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Printable Handouts
Navigable Slide Index
- Introduction
- Goals of genetic studies
- The continuum of variation
- Presentation outline
- Definitions
- Concepts of meiosis
- Meiosis and recombination
- Phasing
- Linkage analysis of phase known family
- Estimation and testing
- Phase unknown example
- Isolating genetic effects in disease causation
- Families for segregation and linkage studies
- Assessing genetic linkage in pedigrees
- Penetrance and linkage parameters
- Penetrance and linkage
- Elston-Stewart algorithm parameters
- Elston-Stewart algorithm formula
- Elston-Stewart algorithm
- Elston-Stewart algorithm for linkage
- Segregation analysis versus linkage analysis
- LOD score
- Implementing the Elston-Stewart algorithm
- Programs using the Elston-Stewart algorithm
- The Lander-Green algorithm
- Implementing the L-G algorithm
- Implementing the L-G algorithm advantages
- How to model larger pedigrees?
- Modeling larger pedigrees
- Biases in θ from an incorrect genetic model
- Effect of locus heterogeneity
- Locus heterogeneity
- Detecting linkage in an uncertain genetic model
- Linkage analysis for uncertain models
- Gene I.B.D.
- Model-free analysis for diseases
- Haseman-Elston test for genetic linkage
- Haseman-Elston family of tests
- Variance-components tests for linkage
- Sequencing of enriched families
- Role of next generation sequence analysis
- Genetic variants
- Annotations
- Integrated annotation and analysis of sequencing
- Study of a large family with multiple cancers
- Questions related to this family
- Approaches
- Parametric and model free analyses
- Whole genome sequences of five samples
- Joint analysis of HNRNPA0 and WIF1
- Time to onset analysis of genes
- Signaling effects of mutations
- Summary
Topics Covered
- Meiosis and linkage
- Family structure and phasing of gametes
- The Elston-Stewart and Lander Green likelihood formulations
- Model-free tests
- Sequencing analysis
- Example of linkage and sequencing in a family study
Talk Citation
Amos, C. (2017, May 29). Linkage and sequence analysis in families [Video file]. In The Biomedical & Life Sciences Collection, Henry Stewart Talks. Retrieved December 6, 2024, from https://doi.org/10.69645/NIGM5817.Export Citation (RIS)
Publication History
Financial Disclosures
- Prof. Christopher Amos has not informed HSTalks of any commercial/financial relationship that it is appropriate to disclose.
Other Talks in the Series: Statistical Genetics
Transcript
Please wait while the transcript is being prepared...
0:00
The title of this presentation is
Linkage and Sequence Analysis
in Families.
My name is Chris Amos.
A reference for this presentation
is current protocols
in human genetics
including several units
in chapter one.
0:18
The goals of genetic studies
include obtaining new insights
into the pathogenesis
of complex diseases like cancer,
developing strategies for characterizing
individual risk for disease,
towards improving early diagnosis
and screening
or developing new strategies
for prevention and treatment.
0:39
And there are a range of effects
from the alleles
that influence a genetic disease
ranging from high risk
but relatively uncommon variants.
Those can be detected
through family studies
and in particular the linkage methods
that I will be describing in this talk.
On the other extreme,
there are low effect sized
common variants
that can be detected
by association studies
and then in the middle
are the low effect
and relatively uncommon
which can be detected
by sequencing of enriched families
that include multiple relatives.
So I will mostly be discussing
those relatively uncommon
but highly penetrant variants
in this talk.
1:27
Topics in this presentation
include meiosis and linkage,
family structure
and phasing of gametes,
the Elston Stewart
and Lander Green likelihood formulations
for linkage analysis,
model-free linkage tests,
sequencing analysis in families,
and finally an example of linkage
and sequencing in a family.