Showing papers on "Chromosome 22 published in 2011"

Aneuploidy in human spermatozoa.

Abstract: We reviewed the frequency and distribution of disomy in spermatozoa obtained by multicolor-FISH analysis on decondensed sperm nuclei in (a) healthy men, (b) fathers of aneuploid offspring of paternal origin and (c) individuals with Klinefelter syndrome and XYY males. In series of healthy men, disomy per autosome is approximately 0.1% but may range from 0.03 (chromosome 8) to 0.47 (chromosome 22). The great majority of authors find that chromosome 21 (0.18%) and the sex chromosomes (0.27%) have significantly elevated frequencies of disomy although these findings are not universal. The total disomy in FISH studies is 2.26% and the estimated aneuploidy (2× disomy) is 4.5%, more than double that seen in sperm karyotypes (1.8%). Increased disomy levels of low orders of magnitude have been reported in spermatozoa of some normal men (stable variants) and in men who have fathered children with Down, Turner and Klinefelter syndromes. These findings suggest that men with a moderately elevated aneuploidy rate may be at a higher risk of fathering paternally derived aneuploid pregnancies. Among lifestyle factors, smoking, alcohol and caffeine have been studied extensively but the compounding effects of the 3 are difficult to separate because they are common lifestyle behaviors. Increases in sex chromosome abnormalities, some autosomal disomies, and in the number of diploid spermatozoa are general features in 47,XXY and 47,XYY males. Aneuploidy of the sex chromosomes is more frequent than aneuploidy of any of the autosomes not only in normal control individuals, but also in patients with sex chromosome abnormalities and fathers of paternally derived Klinefelter, Turner and Down syndromes.

New insights on the origin of B chromosomes in Astyanax scabripinnis obtained by chromosome painting and FISH

Abstract: Chromosome painting (CP) with a probe of B chromosome obtained by microdissection and fluorescence in situ hybridization (FISH) with probes of As51 satellite DNA, C o t−1 DNA, and 18S and 5S rDNA confirmed sharing of some repetitive DNA but not rDNA between A and B chromosomes in the fish Astyanax scabripinnis. Meiotic analysis revealed a pachytene B chromosome bivalent nearly half the size of its mitotic configuration, suggesting a self-pairing of B chromosome arms. Such an isochromosome nature of somatic B chromosome was further evidenced by CP and FISH. All the findings obtained suggest (i) intraspecific origin of B chromosome, and (ii) evolutionary enrichment of repetitive DNA classes, especially those contained in the C o t−1 and the As51 probes, in B chromosome. However, the precise origin of B chromosome in the present species remains to be elucidated by further molecular cytogenetic analysis because of painting of some A chromosome regions with the B chromosome-derived probe.

Genomic content and new insights on the origin of the B chromosome of the cichlid fish Astatotilapia latifasciata

Abstract: B chromosomes are additional chromosomes widely studied in a diversity of eukaryotic groups, including fungi, plants and animals, but their origin, evolution and possible functions are not clearly understood. To further understand the genomic content and the evolutionary history of B chromosomes, classical and molecular cytogenetic analyses were conducted in the cichlid fish Astatotilapia latifasciata, which harbor 1–2 B chromosomes. Through cytogenetic mapping of several probes, including transposable elements, rRNA genes, a repeated DNA genomic fraction (C0t − 1 DNA), whole genome probes (comparative genomic hybridization), and BAC clones from Oreochromis niloticus, we found similarities between the B chromosome and the 1st chromosome pair and chromosomes harboring rRNA genes. Based on the cytogenetic mapping data, we suggest the B chromosome may have evolved from a small chromosomal fragment followed by the invasion of the proto-B chromosome by several repeated DNA families.

Formation of novel CENP-A domains on tandem repetitive DNA and across chromosome breakpoints on human chromosome 8q21 neocentromeres.

