Structural variation in the human genome

Humans have an incredibly complex and intricate genome that has been shaped and modified over time by evolution. About 99.9% of the DNA-sequence in the human genome is conserved between individuals from all over the world, but some variation does exist. Single nucleotide polymorphisms (SNPs) are considered to be the largest contributor to genetic variation in humans since they are so abundant and easily detectable. It is estimated that there are at least 10 million SNPs within the human population but there are also many other types of genetic variants and they occur at dramatically different scales. The variation between genomes in the human population range from single nucleotide polymorphisms to dramatic alterations in the human karyotype.

Human genetic variation is responsible for the phenotypic differences between individuals in the human population. There are different types of genetic variation and it is studied extensively in order to better understand its significance. These studies lead to discoveries associating genetic variants to certain phenotypes as well as their implications in disease. At first, before DNA sequencing technologies, variation was studied and observed exclusively at a microscopic scale. At this scale, the only observations made were differences in chromosome number and chromosome structure. These variants that are about 3 Mb or larger in size are considered microscopic structural variants. This scale is large enough to be visualized using a microscope and include aneuploidies, heteromorphisms, and chromosomal rearrangements. When DNA sequencing was introduced, it opened the door to finding smaller and incredibly more sequence variations including SNPs and minisatellites. This also includes small inversions, duplications, insertions, and deletions that are under 1 kb in size. In the human genome project the human genome was successfully sequenced, which provided a reference human genome for comparison of genetic variation. With improving sequencing technologies and the reference genome, more and more variations were found of several different sizes that were larger than 1 kb but smaller than microscopic variants. These variants ranging from about 1 Kb to 3 Mb in size are considered submicroscopic structural variants. These recently discovered structural variants are thought to play a very significant role in phenotypic diversity and disease susceptibility.

Types of structural variants

Structural variation is an important type of human genetic variation that contributes to phenotypic diversity. There are microscopic and submicroscopic structural variants which include deletions, duplications, and large copy number variants as well as insertions, inversions, and translocations. These are several different types of structural variants in the human genome and they are quite distinctive from each other. A translocation is a chromosomal rearrangement, at the inter- or intra-chromosomal level, where a section of a chromosome changes position but with no change in the whole DNA content. A section of DNA that is larger than 1 kb and occurs in two or more copies per haploid genome, in which the different copies share greater than 90% of the same sequence, are considered to be segmental duplications or low-copy repeats. These are only a few of the several different types of structural variants that have been known to exist in the human genome. A table visualizing these different forms of structural variants, as well as others, is shown in Figure 1.

An inversion is a section of DNA on a chromosome that is reversed in its orientation in comparison to the reference genome. There have been many studies identifying inversions because they have been found to have a big role in many diseases. A study found that forty percent of haemophilia A patients had a factor 8 gene inversion of a certain region that was four hundred kb in size. The inversion breakpoint was found to be around a segmental duplication which is observed in many other inversion events.

It is difficult to completely understand how each structural variant is created. It was previously known that repeated sequences on a chromosome increases the probability of non allelic homologous recombination. These repeated sequences could cause deletions, duplications, inversions, and inverted duplication chromosomes. The products of this mechanism from the sequence repeats is depicted in Figure 2. A study was done on the olfactory receptor gene clusters where they questioned if there was an association between normal rearrangement of 8p and the repeated inverted sequences. The researchers observed that the rearrangement of chromosomes was actually caused by the homologous recombination in the 8p-reps. Therefore, they concluded that the substrate used in order to make rearrangements at the intrachromosomal level are the genes for olfactory receptors. This discovery revealed the role that inverted duplicates have in affecting the development of structural variants. The mechanisms and ways in which structural variants are produced are important to better understand the development of these types of genetic variants.

