Showing papers on "Chromosome 22 published in 2008"

Population-Based Genome-wide Association Studies Reveal Six Loci Influencing Plasma Levels of Liver Enzymes

Abstract: Plasma liver-enzyme tests are widely used in the clinic for the diagnosis of liver diseases and for monitoring the response to drug treatment. There is considerable evidence that human genetic variation influences plasma levels of liver enzymes. However, such genetic variation has not been systematically assessed. In the present study, we performed a genome-wide association study of plasma liver-enzyme levels in three populations (total n = 7715) with replication in three additional cohorts (total n = 4704). We identified two loci influencing plasma levels of alanine-aminotransferase (ALT) (CPN1-ERLIN1-CHUK on chromosome 10 and PNPLA3-SAMM50 on chromosome 22), one locus influencing gamma-glutamyl transferase (GGT) levels (HNF1A on chromosome 12), and three loci for alkaline phosphatase (ALP) levels (ALPL on chromosome 1, GPLD1 on chromosome 6, and JMJD1C-REEP3 on chromosome 10). In addition, we confirmed the associations between the GGT1 locus and GGT levels and between the ABO locus and ALP levels. None of the ALP-associated SNPs were associated with other liver tests, suggesting intestine and/or bone specificity. The mechanisms underlying the associations may involve cis- or trans-transcriptional effects (some of the identified variants were associated with mRNA transcription in human liver or lymphoblastoid cells), dysfunction of the encoded proteins (caused by missense variations at the functional domains), or other unknown pathways. These findings may help in the interpretation of liver-enzyme tests and provide candidate genes for liver diseases of viral, metabolic, autoimmune, or toxic origin. The specific associations with ALP levels may point to genes for bone or intestinal diseases.

Association Studies Reveal Six Loci Influencing Plasma Levels of Liver Enzymes

Abstract: Plasma liver-enzyme tests are widely used in the clinic for the diagnosis of liver diseases and for monitoring the response to drug treatment. There is considerable evidence that human genetic variation influences plasma levels of liver enzymes. However, such genetic variation has not been systematically assessed. In the present study, we performed a genome-wide association study of plasma liver-enzyme levels in three populations (total n ¼ 7715) with replication in three additional cohorts (total n ¼ 4704). We identified two loci influencing plasma levels of alanine-aminotransferase (ALT) (CPN1-ERLIN1-CHUK on chromosome 10 and PNPLA3-SAMM50 on chromosome 22), one locus influencing gamma-glutamyl transferase (GGT) levels (HNF1A on chromosome 12), and three loci for alkaline phosphatase (ALP) levels (ALPL on chromosome 1, GPLD1 on chromosome 6, and JMJD1C-REEP3 on chromosome 10). In addition, we confirmed the associations between the GGT1 locus and GGT levels and between the ABO locus and ALP levels. None of the ALP-associated SNPs were associated with other liver tests, suggesting intestine and/or bone specificity. The mechanisms underlying the associations may involve cis- or trans-transcriptional effects (some of the identified variants were associated with mRNA transcription in human liver or lymphoblastoid cells), dysfunction of the encoded proteins (caused by missense variations at the functional domains), or other unknown pathways. These findings may help in the interpretation of liver-enzyme tests and provide candidate genes for liver diseases of viral, metabolic, autoimmune, or toxic origin. The specific associations with ALP levels may point to genes for bone or intestinal diseases. Plasma liver-enzyme tests are widely used in the clinic to identify patients with liver diseases, to monitor the course and severity of these diseases and the effect of therapies, and to detect drug-induced liver injury. 1,2 These tests also have substantial epidemiologic significance that extends beyond the liver, given that they have been shown to be prospective risk factors for type 2 diabetes, cardiovascular disease, and all-cause mortality in multiple large studies. 3–6 Therefore, it is of interest to identify genes or loci affecting these markers in order to establish whether such loci are also associated with these clinical endpoints. Plasma liver-enzyme levels are influenced by environmental and genetic factors. The estimated heritabilities range from 33% for alanine-aminotransferase (ALT) to 61% for gamma-glutamyl transferase (GGT). 7,8 So far,

Microsatellite accumulation on the Y chromosome in Silene latifolia.