Abstract: Endogenous human centromeres form on megabase-sized arrays of tandemly repeated alpha satellite DNA. Human neocentromeres form epigenetically at ectopic sites devoid of alpha satellite DNA and permit analysis of centromeric DNA and chromatin organization. In this study, we present molecular cytogenetic and CENP-A chromatin immunoprecipitation (ChIP) on CHIP analyses of two neocentromeres that have formed in chromosome band 8q21 each with a unique DNA and CENP-A chromatin configuration. The first neocentromere was found on a neodicentric chromosome 8 with an inactivated endogenous centromere, where the centromeric activity and CENP-A domain were repositioned to band 8q21 on a large tandemly repeated DNA. This is the first example of a neocentromere forming on repetitive DNA, as all other mapped neocentromeres have formed on single copy DNA. Quantitative fluorescent in situ hybridization (FISH) analysis showed a 60% reduction in the alpha satellite array size at the inactive centromere compared to the active centromere on the normal chromosome 8. This neodicentric chromosome may provide insight into centromere inactivation and the role of tandem DNA in centromere structure. The second neocentromere was found on a neocentric ring chromosome that contained the 8q21 tandemly repeated DNA, although the neocentromere was localized to a different genomic region. Interestingly, this neocentromere is composed of two distinct CENP-A domains in bands 8q21 and 8q24, which are brought into closer proximity on the ring chromosome. This neocentromere suggests that chromosomal rearrangement and DNA breakage may be involved in neocentromere formation. These novel examples provide insight into the formation and structure of human neocentromeres.

Differentiation of repetitive DNA sites and sex chromosome systems reveal closely related group in Parodontidae (Actinopterygii: Characiformes).

Abstract: Parodon and Apareiodon lack sufficiently consistent morphological traits to be considered a monophyletic group in Parodontidae. Species within this family are either sex-homomorphic or sex-heteromorphic (i.e., lacking a differentiated sex chromosome system, ZZ/ZW or ZZ/ZW1W2). In this study, a DNA fragment from the heterochromatin segment of the W chromosome of Apareiodon ibitiensis (named WAp) was microdissected and used for in situ mapping of nine Parodontidae species. The species were also characterized using a satellite DNA probe (pPh2004). The species were phylogenetically clustered according to 17 characters, which were examined by both classical and molecular cytogenetic techniques. Given the present results, the single ZZ/ZW sex chromosome system seems to have been derived from a paracentric inversion of a terminal WAp site onto the proximal regions of the short arms of a metacentric chromosome pair, followed by WAp site amplification. We reason that these events restrained recombination and favored differentiation of the W chromosome in some species. Moreover, co-hybridization experiments targeting the WAp and pPh2004 repetitive DNA sites of A. affinis suggest that the ZZ/ZW1W2 sex chromosomes of this species may have arisen from a translocation between the proto-sex chromosome and an autosome. Our phylogenetic analysis corroborates the hypothesis of sex chromosome differentiation and establishes groups of closely related species. The phylogenetic reorganization in response to these new data supports the presence of internal monophyletic groups within Parodontidae.

Chromosome Painting Reveals Asynaptic Full Alignment of Homologs and HIM-8–Dependent Remodeling of X Chromosome Territories during Caenorhabditis elegans Meiosis

Abstract: During early meiotic prophase, a nucleus-wide reorganization leads to sorting of chromosomes into homologous pairs and to establishing associations between homologous chromosomes along their entire lengths. Here, we investigate global features of chromosome organization during this process, using a chromosome painting method in whole-mount Caenorhabditis elegans gonads that enables visualization of whole chromosomes along their entire lengths in the context of preserved 3D nuclear architecture. First, we show that neither spatial proximity of premeiotic chromosome territories nor chromosome-specific timing is a major factor driving homolog pairing. Second, we show that synaptonemal complex-independent associations can support full lengthwise juxtaposition of homologous chromosomes. Third, we reveal a prominent elongation of chromosome territories during meiotic prophase that initiates prior to homolog association and alignment. Mutant analysis indicates that chromosome movement mediated by association of chromosome pairing centers (PCs) with mobile patches of the nuclear envelope (NE)–spanning SUN-1/ZYG-12 protein complexes is not the primary driver of territory elongation. Moreover, we identify new roles for the X chromosome PC (X-PC) and X-PC binding protein HIM-8 in promoting elongation of X chromosome territories, separable from their role(s) in mediating local stabilization of pairing and association of X chromosomes with mobile SUN-1/ZYG-12 patches. Further, we present evidence that HIM-8 functions both at and outside of PCs to mediate chromosome territory elongation. These and other data support a model in which synapsis-independent elongation of chromosome territories, driven by PC binding proteins, enables lengthwise juxtaposition of chromosomes, thereby facilitating assessment of their suitability as potential pairing partners.

