Segmental duplications genomic. Medical search. Frequent questions

DNA duplications and deletions help determine health. (nih.gov)
16. PTEN genomic deletions that characterize aggressive prostate cancer originate close to segmental duplications. (nih.gov)
Comparative genomic hybridization (CGH) was developed to identify pathogenic DNA copy-number changes (e.g., duplications, deletions) on a genome-wide scale, and to map these changes to genomic sequence. (genengnews.com)
It has been suggested that PIR4 sequences may act similarly to segmental duplications, creating recombination events that produce duplications, deletions and inversions. (anthropogeny.org)
Whereas deletions of 16p13.11 have been associated with multiple congenital anomalies, the relevance of duplications of the region is still being debated. (elsevierpure.com)
Complementary deletions and duplications can be generated by interchromatid NAHR involving direct LCRs, deletions will be the only resulting product of intrachromatid NAHR also involving direct LCRs. (biomedcentral.com)
While deletions and duplications are usually related to altered phenotypes, most inversions are considered as being polymorphic variants with no apparent phenotypic effects for the carriers. (biomedcentral.com)
It is well documented that SDs mediate ectopic interactions leading to chromosomal rearrangements such as duplications, deletions, and inversions. (nih.gov)
Genomic structural variations (SVs) are generally defined as deletions (DELs), insertions (INSs), duplications (DUPs), inversions (INVs), and translocations (TRAs) of at least 50 bp in size. (biomedcentral.com)
Imbalanced deletions (DELs) and duplications (DUPs) are also referred to as copy number variations (CNVs), with DUPs comprising tandem and interspersed types depending on the distance between the duplicated copies [ 2 , 3 ]. (biomedcentral.com)
By sequencing PCR products amplified using primers designed to span the deleted regions, we determined the exact size and genomic position of the deletions in all affected samples. (ox.ac.uk)

Table 1 Examples of polymorphic inversions and the related genomic disorders reported to be caused as secondary rearrangements. (biomedcentral.com)
We also detected a wide range of unique structural rearrangements in P. euphratica, including 2,549 translocations, 454 inversions, 121 tandem and 14 segmental duplications. (ttu.edu)

WES employs libraries of oligonucleotides (either DNA or RNA) that target all annotated protein-coding exons (180,000-200,000 different exons depending on the version of gene annotation used), together with physical separation techniques to isolate patient genomic DNA fragments hybridizing to these oligos, in order to reduce the input complexity to next-generation instruments from 3 Gbp of total (haploid) genomic sequence to 30-40 Mbp of exonic genomic sequence. (medscape.com)
The genomes of humans and other primates show an enrichment in Segmental Duplications (SDs) with high sequence identity, plus they present may Copy-Number Variants (CNVs), large genome fragments of which different individuals present different copies. (upf-csic.es)
Aligning to the UMD3.1 cattle genome, we identified segmental duplications comprising 44.6 Mb (~1.73% of the cattle genome) of the autosomal and X chromosomal sequence in the genome of Olimpia (the water buffalo reference animal). (usda.gov)
Such duplications involve the transfer of 1-200 kb blocks of genomic sequence to one or more locations in the genome. (plantlet.org)
It is intriguing that SPANX genes reside within 20-100 kb segmental chromosomal duplications (SDs) with a high level of sequence similarity. (nih.gov)
The technology also increases the density of genomic DNA probes for higher resolution genetic analysis beyond what is used in FISH, genomic microarrays for array comparative genomic hybridization, and solution capture hybridization arrays for sequence enrichment in deep sequencing. (cytognomix.com)
Sequence analysis of deletion and duplication breakpoints indicates that intrachromatid non-allelic homologous recombination (NAHR) between Alu elements is involved in 6 events, while a non-homologous end joining (NHEJ) is implicated in 2 rearrangements. (biomedcentral.com)
We show that the observed genomic properties are characteristic of sequences generated in a simple growth model, where a very short initial random sequence (less than 1 kb) grows mainly by maximally stochastic duplication of short segments (of about 25 b). (biomedcentral.com)
Recent sequence analyses have disclosed an unpredicted extensive segmental duplication of our genome, and the impact of duplicons in triggering genomic disorders is becoming more and more apparent. (uniba.it)
Using genomic sequence from chimpanzee and rhesus macaque, we were able to characterize the breakpoints defining a large pericentric inversion that occurred some time after the split of Homininae from Ponginae, and propose an evolutionary history of the inversion. (inra.fr)
The Human Pangenome Reference Consortium has introduced a significantly more diverse reference human genome sequence, the "pangenome," composed of 94 distinct genome sequences and aiming to reach 700 by 2024, which helps in identifying larger genomic variants and enhancing genomic analysis accuracy. (scitechdaily.com)
Everyone has a unique genome, so using a single reference genome sequence for every person can lead to inequities in genomic analyses. (scitechdaily.com)
Everyone has a unique genome, so using a single reference genome sequence for every person can lead to inequities in genomic analyses," said Adam Phillippy, Ph.D., senior investigator in the Computational and Statistical Genomics Branch within NHGRI's Intramural Research Program and a co-author of the main study. (scitechdaily.com)
Almost 1,500 copy number variable regions, covering around 12% of the genome and containing hundreds of genes, disease loci, functional elements and segmental duplications, have been identified using the HapMap collection, a project describing common patterns of human DNA sequence variation. (wikidoc.org)

