Type Of Structural Variation Research Articles

A model-based clustering method for genomic structural variant prediction and genotyping using paired-end sequencing data.

Structural variation (SV) has been reported to be associated with numerous diseases such as cancer. With the advent of next generation sequencing (NGS) technologies, various types of SV can be potentially identified. We propose a model based clustering approach utilizing a set of features defined for each type of SV events. Our method, termed SVMiner, not only provides a probability score for each candidate, but also predicts the heterozygosity of genomic deletions. Extensive experiments on genome-wide deep sequencing data have demonstrated that SVMiner is robust against the variability of a single cluster feature, and it significantly outperforms several commonly used SV detection programs. SVMiner can be downloaded from http://cbc.case.edu/svminer/.

An Improved Protocol for Sequencing of Repetitive Genomic Regions and Structural Variations Using Mutagenesis and Next Generation Sequencing

The rise of Next Generation Sequencing (NGS) technologies has transformed de novo genome sequencing into an accessible research tool, but obtaining high quality eukaryotic genome assemblies remains a challenge, mostly due to the abundance of repetitive elements. These also make it difficult to study nucleotide polymorphism in repetitive regions, including certain types of structural variations. One solution proposed for resolving such regions is Sequence Assembly aided by Mutagenesis (SAM), which relies on the fact that introducing enough random mutations breaks the repetitive structure, making assembly possible. Sequencing many different mutated copies permits the sequence of the repetitive region to be inferred by consensus methods. However, this approach relies on molecular cloning in order to isolate and amplify individual mutant copies, making it hard to scale-up the approach for use in conjunction with high-throughput sequencing technologies. To address this problem, we propose NG-SAM, a modified version of the SAM protocol that relies on PCR and dilution steps only, coupled to a NGS workflow. NG-SAM therefore has the potential to be scaled-up, e.g. using emerging microfluidics technologies. We built a realistic simulation pipeline to study the feasibility of NG-SAM, and our results suggest that under appropriate experimental conditions the approach might be successfully put into practice. Moreover, our simulations suggest that NG-SAM is capable of reconstructing robustly a wide range of potential target sequences of varying lengths and repetitive structures.

PRISM: Pair-read informed split-read mapping for base-pair level detection of insertion, deletion and structural variants

The development of high-throughput sequencing technologies has enabled novel methods for detecting structural variants (SVs). Current methods are typically based on depth of coverage or pair-end mapping clusters. However, most of these only report an approximate location for each SV, rather than exact breakpoints. We have developed pair-read informed split mapping (PRISM), a method that identifies SVs and their precise breakpoints from whole-genome resequencing data. PRISM uses a split-alignment approach informed by the mapping of paired-end reads, hence enabling breakpoint identification of multiple SV types, including arbitrary-sized inversions, deletions and tandem duplications. Comparisons to previous datasets and simulation experiments illustrate PRISM's high sensitivity, while PCR validations of PRISM results, including previously uncharacterized variants, indicate an overall precision of ~90%. PRISM is freely available at http://compbio.cs.toronto.edu/prism.

Investigation of Inversion Polymorphisms in the Human Genome Using Principal Components Analysis

Despite the significant advances made over the last few years in mapping inversions with the advent of paired-end sequencing approaches, our understanding of the prevalence and spectrum of inversions in the human genome has lagged behind other types of structural variants, mainly due to the lack of a cost-efficient method applicable to large-scale samples. We propose a novel method based on principal components analysis (PCA) to characterize inversion polymorphisms using high-density SNP genotype data. Our method applies to non-recurrent inversions for which recombination between the inverted and non-inverted segments in inversion heterozygotes is suppressed due to the loss of unbalanced gametes. Inside such an inversion region, an effect similar to population substructure is thus created: two distinct “populations” of inversion homozygotes of different orientations and their 1∶1 admixture, namely the inversion heterozygotes. This kind of substructure can be readily detected by performing PCA locally in the inversion regions. Using simulations, we demonstrated that the proposed method can be used to detect and genotype inversion polymorphisms using unphased genotype data. We applied our method to the phase III HapMap data and inferred the inversion genotypes of known inversion polymorphisms at 8p23.1 and 17q21.31. These inversion genotypes were validated by comparing with literature results and by checking Mendelian consistency using the family data whenever available. Based on the PCA-approach, we also performed a preliminary genome-wide scan for inversions using the HapMap data, which resulted in 2040 candidate inversions, 169 of which overlapped with previously reported inversions. Our method can be readily applied to the abundant SNP data, and is expected to play an important role in developing human genome maps of inversions and exploring associations between inversions and susceptibility of diseases.