Integration of genetic and physical maps of the chickpea (Cicer arietinum L.) genome using flow-sorted chromosomes

Abstract: Cultivated chickpea is the third most important legume after field bean and garden pea worldwide. Despite considerable breeding towards improved yield and resistance to biotic and abiotic stresses, the production of chickpea remained stagnant, but molecular tools are expected to increase the impact of current improvement programs. As a first step towards this goal, various genetic linkage maps have been established and markers linked to resistance genes been identified. However, until now, only one linkage group (LG) has been assigned to a specific chromosome. In the present work, mitotic chromosomes were sorted using flow cytometry and used as template for PCR with primers designed for genomic regions flanking microsatellites. These primers amplify sequence-tagged microsatellite site markers. This approach confirmed the assignment of LG8 to the smallest chromosome H. For the first time, LG5 was linked to the largest chromosome A, LG4 to a medium-sized chromosome E, while LG3 was anchored to the second largest chromosome B. Chromosomes C and D could not be flow-sorted separately and were jointly associated to LG6 and LG7. By the same token, chromosomes F and G were anchored to LG1 and LG2. To establish a set of preferably diagnostic cytogenetic markers, the genomic distribution of various probes was verified using FISH. Moreover, a partial genomic bacterial artificial chromosome (BAC) library was constructed and putative single/low-copy BAC clones were mapped cytogenetically. As a result, two clones were identified localizing specifically to chromosomes E and H, for which no cytogenetic markers were yet available.

Studies of genomic imbalances and the MYB-NFIB gene fusion in polymorphous low-grade adenocarcinoma of the head and neck.

Abstract: Polymorphous low-grade adenocarcinoma (PLGA) is a malignancy predominantly originating from the minor salivary glands. The molecular events underlying the pathogenesis of PLGA is poorly understood and no recurrent genetic aberrations have so far been identified. We used genome-wide, high-resolution aCGH analysis to explore genomic imbalances in 9 cases of PLGA. Because of the well-known morphologic similarities between PLGA and adenoid cystic carcinoma (ACC) we also analyzed all tumors for expression of the recently identified ACC-associated MYB-NFIB gene fusion. aCGH analysis revealed that the PLGA genome contains comparatively few copy number alterations (CNAs). Gains/losses of whole chromosomes or chromosome arms were more than twice as common as partial CNAs. Two cases showed gain of chromosome 8 and one case each gain of chromosome 9, loss of chromosome 22 and loss of the Y chromosome. One case showed loss of the entire 6q arm and one case an interstitial deletion of a 33-Mb segment within 6q22.1-q24.3. This region contains the MYB oncogene and the candidate tumor suppressor gene PLAGL1. RT-PCR analysis revealed that one of the 9 PLGAs expressed the ACC-associated MYB-NFIB gene fusion, illustrating the diagnostic difficulties associated with the diagnosis of these morphologically partly overlapping entities. Taken together, our findings indicate that the PLGA genome is genetically stable and contains comparatively few CNAs which is in line with the clinical observation that PLGA is a slow-growing, low-grade carcinoma with low metastatic potential.

Step-by-step evolution of neo-sex chromosomes in geographical populations of wild silkmoths, Samia cynthia ssp.

Abstract: Geographical subspecies of wild silkmoths, Samia cynthia ssp. (Lepidoptera: Saturniidae), differ considerably in sex chromosome constitution owing to sex chromosome fusions with autosomes, which leads to variation in chromosome numbers. We cloned S. cynthia orthologues of 16 Bombyx mori genes and mapped them to chromosome spreads of S. cynthia subspecies by fluorescence in situ hybridization (FISH) to determine the origin of S. cynthia neo-sex chromosomes. FISH mapping revealed that the Z chromosome and chromosome 12 of B. mori correspond to the Z chromosome and an autosome (A1) of S. c. ricini (Vietnam population, 2n=27, Z0 in female moths), respectively. B. mori chromosome 11 corresponds partly to another autosome (A2) and partly to a chromosome carrying nucleolar organizer region (NOR) of this subspecies. The NOR chromosome of S. c. ricini is also partly homologous to B. mori chromosome 24. Furthermore, our results revealed that two A1 homologues each fused with the W and Z chromosomes in a common ancestor of both Japanese subspecies S. c. walkeri (Sapporo population, 2n=26, neo-Wneo-Z) and S. cynthia subsp. indet. (Nagano population, 2n=25, neo-WZ1Z2). One homologue, corresponding to the A2 autosome in S. c. ricini and S. c. walkeri, fused with the W chromosome in S. cynthia subsp. indet. Consequently, the other homologue became a Z2 chromosome. These results clearly showed a step-by-step evolution of the neo-sex chromosomes by repeated autosome–sex chromosome fusions. We suggest that the rearrangements of sex chromosomes may facilitate divergence of S. cynthia subspecies towards speciation.

Two additional reports of deletion on the short arm of the Y chromosome.

