Identifying NAHR mechanism between two distinct Alu elements through breakpoint junction mapping by NGS

Abstract Background: Genomic rearrangements encompass deletions, duplications, inversions, insertions and translocations and may be the cause of several genetic diseases. One of the most frequent mechanisms that generates these rearrangements is the Non-Allelic Homologous Recombination (NAHR). They are caused by a misalignment between regions of high level of similarity, like Low Copy Repeats (LCRs) and Alu sequences. We aimed to sequence the breakpoint of a patient with a single deletion on chromosome 22q13.2 in order to understand the genomic structure of the region involved as well as elucidate the mechanism behind this rearrangement. Investigating breakpoints are of the utmost importance in the understanding the influence of the genomic architecture in clinical assays. Results: We flanked the breakpoint detected by array and then we captured the regions using Illumina Nextera Rapid Capture Custom to sequence with Illumina MiSeq. We found a chimeric read on Chr22:41,026,090, setting a 624,688 bp deletion on Chr22:41,026,112-41,650,780 (hg19). This deletion merges the intronic region of MKL1 and RANGAP1 genes, on two different Alu sequences ( AluSx and AluY, respectively ). Conclusions: The sequence of the breakpoint reveals that Alu elements are an important characteristic of the human genome on generating rearrangements.

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The genomic structure of a human chromosome 22 nucleolar organizer region determined by TAR cloning

Scientific Reports ◽

10.1038/s41598-021-82565-x ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Jung-Hyun Kim ◽

Vladimir N. Noskov ◽

Aleksey Y. Ogurtsov ◽

Ramaiah Nagaraja ◽

Nikolai Petrov ◽

...

Keyword(s):

Genomic Structure ◽

Organizer Region ◽

Nucleolar Organizer Region ◽

Nucleolar Organizer ◽

Chromosome 21 ◽

Reference Sequence ◽

Chromosome 22 ◽

Rdna Variation ◽

High Level ◽

Tar Cloning

AbstractThe rDNA clusters and flanking sequences on human chromosomes 13, 14, 15, 21 and 22 represent large gaps in the current genomic assembly. The organization and the degree of divergence of the human rDNA units within an individual nucleolar organizer region (NOR) are only partially known. To address this lacuna, we previously applied transformation-associated recombination (TAR) cloning to isolate individual rDNA units from chromosome 21. That approach revealed an unexpectedly high level of heterogeneity in human rDNA, raising the possibility of corresponding variations in ribosome dynamics. We have now applied the same strategy to analyze an entire rDNA array end-to-end from a copy of chromosome 22. Sequencing of TAR isolates provided the entire NOR sequence, including proximal and distal junctions that may be involved in nucleolar function. Comparison of the newly sequenced rDNAs to reference sequence for chromosomes 22 and 21 revealed variants that are shared in human rDNA in individuals from different ethnic groups, many of them at high frequency. Analysis infers comparable intra- and inter-individual divergence of rDNA units on the same and different chromosomes, supporting the concerted evolution of rDNA units. The results provide a route to investigate further the role of rDNA variation in nucleolar formation and in the empirical associations of nucleoli with pathology.

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SINE Insertions in Cladistic Analyses and the Phylogenetic Affiliations of Tarsius bancanus to Other Primates

Genetics ◽

10.1093/genetics/157.2.777 ◽

2001 ◽

Vol 157 (2) ◽

pp. 777-784

Author(s):

Jürgen Schmitz ◽

Martina Ohme ◽

Hans Zischler

Keyword(s):

