1. Introduction to Genetics
Debashis Ghosh
Professor and Chair, Biostatistics and Informatics, ColoradoSPH

2. Question we tackle today
What do we mean by a gene?
Steve Mount (ongenetics.blogspot.com):
“A gene is all of the DNA elements required in cis for the properly regulated production of a set of RNAs whose sequences overlap in the genome.  ”
Mark Gerstein (2007, Genome Biology):
“The gene is a union of genomic sequences encoding a coherent set of potentially overlapping functional products”

3. What is a gene? No ``one-size-fits-all” definition
The previous definitions are useful to contextualize data that are generated from experiments
Thinking carefully about evolution and the constraints it has placed on functions is also important

4. From Genotype to Phenotype
Full genotypes (genomes) are coming…But inheritance is complex
Genetic markers are characters inherited in a way that is simple enough to easily track
Want to find genetic markers that explain or predict phenotypes
e.g., disease, susceptibility
Ideally, the marker would be causative
But that is rare

5. Alleles as Genes
At each gene locus, we have two alleles, one transmitted to us by our father, and one by our mother.
Usual assumption: Each parent randomly transmits one of his/her alleles to the child
For real datasets, this is identical to DNA variants referred to as single-nucleotide polymorphisms (SNPs)

6. Diploid Inheritance From Mom From Dad Heterozygote From Mom From Dad
Homozygote

7. Phenotypic Dominance From Mom From Dad Heterozygote
Light blue dominant
Dark blue recessive
Mixed Dominance
Dark blue dominant
Light blue recessive

8. Recessive Phenotype Only Visible in Homozygote
Diploid Inheritance
Dark Blue
Is Dominant
Heterozygote
Recessive Phenotype Only Visible in Homozygote
Homozygote

9. Mendelian Ratios

10. Recombination From Grandma From Grandpa
Chromosomal Segment in Mom (she’s a diploid, remember)
From Mom
From Dad
Chromosomal Segment in You (You’re diploid too)

11. Sister Chromatids Recombine (Cross Over) During Meiosis
Crossing Over
From Grandma
From Grandpa
Sister Chromatids Recombine (Cross Over) During Meiosis
Inherited by You
Lost (Except in
Tetrad Analysis)
Products of Meiosis

12. Recombination: Basic Points
Recombination switches which chromosome in the parent (i.e., originating from which grandparent) is passed along to the offspring
Alleles physically adjacent on a chromosome are more likely to be passed on together than alleles far apart
Alleles very far apart or on different chromosomes are inherited randomly

13. Finding Disease Genes Assemble data set of probands
Assemble data set of control population
Might have pedigree if runs in families
Might have trios to determine linkage
Proband plus two parents
Look for linkage between genetic markers and disease
In pedigree
In dataset of less related individuals

14. Genetic Markers Polymorphic in population Haplotype
Different variants in different individuals
Single Nucleotide Polymorphism (SNP)
Variable Number of Tandem Repeats (VNTR)
minisatellites
Short Tandem Repeats (STR)
Microsatellites
Very high mutation rate: strand slippage
Haplotype
A set of closely linked SNPs inherited as unit

15. Linkage Analysis Set of variable markers distributed throughout genome
Identify linkage regions (haplotypes) that cosegregate (are inherited) with disease or trait

16. Pedigree Analysis
Tabulate the occurrence of a trait in an extended family
Pedigree is family’s mating history

17. Assumptions and Complications
Single gene with Mendelian inheritance
Best use of extended families
Few extended families with trait
Quantitative traits are multigenic
Includes most widespread or “common” inherited diseases
Sib pairs are best for complex traits with incomplete penetrance (see next slide)

18. Incomplete Penetrance
Not everyone with genotype will have the disease
Delayed or adult onset
Mild or undetectable symptoms
Environmental and developmental factors
Unknown genetic factors
Disease allele = increase probability of disease, relative risk
We don’t always know in pedigree who has the disease genotype!