Abstract: Deletions on the short arm of the Y chromosome involving the amelogenin Y gene (AMELY), located on Yp11.2, can be misleading for sex typing with serious consequences in forensic applications and prenatal diagnosis. In this study, we describe two AMELY null cases concerning two unrelated Italian males from Northeast Italy. PCR amplification of short tandem repeats on the Y chromosome (Y-STRs) showed a lack of AMELY and DYS458 markers. The presence of all the other markers located on the Y chromosome and of the SRY gene in both samples led us to conclude that a deletion had occurred in a portion of the short arm of the Y chromosome. Twenty-three Y-specific sequence tagged sites (STSs) were chosen to delineate the deletion's length, which was estimated to be in the range of 3.35-3.87Mb for one sample and 1.51-2.58Mb for the other. These and previous findings suggest that in all cases where potential AMELY drop out has occurred, it should be used additional specific Y chromosome markers or human DNA quantification methods that specifically quantify male DNA using target male genomic markers, which not being located within the deletion regions, allow an accurate sex identification.

Detection of uniparental isodisomy in autosomal recessive mitochondrial DNA depletion syndrome by high-density SNP array analysis

Abstract: Mitochondrial DNA (mtDNA) depletion syndrome encompasses a heterogeneous group of disorders characterized by a reduction in the mtDNA copy number. We identified two patients with clinical presentations consistent with mtDNA depletion syndrome (MDS), who were subsequently found to have apparently homozygous point mutations in TYMP and DGUOK, two of the nine nuclear genes commonly associated with these disorders. Further sequence analyses of parents indicated that in each case only one parent; the mother of the first and the father of the second, was a heterozygous carrier of the mutation identified in the affected child. The presence of underlying deletions was ruled out by use of a custom target array comparative genomic hybridization (CGH) platform. A high-density single-nucleotide polymorphism (SNP) array analysis revealed that the first patient had a region of copy-neutral absence of heterozygosity (AOH) consistent with segmental isodisomy for an 11.3 Mb region at the long-arm terminus of chromosome 22 (including the TYMP gene), and the second patient had results consistent with complete isodisomy of chromosome 2 (where the DGUOK gene is located). The combined sequencing, array CGH and SNP array approaches have demonstrated the first cases of MDS due to uniparental isodisomy. This diagnostic scenario also demonstrates the necessity of comprehensive examination of the underlying molecular defects of an apparently homozygous mutation in order to provide patients and their families with the most accurate molecular diagnosis and genetic counseling.

Analysis of cytogenetic aberrations in sporadic vestibular schwannoma by comparative genomic hybridization.

Abstract: Vestibular schwannomas (VS) are benign tumors of the nervous system that are usually sporadic but also occur in the inherited disorder neurofibromatosis type 2 (NF2). The NF2 gene is a tumor suppressor gene located on chromosome 22. Loss of the NF2 protein product, Merlin, is universal in both sporadic and NF2-related schwannomas and the loss or mutation of the gene is the only established causative event underlying schwannoma formation. Comparative genomic hybridization (CGH) was used to screen 20 sporadic VS to identify additional chromosomal regions that may harbor genes involved in VS-tumorigenesis. The most common change were losses on chromosome 22q. Additionally, losses were observed on chromosome 9p indicating a possible participation of the CDKN2A tumor suppressor gene in the genesis of VS. Gains were observed on 17q, 19p and 19q, which have been reported before in malignant peripheral nerve sheath tumors that are associated with neurofibromatosis type 1. Importantly, high level amplifications have been observed on 16p and 16q as well as on 9q, suggesting the possible involvement of several oncogenes in the tumorigenesis of VS. Our data suggest the involvement of various oncogenes and tumor suppressor genes might play a role in the genesis of the vestibular schwannomas apart from the inactivation of the NF2 gene.