New World ◽

World Monkey ◽

Old World ◽

Alu Elements ◽

Alu Sequences ◽

Short Interspersed Elements ◽

Divergence Point ◽

Tarsius Bancanus ◽

Cladistic Analyses ◽

The Common

Abstract Transpositions of Alu sequences, representing the most abundant primate short interspersed elements (SINE), were evaluated as molecular cladistic markers to analyze the phylogenetic affiliations among the primate infraorders. Altogether 118 human loci, containing intronic Alu elements, were PCR analyzed for the presence of Alu sequences at orthologous sites in each of two strepsirhine, New World and Old World monkey species, Tarsius bancanus, and a nonprimate outgroup. Fourteen size-polymorphic amplification patterns exhibited longer fragments for the anthropoids (New World and Old World monkeys) and T. bancanus whereas shorter fragments were detected for the strepsirhines and the outgroup. From these, subsequent sequence analyses revealed three Alu transpositions, which can be regarded as shared derived molecular characters linking tarsiers and anthropoid primates. Concerning the other loci, scenarios are represented in which different SINE transpositions occurred independently in the same intron on the lineages leading both to the common ancestor of anthropoids and to T. bancanus, albeit at different nucleotide positions. Our results demonstrate the efficiency and possible pitfalls of SINE transpositions used as molecular cladistic markers in tracing back a divergence point in primate evolution over 40 million years old. The three Alu insertions characterized underpin the monophyly of haplorhine primates (Anthropoidea and Tarsioidea) from a novel perspective.

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Rearrangements of the Williams–Beuren syndrome locus: molecular basis and implications for speech and language development

Expert Reviews in Molecular Medicine ◽

10.1017/s146239940700035x ◽

2007 ◽

Vol 9 (15) ◽

pp. 1-16 ◽

Cited By ~ 83

Author(s):

Lucy R. Osborne ◽

Carolyn B. Mervis

Keyword(s):

Language Development ◽

Language Impairment ◽

Short Term Memory ◽

Relative Strength ◽

Genomic Rearrangements ◽

Speech And Language ◽

Human Speech ◽

Hyperactivity Disorder ◽

Low Copy Repeats ◽

Speech And Language Development

AbstractThe Williams–Beuren syndrome (WBS) locus on human chromosome 7q11.23 is flanked by complex chromosome-specific low-copy repeats that mediate recurrent genomic rearrangements of the region. Common genomic rearrangements arise through unequal meiotic recombination and result in complex but distinct behavioural and cognitive phenotypes. Deletion of 7q11.23 results in WBS, which is characterised by mild to moderate intellectual disability or learning difficulties, with relative cognitive strengths in verbal short-term memory and in language and extreme weakness in visuospatial construction, as well as anxiety, attention-deficit hyperactivity disorder and overfriendliness. By contrast, duplication results in severely delayed speech and expressive language, with relative strength in visuospatial construction. Although deletion and duplication of the WBS region have very different effects, both cause forms of language impairment and suggest that dosage-sensitive genes within the region are important for the proper development of human speech and language. The spectrum and frequency of genomic rearrangements at 7q11.23 presents an exceptional opportunity to identify gene(s) directly involved in human speech and language development.

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Research and Management of Rare Diseases in the COVID-19 Pandemic Era: Challenges and Countermeasures

Frontiers in Public Health ◽

10.3389/fpubh.2021.640282 ◽

2021 ◽

Vol 9 ◽

Author(s):

Sanjana Fatema Chowdhury ◽

Syed Muktadir Al Sium ◽

Saeed Anwar

Keyword(s):

