Fine-mapping subtelomeric deletions and duplications by comparative genomic hybridization in 42 individuals

ArticleinAmerican Journal of Medical Genetics Part A 146A(6):730-9 · March 2008with39 Reads
DOI: 10.1002/ajmg.a.32216 · Source: PubMed
Abstract
Human subtelomere regions contain numerous gene-rich segments and are susceptible to germline rearrangements. The availability of diagnostic test kits to detect subtelomeric rearrangements has resulted in the diagnosis of numerous abnormalities with clinical implications including congenital heart abnormalities and mental retardation. Several of these have been described as clinically recognizable syndromes (e.g., deletion of 1p, 3p, 5q, 6p, 9q, and 22q). Given this, fine-mapping of subtelomeric breakpoints is of increasing importance to the assessment of genotype-phenotype correlations in these recognized syndromes as well as to the identification of additional syndromes. We developed a BAC and cosmid-based DNA array (TEL array) with high-resolution coverage of 10 Mb-sized subtelomeric regions, and used it to analyze 42 samples from unrelated patients with subtelomeric rearrangements whose breakpoints were previously either unmapped or mapped at a lower resolution than that achievable with the TEL array. Six apparently recurrent subtelomeric breakpoint loci were localized to genomic regions containing segmental duplication, copy number variation, and sequence gaps. Small (1 Mb or less) candidate gene regions for clinical phenotypes in separate patients were identified for 3p, 6q, 9q, and 10p deletions as well as for a 19q duplication. In addition to fine-mapping nearly all of the expected breakpoints, several previously unidentified rearrangements were detected.
    • "Reads were mapped to the 15kb subtelomere reference using bowtie[238]. Many subtelomeres are duplicon rich with duplicon-specific nucleotide sequence similarities ranging from 90 to 99% between individual members of duplicon families that occur on separate subtelomeres[162,164,252,253]. To deal with this issue, we required a perfect match to retain a read, and all perfect matches of a given read to positions within the reference assemblies were recorded. "
    [Show abstract] [Hide abstract] ABSTRACT: The telomere is a specialized simple sequence repeat found at the end of all linear chromosomes. It acts as a substrate for telomere binding factors that in coordination with other interacting elements form what is known as the shelterin complex to protect the end of the chromosome from the DNA damage repair machinery. The telomere shortens with each cell division, and once critically short is no longer able to perform this role. Short dysfunctional telomeres result in cellular senescence, apoptosis, or genome instability. Telomere length is regulated by many factors including cis-acting elements in the proximal sequence which is known as the subtelomere. The Riethman lab played a pivotal role in generating the reference sequence of the subtelomere in both the human and mouse genomes, providing an essential resource for this work. Short high throughput sequencing (HTS) reads generated from the simple repeat containing telomere or the segmental duplication rich subtelomere cannot be aligned to a reference genome uniquely. They are filtered and excluded from many HTS analysis methods. A ChIP-Seq analysis pipeline was developed to incorporate these multimapping reads to study DNA-protein interactions in the subtelomere. This pipeline was employed to search for factors regulating the expression TERRA, an essential long non-coding RNA, and to better characterize their transcription start sites. ChIP-seq analysis in the human subtelomere found colocalization of CTCF and Cohesin directly adjacent to the telomere and throughout the subtelomere specific repeats. Follow up functional studies showed this binding regulated TERRA transcription at these sites. Extending these analyses in the mouse genome showed very different patterns of CTCF and cohesin binding, with no evidence of binding at apparent sites of TERRA transcription. Mouse subtelomere sequence analysis showed the co-occurence of two repeats at sites of putative TERRA expression, MurSatRep1 and MMSAT4, one of which was previously shown to be expressed in lincRNAs. The Telomere Analysis from SEquencing Reads(TASER) pipeline was developed to capture telomere information from HTS data sets and used to investigate telomere changes that occur in prostate cancer. TASER analysis of 53 paired prostate tumor and normal samples revealed an overall decrease in telomere length in tumor samples relative to matched paired normal tissue, especially sequence containing the exact canonical telomere repeat. Multimapping reads contain important information, that when used properly, help elucidate understanding of telomere biology, cancer biology, and genome regulation and stability.