Abstract: The dioecious plant Silene latifolia possesses evolutionarily young sex chromosomes, and so serves as a model system to study the early stages of sex chromosome evolution. Sex chromosomes often differ distinctly from autosomes in both their structure and their patterns of evolution. The S. latifolia Y chromosome is particularly unique owing to its large size, which contrasts with the size of smaller, degenerate mammalian Y chromosomes. It is thought that the suppression of recombination on the S. latifolia Y chromosome could have resulted in the accumulation of repetitive sequences that ac- count for its large size. Here we used fluorescence in situ hybridization (FISH) to study the chromosomal distribution of various microsatellites in S. latifolia including all possible mono-, di-, and tri-nucleotides. Our results demonstrate that a majority of microsatellites are accumulated on the q arm of the Y chromosome, which stopped recombining relatively re- cently and has had less time to accumulate repetitive DNA sequences compared with the p arm. Based on these results we can speculate that microsatellites have accumulated in regions that predate the genome expansion, supporting the view that the accumulation of repetitive DNA sequences occurred prior to, not because of, the degeneration of genes.

Evidence of a four-hit mechanism involving SMARCB1 and NF2 in schwannomatosis-associated schwannomas.

Abstract: Schwannomatosis is characterized by the onset of multiple intracranial, spinal, or peripheral schwannomas, without involvement of the vestibular nerve, which is instead pathognomonic of neurofibromatosis type 2 (NF2). Recently, a schwannomatosis family with a germline mutation of the SMARCB1 gene on chromosome 22 has been described. We report on the molecular analysis of the SMARCB1 and NF2 genes in a series of 21 patients with schwannomatosis and in eight schwannomatosis-associated tumors from four different patients. A novel germline SMARCB1 mutation was found in one patient; inactivating somatic mutations of NF2, associated with loss of heterozygosity (LOH) of 22q, were found in two schwannomas of this patient. This is the second report of a germline SMARCB1 mutation in patients affected by schwannomatosis and the first report of SMARCB1 mutations associated with somatic NF2 mutations in schwannomatosis-associated tumors. The latter observation suggests that a four-hit mechanism involving the SMARCB1 and NF2 genes may be implicated in schwannomatosis-related tumorigenesis. Hum Mutat 29(2), 227–231, 2008. © 2007 Wiley-Liss, Inc.

Detailed analysis of 22q11.2 with a high density MLPA probe set.

Abstract: The presence of chromosome-specific low-copy repeats (LCRs) predisposes chromosome 22 to deletions and duplications. The current diagnostic procedure for detecting aberrations at 22q11.2 is chromosomal analysis coupled with fluorescence in situ hybridization (FISH) or PCR-based multiplex ligation dependent probe amplification (MLPA). However, there are copy number variations (CNVs) in 22q11.2 that are only detected by high-resolution platforms such as array comparative genomic hybridization (aCGH). We report on development of a high-definition MLPA (MLPA-HD) 22q11 kit that detects copy number changes at 37 loci on the long arm of chromosome 22. These include the 3-Mb region commonly deleted in DiGeorge/velocardiofacial syndrome (DGS/VCFS), the cat eye syndrome (CES) region, and more distal regions in 22q11 that have recently been shown to be deleted. We have used this MLPA-HD probe set to analyze 363 previously well-characterized samples with a variety of different rearrangements at 22q11 and demonstrate that it can detect copy number alterations with high sensitivity and specificity. In addition to detection of the common recurrent deletions associated with DGS/VCFS, variant and novel chromosome 22 aberrations have been detected. These include duplications within as well as deletions distal to this region. Further, the MLPA-HD detects deletion endpoint differences between patients with the common 3-Mb deletion. The MLPA-HD kit is proposed as a cost effective alternative to the currently available detection methods for individuals with features of the 22q11 aberrations. In patients with the relevant phenotypic characteristics, this MLPA-HD probe set could replace FISH for the clinical diagnosis of 22q11.2 deletions and duplications.

Chromatin Structure and Physical Mapping of Chromosome 6 of Potato and Comparative Analyses With Tomato

Abstract: Potato (Solanum tuberosum) has the densest genetic linkage map and one of the earliest established cytogenetic maps among all plant species. However, there has been limited effort to integrate these maps. Here, we report fluorescence in situ hybridization (FISH) mapping of 30 genetic marker-anchored bacterial artificial chromosome (BAC) clones on the pachytene chromosome 6 of potato. The FISH mapping results allowed us to define the genetic positions of the centromere and the pericentromeric heterochromatin and to relate chromatin structure to the distribution of recombination along the chromosome. A drastic reduction of recombination was associated with the pericentromeric heterochromatin that accounts for ∼28% of the physical length of the pachytene chromosome. The pachytene chromosomes 6 of potato and tomato (S. lycopersicum) share a similar morphology. However, distinct differences of heterochromatin distribution were observed between the two chromosomes. FISH mapping of several potato BACs on tomato pachytene chromosome 6 revealed an overall colinearity between the two chromosomes. A chromosome inversion was observed in the euchromatic region of the short arms. These results show that the potato and tomato genomes contain more chromosomal rearrangements than those reported previously on the basis of comparative genetic linkage mapping.

