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Concept: Chromosomes

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Microarray-based comparative genomic hybridization (array-CGH) led to the discovery of genetic abnormalities among patients with complex phenotype and normal karyotype. Also several apparently normal individuals have been found to be carriers of cryptic imbalances, hence the importance to perform parental investigations after the identification of a deletion/duplication in a proband. Here, we report the molecular cytogenetic characterization of two individuals in which the microdeletions/duplications present in their parents could have predisposed and facilitated the formation of pathogenic different copy number variations (CNVs). In family 1, a 4-year-old girl had a pathogenic 10.5 Mb duplication at 15q21.2q22.2, while her mother showed a 2.262 Mb deletion at 15q13.2q13.3; in family 2, a 9-year-old boy had a 1.417 Mb deletion at 22q11.21 and a second paternal deletion of 247 Kb at 22q11.23 on the same chromosome 22. Chromosome 22 at band q11.2 and chromosome 15 at band q11q13 are considered unstable regions. We could hypothesize that 15q13.2q13.3 and 22q11.21 deletions in the two respective parents might have increased the risk of rearrangements in their children. This study highlights the difficulty to make genetic counseling and predict the phenotypic consequences in these situations.

Concepts: DNA, Gene, Genetics, Copy number variation, Chromosome, Cytogenetics, Chromosomes, Metaphase

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Current cell-free DNA assessment of fetal chromosomes does not analyze and report on all chromosomes. Hence, a significant proportion of fetal chromosomal abnormalities are not detectable by current non-invasive methods. Here we report the clinical validation of a novel non-invasive prenatal test designed to detect genome-wide gains and losses of chromosomal material ≥7 Mb and losses associated with specific deletions <7 Mb.

Concepts: DNA, Gene, Cell, Species, Chromosome, Cytogenetics, Chromosomes, Chromatin

28

The Ashkenazi Jewish population has a several-fold higher prevalence of Crohn’s disease (CD) compared with non-Jewish European ancestry populations and has a unique genetic history. Haplotype association is critical to CD etiology in this population, most notably at NOD2, in which three causal, uncommon and conditionally independent NOD2 variants reside on a shared background haplotype. We present an analysis of extended haplotypes that showed significantly greater association to CD in the Ashkenazi Jewish population compared with a non-Jewish population (145 haplotypes and no haplotypes with P-value <10(-3), respectively). Two haplotype regions, one each on chromosomes 16 and 21, conferred increased disease risk within established CD loci. We performed exome sequencing of 55 Ashkenazi Jewish individuals and follow-up genotyping focused on variants in these two regions. We observed Ashkenazi Jewish-specific nominal association at R755C in TRPM2 on chromosome 21. Within the chromosome 16 region, R642S of HEATR3 and rs9922362 of BRD7 showed genome-wide significance. Expression studies of HEATR3 demonstrated a positive role in NOD2-mediated NF-κB signaling. The BRD7 signal showed conditional dependence with only the downstream rare CD-causal variants in NOD2, but not with the background haplotype; this elaborates NOD2 as a key illustration of synthetic association.Genes and Immunity advance online publication, 25 April 2013; doi:10.1038/gene.2013.19.

Concepts: Gene, Mutation, Chromosome, Genetic genealogy, Chromosomes, Jews, Jewish ethnic divisions, Ashkenazi Jews

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A eukaryotic chromosome consists of a centromere, two telomeres and a number of replication origins, and “artificial chromosomes” can be created in yeast and mammals when these three elements are artificially joined and introduced into cells. Plant artificial chromosomes (PACs) have been anticipated as new vectors for the development of new crops and as tools for basic research on chromosomes. However, indisputable PAC formation has not yet been confirmed. Here, we present a method for generating PACs in the model plant Arabidopsis thaliana using the Cre/LoxP and Activator (Ac)/Dissociation (Ds) element systems. The successfully generated PAC, designated “AtARC1 (A. thaliana artificial ring chromosome 1)”, originated from a centromeric edge of the long arm of chromosome 2, yet the size (2.85 Mb) is much smaller than that of the original chromosome (26.3 Mb). Although AtARC1 contains only a short centromere domain consisting of 180-bp repeats approximately 250 kb in length, compared with the domain on the original chromosome 2 (3 Mb), the centromere-specific histone H3 (HTR12) was detected on the centromeric region. This result supported the observed stability of the PAC during mitosis in the absence of selection and the transmission of the PAC to the next generation through meiosis. Because AtARC1 contains a unique LoxP site driven by the CaMV 35S promoter, it is possible to introduce a selectable marker and desired transgenes into AtARC1 at the LoxP site using the Cre recombinase. Therefore, AtARC1 meets the criteria for a PAC and is a promising vector. © 2013 The Authors. The Plant Journal © 2013 Blackwell Publishing Ltd.