The relative intensity of test and reference signals at a given genomic position indicates the relative copy number of those sequences in the test and reference genomes. (genengnews.com)
With the availability of complete genome sequences, the ability to probe multiple genes in a single experiment using DNA microarrays provides an unprecedented tool for genomic research. (biomedcentral.com)
The design criteria permit inclusion of highly divergent interspersed repeated sequences that don't cross-hybridize to other genomic locations. (cytognomix.com)
If desired, ab-initio probes can optionally exclude segmental duplications and self-chain blocks of low copy sequences capable of cross-hybridizing to undesirable genomic targets. (cytognomix.com)
Aside from FISH, genomic microarrays, and NGS capture reagents, ab-initio single copy sequences have been used to identify stable genes in breast tumour genomes, whose products are often targets of chemotherapy agents (US Pat. (cytognomix.com)
We compare the distributions of occurrence frequencies of oligonucleotides two to ten bases long (2 to 10-mers) in microbial complete genomes with corresponding distributions obtained from random sequences and find that the genomic distributions are uniformly many times wider in a universal manner, that is, the same for all microbial complete genomes. (biomedcentral.com)
To understand these genomic differences, scientists create reference human genome sequences for use as a "standard" - a digital amalgamation of human genome sequences that can be used as a comparison to align, assemble and study other human genome sequences. (scitechdaily.com)

These duplication regions include interspersed repeats and duplicons that have exon-intron structure. (anthropogeny.org)
The presence of segmental duplications or low-copy repeats (LCR) throughout the human genome plays a significant role in the formation of variation through NAHR [ 2 , 3 ]. (biomedcentral.com)
LCRs of the 15q11-q13 region are built by duplications of the HERC2 gene/pseudogene which form blocks called END-repeats that are oriented both in direct or indirect orientations [ 9 ]. (biomedcentral.com)
The yellow path that loops around itself and repeats the same nucleotides represents a duplication variant. (scitechdaily.com)

Characterisation of interstitial duplications and triplications of chromosome 15q11-q13. (nih.gov)
Telomeres and subtelomeres, the genomic regions located at chromosome extremities, are essential for genome stability in eukaryotes. (ibpc.fr)
Intrachromosomal duplications occur within a particular chromosome or chromosomal arm. (plantlet.org)
Involved are: 1) aspects of gene duplication and evolution and 2) specialized features of mitosis -- particularly the centromere structure and function that underlie proper chromosome segregation. (nih.gov)
The chromosome is remarkable in having the lowest rate of segmental duplication in the genome. (inra.fr)

The knowledge that specific genetic diseases are caused by recurrent chromosomal aberrations has indicated that genomic instability might be directly related to the structure of the regions involved. (nih.gov)
Pericentric regions are also enriched for segmental duplications (SDs), which are known to be hotspots of chromosomal rearrangement and one third of human-specific SDs reside within pericentromeric regions. (anthropogeny.org)
Our overall goal is to understand why particular chromosomal regions and genes are prone to generate genomic disorders. (nih.gov)
The de novo assembly of a European wild boar genome revealed unique patterns of chromosomal structural variations and segmental duplications. (nih.gov)

Segmental duplications have emerged as a significant factor in the aetiology of disorders that are caused by abnormal gene dosage. (nih.gov)
Invertebrates have a single NCX gene, whereas vertebrate species have multiple NCX genes as a result of at least two duplication events. (biomedcentral.com)
Interpretation of expression dynamics in physiological, developmental and evolutionary comparisons is complicated by the diversity in NCX homologs arising from both splice variants and gene/genome duplications. (biomedcentral.com)
Lineage-specific gene duplication and loss in human and great ape evolution. (anthropogeny.org)
The first of these topics, gene duplication and evolution, is the basis for divergence and in some cases for the supply of variants of genes that predispose to cancer. (nih.gov)
In many populations, large genomic rearrangements account for approximately 10% of mutations in the LDLR gene. (biomedcentral.com)
Our study thus describes for the first time NHEJ as a mechanism involved in genomic rearrangements in the LDLR gene. (biomedcentral.com)
However, small subsets of gene families such as MORPHEUS, LRRC37 and SPATA31, which have been subjected to a burst of segmental duplications, are found within the paralogous genomic regions in human. (bau.edu.tr)
A synteny analysis suggested that segmental duplication was a key driver in the expansion of the GASA gene family. (biomedcentral.com)
Equally surprising, this is a partial gene created from an incomplete duplication of its "parent" gene in the prehistoric human genome. (washington.edu)
Gene duplication is an important driving force in creating physical changes in living things during evolution, explained the researchers studying the SRGAP2 gene family. (washington.edu)
The incomplete duplication of the gene may account for its behavior. (washington.edu)
Although many mammals have the gene, the segmental duplications occurred exclusively in humans. (washington.edu)