45S rDNA regions are chromosome fragile sites expressed as gaps in vitro on metaphase chromosomes of root-tip meristematic cells in Lolium spp.

Abstract: BackgroundIn humans, chromosome fragile sites are regions that are especially prone to forming non-staining gaps, constrictions or breaks in one or both of the chromatids on metaphase chromosomes either spontaneously or following partial inhibition of DNA synthesis and have been well identified. So far, no plant chromosome fragile sites similar to those in human chromosomes have been reported.Methods and ResultsDuring the course of cytological mapping of rDNA on ryegrass chromosomes, we found that the number of chromosomes plus chromosome fragments was often more than the expected 14 in most cells for Lolium perenne L. cv. Player by close cytological examination using a routine chromosome preparation procedure. Further fluorescent in situ hybridization (FISH) using 45S rDNA as a probe indicated that the root-tip cells having more than a 14-chromosome plus chromosome fragment count were a result of chromosome breakage or gap formation in vitro (referred to as chromosome lesions) at 45S rDNA sites, and 86% of the cells exhibited chromosome breaks or gaps and all occurred at the sites of 45S rDNA in Lolium perenne L. cv. Player, as well as in L. multiflorum Lam. cv. Top One. Chromatin depletion or decondensation occurred at various locations within the 45S rDNA regions, suggesting heterogeneity of lesions of 45S rDNA sites with respect to their position within the rDNA region.ConclusionsThe chromosome lesions observed in this study are very similar cytologically to that of fragile sites observed in human chromosomes, and thus we conclude that the high frequency of chromosome lesions in vitro in Lolium species is the result of the expression of 45S rDNA fragile sites. Possible causes for the spontaneous expression of fragile sites and their potential biological significance are discussed.

Defining Regions and Rearrangements of the Silene latifolia Y Chromosome

Abstract: We combine data from published marker genotyping of three sets of S. latifolia Y chromosome deletion mutants with changed sex phenotypes and add genotypes for several new genic markers to refine the deletion map of the Y chromosome and compare it with the X chromosome genetic map. We conclude that the Y chromosome of this species has been derived through multiple rearrangements of the ancestral gene arrangement and that none of the rearrangements so far detected was involved in stopping X–Y recombination. Different Y genotypes may also differ in their gene content and possibly arrangements, suggesting that mapping the Y-linked sex-determining genes will be difficult, even if many further genic markers are obtained. Even in determining the map of Y chromosome markers to discover all the rearrangements, physical mapping by FISH or other experiments will be essential. Future deletion mapping work should ensure that markers are studied in the parents of deletion mutants and should probably include additional deletions that were not ascertained by causing mutant sex phenotypes.

Copy number variation on the human Y chromosome

Abstract: The Y chromosome is unusual in being constitutively haploid and escaping recombination for most of its length This has led to a correspondingly unusual genomic landscape, rich in segmental duplications, which provide a potent environment for the generation of copy number variation (CNV) Interest in the chromosome comes from diverse fields, including infertility research, population genetics, forensics, and genealogy Together with inclusion in more systematic surveys, this has led to the ascertainment of a variety of CNVs Assessment in the context of the well-resolved Y phylogeny allows their mutational history to be deciphered and an estimation of mutation rate The functional consequences of variants are moderated by the specialization of the chromosome and the presence of functionally equivalent X-chromosomal homologues for some genes However, deletions of the AZFa, b, and c regions cause impaired spermatogenesis, while partial deletions and duplications within these regions, and deletions and duplications elsewhere, may be selectively neutral or have subtle phenotypes

Correspondence of tumor localization with tumor recurrence and cytogenetic progression in meningiomas.

Abstract: Objective Meningiomas are mostly benign tumors that originate from the coverings of the brain and spinal cord. Cytogenetically, they reveal a normal karyotype or, typically, monosomy of chromosome 22. Progression of meningiomas is associated with a non-random pattern of secondary losses of other autosomes. