All of them correspond to deletions located in homopolymeric stretches.
Anna Ruiz, Gemma Llort, Carmen Yagüe, Neus Baena, Marina Viñas, Montse Torra, AnnaBrunet, Miquel A. Seguí, Eugeni Saigí, Miriam Guitart 2014, 'Genetic Testing in Hereditary Breast and Ovarian Cancer Using Massive Parallel Sequencing',BioMed Research Internationalhttp://dx.doi.org/10.1155/2014/542541. Retrieved from DOAJ CC BY 4.0 (https://creativecommons.org/licenses/by-sa/4.0/legalcode)
Proteins containing long, homopolymeric stretches of glutamine are especially prone to form aggregates.
Caldwell Guy A, Caldwell Kim A, Hajjar Connie, Sharma Pratima, Howard Rebecca A, duBreuil Rusla, Moore Rhonda, Boyd Lynn 2007, 'Ubiquitin conjugating enzymes participate in polyglutamine protein aggregation', BMC Cell Biologyhttp://www.biomedcentral.com/1471-2121/8/32. Retrieved from DOAJ CC BY 4.0 (https://creativecommons.org/licenses/by-sa/4.0/legalcode)
Sixteen of the 29 coding regions have homopolymeric tracts characteristic of translational phase variation.
Weinstock George M, Langdon Rebecca R, Linton James D, Loman Nicholas J, Snyder LoriAS, Wren Brendan W, Pallen Mark J 2010, 'Simple sequence repeats in Helicobacter canadensis and their role in phasevariable expression and C-terminal sequence switching', BMC Genomicshttp://www.biomedcentral.com/1471-2164/11/67. Retrieved from DOAJ CC BY 4.0 (https://creativecommons.org/licenses/by-sa/4.0/legalcode)
We also developed a new software tool, hp_caller, to perform accurate genotyping at homopolymeric repeat loci.
Daniel E. Eyler, Kylie A. Burnham, Thomas E. Wilson, Patrick J. O'Brien 2017, 'Mechanisms of glycosylase induced genomic instability', PLOS ONE10.1371/journal.pone.0174041. Retrieved from PLOS CC BY 4.0 (https://creativecommons.org/licenses/by-sa/4.0/legalcode)
Both the repeat length itself and mismatch repair deficiency were shown to influence the genetic instability of the homopolymeric tracts.
Kristian Alfsnes, Xavier Raynaud, Tone Tønjum, Ole Herman Ambur 2014, 'Mathematical and Live Meningococcal Models for Simple Sequence Repeat Dynamics – CoherentPredictions and Observations', PLoS ONE10.1371/journal.pone.0101637. Retrieved from PLOS CC BY 4.0 (https://creativecommons.org/licenses/by-sa/4.0/legalcode)
In cleaned data the error frequency was similar in homopolymeric and non-homopolymeric regions, but varied considerably across sites.
Johanna Brodin, Mattias Mild, Charlotte Hedskog, Ellen Sherwood, Thomas Leitner, BjörnAndersson, Jan Albert 2013, 'PCR-induced transitions are the major source of error in cleaned ultra-deep pyrosequencingdata.', PLoS ONEhttp://europepmc.org/articles/PMC3720931?pdf=render. Retrieved from PLOS CC BY 4.0 (https://creativecommons.org/licenses/by-sa/4.0/legalcode)
In agreement with previous observations these higher rates were strongly associated with homopolymeric stretches on the 454platform.
Archer John, Baillie Greg, Watson Simon J, Kellam Paul, Rambaut Andrew, RobertsonDavid L 2012, 'Analysis of high-depth sequence data for studying viral diversity: a comparison ofnext generation sequencing platforms using Segminator II', BMC Bioinformaticshttp://www.biomedcentral.com/1471-2105/13/47. Retrieved from DOAJ CC BY 4.0 (https://creativecommons.org/licenses/by-sa/4.0/legalcode)
We compare the properties of these conformations to those of the standard proteins, as wellas to other homopolymeric tracts.
Àngel Gómez-Sicilia, Mateusz Sikora, Marek Cieplak, Mariano Carrión-Vázquez 2015, 'An Exploration of the Universe of Polyglutamine Structures.', PLoS Computational Biologyhttp://europepmc.org/articles/PMC4619799?pdf=render. Retrieved from PLOS CC BY 4.0 (https://creativecommons.org/licenses/by-sa/4.0/legalcode)