Abstract 4947: Analysis of structural mutations in cancer genomes

Abstract In our group, we have extensively sequenced various cancer genomes (breast cancer, ovarian cancer and melanoma) using a range of genome-wide sequencing approaches, including DNA-PET, RNA-SEQ and exome-capture sequencing. Taking each tumor as a system of its own, we aim to integrate the different outputs of these technologies to explore the composite of hard-wired changes that drive tumorgenesis in different cancers. One type of hard-wired changes is copy number alterations, where the cancer genome tends to gain oncogenes and lose tumor suppressors by DNA amplifications and deletions respectively. While copy number variation data are now a standard output of the DNA-PET pipeline, the accurate prediction of copy number gains and losses is further complicated by several issues, including normal tissue contamination, tumor heterogeneity and aneuploidy. I will present my current work to deconvolute the contribution of these factors to the copy number profile. I will also discuss the classification of our sequenced cancer genomes into various chromotypes based on their unique copy number signatures. I will show how different chromotypes are enriched in specific types of structural variations, which may underlay alternative mechanisms of genomic instability promoting cancer evolution. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4947. doi:1538-7445.AM2012-4947

Detection of copy number alterations in acute myeloid leukemia and myelodysplastic syndromes

Chromosomal deletions and amplifications that occur in affected cells from patients with myelodysplastic syndromes and acute myeloid leukemia often contain genes that contribute to disease pathogenesis. Identification of copy number alterations (deletions and amplifications) and regions of copy neutral loss of heterozygosity using array-based platforms has led to the identification of genes that are commonly mutated in myeloid malignancies. In this article, we review the literature and highlight the array-based studies that directly compare matched normal and tumor samples from the same individual to identify somatic alterations. We also discuss the use of next-generation sequencing to identify all types of structural variants, including copy number alterations and copy neutral loss of heterozygosity, and provide an outlook for how this technology may be used to interrogate cancer genomes.

Predicting Target DNA Sequences of DNA-Binding Proteins Based on Unbound Structures

DNA-binding proteins such as transcription factors use DNA-binding domains (DBDs) to bind to specific sequences in the genome to initiate many important biological functions. Accurate prediction of such target sequences, often represented by position weight matrices (PWMs), is an important step to understand many biological processes. Recent studies have shown that knowledge-based potential functions can be applied on protein-DNA co-crystallized structures to generate PWMs that are considerably consistent with experimental data. However, this success has not been extended to DNA-binding proteins lacking co-crystallized structures. This study aims at investigating the possibility of predicting the DNA sequences bound by DNA-binding proteins from the proteins' unbound structures (structures of the unbound state). Given an unbound query protein and a template complex, the proposed method first employs structure alignment to generate synthetic protein-DNA complexes for the query protein. Once a complex is available, an atomic-level knowledge-based potential function is employed to predict PWMs characterizing the sequences to which the query protein can bind. The evaluation of the proposed method is based on seven DNA-binding proteins, which have structures of both DNA-bound and unbound forms for prediction as well as annotated PWMs for validation. Since this work is the first attempt to predict target sequences of DNA-binding proteins from their unbound structures, three types of structural variations that presumably influence the prediction accuracy were examined and discussed. Based on the analyses conducted in this study, the conformational change of proteins upon binding DNA was shown to be the key factor. This study sheds light on the challenge of predicting the target DNA sequences of a protein lacking co-crystallized structures, which encourages more efforts on the structure alignment-based approaches in addition to docking- and homology modeling-based approaches for generating synthetic complexes.