Human Chromosome Variation: Heteromorphism and Polymorphism

Abstract: Foreword.- Preface to Second Edition.- Acknowledgements.- List of Contributors.- A. HUMAN CHROMOSOME METHODS AND NOMENCLATURE.- 1. Introduction.- 2. Chromosome Heteromorphism.- 2.1 Chromosome Banding Techniques and Mechanisms.- 2.2 Other DNA-Binding Fluorochromes.- 2.3 Sister Chromatid Exchange Staining (SCE).- 2.4 Replication Banding.- 2.5 High Resolution Banding and Special Treatments.- 2.6 Satellite DNA in Heteromorphic Regions.- 2.7 Single nucleotide polymorphisms (SNPs).- 2.8 Fluorescence In Situ Hybridization (FISH).- 3. Frequencies Of Heteromorphisms.- 3.1 By Q- and C-banding.- 3.2 Specialized Banding Studies.- 4. Clinical Populations.- 4.1 Spontaneous Abortions and Reproductive Failure.- 4.2 Non-disjunction.- 4.3 Satellite Association.- 4.4 Cancer.- 5. Euchromatic Variants.- B. CHROMOSOME HETEROMORPHISM (SUMMARIES).- Chromosome 1.- Chromosome 2.- Chromosome 3.- Chromosome 4.- Chromosome 5.- Chromosome 6.- Chromosome 7.- Chromosome 8.- Chromosome 9.- Chromosome 10.- Chromosome 11.- Chromosome 12.- Chromosome 13.- Chromosome 14.- Chromosome 15.- Chromosome 16.- Chromosome 17.- Chromosome 18.- Chromosome 19.- Chromosome 20.- Chromosome 21.- Chromosome 22.- Chromosome X.- Chromosome Y.- C. Fish Variants.- 1. FISH Results With Centromeric Repeats.- 2. Subtelomeric Deletions/Duplications: Normal Variation or Chromosome Abnormality.- D. Fragile Sites.- E. Comparative Genomic Hybridization-Microarray Analysis, Copy Number Variants, and Clinical Interpretation.- 1. Introduction.- 2. Case Discussions.- 2.1 Cases where the interpretation of clinical significance is clear and the diagnosis provides good prognostic information.- 2.2 Cases where interpretation of clinical significance is clear but the finding gives less defined prognosis.- 2.3 Cases of familial change with unclear significance or prognosis.- 3. Summary.- Index

DNA methylation patterns of Brachypodium distachyon chromosomes and their alteration by 5-azacytidine treatment

Abstract: Sequential immunolocalisation of 5-methylcytosine (5-MeC) and fluorescence in situ hybridisation with chromosome-specific BAC clones were performed on Brachypodium distachyon mitotic metaphase chromosomes to determine specific DNA methylation patterns of each chromosome in the complement. In the majority of cells examined, chromosomes Bd4 and Bd5, which bear the loci of 5S and 35S ribosomal DNA, respectively, had characteristic 5-MeC patterns. In contrast, the distribution of 5-MeC along the metacentric chromosome pairs Bd1, Bd2 and Bd3 was more variable. There were numerous differences in distribution of methylated sites between homologous chromosomes as well as between chromosome arms. Some chromosome sites, such as pericentromeric regions, were highly methylated in all chromosomes. Additionally, the influence of a hypomethylating agent, 5-azacytidine, on B. distachyon chromosome methylation patterns was confirmed. It was found that some chromosome pairs underwent demethylation more easily than others, but there was no apparent regularity in demethylation of particular chromosome segments.

Identification of copy number variants on human chromosome 22 in patients with a variety of clinical findings.

Abstract: The aims of this study were to create a copy number variant (CNV) profile of human chromosome 22 and to establish a genotype-phenotype correlation for patients with genomic abnormalities on chromosome 22. Thus, 1,654 consecutive pediatric patients with a diversity of clinical findings were evaluated by high-resolution chromosomal microarray analysis (CMA). We identified 25 individuals with abnormal CNVs on chromosome 22, representing 1.5% of the cases analyzed in this cohort. Meanwhile, we detected 1,298 benign CNVs on this chromosome in these individuals. Twenty-one of the 25 abnormal CNVs and the majority of the benign CNVs occurred through involvement of the 8 unstable genomic regions enriched with low copy repeats (LCR22A-H). The highly dynamic status of LCR22s within the 22q11 region facilitates the formation of diverse genomic abnormalities. This CNV profile provides a general perspective of the spectrum of chromosome 22 genomic imbalances and subsequently improves the CNV-phenotype correlations.

The Cytogenetic Map of the Poncirus trifoliata (L.) Raf. — A Nomenclature System for Chromosomes of All Citric Species

Abstract: A cytogenetic map was established for the trifoliate orange, Poncirus trifoliata. Chromosome size, centromere position and CMA+ heterochromatin content were determined for each chromosome pair, together with the position of BAC clones previously described as chromosome-specific markers. Although P. trifoliata is a true biological species, heteromorphisms for the size of the heterochromatic bands in two chromosome pairs were observed. A minimum set of four BACs was proposed for chromosome identification in P. trifoliata, as well as a chromosome nomenclature that can be applied to all citrus species. The Ctv locus was assigned to chromosome 9 and the remaining linkage groups can now be integrated to this physical map. This standard nomenclature for trifoliate orange will be valuable for genome-sequencing projects in all citrus species.

Recovery of a telomere-truncated chromosome via a compensating translocation in maize.

