1. The Genetics of Spina Bifida
Laura E. Mitchell, PhD

4. “The proper study of mankind is man.” Alexander Pope

5. Aggregation
Segregation
Linkage
Association
Sequence

6. Aggregation Sequence Association Linkage Segregation Penrose 1946
Majority ’s

7. Majority ~ 95% look like this

8. 3% - 5%
Either SB or the related conditions SB

9. 1-2%

10. ~ 0.5%

11. Rapid decline with degree of relationship
RISK
Increased
# of affected
Rapid decline with degree of relationship
These familial patterns are consistent with…

12. Multifactorial Threshold Model
Today, conditions that fit the MTF model tend to be referred to as…
Human Genetics and Genomics, Figure 5-2, B.R. Korf (3rd Edition)

13. Complex Diseases
Once familial aggregation is established, then next steps in defining the genetic contribution to a condition may include…

14. Linkage Segregation Sequence Association Aggregation
Segregation analyses – formal statistical modeling of the familial data to identify the underlying model of inheritance
Linage analyses – co-segregation of disease and genetic markers to identify the region of the genome harboring disease related genes
However, both approaches require data from families that look like this…

15. Which are rare/non-existent for SB.
Consequently, these two steps have been largely omitted for SB due to lack of the raw materials required.

16. Association Candidate genes/pathways Genome-wide Sequence Aggregation
1992
Low-resolution genetic linkage map of entire human genome published.
Candidate genes/pathways
Genome-wide

17. Common Variants
Disease-related (not disease-causing) genetic variants will be observed in the general population…

18. As illustrated here, by the individuals carry a blue sphere (high risk genotype)…

19. But will be even more common in individuals with the disease of interest…
This type of association can be studied using the famililar…

20. Case - Control Cases 7/20 Controls 3/20
However, the case-control design has some limitation, the most notable being difficulties associated with selection of an appropriate control group.
Fortunately, in 1993 a new design that is exceptionally well suited for studies of birth defects and other pediatric conditions was described.
Cases
7/20
Controls
3/20

21. Triad
This was a family-based approach that is often referred to as a triad or trio design, because it is based on the analysis of genetic data from an affected individual and his/her parents.

22. CT
This design assesses the transmission of alleles from parents with a heterozygous genotype to their affected offspring.
If there is not relationship between the genotype and disease, then…

23. CT EXPECTED C = 50 T = 50 Mendelian transmission…
However, if gene is assocated with disease risk

24. CT OBSERVED EXPECTED C = 30 C = 50 T = 70 T = 50
The high risk allele (in this case T) will be over-represented among affected offspring.
Association is tested by comparing the observed data with the Mendelian expectation.

25. EPIDEMIOLOGY GENETICS
Now, up until the 1990’s, genetics and epidemiology were largely working independently…
1990’s

26. EPIDEMIOLOGY GENETICS
Folic Acid
Association
GENETICS
But as Sarah told you, about this time the link between FA and NTDs was established and progress on the HGP provided the ability to due genetic association studies.
Given this timing, it is not surprising that what followed was an interest by both G and E in studies evaluating genetic variation within folate related genes as SB risk factors.
1990’s

27. EPIDEMIOLOGY GENETICS
Folic Acid
Association
GENETICS
And the two fields have been much more closely united since that time.
1990’s

28. Folic
Acid CT
In addition, provided perfect paradigm for study of gene/environment interactions…

29. Folic
Acid TT CT
As well as raising interest in the role that the maternal genotype plays…an area that has been of particular interest to my research group.

30. MTHFR C677T Child OR = 1.8 (1.4-2.1) Mother OR=1.9 (1.5-2.4)
The most frequently studied, and widely recognized folate-related gene variant is C677T of MTHFR (involved in conversion to intracellular form)
Numerous studies, looking at both child and mothers genotype – majority suggesting increase in risk associated with T allele. However, not clear whether one or both related, in addition….
Mother
OR=1.9 ( )
Vollest and Botto, 2004

31. MTHFR C677T Mother OR=1.9 (1.5-2.4) GENOTYPE CASE MOTHERS
CONTROL MOTHERS CC
368
816 CT
567
885 TT
226 (19%)
212 (11%)
Because this is common variant, ~10% of women who have not had an affected child have the high risk genotype – therefore not appropriate as screening tool – recommendations regarding folate intake would remain unchanged.
Mother
OR=1.9 ( )
Vollest and Botto, 2004

32. Obesity/Diabetes-Related
Maternal Genotypes
N=737 NTD triads
Fat mass and obesity associated gene (FTO)
Leptin (LEP)
T-cell factor 7-like 2 (TCF7L-2)
Another area where epidemiology has guided genetic studies relates to associate with diabetes/obesity…
Lupo et al. Am J Epidemiology (in press)

33. Genetic Suspects Folate pathway Obesity/diabetes-related
Planar cell polarity pathway
Overall, candidate gene association studies have provided evidence for….

34. GWAS
No GWAS – numbers…
No doubt that candidate based work will continue even as we move forward into the most recent arena of…

35. Sequence Candidate genes/pathways Exomes Genomes Association
Aggregation
Association
Sequence
Sequencing – This represents a paradigm shift in that the underlying hyp is:
Candidate genes/pathways
Exomes
Genomes

36. Rare Variants
That rare variants contribute to the risk of disease – such variants are not captured in association studies, so have not yet been explored in a major way
For SB, sequencing to date has largely focused on candidate genes…

37. Such as VANGL2 – a PCP gene
6 rare
PCP - Gene
6 rare, novel variants

38. PCP genes seem to be one area where studies in mice and humans are converging

39. Pathways
Spectrum of Variants

41. NH- Homocysteine
Hispanic – Purine

42. Complex Diseases are Complex

43. Bioinformatics
Pathways
Interactions