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Journal ArticleDOI

Class II Analphoid Chromosome in a Child with Aberrant Chromosome 7: A Rare Cytogenetic Association

TL;DR: A case with a very rarely reported class II neocentromere formation in an aberrant chromosome 7 is presented, and analysis revealed that the linear acentric fragment was part of the 7q region, which suggests that there could be a possible McClintock mechanism.
Abstract: A neocentromere is a functional centromere that has arisen within a region not known to have a centromere. We present a case with a very rarely reported class II neocentromere formation in an aberrant chromosome 7. A 22-month-old male was referred because of dysmorphic features. Banding cytogenetics was performed, and a ring 7 and a supernumerary marker chromosome along with a normal chromosome 7 were found. In situ hybridization using a centromeric probe revealed 46 signals, of which 2 signals for chromosome 7 were observed, one on the normal and one on the ring chromosome. Further analysis using FISH revealed that the linear acentric fragment was part of the 7q region, which suggests that there could be a possible McClintock mechanism.
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Journal ArticleDOI
TL;DR: This is the first patient carrying a mosaic neocentric SRC derived from the long arm of chromosome 7.1q31 present in low mosaic and contributes to the delineation of the partial trisomy 7q phenotype.
Abstract: Supernumerary ring chromosomes (SRC) are usually derived from regions adjacent to the centromere. Their identification may be challenging, particularly in case of low mosaicism. Here, we report on a patient who was referred for major in utero growth retardation, severe developmental delay, facial dysmorphism, cleft palate, and hypospadias. The karyotype showed a small SRC in mosaic. The combination of FISH, M-FISH and array-CGH was necessary for a complete characterization of this SRC. M-FISH revealed that the SRC originated from chromosome 7. Array-CGH performed with a 400K oligonucleotide array showed a gain in region 7q22.1q31.1 present in low mosaic. This result was confirmed by FISH using BAC probes specific for chromosome 7. The SRC was a neocentric ring derived from 7q22.1q31.1 and was found in only 8% of the cells. This is the first patient carrying a mosaic neocentric SRC derived from the long arm of chromosome 7. Our study emphasizes the need to combine different techniques and to use adapted bioinformatic tools for low-mosaicism marker identification. It also contributes to the delineation of the partial trisomy 7q phenotype.

3 citations


Cites background from "Class II Analphoid Chromosome in a ..."

  • ...Only 3 neocentric markers derived from chromosome 7 have been reported until now [Lamb et al., 1998; Warburton, 2004; Kumar et al., 2015]....

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  • ...html), and only 3 neocentric markers derived from chromosome 7 have been reported to date [Lamb et al., 1998; Warburton, 2004; Kumar et al., 2015]....

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  • ...SRC derived from chromosome 7, r(7), are rare cytogenetic events (16 cases in the sSMC database, http://ssmc-tl. com/sSMC.html), and only 3 neocentric markers derived from chromosome 7 have been reported to date [Lamb et al., 1998; Warburton, 2004; Kumar et al., 2015]....

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Journal ArticleDOI
TL;DR: In this paper , the impacts of soil and water conservation practices on soil moisture in the Debre Mewi and Sholit watersheds, Abbay basin, Ethiopia were investigated by using satellite-synchronized 63 soil moisture samples, systematically collected from two treatment slope positions, two treatment positions, and two depths.
Abstract: Soil and water conservation (SWC) practices have been widely implemented to reduce surface runoff in the Debre Mewi watershed. However, studies on the issue have disproportionately focused on the lost or preserved soils, expressed in tons per hectare, while the impacts on the lost or preserved moisture were inadequately addressed. This study aimed to investigate the impacts of soil and water conservation practice on soil moisture in the Debre Mewi and Sholit watersheds, Abbay basin, Ethiopia. We compared soil moisture between the treated (Debre Mewi) and the untreated (Sholit) watersheds with SWCs, based on Sentinel-1A data and the field-measured soil moisture, Leaf Area Index (LAI), and water cloud model (WCM). Field-measurement was based on satellite-synchronized 63 soil moisture samples, systematically collected from the two treatment slope positions, two treatment positions, and two depths. We employed ANOVA to compare samples and discern patterns along space and time. The result indicated that the LAI, a predictor of crop yield, was higher in the SWC treated watershed, demonstrating the potential of conserving moisture for boosting crop production. In addition, the results reveal that the higher soil moisture was recorded on the grasslands of the treated watershed at a depth of 15–30 cm, while the lowest was from croplands and eucalyptus trees at 0–15 cm depth. A higher correlation was observed between the measured and estimated soil moisture across three stages of crop development. The soil moisture estimation using WCM from the Sentinel-1 satellite data gives promising results with good correlation (R2 = 0.69, 0.43 and 0.75, RMSE = 0.16, 2.24 and 0.02, and in Sholit (0.7539, 0.933, and 0.3673 and the RMSEs are 0.17%, 0.02%, and 1.02%) for different dates: August, September, and November 2020, respectively. We conclude that in the face of climate change-induced rainfall variability in tropical countries, predicted to elongate the dry spell during the cropping season, the accurate measurement of soil moistures with the mix of satellite and in-situ data could support rain-fed agriculture planning and assist in fine-tuning the climate adaptation measures at the local and regional scales.