Abstract: Maize-engineered minichromosomes are easily recovered from telomere-truncated B chromosomes but are rarely recovered from A chromosomes. B chromosomes lack known genes, and their truncation products are tolerated and trans- mitted during meiosis. In contrast, deficiency gametes resulting from truncated A chromosomes prevent their transmission. We report here a de novo compensating translocation that permitted recovery of a large truncation of chromosome 1 in maize. The truncation (trunc-1) and translocation with chromosome 6 (super-6) occurred during telomere-mediated trunca- tion experiments and were characterized using single-gene fluorescent in situ hybridization (FISH) probes. The truncation contained a transgene signal near the end of the broken chromosome and transmitted together with the compensating trans- location as a heterozygote to approximately 41%-55% of progeny. Transmission as an addition chromosome occurred in ~15% of progeny. Neither chromosome transmitted through pollen. Transgene expression (Bar) cosegregated with trunc-1 transcriptionally and phenotypically. Meiosis in T1 plants revealed eight bivalents and one tetravalent chain composed of chromosome 1, trunc-1, chromosome 6, and super-6 in diplotene and diakinesis. Our data suggest that de novo compensat- ing translocations allow recovery of truncated A chromosomes by compensating deficiency in female gametes and by af- fecting chromosome pairing and segregation. The truncated chromosome can be maintained as an extra chromosome or together with the super-6 as a heterozygote.

Chronic myeloid leukemia: cytogenetic methods and applications for diagnosis and treatment.

Abstract: Chronic myeloid leukemia (CML) is a clonal myeloproliferative disease caused by recombination between the BCR gene on chromosome 22 and the ABL1 gene on chromosome 9. This rearrangement generates the BCR-ABL1 fusion gene that characterizes leukemic cells in all CML cases. In about 90% of cases, the BCR-ABL1 rearrangement is manifest cytogenetically by the Philadelphia (Ph) chromosome, a derivative of the reciprocal translocation t(9;22)(q34;q11.2). For the remaining cases, recombination may be more complex, involving BCR, ABL1, and genomic sites on one or more other chromosomal regions, or it may occur cryptically within an apparently normal karyotype. Detection of the Ph and associated t(9;22) translocation is a recognized clinical hallmark for CML diagnosis. The disease has a natural multistep pathogenesis, and during chronic phase CML, the t(9;22) or complex variant is usually the sole abnormality. In 60-80% of cases, additional cytogenetic changes appear and often forecast progression to an accelerated disease phase or a terminal blast crisis. Because new frontline therapies such as imatinib specifically target the abnormal protein product of the BCR-ABL1 fusion gene to eliminate BCR-ABL1 positive cells, there is a new reliance on the cytogenetic evaluation of bone marrow cells at diagnosis, then at regular posttreatment intervals. Combined with other parameters, presence or absence of Ph-positive cells in the bone marrow is a powerful early indicator for clinical risk stratification. Cytogenetic changes detected at any stage during treatment, including in the BCR-ABL1-negative cells, may also provide useful prognostic information. Laboratory methods detailed here extend from initial collection of peripheral blood or bone marrow samples through cell culture with or without synchronization, metaphase or interphase harvest, hypotonic treatment and fixation, slide preparation for G-banding or fluorescent in situ hybridization (FISH), and final interpretation.

Combined 22q11.1-q11.21 deletion with 15q11.2-q13.3 duplication identified by array-CGH in a 6 years old boy

Abstract: Deletions of chromosome 22q11 are present in over 90% of cases of DiGeorge or Velo-Cardio-Facial syndrome (DGS/VCFS). 15q11-q13 duplication is another recognized syndrome due to rearrangements of several genes, belonging to the category of imprinted genes. The phenotype of this syndrome varies but has been clearly associated with developmental delay and autistic spectrum disorders. Co-existence of the two syndromes has not been reported so far. Here we report a 6-year-old boy presenting growth retardation, dysmorphic features and who exhibited learning difficulties. Fluorescence in situ hybridization (FISH) analysis of the proband revealed a deletion of DiGeorge Syndrome critical region (TUPLE). Array-CGH analysis revealed an interstitial duplication of 12 Mb in size in the area 15q11.2-q13.3, combined with a 3.2 Mb deletion at region 22q11.1-q11.21. FISH analysis in the mother showed a cryptic balanced translocation between chromosome 15 and chromosome 22 (not evident by classic karyotyping). The clinical manifestations could be related to both syndromes and the importance of array-CGH analysis in cases of unexplained developmental delay is emphasized. The present case further demonstrates how molecular cytogenetic techniques applied in the parents were necessary for the genetic counseling of the family.