Concepts: DNA, Histone, Eukaryote, Chromosome, Model organism, Chromosomes, Arabidopsis thaliana, Meiosis

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Context:Pseudohypoparathyroidism type 1b (PHP1b) is the result of end-organ resistance to PTH and other hormones such as TSH in the absence of any features of Albright’s hereditary osteodystrophy. Patients with PHP1b show imprinting abnormalities at the complex GNAS locus. The molecular cause of autosomal dominant familial PHP1b has been well-defined with identification of microdeletions within the GNAS locus or the nearby STX16, but the molecular mechanism of the GNAS imprinting defects in sporadic PHP1b cases remains elusive.Objective:We investigated the underlying molecular mechanism of GNAS imprinting defects in two patients with sporadic PHP1b.Results:We identified paternal uniparental disomy of the long arm of chromosome 20 (patUPD20) in two unrelated patients with sporadic PHP1b. This provides an explanation for the patients' GNAS methylation abnormalities and hormone resistance. Our data and a review of the six published cases of patUPD20 suggest that high birth weight and/or early-onset obesity and macrocephaly may also represent features of patUPD20.Conclusion:We suggest that patUPD20 should be considered in the evaluation of patients with sporadic PHP1b.

Concepts: DNA, Biology, Chromosome, Cytogenetics, Chromosomes, Aneuploidy, Pseudohypoparathyroidism, RIC8A

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Objective: Custom genotyping of markers in families with familial idiopathic scoliosis were used to fine-map candidate regions on chromosomes 9 and 16 in order to identify candidate genes that contribute to this disorder and prioritize them for next-generation sequence analysis. Methods: Candidate regions on 9q and 16p-16q, previously identified as linked to familial idiopathic scoliosis in a study of 202 families, were genotyped with a high-density map of single nucleotide polymorphisms. Tests of linkage for fine-mapping and intra-familial tests of association, including tiled regression, were performed on scoliosis as both a qualitative and quantitative trait. Results and Conclusions: Nominally significant linkage results were found for markers in both candidate regions. Results from intra-familial tests of association and tiled regression corroborated the linkage findings and identified possible candidate genes suitable for follow-up with next-generation sequencing in these same families. Candidate genes that met our prioritization criteria included FAM129B and CERCAM on chromosome 9 and SYT1, GNAO1, and CDH3 on chromosome 16.

Concepts: DNA, Gene, Genetics, Chromosome, Single-nucleotide polymorphism, Chromosomes, Qualitative research, Genotyping

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Hoolock gibbons (genus Hoolock) are a group of very endangered primate species that belong to the small ape family (family Hylobatidae). The entire population that is distributed in the northeast and southeast of Bangladesh is estimated to include only around 350 individuals. A conservation program is thus necessary as soon as possible. Genetic markers are significant tools for planning such programs. In this study, we examined chromosomal characteristics of two western hoolock gibbons that were captured in a Bangladesh forest. During chromosome analysis, we encountered two chromosome variations that were observed for the first time in the wild-born western hoolock gibbons (Hoolock hoolock). The first one was a nonhomologous centromere position in chromosome 8 that was observed in the two examined individuals. The alteration was identical in the two individuals, which were examined by G-band and DAPI-band analyses. Chromosome paint analyses revealed that the difference in the centromere position was due to a single small pericentric inversion. The second variation was a heterozygous elongation in chromosome 9. Analysis by sequential techniques of fluorescence in situ hybridization with 18S rDNA and silver nitrate staining revealed a single and an inverted tandem duplication, respectively, of the nucleolus organizer region in two individuals. These chromosome variations provide useful information for the next steps to consider the evolution and conservation of the hoolock gibbon.