2 citations

Journal ArticleDOI
TL;DR: It is concluded that an integrated genome-wide copy number variation analysis, if possible associated to FISH and gene expression studies, could facilitate in the future the difficult task of establishing accurate genotype-phenotype correlations and help to improve genetic counselling.
Abstract: Analphoid supernumerary marker chromosomes (aSMC) constitute one of the smallest groups of SMC, and are characterized by a centromeric constriction but no detectable alpha-satellite DNA. These marker chromosomes cannot be properly identified by conventional banding techniques alone, and molecular cytogenetic methods are necessary for a detailed characterization. Analphoid SMC derived from chromosome 7 are extremely rare, with only five cases reported so far. In this work we report an aSMC involving the terminal long arm of chromosome 7 in a 10-year-old boy with multiple dysmorphic features and severe development delay. Cytogenetic analysis revealed a mosaic karyotype with the presence of an extra SMC, de novo, in 20% of lymphocytes and 73% of fibroblast cells. Next, we performed FISH analysis with multiple DNA probes and cCGH analysis. This identified the origin of the SMC as an analphoid marker resulting of invdup rearrangement of 7q35-qter region. Affimetrix CytoScan HD array analysis redefined the aSMC as a 15.42 Mb gain at 7q35-q36.3 (minimum tetraplicated region-chr7: 143,594,973-159,119,707; GRCh37/hg19) of maternal origin that encloses 67 OMIM genes, 16 of which associated to disease. Uniparental disomy of chromosome 7 (UPD 7) has been excluded. We report the first patient with an aSMC(7) derived from the terminal 7q region who has been molecularly and clinically full characterized. The use of SNParray in the characterization of SMC reveals to be a powerful tool, giving information not only about copy number variation but also about loss-of-heterozygosity and parental origin. We conclude that an integrated genome-wide copy number variation analysis, if possible associated to FISH and gene expression studies, could facilitate in the future the difficult task of establishing accurate genotype-phenotype correlations and help to improve genetic counselling.

1 citations


Cites background from "Class II Analphoid Chromosome in a ..."

  • ...reported a child with dysmorphic features and developmental delay, who presented a complex chromosome rearrangement involving chromosome 7 and resulting of a class II/McClintock mechanism [6]....

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References
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Journal ArticleDOI

4,888 citations


"Class II Analphoid Chromosome in a ..." refers methods in this paper

  • ...Banding Cytogenetics A human leukocyte culture was used for metaphase slide preparation followed by GTG banding to observe numerical and structural chromosome aberrations [Seabright, 1971]....

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Journal ArticleDOI
TL;DR: Recent research has focused on the role of neocentromeres in evolution and speciation, as well as in disease development and the understanding of the organization and epigenetic maintenance of the centromere.
Abstract: Since the discovery of the first human neocentromere in 1993, these spontaneous, ectopic centromeres have been shown to be an astonishing example of epigenetic change within the genome. Recent research has focused on the role of neocentromeres in evolution and speciation, as well as in disease development and the understanding of the organization and epigenetic maintenance of the centromere. Here, we review recent progress in these areas of research and the significant insights gained.

356 citations


"Class II Analphoid Chromosome in a ..." refers background in this paper

  • ...Neocentromeres are analphoid DNA sequences, forming new sites of assembly of functional kinetochores at ectopic loci that rescue chromosome fragments [Marshall et al., 2008] and restore their ability to segregate efficiently [Blom et al....

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  • ...To date, more than 100 neocentromeres have been characterized in humans [Marshall et al., 2008; Alonso et al., 2010; Klein et al., 2012], and they show remarkable diversity in chromosome position and associated DNA sequences [Burrack and Berman, 2012]....