Mouse artificial chromosome vector

Abstract: Disclosed is a mouse artificial chromosome vector, comprising: a natural centromere derived from a mouse chromosome; a mouse-chromosome-derived long-arm fragment formed by deleting a long-arm distal region at a mouse chromosome long-arm site proximal to the centromere; and a telomere sequence, wherein the vector is stably retained in a cell and/or tissue of a mammal. In addition, disclosed are cells or non-human animals comprising the vector, and use of the cells or non-human animals.

Clinical utility gene card for: Deletion 22q13 syndrome

Abstract: 1.5 Mutational spectrum Phelan-McDermid syndrome can result from simple 22q13 deletions, ring chromosomes and unbalanced translocations.1–5 The deletions are extremely variable in size, ranging from 95 kb to 9 Mb. The gene responsible for the core neurological features is SHANK3, which has been found to be mutated in patients with autism spectrum disorders and intellectual disability.6–9 55% de novo deletion 22q13.3 of the paternally derived chromosome 20% de novo deletion 22q13.3 of the maternally derived chromosome 10% paternal structural rearrangement 10% maternal structural rearrangement 4% de novo unbalanced rearrangement o1% mutations within SHANK3 gene (only a small number of studies have sequenced SHANK3, so the frequency may be underestimated).6–10 Deletions of 22q13, not including the SHANK3 gene, have been reported in two unrelated individuals with Phelan-McDermid syndrome.11

Five opitz G/B.B.B syndrome cases report with two chromosomal abnormalities; x chromosome duplication (47, XXY) and translocation 46XX t(3q;4q)

Abstract: Opitz G/BBB syndrome is a genetic condition that affects several structures along the midline of the body. The most common features of this condition are wide-spaced eyes (hypertelorism) with structural defects of the larynx, trachea, and/or esophagus causing breathing problems and difficulty swallowing (dysphagia). Some times in males, the urethra opening on the underside of the penis (hypospadias) is observed. Mild intellectual disability occurs in 30% approximately of patients with Opitz G/BBB syndrome (GBBBS), most likely caused by structural defects in the brain. About half of affected individuals also have cleft lip with or without a cleft palate as in this study. Some have cleft palate alone. Heart defects, imperforate anus, and brain defects such as absence of the corpus callosum. Facial abnormalities that may be seen in this disorder include a flat nasal bridge, thin upper lip, and low set ears. There are two forms of Opitz G/BBB syndrome, which are distinguished by their genetic causes and patterns of inheritance. The X-linked form of Opitz G/BBB syndrome is caused by a mutation in a specific gene, MID1, on the X chromosome. Autosomal dominant Opitz G/BBB syndrome is caused by a mutation in an as-yet unidentified gene on chromosome 22. Two chromosomal aberrations in this study were observed in two patients; chromosome duplication 47,XXY and translocation 46,XX t(3;4). However one patient with oral encephalocele presented normal karyotype 46,XY. Key words: Hypertelorism, cleft lip with or without cleft palate, chromosomes, klinefelter syndrome, chromosomal translocation

Polymorphism in a Human Chromosome-Specific Interstitial Telomere-Like Sequence at 22q11.2

Abstract: Interstitial telomeric sequences (ITSs) are common in human. We previously reported the presence of an ITS at 22q11.2 which is in the vicinity of the genomically unstable region involved in 22q11 rear

HIV associated dementia and HIV encephalitis II: Genes on chromosome 22 expressed in individually microdissected Globus pallidus neurons (Preliminary analysis).

Abstract: We analyzed RNA gene expression in neurons from 16 cases in four categories, HIV associated dementia with HIV encephalitis (HAD/HIVE), HAD alone, HIVE alone, and HIV-1-positive (HIV+)with neither HAD nor HIVE. We produced the neurons by laser capture microdissection (LCM) from cryopreserved globus pallidus. Of 55,000 gene fragments analyzed, expression of 197 genes was identified with significance (p = 0.005).We examined each gene for its position in the human genome and found a non-stochastic occurrence for only seven genes, on chromosome 22. Six of the seven genes were identified, CSNK1E (casein kinase 1 epsilon), DGCR8 (Di George syndrome critical region 8), GGA1 (Golgi associated gamma adaptin ear containing ARF binding protein 1), MAPK11 (mitogen activated protein kinase 11), SMCR7L (Smith-Magenis syndrome chromosome region candidate 7-like), andTBC1D22A (TBC1 domain family member 22A). Six genes (CSNK1E, DGCR8, GGA1, MAPK11, SMCR7L, and one unidentified gene) had similar expression profiles across HAD/HIVE, HAD, and HIVE vs. HIV+ whereas one gene (TBC1D22A) had a differing gene expression profile across these patient categories. There are several mental disease-related genes including miRNAs on chromosome 22 and two of the genes (DGCR8 and SMCR7L) identified here are mental disease-related. We speculate that dysregulation of gene expression may occur through mechanisms involving chromatin damage and remodeling. We conclude that the pathogenesis of NeuroAIDS involves dysregulation of expression of mental disease-related genes on chromosome 22 as well as additional genes on other chromosomes. The involvement of these genes as well as miRNA requires additional investigation since numerous genes appear to be involved.

