lod score
o 𝜃=0 Highest lod score ® no recombinants
o Only recombination fractions between 0 and 0.5 are meaningful
Positive lod score: Evidence in favour for linkage
Negative lod score: Evidence against linkage
Threshold of significance
• Z = 3.0 Threshold for linkage
• p = 0.05 Threshold of significance
• Z = -2 Linkage can be rejected
• Threshold lod score for a study using n markers:
3 + log(n)
If there is a Mendelian condition the causative variant must be somewhere in the
genome. If one location is excluded, then the probability that the character maps to
another location is raised.
Significant linkage
Autosomal dominant: DNA of 10 patients
Autosomal recessive: DNA of 5 patients
Identify the causative variant
• Is the variant localised in a gene that is linked to the phenotype
• Unrelated affected people should all have the mutation, but healthy controls
not
Loss-of-function mutations: show allelic heterogeneity
Gain-of-function mutations: show no allelic heterogeneity
Genes & Genomes
BMW20605 2019-2020
Marieke Roos
,2
Week 4. Gene mapping: linkage, de novo mapping and
homozygosity mapping
H17. Mapping and identifying genes for monogenic disorders
17.1 Positional cloning
Positional cloning: Identify the disease genes by first mapping them to a
precise chromosomal location
To minimize the amount of Sanger sequencing
Linkage analysis
Determine the distance between two loci
o Test if the marker is close to the disease mutation
Recombination fraction
• Recombination: During meiotic cell division
During prophase of meiosis I
Individual chromatids exchange segments at crossovers
• Recombination fraction: The proportion of
gametes that are recombinant for two loci:
𝑛𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝑟𝑒𝑐𝑜𝑚𝑏𝑖𝑛𝑎𝑛𝑡𝑠
𝑛𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝑛𝑜𝑛𝑟𝑒𝑐𝑜𝑚𝑏𝑖𝑛𝑎𝑛𝑡𝑠
• The recombination fraction between two loci is a
measure of their distance on the chromosome
• When two loci are on different chromosomes,
50% will be recombinant
Linked loci Unlinked loci
Markers on the same chromosome Markers are on different chromosomes
Both markers on the same arm Markers are on different arms
Recombination fraction 𝜃 < 50% Recombination fraction 𝜃 = 50%
Marker
A suitable genetic marker would have the following characteristics:
o It should show a clean patterns of Mendelian inheritance, so that the
genotype can always be inferred from the phenotype
o It should be easily available
o The locus should be highly polymorphic
o Markers should be spread at known chromosomal locations across the entire
genome
If there is no recombination, the marker is linked
, 3
Rules
• The person which is used to set the hypothesis doesn’t count
• Affected people from out of the family doesn’t count
LOD score
• Calculate the likelihood of the pedigree, on the alternative assumptions that
the loci are linked or not linked
• Odds: The ratio of Linked/Unlinked
• LOD score: Logarithm of the odds
𝑝𝑟𝑜𝑏𝑎𝑏𝑖𝑙𝑖𝑡𝑦 𝑜𝑓 𝑓𝑖𝑛𝑑𝑖𝑛𝑔 𝑥 𝑅 𝑎𝑛𝑑 𝑦 𝑁𝑅 𝑖𝑓 𝜃 = 𝜃 ∗
𝑂𝑑𝑑𝑠 =
𝑝𝑟𝑜𝑏𝑎𝑏𝑖𝑙𝑖𝑡𝑦 𝑜𝑓 𝑓𝑖𝑛𝑑𝑖𝑛𝑔 𝑥 𝑅 𝑎𝑛𝑑 𝑦 𝑁𝑅 𝑖𝑓 𝜃 = 0.5
𝐿𝑂𝐷 = log(𝑜𝑑𝑑𝑠)
Linkage Nonrecombinants: (1 − 𝜃) 𝜃 " ∗ (1 − 𝜃)#
Linkage Recombinants: 𝜃 𝐿𝑂𝐷 = log F H
0.5"$#
No linkage: 0.5"$#
The most likely recombination fraction is the one with the highest lod score
o 𝜃=0 Highest lod score ® no recombinants
o Only recombination fractions between 0 and 0.5 are meaningful
Positive lod score: Evidence in favour for linkage
Negative lod score: Evidence against linkage
Threshold of significance
• Z = 3.0 Threshold for linkage
• p = 0.05 Threshold of significance
• Z = -2 Linkage can be rejected
• Threshold lod score for a study using n markers:
3 + log(n)
If there is a Mendelian condition the causative variant must be somewhere in the
genome. If one location is excluded, then the probability that the character maps to
another location is raised.
Significant linkage
Autosomal dominant: DNA of 10 patients
Autosomal recessive: DNA of 5 patients
Identify the causative variant
• Is the variant localised in a gene that is linked to the phenotype
• Unrelated affected people should all have the mutation, but healthy controls
not
Loss-of-function mutations: show allelic heterogeneity
Gain-of-function mutations: show no allelic heterogeneity