    Full-text · Article · Jan 2014 · The EMBO Journal
    • ") is a contiguous gene deletion syndrome characterized by various anomalies including ocular anterior segment dysgenesis reminiscent of Axenfeld– Rieger syndrome (ARS), hypertelorism, down-slanting palpebral fissures, flat nasal bridge, dental anomalies, congenital heart defects, Dandy–Walker malformation, hearing loss, and developmental delay. The many patients described to date had terminal 6p25 deletions [Law et al., 1998; Nishimura et al., 1998; Gould et al., 2004; Le Caignec et al., 2005; Rosenberg et al., 2006; Martinez-Glez et al., 2007; DeScipio et al., 2008; Martinet et al., 2008], interstitial 6p25 deletions [van Swaay et al., 1988; Davies et al., 1999; Lehmann et al., 2002; Koolen et al., 2005; Chanda et al., 2008; D'Haene et al., 2011], or mixed 6p25 deletions [Bedoyan et al., 2011]. However, molecular characterization of the deletion was performed in only a minority of patients (using FISH and/or STS marker analysis in 26 cases and array-CGH or SNP chips in 18 cases). "
    [Show abstract] [Hide abstract] ABSTRACT: FOXC1 deletion, duplication, and mutations are associated with Axenfeld-Rieger anomaly, and Dandy-Walker malformation spectrum. We describe the clinical history, physical findings, and available brain imaging studies in three fetuses, two children, and one adult with 6p25 deletions encompassing FOXC1. Various combinations of ocular and cerebellar malformations were found. In all three fetuses, necropsy including detailed microscopic assessments of the eyes and brains showed ocular anterior segment dysgenesis suggestive of Axenfeld-Rieger anomaly. Five 6p25 deletions were terminal, including two derived from inherited reciprocal translocations; the remaining 6p25 deletion was interstitial. The size and breakpoints of these deletions were characterized using comparative genomic hybridization arrays. All six deletions included FOXC1. Our data confirm that FOXC1 haploinsufficiency plays a major role in the phenotype of patients with 6p25 deletions. Histopathological features of Axenfeld-Rieger anomaly were clearly identifiable before the beginning of the third-trimester of gestation. © 2012 Wiley Periodicals, Inc.
    Full-text · Article · Oct 2012
    • "Reads were mapped to the subtelomere reference using bowtie (Langmead et al, 2009). Many subtelomeres are duplicon rich with duplicon-specific nucleotide sequence similarities ranging from 90 to 99% between individual members of duplicon families that occur on separate subtelomeres (Linardopoulou et al, 2005; Riethman et al, 2005; Ambrosini et al, 2007; Descipio et al, 2008). To deal with this issue, we required a perfect match to retain a read, and all perfect matches of a given read to positions within the reference assemblies were recorded. "
    [Show abstract] [Hide abstract] ABSTRACT: The contribution of human subtelomeric DNA and chromatin organization to telomere integrity and chromosome end protection is not yet understood in molecular detail. Here, we show by ChIP-Seq that most human subtelomeres contain a CTCF- and cohesin-binding site within ∼1-2 kb of the TTAGGG repeat tract and adjacent to a CpG-islands implicated in TERRA transcription control. ChIP-Seq also revealed that RNA polymerase II (RNAPII) was enriched at sites adjacent to the CTCF sites and extending towards the telomere repeat tracts. Mutation of CTCF-binding sites in plasmid-borne promoters reduced transcriptional activity in an orientation-dependent manner. Depletion of CTCF by shRNA led to a decrease in TERRA transcription, and a loss of cohesin and RNAPII binding to the subtelomeres. Depletion of either CTCF or cohesin subunit Rad21 caused telomere-induced DNA damage foci (TIF) formation, and destabilized TRF1 and TRF2 binding to the TTAGGG proximal subtelomere DNA. These findings indicate that CTCF and cohesin are integral components of most human subtelomeres, and important for the regulation of TERRA transcription and telomere end protection.
    Full-text · Article · Sep 2012
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