Sequence organization of the human chromosome 2q telomere

Macina, Roberto A.; Negorev, Dmitri; Spais, Chrysanthe; Ruthig, Lisa A.; Hu, Xue-Lan; Riethman, Harold

doi:10.1093/hmg/3.10.1847

Cited by 57 publications

(45 citation statements)

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“…Data on polymorphic telomeres are from Riethman, unpubl. results;Wilke et al (1991); Ijdo et al (1992); Cook et al (1994); Macina et al (1994Macina et al ( , 1995; Martin-Gallardo et al (1995); Reston et al (1995); Monfouilloux et al (1998);Trask et al (1998);van Overveld et al (2000). sequences were not already identified by the BLAST analysis described above; for the most part, the regions identified by WSSD were consistent with our analyses, although each method missed a small percentage of the duplications.…”

Section: Sequence Organization Of Subtelomeric Dnasupporting

confidence: 89%

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Mapping and Initial Analysis of Human Subtelomeric Sequence Assemblies

Riethman¹,

Ambrosini²,

Castañeda³

et al. 2004

Genome Res.

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115

119

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Physical mapping data were combined with public draft and finished sequences to derive subtelomeric sequence assemblies for each of the 41 genetically distinct human telomere regions. Sequence gaps that remain on the reference telomeres are generally small,well-defined,and for the most part,restricted to regions directly adjacent to the terminal (TTAGGG)n tract. Of the 20.66 Mb of subtelomeric DNA analyzed, 3.01 Mb are subtelomeric repeat sequences (Srpt),and an additional 2.11 Mb are segmental duplications. The subtelomeric sequence assemblies are enriched >25-fold in short,internal (TTAGGG)n-like sequences relative to the rest of the genome; a total of 114 (TTAGGG)n-like islands were found,55 within Srpt regions,35 within one-copy regions,11 at one-copy/Srpt or Srpt/segmental duplication boundaries,and 13 at the telomeric ends of assemblies. Transcripts were annotated in each assembly,noting their mapping coordinates relative to their respective telomere and whether they originate in duplicated DNA or single-copy DNA. A total of 697 transcripts were found in 15.53 Mb of one-copy DNA,76 transcripts in 2.11 Mb of segmentally duplicated DNA,and 168 transcripts in 3.01 Mb of Srpt sequence. This overall transcript density is similar (within ∼10%) to that found genome-wide. Zinc finger-containing genes and olfactory receptor genes are duplicated within and between multiple telomere regions

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Section: Sequence Organization Of Subtelomeric Dnasupporting

confidence: 89%

“…Large variant alleles of many human subtelomeric regions exist, and are believed to consist entirely of subtelomeric repeats (Wilkie et al 1991;Macina et al 1994Macina et al , 1995Trask et al 1998;Mefford and Trask 2002). For example, Wilkie et al (1991) found that three alleles varying in length up to 260 kb exist at the 16p telomere.…”

mentioning

confidence: 99%

Mapping and Initial Analysis of Human Subtelomeric Sequence Assemblies

Riethman¹,

Ambrosini²,

Castañeda³

et al. 2004

Genome Res.

Self Cite

115

119

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“…A polymorphism at the 2q telomere was first identified by Macina et al 29 Deletion of 2qtel has been reported in study populations with a frequency ranging from 1.5% to 8.2%. 19,[23][24][25]27 When all the data are considered, the average prevalence of the 2qtel deletion is approximately 5%.…”

Section: Discussionmentioning

confidence: 95%

Detection of submicroscopic aberrations in patients with unexplained mental retardation by fluorescence in situ hybridization using multiple subtelomeric probes

Fan

Zhang

Speevak

et al. 2001

Genetics in Medicine

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Purpose: To further assess the frequency of subtelomeric aberrations in a selected population and to examine the feasibility of a clinical testing. Methods: Patients were selected based on the following criteria: (1) mental retardation (IQ Ͻ 70) or developmental delay with dysmorphic features; (2) a normal karyotype at the level of resolution of 450 to 500 bands; and (3) exclusion of other possible etiologies by a full genetic assessment and relevant tests. Fluorescence in situ hybridization (FISH) was performed using multiple subtelomeric probes.Abnormal findings were confirmed by 24-color spectral karyotyping or FISH with a specific subtelomeric probe, and family studies were carried out to determine inheritance. Results: Clinically significant aberrations were detected in 6 of 150 proband patients (4%), while deletion of the 2q subtelomeric region appeared to be a common variant (6%). Conclusions: FISH with multiple subtelomeric probes is a valuable clinical test for establishing a definitive diagnosis for patients with unexplained mental retardation/developmental disorders. Genet Med 2001:3(6):416 -421.

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“…24 However, some subtelomeric DNA is noncoding, polymorphic with no clinical significance, or both. 30 In particular, the subtelomeric region of chromosome 2q has been shown to exhibit a chromosome length polymorphism 31 and a 2q polymorphism detectable using the Cytocell indirect probe (PAC 1011O17) has been reported. 32 (Note that this reference 32 reports that the direct 2q telomere probe [P1 210E14] for the generation 2 Cytocell device revealed normal results for the patients with the polymorphism.)…”

Section: Discussionmentioning

confidence: 99%

Pilot assessment of the subtelomeric regions of children with autism: Detection of a 2q deletion

Wolff

Clifton

Karr

et al. 2002

Genetics in Medicine

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Purpose: Autism is a chronic neurodevelopmental disorder characterized by deficits in reciprocal social interaction, language and communication, and by the presence of stereotypical behaviors. The disorder is a complex genetic trait with no known predisposing genes. We report the results of a pilot project to screen for aberrations in the gene-rich subtelomeric chromosomal regions of a cohort of children with autism. Methods: For our pilot project, we used a multiprobe system that includes probes for the subtelomeric regions of all human chromosomes. We assessed the subtelomeric regions of chromosomes from 10 children with a diagnosis of autism. Results: The screen identified one child with an apparent deletion of the subtelomeric region of chromosome 2q; nine children and pooled control samples yielded normal results. The deletion in our patient was confirmed with two other subtelomeric probes and a targeted cytogenetic study revealed a subtle difference in appearance for one chromosome 2 homologue. Conclusion: There have been several reports of children with dysmorphic features, autistic behaviors, and 2q deletions detectable with standard cytogenetic techniques. It may be that the distal region of chromosome 2q harbors a gene or genes that may predispose to autism. Genet Med 2002:4(1):10 -14.

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Sequence organization of the human chromosome 2q telomere

Cited by 57 publications

References 0 publications

Mapping and Initial Analysis of Human Subtelomeric Sequence Assemblies

Mapping and Initial Analysis of Human Subtelomeric Sequence Assemblies

Detection of submicroscopic aberrations in patients with unexplained mental retardation by fluorescence in situ hybridization using multiple subtelomeric probes

Pilot assessment of the subtelomeric regions of children with autism: Detection of a 2q deletion

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