Alternatively, many genomic regions are duplicated intact as 'segmental duplications', some of which contain either parts or all of coding genes that appear to be nonfunctional and are in the process of deteriorating through random mutation on an evolutionary timescale. (medscape.com)
Procesos que se dan en distintos organismos, por el que surgen nuevos genes. (bvsalud.org)
DNA microarrays provide the ability to interrogate multiple genes in a single experiment and have revolutionized genomic research. (biomedcentral.com)
We evaluated the organization of these sets of genes through three aspects: number of chromosomes involved, genomic distance, spatial intra-chromosomic distance. (univ-lyon1.fr)
Most genes in the human genome are found within the orthologous genomic segments. (bau.edu.tr)
Investigating human genomic variations holds great potential for identifying genes that might underlie differences in disease resistance (e.g. (wikidoc.org)

Multiple pericentric regions in humans have also undergone lineage-specific duplication events and have duplicated to novel pericentric regions of other nonhomologous chromosomes. (anthropogeny.org)
The duplication of chromosomes occurs chiefly when they are in the extended stage (interphase). (plantlet.org)
In human DNA, the pericentromeric and subtelomeric regions of chromosomes are filled with segmental duplications but they are much less common in the Saccharomyces, nematode and fruit fly genomes. (plantlet.org)
For example, a 9.5 kb genomic segment from the human adrenoleukodystrophy locus from Xq28 has been duplicated to regions near the centromeres of chromosomes 2, 10, 16 and 22. (plantlet.org)
FISH signals on metaphase and interphase chromosomes (left panel), and WSSD coverages and segmentally duplicated regions according to the nodiv_N method of the genomic loci (right panel) of VV40024H153C18 single (A) and VV40024H153D21 duplicated (B) clones. (biomedcentral.com)

Copy number variants (CNVs) contribute significantly to human genomic variation, with over 5000 loci reported, covering more than 18% of the euchromatic human genome. (ox.ac.uk)

Using a pericentromeric interspersed repeat to recapitulate the phylogeny and expansion of human centromeric segmental duplications. (anthropogeny.org)
In Arabidopsis there are 24 segmental duplications that account for 58% of the genome but only one is in the centromeric region. (plantlet.org)

Using a read depth approach based on next-generation sequencing, we performed a genome-wide analysis of segmental duplications (SDs) and associated copy number variants (CNVs) in water buffalo (Bubalus bubalis). (usda.gov)

Resolving genomic disorder-associated breakpoints within segmental DNA duplications using massively parallel sequencing[J]. Nat Protoc, 2014,9(6):1496-1513. (magtech.com.cn)
Subsequent analyses of deletion and duplication breakpoints were performed using long-range PCR, PCR, and DNA sequencing. (biomedcentral.com)

Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars. (nih.gov)

Since its first description in 1992, CGH has been rapidly adopted as the method of choice for analysis of DNA copy-number changes associated with cancer, genomic disorders, genetic disease, and other complex phenotypes. (genengnews.com)
This high-quality genome represents a valuable resource for poplar breeding and genetic improvement in the future, as well as comparative genomic analysis with other Salicaceae species. (ttu.edu)

We found no enrichment of LINE elements or segmental duplications, in contrast to other reports. (ox.ac.uk)

This situation could have important implications, as they have been described as predisposing haplotypes for genomic disorders. (biomedcentral.com)
Nevertheless, it has been postulated that they can increase the likelihood of secondary rearrangements leading to recurrent genomic disorders in the offspring [ 7 ] (Table 1 ). (biomedcentral.com)

Molecular mechanisms for CMT1A duplication and HNPP deletion. (nih.gov)
We report detailed clinical and molecular characterization of 10 patients with duplication and 4 patients with deletion of 16p13.11. (elsevierpure.com)
We enumerate potential good algorithms for each SV category, among which GRIDSS, Lumpy, SVseq2, SoftSV, Manta, and Wham are better algorithms in deletion or duplication categories. (biomedcentral.com)

