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.

Characterization of a de novo Supernumerary Neocentric Ring Chromosome Derived from Chromosome 7.

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.

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Impacts of Soil and Water Conservation Practice on Soil Moisture in Debre Mewi and Sholit Watersheds, Abbay Basin, Ethiopia

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.

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Molecular characterization of a rare analphoid supernumerary marker chromosome derived from 7q35 → qter: a case report.

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.

Rangasamy Ashok Kumar

Papers

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