A Census of Tandemly Repeated Polymorphic Loci in Genic Regions Through the Comparative Integration of Human Genome Assemblies

Abstract

Polymorphic Tandem Repeat (PTR) is a common form of polymorphism in the human genome. A PTR consists in a variation found in an individual (or in a population) of the number of repeating units of a Tandem Repeat (TR) locus of the genome with respect to the reference genome. Several phenotypic traits and diseases have been discovered to be strongly associated with or caused by specific PTR loci. PTR are further distinguished in two main classes: Short Tandem Repeats (STR) when the repeating unit has size up to 6 base pairs, and Variable Number Tandem Repeats (VNTR) for repeating units of size above 6 base pairs. As larger and larger populations are screened via high throughput sequencing projects, it becomes technically feasible and desirable to explore the association between PTR and a panoply of such traits and conditions. In order to facilitate these studies, we have devised a method for compiling catalogs of PTR from assembled genomes, and we have produced a catalog of PTR for genic regions (exons, introns, UTR and adjacent regions) of the human genome (GRCh38). We applied four different TR discovery software tools to uncover in the first phase 55,223,485 TR (after duplicate removal) in GRCh38, of which 373,173 were determined to be PTR in the second phase by comparison with five assembled human genomes. Of these, 263,266 are not included by state-of-the-art PTR catalogs. The new methodology is mainly based on a hierarchical and systematic application of alignment-based sequence comparisons to identify and measure the polymorphism of TR. While previous catalogs focus on the class of STR of small total size, we remove any size restrictions, aiming at the more general class of PTR, and we also target fuzzy TR by using specific detection tools. Similarly to other previous catalogs of human polymorphic loci, we focus our catalog toward applications in the discovery of disease-associated loci. Validation by cross-referencing with existing catalogs on common clinically-relevant loci shows good concordance. Overall, this proposed census of human PTR in genic regions is a shared resource (web accessible), complementary to existing catalogs, facilitating future genome-wide studies involving PTR.

DNA Hypermethylation and Unstable Repeat Diseases: A Paradigm of Transcriptional Silencing to Decipher the Basis of Pathogenic Mechanisms

“…In patients with familial cortical myoclonic tremor with epilepsy (FCMTE; MIM 615400), LRS sequencing identified, as the causative mutations, intronic repeat expansions in SAMD12 [ 80 ]. Recently, various applications of massively parallel sequencing coupled with innovative algorithms have also contributed to identifying new repeat loci, highlighting the importance of considering the genetic contribution of unstable repeats, where these lack a clear genetic cause [ 51 , 52 , 53 , 81 , 82 ]. In addition, a genome-wide DNA methylation assay has been successfully applied to the molecular diagnosis of genetically unresolved cases, uncovering new hypervariable trinucleotide repeat loci [ 72 , 83 ].…”

A human-specific VNTR in the TRIB3 promoter causes gene expression variation between individuals

“…In the current era of human genetic studies, powered mainly by short-read sequencing and SNP microarrays, VNTRs have been addressed comparatively less than other types of variants due to technological constraints. Nevertheless, more than a hundred thousand polymorphic tandem repeats have been described that localize within or near genes in the human genome, representing considerable potential to alter the protein coding or regulatory sequences of genes [ 52 ]. In the current article, we characterize copy number variation in a 33-bp tandem repeat localized to the promoter region of human TRIB3 and uncover that alleles with a higher copy number of the 33-bp repeating element lead to elevated TRIB3 gene expression level.…”

Non-canonical RNA-DNA differences and other human genomic features are enriched within very short tandem repeats

“…In the past decade, although many efforts were dedicated to calling STR variations from Next-Generation Sequencing data, an updated census of STR in the human reference genome is surprisingly unobserved. As a preparation step to their major analyses, two studies [8,9] compiled STR catalogs in GRCh37 and GRCh38, respectively; both works employed ad hoc procedures and custom parameters, thus generating highly customized datasets unsuitable for general use. In particular, both catalogs were initially generated by an inference-based algorithm TRF [10], so by definition they represented a mixture of perfect and imperfect STRs.…”