Concepts: DNA, Chromosome, Chromosomes, Primate, Ape, Gibbon, Gibbons, Bunopithecus sericus

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Small supernumerary marker chromosomes (sSMC) are structurally abnormal chromosomes, generally equal in size or smaller than a chromosome 20 of the same metaphase spread. Most of them are unexpectedly detected in routine karyotype analyses, and it is usually not easy to correlate them with a specific clinical picture. A small group of sSMCs is derived from more than one chromosome, called complex sSMCs. Here, we report on a patient with a de novo complex sSMC, derived from chromosomes 8 and 14. Banding karyotype analysis, multiplex ligation-dependent probe amplification (MLPA), single nucleotide polymorphism (SNP)-based array, and fluorescence in situ hybridization (FISH) were performed to investigate its origin. Array and FISH analyses revealed a der(14)t(8;14)(p23.2;q22.1)dn. The propositus presents some clinical features commonly found in patients with partial duplication or triplication of 8p and 14q. This is the first report describing a patient with a congenital der(14)t(8;14)(p23.2;q22.1)dn sSMC.

Concepts: DNA, Molecular biology, Chromosome, Cell cycle, Cytogenetics, Chromosomes, In situ hybridization, Small supernumerary marker chromosome

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The vast majority of the mouse and human genomes consist of repetitive elements (REs), while protein-coding sequences occupy only ∼3 %. It has been reported that the Y chromosomes of both species are highly populated with REs although at present, their complete sequences are not available in any public database. The recent update of the mouse genome database (Build 38.1) from the National Center for Biotechnology Information (NCBI) indicates that mouse chromosome Y is ∼92 Mb in size, which is substantially larger than the ∼16 Mb reported previously (Build 37.2). In this study, we examined how REs are arranged in mouse chromosome Y (Build 38.1) using REMiner-II, a RE mining program. A combination of diverse REs and RE arrays formed large clusters (up to ∼28 Mb in size) and most of them were directly or inversely related. Interestingly, the RE population of human chromosome Y (NCBI Build 37.2-current) was less dense, and the RE/RE array clusters were not evident in comparison to mouse chromosome Y. The annotated gene loci were distributed in five different regions and most of them were surrounded by unique RE arrays. In particular, tandem RE arrays were embedded into the introns of two adjacent gene loci. The findings from this study indicate that the large and interrelated clusters of REs and RE arrays predominantly represent the unique organizational pattern of mouse chromosome Y. The potential interactions among the clusters, which are populated with various interrelated REs and RE arrays, may play a role in the structural configuration and function of mouse chromosome Y.

Concepts: DNA, Gene, Human genome, Genome, Chromosome, Chromosomes, Y chromosome, XY sex-determination system

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Somatic mosaicism is present in slightly more than 50% of small supernumerary marker chromosome (sSMC) carriers. Interestingly, non-acrocentric derived sSMC show mosaicism much more frequently than acrocentric ones. sSMC can be present in different mosaic rates, which may go below 5% of the studied cells. Also cryptic mosaicism can be present and mosaics may be differently expressed in different tissues of the body. Even though in the overwhelming majority of the cases somatic sSMC mosaicism has no direct clinical effect, there are also cases with altered clinical outcomes due to mosaicism. Also clinically important is the fact that a de novo sSMC, even present in mosaic, may be a hint of uniparental disomy (UPD). As it is under discussion to possibly replace standard karyotyping by methods like array-CGH, the impracticality of the latter to detect low-level sSMC mosaics and/or UPD has to be considered as well. Overall, sSMC mosaicism has to be studied carefully in each individual case, as it can be extremely informative and of importance, especially for prenatal genetic counseling.

Concepts: DNA, Gene, Chromosome, Cytogenetics, Chromosomes, Aneuploidy, Y chromosome, Small supernumerary marker chromosome