Structural variation in the human genome

Structural Variation

Structural variation in the human genome is operationally defined as genomic alterations, varying between individuals, that involve DNA segments larger than 1 kilo base (kb), and could be either microscopic or submicroscopic.[1] This definition distinguishes them from smaller variants that are less than 1 kb in size such as short deletions, insertions, and single nucleotide variants.

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.[1] Single nucleotide polymorphisms (SNPs) are considered to be the largest contributor to genetic variation in humans since they are so abundant and easily detectable.[2] 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.[1] The variation between genomes in the human population range from single nucleotide polymorphisms to dramatic alterations in the human karyotype.[3]

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.[1] This scale is large enough to be visualized using a microscope and include aneuploidies, heteromorphisms, and chromosomal rearrangements.[1] 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.[1] 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.[1] These recently discovered structural variants are thought to play a very significant role in phenotypic diversity and disease susceptibility.

  1. ^ a b c d e f g Feuk, L.; Carson, A.R.; Schere, S.W. (2006). "Structural variation in the human genome". Nature Reviews Genetics. 7 (2): 85–97. doi:10.1038/nrg1767. PMID 16418744. S2CID 17255998.
  2. ^ Nguyen, D.Q.; Webber, C.; Ponting, C.P. (2006). "Bias of selection on human copy-number variants". PLOS Genetics. 2 (2): e20. CiteSeerX 10.1.1.276.7715. doi:10.1371/journal.pgen.0020020. PMC 1366494. PMID 16482228.
  3. ^ Kidd, J.M.; Cooper, G.M.; Donahue, W.F.; Hayden, H.S.; Sampas, N.; Graves, T.; Hansen, N.; Teauge, B.; Alkan, C.; Antonacci, F.; Haugen, E.; Zerr, T.; Yamada, N.A.; Tsang, P.; Newman, T.L.; Tuzun, E.; Cheng, Z.; Ebling, H.M.; Tusneem, N.; David, R.; Gillett, W.; Phelps, K.A.; Weaver, M.; Saranga, D.; Brand, A.; Tao, W.; Gustafson, E.; McKernan, K.; Chen, L.; Malig, M.; Smith, J.D.; Korn, J.M.; McCarroll, S.A.; Altshuler, D.A.; Peiffer, D.A.; Dorschner, M.; Stamatoyannopoulos, J.; Schwartz, D.; Nickerson, D.A.; Mullikin, J.C.; Wilson, R.K.; Bruhn, L.; Olson, M.V.; Kaul, R.; Smith, D.R.; Eichler, E.E. (2008). "Mapping and sequencing of structural variation from eight human genomes". Nature. 453 (7191): 56–64. Bibcode:2008Natur.453...56K. doi:10.1038/nature06862. PMC 2424287. PMID 18451855.