Chromosome 22q11.2 microdeletion syndrome

Abstract: Chromosome 22q11.2 microdeletion syndrome is the most common microdeletion syndrome in humans. It involves the loss of genetic material on the short arm of one of the chromosome 22 alleles. Until advanced testing was available, this syndrome was known by various names including DiGeorge syndrome and velo-cardio-facial syndrome. This syndrome has a varied presentation with significant abnormalities including congenital heart disease, hypocalcemia, immunologic deficiencies, learning disabilities, and behavioral problems. A multidisciplinary approach is required to diagnose and manage the varied manifestations.

Translocation Frequencies and Chromosomal Proximities for Selected Mouse Chromosomes in Primary B Lymphocytes

Abstract: Chromosome positions within the nucleus of mammalian cells are nonrandom and it is assumed that chromosomal neighborhoods affect the probability of translocations. Four chromosomes can be involved in c-myc-activating chromosomal translocations in mouse plasmacytoma (PCT): the c-myc gene on mouse chromosome 15 can be juxtaposed to either one of the immunoglobulin (Ig) loci on chromosomes 12 (IgH), 16 (Igλ), or 6 (Igκ). In the BALB/c mouse, the translocation between chromosomes 12 and 15, T(12;15), is most common (90%) while the other two possible translocations, T(6;15) and T(16;15), are much less common (<10%). In contrast, in the BALB/cRb6.15 mouse, T(6;15) is found with the same frequency as T(12;15). We, therefore, examined the distance between chromosomes 15 and 12, 6, and 16 in primary mouse B lymphocytes in order to examine the effect of the chromosome proximity on the translocation frequency. We performed three-dimensional fluorescent in situ hybridization (3D-FISH) with chromosome paints. We acquired three-dimensional image stacks with 90 slices per stack and used constrained iterative deconvolution. The nucleus and chromosomes were segmented from this image stack and the interchromosomal distances were measured. Chromosomes 6 and 15 were found in close proximity in BALB/cRb6.15 mice (82%), whereas they did not share this neighborhood relationship in BALB/c mice. No other chromosome combinations showed such a high percentage of close proximities in either mouse strain. Chromosome positions contribute to translocation frequencies in mouse PCTs. The BALB/cRb6.15 mouse data argue for a proximity relationship of chromosomes that engage in illegitimate recombination. These positions are not, however, the only contributing factor as the T(12;15) translocation preference in BALB/c mice could not be supported by significantly elevated proximity of chromosomes 12 and 15 versus 12 and 16 or 12 and 6. Moreover, while there is a significant increase in T(6;15) in BALB/cRb6.15 mice, T(12;15) still occurs in this mouse strain. © 2011 International Society for Advancement of Cytometry

Molecular and cytological characterization of repetitive DNA sequences from the centromeric heterochromatin of Sciara coprophila

Abstract: Sciara coprophila (Diptera, Nematocera) constitutes a classic model to analyze unusual chromosome behavior such as the somatic elimination of paternal X chromosomes, the elimination of the whole paternal, plus non-disjunction of the maternal X chromosome at male meiosis. The molecular organization of the heterochromatin in S. coprophila is mostly unknown except for the ribosomal DNA located in the X chromosome pericentromeric heterochromatin. The characterization of the centromeric regions, thus, is an essential and required step for the establishment of S. coprophila as a model system to study fundamental mechanisms of chromosome segregation. To accomplish such a study, heterochromatic sections of the X chromosome centromeric region from salivary glands polytene chromosomes were microdissected and microcloned. Here, we report the identification and characterization of two tandem repeated DNA sequences from the pericentromeric region of the X chromosome, a pericentromeric RTE element and an AT-rich centromeric satellite. These sequences will be important tools for the cloning of S. coprophila centromeric heterochromatin using libraries of large genomic clones.

Soft tissue tumors: Extraskeletal myxoid chondrosarcoma

Abstract: Review on Soft tissue tumors: Extraskeletal myxoid chondrosarcoma, with data on clinics, and the genes involved.