Rare Disease ◽

Rare Diseases ◽

Genetic Diseases ◽

Management Strategies ◽

Routine Care ◽

Ongoing Research ◽

The People ◽

Number Of Patients ◽

High Level ◽

Disease Community

The ongoing coronavirus disease 2019 (COVID-19) pandemic has disrupted every aspect of our life. The need to provide high-level care for an enormous number of patients with COVID-19 infection during this pandemic has impacted resourcing for and restricted the routine care of all non-COVID-19 conditions. Since the beginning of the pandemic, the people living with rare disorders, who represent a marginalized group of the population even in a normal world, have not received enough attention that they deserve. Due to the pandemic situation, they have experienced (and experiencing) an extreme inadequacy of regular clinical services, counseling, and therapies they need, which have made their life more vulnerable and feel more marginalized. Besides, the clinicians, researchers, and scientists working on rare genetic diseases face extra challenges due to the pandemic. Many ongoing research projects and clinical trials for rare and genetic diseases were stalled to avoid patients' and research staff's transmission to COVID-19. Still, with all the odds, telehealth and virtual consultations for rare disease patients have shown hope. The clinical, organizational, and economic challenges faced by institutions, patients, their families, and the caregivers during the pandemic indicate the importance of ensuring continuity of care in managing rare diseases, including adequate diagnostics and priority management strategies for emergencies. In this review, we endeavored to shed light on the issues the rare disease community faces during the pandemic and the adaptations that could help the rare disease community to better sustain in the coming days.

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Antimicrobial Resistance and Genomic Characterization of OXA-48- and CTX-M-15-Co-Producing Hypervirulent Klebsiella pneumoniae ST23 Recovered from Nosocomial Outbreak

Antibiotics ◽

10.3390/antibiotics9120862 ◽

2020 ◽

Vol 9 (12) ◽

pp. 862

Author(s):

Elvira Shaidullina ◽

Andrey Shelenkov ◽

Yuri Yanushevich ◽

Yulia Mikhaylova ◽

Dmitriy Shagin ◽

...

Keyword(s):

Klebsiella Pneumoniae ◽

Illumina Miseq ◽

Type I ◽

Nosocomial Outbreak ◽

Recent Emergence ◽

Genomic Characterization ◽

Global Threat ◽

High Level ◽

Sepsis And Septic Shock

Multidrug resistance (MDR) and hypervirulence (hv) have been long considered distinct evolutionary traits for Klebsiella pneumoniae (Kp), a versatile human pathogen. The recent emergence of Kp strains combining these traits poses a serious global threat. In this article, we describe the phenotypic and genomic characteristics of an MDR hvKp isolate, MAR14-456, representative of a nosocomial outbreak in Moscow, Russia, that was recovered from a postoperative wound in a patient who later developed multiple abscesses, fatal sepsis, and septic shock. Broth microdilution testing revealed decreased susceptibility of MAR14-456 to carbapenems (MICs 0.5–2 mg/L) and a high-level resistance to most β-lactams, β-lactam-β-lactamase-inhibitor combinations, and non-β-lactam antibiotics, except ceftazidime-avibactam, amikacin, tigecycline, and colistin. Whole-genome sequencing using Illumina MiSeq and ONT MinION systems allowed to identify and completely assemble two conjugative resistance plasmids, a typical ‘European’ epidemic IncL/M plasmid that carries the gene of OXA-48 carbapenemase, and an IncFIIK plasmid that carries the gene of CTX-M-15 ESBL and other resistance genes. MLST profile, capsular, lipopolysaccharide, virulence genes encoded on chromosome and IncHI1B/FIB plasmid, and the presence of apparently functional type I-E* CRISPR-Cas system were all characteristic of hvKp ST23, serotype K1-O1v2. Phylogenetic analysis showed the closest relatedness of MAR14-456 to ST23 isolates from China. This report highlights the threat of multiple resistance acquisition by hvKp strain and its spread as a nosocomial pathogen.

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Migration and Hereditary Disease in the Saguenay Population of Eastern Quebéc

International Migration Review ◽

10.1177/019791838702100308 ◽

1987 ◽

Vol 21 (3) ◽

pp. 592-608 ◽

Cited By ~ 2

Author(s):

Margaret I. Gradie ◽

Danielle Gauvreau

Keyword(s):

Genetic Structure ◽

Genetic Disease ◽

Genetic Diseases ◽

Large Population ◽

Hereditary Disease ◽

Genetic Homogeneity ◽

Preliminary Results ◽

Consanguineous Marriages ◽

High Level ◽

The Relationship

This article examines the relationship between migration and genetic disease in the situation of the Saguenay region of Quέbec. This large population shows an elevated incidence of several genetic diseases. The process of migration, which created the population, is thought to be a major factor in determining the genetic structure of the contemporary population. Preliminary results suggest that although consanguineous marriages are not and never were frequent in the population, socially, kinship was important in determining migration and persistence, leading to a high level of genetic homogeneity today.