Characterization of six human disease-associated inversion polymorphisms

The human genome is a highly dynamic structure that shows a wide range of genetic polymorphic variation. Unlike other types of structural variation, little is known about inversion variants within normal individuals because such events are typically balanced and are difficult to detect and analyze by standard molecular approaches. Using sequence-based, cytogenetic and genotyping approaches, we characterized six large inversion polymorphisms that map to regions associated with genomic disorders with complex segmental duplications mapping at the breakpoints. We developed a metaphase FISH-based assay to genotype inversions and analyzed the chromosomes of 27 individuals from three HapMap populations. In this subset, we find that these inversions are less frequent or absent in Asians when compared with European and Yoruban populations. Analyzing multiple individuals from outgroup species of great apes, we show that most of these large inversion polymorphisms are specific to the human lineage with two exceptions, 17q21.31 and 8p23 inversions, which are found to be similarly polymorphic in other great ape species and where the inverted allele represents the ancestral state. Investigating linkage disequilibrium relationships with genotyped SNPs, we provide evidence that most of these inversions appear to have arisen on at least two different haplotype backgrounds. In these cases, discovery and genotyping methods based on SNPs may be confounded and molecular cytogenetics remains the only method to genotype these inversions.

Thrombin-like enzymes from venom gland of Deinagkistrodon acutus: cDNA cloning, mechanism of diversity and phylogenetic tree construction1

To clone cDNAs of thrombin-like enzymes (TLEs) from venom gland of Deinagkistrodon acutus and analyze the mechanisms by which their structural diversity arose. Reverse transcription-polymerase chain reaction and gene cloning techniques were used, and the cloned sequences were analyzed by using bioinformatics tools. Novel cDNAs of snake venom TLEs were cloned. The possibilities of post-transcriptional recombination and horizontal gene transfer are discussed. A phylogenetic tree was constructed. The cDNAs of snake venom TLEs exhibit great diversification. There are several types of structural variations. These variations may be attributable to certain mechanisms including recombination.

Discovery of Human Inversion Polymorphisms by Comparative Analysis of Human and Chimpanzee DNA Sequence Assemblies

With a draft genome-sequence assembly for the chimpanzee available, it is now possible to perform genome-wide analyses to identify, at a submicroscopic level, structural rearrangements that have occurred between chimpanzees and humans. The goal of this study was to investigate chromosomal regions that are inverted between the chimpanzee and human genomes. Using the net alignments for the builds of the human and chimpanzee genome assemblies, we identified a total of 1,576 putative regions of inverted orientation, covering more than 154 mega-bases of DNA. The DNA segments are distributed throughout the genome and range from 23 base pairs to 62 mega-bases in length. For the 66 inversions more than 25 kilobases (kb) in length, 75% were flanked on one or both sides by (often unrelated) segmental duplications. Using PCR and fluorescence in situ hybridization we experimentally validated 23 of 27 (85%) semi-randomly chosen regions; the largest novel inversion confirmed was 4.3 mega-bases at human Chromosome 7p14. Gorilla was used as an out-group to assign ancestral status to the variants. All experimentally validated inversion regions were then assayed against a panel of human samples and three of the 23 (13%) regions were found to be polymorphic in the human genome. These polymorphic inversions include 730 kb (at 7p22), 13 kb (at 7q11), and 1 kb (at 16q24) fragments with a 5%, 30%, and 48% minor allele frequency, respectively. Our results suggest that inversions are an important source of variation in primate genome evolution. The finding of at least three novel inversion polymorphisms in humans indicates this type of structural variation may be a more common feature of our genome than previously realized.

1H and 13C NMR Study of 1-Hydrazino-2,3-dihydro-1H-pyrazolo[1,2-a]pyridazine-5,8-diones and -1H-pyrazolo[1,2-b]phthalazine-5,10-diones and Their Ring-Chain Tautomerism

