Nucleotide variation in the human genome Nieves García Gisbert

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

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

Recent history of human population Human global population has grown from a 5 million people to 7 billion, in only 10.000 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):

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

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

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

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 10,000-100,000 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

Presence of rare variants Coventry, Alex, et al., 2010. 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)

Presence of rare variants Tennessen, Jacob A., et al., 2012. 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

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

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

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

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

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