19. Evaluating Linkage
Remember, individual is a recombinant with respect to two genes, A and B, if inherits the allele from one parental chromatid at A and inherits the allele from the other parental chromatid at B
The recombination fraction is the probability that a child is recombinant
If A and B are tightly linked, then is small

20. Simple LOD Scores Total number of offspring, P
Number of recombinant offspring, R
Likelihood of the Data =
Maximum likelihood estimate
LOD score for linkage in pedigree is

21. Complications
Need to know phase, genotypes of parents, to identify recombinants
Can estimate informativeness of additional data depending on heterozygosity of markers
Many disease versus marker comparisons are involved
Multiple comparisons
But, markers are not independent
Population structure
LOD scores > 3 (1000:1) give general sense; >5 very strong

22. Population structure
Genetic markers have different patterns in different populations; this has the possibility of confounding associations between genetic markers with disease phenotypes.

23. Realistic Complications
Include Penetrance(X|G)
Likelihood of observing trait X given the genotype G
Prior(G)
Likelihood of observing the genotype in an individual
Transmit(Gm|Gk,Gl, )
Probability that offpring will have genotype Gm given parental genotypes Gk and Gl, and the recombination parameter

24. LOD Graph Can look at LOD score over a range of 's, not just MLE.
Usual assumption is LOD > 3 is evidence for linkage, LOD < -2 is evidence for exclusion
Example: 27 recombinants
Out of 139 gametes
(example from S. Purcell)

25. Recombination Probability and Distance along Chromosome
Recombination does not increase linearly
Multiple recombination events possible over greater distances, but also interference
Can estimate genetic distance from recombination rates
Measure in Morgans, or cM
the expected number of crossovers, is additive

26. Mapping Functions Haldane’s mapping function
Crossovers are assumed random and independent
Kosambi’s mapping function
Models interference: crossovers not too close
Most popular

27. Genetic versus Physical
Mapping is not simple
Recombination rate varies along chromosomes
Male versus Female
Men 28.51M over whole genome
1.05 Mb/cM
Women 42.96M (excluding X)
0.88 Mb/cM
In Drosophila, about 0.4 Mb/cM

28. Modeling Penetrance Single locus, three genotypes If
Disease is Mendelian dominant
Disease is Mendelian recessive
Spontaneous mutations:
incomplete penetrance:

29. Extending Analysis SNPs scattered throughout genome
LOD scores for regions, not individual marker
Multipoint linkage analysis
Establish order relationship among 3+ markers
Non-parametric analysis can be better for complex traits, incomplete penetrance
Work with affected siblings
Less statistical power than model-based methods
Identical by descent (IBD) versus chance

30. Non-Parametric Concerning siblings or other relatives
Need “both affected” and “only one affected” pairs
Correlate shared IBD alleles with affected state, proportion in two classes
High correlation means linkage to disease
Mention
T1D

31. (Genomewide) Association Studies
Correlate markers with disease over a large population
Marker may be disease (rare)
Large regions of chromosome in linkage disequilibrium with disease allele
Marker is in disease gene haplotype
Regions of chromosome tend to be inherited as a unit
Tapers off over time due to recombination

32. Association Studies Linkage disequilibrium varies among populations
Depends on population structure, age
coalescent
Europeans have a lot, African populations only a little
Population of human origin is more diverse, older
Need dense, cheap markers over genome: Genome Wide Association Studies (GWAS)

33. QTL and GWAS
Quantitative Traits, polygenic traits that are assumed to have additive effects
Height, heart disease
Quixotic Trait Loci?
Each gene has a small effect
Huge genotyping efforts now paying off
BUT only a small fraction of genetic component is accounted for even in huge studies
Tradeoffs of including broader human population

34. Common Disease versus Rare Variants
Common disease, common variants: The most frequently occurring alleles/SNPs should explain most of the etiology of a disease.
- Current studies do NOT show this to be the case.
Newer paradigm: rare variants
- occur less frequently but have larger associations with disease

35. Sullivan, Daly and Donovan, Nature Reviews Genetics, 2012

36. Different results in different populations Heritability
What makes a gene matter to a disease?
Take advantage of human phenotyping
What genes CAN contribute to disease or modification of disease?
A golden age of personal genomics?

37. Acknowledgments
David Pollock, Biochemistry and Molecular Genetics