Treatment of 1-hydroxy-2,3-dihydro-1H-pyrazolo[1,2-a]pyridazine-5,8-diones and -1H-pyrazolo[1,2-b]phthalazine-5,10-diones with hydrazides produces corresponding acylhydrazino derivatives. In this work, ten new hydrazino derivatives were synthesized, and their properties were studied by 1H and 13C NMR spectroscopy. These compounds exhibited several types of structural variation, including ring-chain tautomerism, cis-trans isomerism with respect to the substituents in the pyrazole ring, and (E)/(Z) rotamerism with respect to the nitrogen−carbon hydrazide bond with partial double-bond character. In [D6]DMSO, 2,3-dihydro-1H-pyrazolo[1,2-a]pyridazine-5,8-dione derivatives were found mainly as linear tautomers, whereas 2,3-dihydro-1H-pyrazolo[1,2-b]phthalazine-5,10-dione derivatives favored cyclic tautomers. For the latter compounds, a six-component equilibrium was found, consisting of a linear and of cis and trans cyclic tautomers, all of which had two rotamers, (E) and (Z). (© Wiley-VCH Verlag GmbH, 69451 Weinheim, Germany, 2002)

Exploring repeated measures data sets for key features using Principal Components Analysis

Repeated measures data sets are a very common data structure in marketing, ranging from weekly household purchase data obtained via supermarket scanners, household penetration rates for products over time, panel survey questionnaire responses, etc. In many circumstances, it is desirable to glean key features of the data without having to run a formal model and/or perform a large number of exploratory analyses. Such features of interest may include defining market segments, identifying change points (a sudden shift in aggregate behavior), and, in general, identifying “typical” behavior patterns. In this research, we apply an exploratory approach for analyzing repeated measures data sets, initially considered by Tucker [Psychometrika 23 (1958) 19] and fully explicated in Jones and Rice [Am. Stat. 46 (1992)], that utilizes Principal Components Analysis (as its core), regression, and simple bivariate plots. It is clearly our intention, via the algorithm provided, that a user can read this manuscript and then sit down at his or her computer and implement the approach immediately. We first demonstrate our approach on simulated data, therefore providing a “blueprint” for users of this approach, i.e. we simulate different types of structural variation and provide the corresponding principal component rotation curves, and how to glean features from them. Our approach is then applied to a data set on cumulative penetration rates for a set of durable products.

Développement de la construction argumentale de trois verbes essentiels : mettre, prendre, donner

C. Martinot, The development of the argument structure of three essential verbs: mettre ('to put'), prendre ('to take'), donner ('to give') The verbs mettre ('to puť), prendre ('to take'), and donner ('to give'), which are very frequent and used very early with various semantic values, present different types of structural variations: they vary just as well according to the presence vs omission of their arguments in the target language as according to the nature of these arguments (pronominal, adverbial, or nominal). Nonetheless, with all three verbs the same relation was found between two otherwise independent phenomena, namely the lexical diversity of the nominal arguments increases as a function of verbal morphology in the following order: uninflected infinitival form, inflected form, complex form. These results are based on a thousand utterances produced by two-to four -year-old children.

Methods for displaying macromolecular structural uncertainty: Application to the globins

Most molecular graphics programs ignore any uncertainty in the atomic coordinates being displayed. Structures are displayed in terms of perfect points, spheres, and lines with no uncertainty. However, all experimental methods for defining structures, and many methods for predicting and comparing structures, associate uncertainties with each atomic coordinate. We have developed graphical representations that highlight these uncertainties. These representations are encapsulated in a new interactive display program, PROTEAND. PROTEAND represents structural uncertainty in three ways: (1) The traditional way: The program shows a collection of structures as superposed and overlapped stick-figure models. (2) Ellipsoids: At each atom position, the program shows an ellipsoid derived from a three-dimensional Gaussian model of uncertainty. This probabilistic model provides additional information about the relationship between atoms that can be displayed as a correlation matrix. (3) Rigid-body volumes: Using clouds of dots, the program can show the range of rigid-body motion of selected substructures, such as individual α helices. We illustrate the utility of these display modalities by the applying PROTEAND to the globin family of proteins, and show that certain types of structural variation are best illustrated with different methods of display.