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The 22q11 low copy repeats are characterized by unprecedented size and structure variability

10.1101/403873 ◽

2018 ◽

Cited By ~ 4

Author(s):

Wolfram Demaerel ◽

Yulia Mostovoy ◽

Feyza Yilmaz ◽

Lisanne Vervoort ◽

Steven Pastor ◽

...

Keyword(s):

De Novo ◽

Phenotypic Variability ◽

Chromosomal Rearrangements ◽

Deletion Syndrome ◽

Genomic Disorder ◽

Genome Variability ◽

Low Copy Repeats ◽

Different Populations ◽

High Level

Abstract:Low copy repeats (LCRs) are recognized as a significant source of genomic instability, driving genome variability and evolution. The chromosome 22 LCRs (LCR22s) are amongst the most complex regions in the genome and their structure remains unresolved. These LCR22s mediate non-allelic homologous recombination (NAHR) leading to the 22q11 deletion syndrome (22q11DS), causing the most frequent genomic disorder. Using fiber FISH optical mapping, we have de novo assembled the LCR22s in 33 cell lines. We observed a high level of variation in LCR22 structures, including 26 different haplotypes of LCR22A with alleles ranging from 250 Kb to over 2,000 Kb. An additional four haplotypes were detected using Bionano mapping. Further, Bionano maps generated from 154 individuals from different populations suggested significantly different LCR22 haplotype frequencies between populations. Furthermore, haplotype analysis in nine 22q11DS patients resulted in the localization of the NAHR site to a 160 Kb paralog between LCR22A and –D in seven patients and to a 31 Kb region in two individuals with a rearrangement between LCR22A and –B.. This 31 Kb region contains a palindromic AT-rich repeat known to be a driver of chromosomal rearrangements. Our study highlights an unprecedented level of polymorphism in the structure of LCR22s, which are likely still evolving. We present the most comprehensive map of LCR22 variation to date, paving the way towards investigating the role of LCR variation as a driver of 22q11 rearrangements and the phenotypic variability in 22q11DS patients as well as in the general population.

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Protein disulphide isomerase family in bread wheat (Triticum aestivum L.): genomic structure, synteny conservation and phylogenetic analysis

Plant Genetic Resources ◽

10.1017/s1479262111000232 ◽

2011 ◽

Vol 9 (2) ◽

pp. 342-346 ◽

Cited By ~ 1

Author(s):

E. d'Aloisio ◽

A. R. Paolacci ◽

A. P. Dhanapal ◽

O. A. Tanzarella ◽

E. Porceddu ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Gene Family ◽

Bread Wheat ◽

Plant Species ◽

Genomic Structure ◽

Triticum Aestivum L ◽

Protein Disulphide Isomerase ◽

Homoeologous Genes ◽

Genes Encoding ◽

High Level

Eight genes encoding protein disulphide isomerase (PDI)-like proteins in bread wheat were cloned and characterized and their genomic structure was compared with that of homoeologous genes isolated from other plant species. Fourteen wheat cDNA sequences of PDI-like genes were amplified and cloned; eight of them were relative to distinct PDI-like genes, whereas six corresponded to homoeologous sequences. Also, the genomic sequences of the eight non-homoeologous genes were amplified and cloned. Phylogenetic analysis, which included eight genes encoding PDI-like proteins and the gene encoding the typical PDI, assigned at least one of them to each of the eight major clades identified in the phylogenetic tree of the PDI gene family of plants. The close chromosome synteny between wheat and rice was confirmed by the location of the homoeologous genes of the PDI family in syntenic regions of the two species. Within the same phylogenetic group, a high level of conservation, in terms of sequence homology, genomic structure and domain organization, was detected between wheat and the other plant species. The high level of conservation of sequence and genomic organization within the PDI gene family, even between distant plant species, might be ascribed to the key metabolic roles of their protein products.

