1. Nucleotide variation in the human genome
Nieves García Gisbert

2. How variable is the human genome?
We are identical in 99,5 % of our genome sequence
Human genome has about 10 million polymorphisms
Recent projects studying variability in humans:
Single Nucleotide Polymorphism (SNP): variation in a single nucleotide that occurs at a specific position in the genome

3. 7,000,000,000 5,000,000 How many humans are we now in the world?
How many humans were 10,000 years ago?
5,000,000

4. Recent history of human population
Human global population has grown from a 5 million people to 7 billion, in only years
x3 increase in 400 generations
Recent explosive human population growth has resulted in an excess of rare genetic variants
Keinan, Alon, et al. "Recent explosive human population growth has resulted in an excess of rare genetic variants." (2012):

5. Previous studies Recent studies
limited sample size of these studies (at most 60 individuals)
only allowed capturing variants of frequency as low as ~1% in the sample
limited view of rare variants in the population
only focused in common variants
higher number of individuals are studied, having a bigger sample size
allowed to detect all kind of variants, including the less frequent
It has been observed an excess of rare variants compared to what was expected
explosive human population growth

6. Identifying rare variants
Singletons: rare variants, which are only found in one individual in the population sample. Doubletons are found twice.
Variants considered rare in population require sequencing of a large sample of individuals.
Now it is economically possible, but there are other problems:
How to distinguish false positives from rare SNP variants?
False positives: are errors in sequencing that may be considered as variants
For example:
(20,000 times the sequence)
Gene
10,000 individuals
2 errors in each bp
Sequencing method:
error rate: 1 error per 10,000 mb

7. Identifying rare variants
Singletons: rare variants, which are only found in one individual in the population sample. Doubletons are found twice.
Variants considered rare in population require sequencing of a larger sample of individuals.
Now it is economically possible, but there are other problems:
How to distinguish false positives from rare SNP variants?
Rare variants have such a low frequency that they are considered not reliable
second validation of rare variants with other sequencing methods

8. Recent variants are mostly rare variants
Due to the explosion in population growth in the last years, there is a high presence of new and rare variants
A larger sample allow identification of rarer polymorphisms that are due to more recent mutations. An estimation is:
- SNPs with >5% frequency have 10, ,000 years
- SNPs with 5% frequency only 8% have 10,000 years less than 1% have 2,500 years
Rare variants add information about changes that have occur during this recent epochs of accelerated explosive growth

9. Presence of rare variants
Coventry, Alex, et al., In collaboration with the Atherosclerosis Risk community, they resequenced KCNJII and HHEX genes in 10,422 individuals
10,422 individuals
Is this just because this genes are more likely to have this rare variants?
two genes: KCNJII, HHEX
Of all the SNVs that were found, 50% were singletons (only present in one of the individuals)

10. Presence of rare variants
Tennessen, Jacob A., et al., They try to identify and understand variants related with complex diseases
2440 exomes where sequenced
503,481 SNV were identified in 15,583 genes
82% SNVs were novel, previously unknown. 48,9% of this are nonsynonymous
75% SNVs were singletons
110 genes had a higher proportion of rare variants
Including six histone related genes, highly conserved and with great selective constraint

11. Presence of rare variants
Tennessen, Jacob A., et al., 2012.
They analyzed found SNVs using function predictors
Combined software:
Gives a score to a concrete aa change in the protein to predict if its function or conformation is altered
95.7% variants with functional importance are rare SNVs

12. Rare variants and disease
it is not clear which is the medical implication of an excess of rare genetic variation
as these variants are so recent, they appear as novel mutation, with little time for natural selection to operate
rare variants appear in high conserved places, and sometimes are nonsynonymous, they may have a role in disease
risk for more complex disease may be due to this rapid expansion of rare variants

13. Rare variants and disease
Rare diseases
When affecting to certain genes
Rare variants
For example, autism, mental retardation, epilepsy and schizophrenia have been shown to be influenced by rare variants that affect genes
Studying common variants has not been enough to determine the cause of many common diseases
Common diseases

14. Conclusions
Studying this rare variants require large sample size studies
As these variants are so recent, they appear as novel mutation, with little time for natural selection to operate.
Majority of protein coding variation is evolutionary recent, rare, and probably deleterious
Rare variants are contributing to human phenotypic variation and disease susceptibility, but it is not known how. It is not clear which is the medical implication of an excess of rare genetic variation
Evaluation of rare variants found is needed to understand disease

15. Bibliography
Keinan, Alon, and Andrew G. Clark. "Recent explosive human population growth has resulted in an excess of rare genetic variants." science  (2012):
Goldstein, D.B., and Cavalleri, G.L Genomics: Understanding human diversity. Nature 437:
Tennessen, Jacob A., et al. "Evolution and functional impact of rare coding variation from deep sequencing of human exomes." science  (2012):
Sachidanandam, Ravi, et al. "A map of human genome sequence variation containing million single nucleotide polymorphisms." Nature  (2001):
Cirulli, Elizabeth T., and David B. Goldstein. "Uncovering the roles of rare variants in common disease through whole-genome sequencing." Nature Reviews Genetics  (2010):