Copy-number variation

Copy-number variants are defined as sections of DNA that exist in a variable copy number when comparing it to the reference genome and are larger than 1 kb in size. This definition is broad and includes deletions, duplications, and large copy number variants. If the copy number variant is present in 1% or more of the population then it is also considered a copy-number polymorphism. There was a study on the global variation in copy number in the human genome which questioned the characteristics of copy number variants in the human genome. It was known that copy number variation in the human genome is important but at this point of time, it had not yet been fully understood. Human genome variation itself is very diverse as there are many types including inversions, duplication, SNPs, and other forms. They surveyed the genomes of 270 individuals, from a variety of populations, for copy number variants with technologies such as SNP arrays. Their results showed that many copy number variants had specific arrangements of linkage disequilibrium which revealed the copy number variation in all of the different populations. The study concluded that twelve percent of the genome contained CNVRs. They were found to be involved in more of the DNA in each genome than single nucleotide polymorphisms. This was a remarkable discovery since single nucleotide polymorphisms have been known to be the greatest in number in the human genome. In terms of size, however, these types of structural variants were found to have a larger presence in the human genome.

The copy number variants continued to be studied as several studies continued to reveal the depth of their presence and their significance. A study was conducted that questioned the role of the organization of copy number variants and wondered what type of duplications they are. It was known that copy number variation plays a big role in many human diseases but at the time large scale studies of these duplications had not been done. They decided to sequence 130 breakpoints from 112 individuals that contained 119 known CNVs by doing whole genome sequencing as well as next generation sequencing. They found that tandem duplications comprised 83% of the CNVs while 8.4% were triplications, 4.2% were adjacent duplications, 2.5% were insertional translocations, and 1.7% were other complex rearrangements. The copy number variants were predominantly tandem duplications which made it the most common type of copy number variant in the human genome according to the results of the study on this population. More was needed on the mechanistic side of the formation of structural variants. There was a study that focused on the mechanisms of very interesting and rare pathogenic copy number variants. The researchers knew that copy number variation is important in genome structural variation and contributes to human genetic disease but the actual mechanisms of most of the new and few pathogenic copy number variants had not been known. They used sequencing technologies to sequence breakpoint areas of many rare pathogenic copy number variants which was the biggest and most in depth analysis of copy number variants. They saw that the genomic architectural features were very important in the human genome and they were associated with about eighty-one percent of breakpoints. They concluded that tandem duplications and microdeletions that are rare and pathogenic do not happen in the human genome by chance. Instead, they arise from many different genomic architectural features. It was a very interesting result in that the certain architectural features of the genome physically made it possible and probable to develop certain rare and pathogenic structural variants.

Structural variation can be seen as an avenue of genome modification for adaptation by evolution. A study was conducted on ancestral diet and the evolution of the human amylase gene copy number. The consumption of starch became a huge component of the human diet with the development of agricultural societies. Amylase is the enzyme that breaks down starch and its copy number varies. These observations led to the question of whether or not the differences in starch consumption between different populations created natural selection pressures on the enzyme amylase. They tested for the differences in the amylase protein expression in saliva from different populations and compared their expression to their copy number in their respective genomes. Then they compared the starch consumption of different populations to their copy number of the amylase gene. They found that there was more amylase protein expression in saliva from people that had higher amylase copy number in their genome and there was also an association between groups of people with high starch diets and a larger amylase gene copy number. This study brought exciting results as structural variation proved an involvement in the evolution of the human population by increasing its amylase copy number over time.

The 1000 genomes project was able to successfully produce the DNA sequence of the human genome. They provided much sequencing data from many populations to analyze as well as a reference human genome for comparison and future studies. One study took advantage of this resource to question the structural variation differences between genomes from whole genome sequence data. It was known that human diseases are affected by duplications and deletions and that copy number analysis is common but multiallelic copy number variants (mCNVs) were not as well studied. The researchers got their data from the 1000 genomes project and analyzed 849 different genomes from a variety of populations that were sequenced in order to find large mCNVs. From their analysis, they found that mCNVs create most genetic variation in gene dosage compared to other structural variants and that the gene expression variation is created by the dosage diversity of genes created by mCNVs. The study underlined the great significance that structural variants, especially mCNVs, have on gene dosage which leads to variable gene expressions and human phenotypic diversity in the population.