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Breakpoint junction analysis for complex genomic rearrangements with the caldera volcano‐like pattern

Human Mutation ◽

10.1002/humu.24108 ◽

2020 ◽

Vol 41 (12) ◽

pp. 2119-2127

Author(s):

Tomoe Yanagishita ◽

Taichi Imaizumi ◽

Keiko Yamamoto‐Shimojima ◽

Tamami Yano ◽

Nobuhiko Okamoto ◽

...

Keyword(s):

Genomic Rearrangements ◽

Breakpoint Junction

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Plasmid mediated penicillin and tetracycline resistance among Neisseria gonorrhoeae isolates from Kenya

BMC Infectious Diseases ◽

10.1186/s12879-020-05398-5 ◽

2020 ◽

Vol 20 (1) ◽

Author(s):

Mary Wandia Kivata ◽

Margaret Mbuchi ◽

Fredrick Eyase ◽

Wallace Dimbuson Bulimo ◽

Cecilia Katunge Kyanya ◽

...

Keyword(s):

Drug Resistance ◽

Antibiotic Resistance ◽

Antimicrobial Resistance ◽

Neisseria Gonorrhoeae ◽

De Novo ◽

Antibiotic Resistance Genes ◽

Tetracycline Resistance ◽

Illumina Miseq ◽

Miseq Platform ◽

High Level

Abstract Background Treatment of gonorrhea is complicated by the development of antimicrobial resistance in Neisseria gonorrhoeae (GC) to the antibiotics recommended for treatment. Knowledge on types of plasmids and the antibiotic resistance genes they harbor is useful in monitoring the emergence and spread of bacterial antibiotic resistance. In Kenya, studies on gonococcal antimicrobial resistance are few and data on plasmid mediated drug resistance is limited. The present study characterizes plasmid mediated resistance in N. gonorrhoeae isolates recovered from Kenya between 2013 and 2018. Methods DNA was extracted from 36 sub-cultured GC isolates exhibiting varying drug resistance profiles. Whole genome sequencing was done on Illumina MiSeq platform and reads assembled de-novo using CLC Genomics Workbench. Genome annotation was performed using Rapid Annotation Subsystem Technology. Comparisons in identified antimicrobial resistance determinants were done using Bioedit sequence alignment editor. Results Twenty-four (66.7%) isolates had both β-lactamase (TEM) and TetM encoding plasmids. 8.3% of the isolates lacked both TEM and TetM plasmids and had intermediate to susceptible penicillin and tetracycline MICs. Twenty-six (72%) isolates harbored TEM encoding plasmids. 25 of the TEM plasmids were of African type while one was an Asian type. Of the 36 isolates, 31 (86.1%) had TetM encoding plasmids, 30 of which harbored American TetM, whereas 1 carried a Dutch TetM. All analyzed isolates had non-mosaic penA alleles. All the isolates expressing TetM were tetracycline resistant (MIC> 1 mg/L) and had increased doxycycline MICs (up to 96 mg/L). All the isolates had S10 ribosomal protein V57M amino acid substitution associated with tetracycline resistance. No relation was observed between PenB and MtrR alterations and penicillin and tetracycline MICs. Conclusion High-level gonococcal penicillin and tetracycline resistance in the sampled Kenyan regions was found to be mediated by plasmid borne blaTEM and tetM genes. While the African TEM plasmid, TEM1 and American TetM are the dominant genotypes, Asian TEM plasmid, a new TEM239 and Dutch TetM have emerged in the regions.

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