Copy number variation (CNV) represents a major source of genomic variation. (usda.gov)

Despite their importance in disease and evolution, highly identical segmental duplications (SDs) are among the last regions of the human reference genome (GRCh38) to be fully sequenced. (nih.gov)
Interestingly, we found a nonrandom spatial distribution of aberrantly methylated regions across the genome that showed a tendency to concentrate in relatively small genomic regions. (nih.gov)
The hypermethylation events usually occurred in the proximity of the transcription start site in CpG island promoters, whereas hypomethylation events were frequently found in regions of segmental duplication. (nih.gov)

The diagnosis of 7q11.23 duplication syndrome is established by detection of a recurrent 1.5- to 1.8-Mb heterozygous duplication of the Williams-Beuren syndrome critical region . (nih.gov)

Additionally, we performed array Comparative Genomic Hybridization (aCGH) experiments using the 14 water buffalos as test samples and Olimpia as the reference. (usda.gov)

Moreover, the additional steps of the hybrid capture itself, and attendant PCR amplifications, increase statistical sample biases inherent in the entire process, so that higher average coverage is required for WES versus WGS to increase the probability of capture of both alleles at most diploid genomic sites. (medscape.com)

The timing of the duplication coincides with evolutionary changes in the brain anatomy in species of the genus Homo . (washington.edu)

Analysis of genomic structural diversity in wolf-like canids. (univ-lyon1.fr)

In order to understand the ancestral dog genome organization, we designed a high density custom 720K probes NimbleGen aCGH chip based on all known dog CNV and segmental duplication and genotyped 15 wolves from 11 populations, with a wide distribution (including Europe, Asia and America), 5 dogs (Dingo, Basenji, Beagle, Boxer and Dachshund) and three outgroups (red wolf, coyote and golden jackal). (univ-lyon1.fr)

In a typical CGH experiment, genomic DNA isolated from test and reference cell populations are differentially labeled with fluorescent dyes and cohybridized to a target representation of the genome. (genengnews.com)
Sample preparation-Genomic DNA (gDNA) from test and reference cell populations are isolated using standard molecular biology techniques. (genengnews.com)

The new analysis suggests that it's the frequency of segmental duplications , or DNA sections very similar to other sections, that are the cause. (sciencealert.com)

These observations suggest that the predisposition to prostate cancer in some HPCX families may have resulted from genomic rearrangements mediated by SDs. (nih.gov)
DNA diagnostics of large genomic rearrangements was based on Multiple Ligation dependent Probe Amplification (MLPA). (biomedcentral.com)
In set of 1441 unrelated FH patients, large genomic rearrangements were found in 37 probands. (biomedcentral.com)

These data depict a definitive molecular portrait of a diploid human genome that provides a starting point for future genome comparisons and enables an era of individualized genomic information. (jcvi.org)
The period of this partial duplication even corresponds to the transition of the slender, upright African pre-human primate genus, Australopithecus , to the larger-brained genus, Homo . (washington.edu)

Under conditions of DNA replication stress, required for the repair of broken replication forks through break-induced replication (BIR), a mechanism that may induce segmental genomic duplications of up to 200 kb (PubMed:24310611). (nih.gov)

[7] Some genomic differences may not affect fitness. (wikidoc.org)

Primate segmental duplications: crucibles of evolution, diversity and disease. (anthropogeny.org)

We found that patients with duplication of the region have varied clinical features including behavioral abnormalities, cognitive impairment, congenital heart defects and skeletal manifestations, such as hypermobility, craniosynostosis and polydactyly. (elsevierpure.com)

7q11.23 duplication syndrome is transmitted in an autosomal dominant manner. (nih.gov)

We wanted to take advantage of some new technologies that allow us to create more complete cat genomic maps. (sciencealert.com)

Anatomy18

Organisms12

Diseases14

Chemicals and Drugs7

Analytical, Diagnostic and Therapeutic Techniques and Equipment17

Psychiatry and Psychology1

Phenomena and Processes78

Disciplines and Occupations2

Technology, Industry, Agriculture1

Information Science7

Health Care1

Deletions11

Inversions2

Sequence14

Sequences7

Repeats4

Chromosome5

Chromosomal4

Gene13

Genes6

Chromosomes5

Loci1

Centromeric2

Genome-wide1

Breakpoints2

Analyses1

Genetic2

Enrichment1

Disorders2

Deletion3

Variation1

Regions3

Recurrent1

Comparative1

Alleles1

Species1

Structural1

ACGH1

Populations2

Analysis1

Rearrangements3

Human2

Mechanism1

Differences1

Diversity1

Found1

Syndrome1

Complete1