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  • ...Neocentromeres have been identified in 21 of the 22 autosomes as well as in the X and Y sex chromosomes [Marshall et al., 2008; Liehr et al., 2010]....

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  • ...…either an inverted duplication (inv dup) of the distal part of a chromosome arm resulting in an unbalanced karyotype (class I) or a balanced chromosomal rearrangement into linear and circular marker chromosomes after an interstitial deletion (class II/McClintock mechanism) [Marshall et al., 2008]....

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  • ...The present report is a marked association of the rarer class II analphoid chromosome [Marshall et al., 2008]....

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Journal Article
TL;DR: A mechanism of formation of the mar del(10) chromosome involving the activation of a latent intercalary centromere at 10q25 is supported by cytogenetic and FISH results.
Abstract: We report the investigation of an unusual human supernumerary marker chromosome 10 designated "mar del(10)." This marker is present together with two other marker chromosomes in the karyotype of a boy with mild developmental delay. It has a functional centromere at a primary constriction and is mitotically stable. Fluorescence in situ hybridization (FISH) using alpha-satellite and satellite III DNA as probes failed to detect any signal at the primary constriction site. CENP-B protein could not be demonstrated, although the presence of at least some centromeric proteins was confirmed using a CREST antiserum. Consideration of these and other cytogenetic and FISH results supports a mechanism of formation of the mar del(10) chromosome involving the activation of a latent intercalary centromere at 10q25.

273 citations


Additional excerpts

  • ...2 [Voullaire et al., 1993; Maraschio et al., 1996; Warburton et al., 2003]....

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Journal ArticleDOI
TL;DR: The centromere is essential for the proper segregation and inheritance of genetic information as discussed by the authors, and it forms a primary constriction and assemble a functional kinetochore, despite the complete absence of normal centromeric α-satellite DNA.
Abstract: The centromere is essential for the proper segregation and inheritance of genetic information. Neocentromeres are ectopic centromeres that originate occasionally from noncentromeric regions of chromosomes. Despite the complete absence of normal centromeric α-satellite DNA, human neocentromeres are able to form a primary constriction and assemble a functional kinetochore. Since the discovery and characterization of the first case of a human neocentromere in our laboratory a decade ago, 60 examples of constitutional human neocentromeres distributed widely across the genome have been described. Typically, these are located on marker chromosomes that have been detected in children with developmental delay or congenital abnormalities. Neocentromeres have also been detected in at least two types of human cancer and have been experimentally induced in Drosophila. Current evidence from human and fly studies indicates that neocentromere activity is acquired epigenetically rather than by any alteration to the DNA sequence. Since human neocentromere formation is generally detrimental to the individual, its biological value must lie beyond the individual level, such as in karyotype evolution and speciation.

260 citations

Journal ArticleDOI
TL;DR: The process of centromere repositioning during primate chromosomal evolution may depend on the acquisition and subsequent fixation of neocentromeres, and this remarkable plasticity in the position of centromeres has important implications for human cytogenetics and chromosome evolution.
Abstract: Neocentromeres are rare human chromosomal aberrations where a new centromere has formed in a previously non-centromeric location. The emergence of new centromeres on a chromosome that already contains an endogenous centromere would be a highly deleterious event which would lead to dicentricity and mitotic instability. Nonetheless, neocentromere formation appears to provide a mechanism for the acquisition of a new centromere. Neocentromeres are most often observed on chromosomal arm fragments that have separated from an endogenous centromere, and therefore actually lead to mitotic stability of what would have been an acentric fragment. Neocentromeres have recently also been observed on apparently unrearranged chromosomes where the endogenous centromere has been inactivated. Furthermore, the process of centromere repositioning during primate chromosomal evolution may depend on the acquisition and subsequent fixation of neocentromeres. This remarkable plasticity in the position of centromeres has important implications for human cytogenetics and chromosome evolution, and provides an opportunity to further our understanding of the process of centromere formation and structure.

152 citations


"Class II Analphoid Chromosome in a ..." refers background in this paper

  • ...To our knowledge, the neocentric association in chromosome 7 was studied in 4 cases, of which 3 cases were reported on aberrant chromosomes 7 with an unclear position of the neocentromere [Lamb et al., 1998; Warbur- ton, 2004; Ebrahim et al., 2008]....

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  • ...To our knowledge, the neocentric association in chromosome 7 was studied in 4 cases, of which 3 cases were reported on aberrant chromosomes 7 with an unclear position of the neocentromere [Lamb et al., 1998; Warburton, 2004; Ebrahim et al., 2008]....

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