Isolation of Insertion Sequence IS RLd TAL1145-1 from a Rhizobium sp. ( Leucaena diversifolia ) and Distribution of Homologous Sequences Identifying Cross-Inoculation Group Relationships

Insertion sequence (IS) element ISRLdTAL1145-1 from Rhizobium sp. (Leucaena diversifolia) strain TAL 1145 was entrapped in the sacB gene of the positive selection vector pUCD800 by insertional inactivation. A hybridization probe prepared from the whole 2.5-kb element was used to determine the distribution of homologous sequences in a diverse collection of 135 Rhizobium and Bradyrhizobium strains. The IS probe hybridized strongly to Southern blots of genomic DNAs from 10 rhizobial strains that nodulate both Phaseolus vulgaris (beans) and Leucaena leucocephala (leguminous trees), 1 Rhizobium sp. that nodulates Leucaena spp., 9 R. meliloti (alfalfa) strains, 4 Rhizobium spp. that nodulate Sophora chrysophylla (leguminous trees), and 1 nonnodulating bacterium associated with the nodules of Pithecellobium dulce from the Leucaena cross-inoculation group, producing distinguishing IS patterns for each strain. Hybridization analysis revealed that ISRLdTAL1145-1 was strongly homologous with and closely related to a previously isolated element, ISRm USDA1024-1 from R. meliloti, while restriction enzyme analysis found structural similarities and differences between the two IS homologs. Two internal segments of these IS elements were used to construct hybridization probes of 1.2 kb and 380 bp that delineate a structural similarity and a difference, respectively, of the two IS homologs. The internal segment probes were used to analyze the structures of homologous IS elements in other strains. Five types of structural variation in homolog IS elements were found. The predominate IS structural type naturally occurring in a strain can reasonably identify the strain's cross-inoculation group relationships. Three IS structural types were found in Rhizobium species that nodulate beans and Leucaena species, one of which included the designated type IIB strain of R. tropici (CIAT 899). Weak homology to the whole IS probe, but not with the internal segments, was found with two Bradyrhizobium japonicum strains. The taxonomic and ecological implications of the distribution of ISRLdTAL1145-1 are discussed.

Different types of structural variation in STRs: HumFES/FPS, HumVWA and HumD21S11.

Alleles of the STR systems HumFES/FPS, HumVWA and HumD21S11 were sequenced and analyzed. Sequence data revealed 3 different systems concerning the complexity of their sequence structure. HumFES/FPS belongs to the STR polymorphism with a simple repeat structure. Only 2 subtypes were found with a base substitution in the 5'-flanking region and no variation in the repeat region. In the STR system HumVWA the sequence structure of the repeat region is more complex, because 2 tetranucleotide units TCTA and TCTG were present. Additionally allele 14 revealed a completely different sequence structure leading to a different electrophoretic mobility. The repeat region of HumD21S11 is compound in structure. The possibility of variation at 3 positions leads to the occurrence of microheterogeneities in fragments of apparent length. In the upper allele range alleles arise with an additional incomplete TA-repeat.

Polytypes and polytypism

Abstract The definition of polytypism recommended by the IMA/IUCr joint committee on nomenclature is reviewed in the light of the structural variation observed in mineral and alloy systems. As a result of this review it is concluded that previous definitions of polytypism are too restrictive to be practical, and a definition which emphasises the structural basis of polytypism is proposed: “Polytypism arises from the different modes of stacking of one or more structurally compatible modules.” The various types of structural variation included under this definition are described using as examples minerals, ceramics, and alloys.

STRUCTURE OF FLORAL NECTARIES OF ALFALFA (MEDICAGO SATIVA L.) IN RELATION TO NECTAR PRODUCTION

Alfalfa (Medicago sativa L.) plants differ in nectar volume production per floret. These differences are heritable, but no information is available on what type of structural variation may be responsible for these differences. One high, one intermediate, and one low nectar‐volume‐producing clone was selected from each of two alfalfa cultivars. Results from light and scanning electron microscopy indicated that alfalfa has an annular nectary located on the staminal column and primarily on the receptacle. It is composed of several cell layers subtended by vascular bundles containing both xylem and phloem. Vascular tissue does not extend into nectariferous tissue. Permanently open stomata are present in the epidermal layer and are thought to function in nectar secretion. These stomata did not respond to stimuli known to affect leaf stomata. Number of stomata per nectary among the six clones ranged from 24.7 ± 1.9 to 6.8 ± 0.5. Nectar‐reservoir diameters among clones ranged from 1.07 ± 0.09 mm to 0.70 ± 0.01 mm. Clones producing the most nectar were characterized by a large nectar reservoir and moderate to high numbers of stomata.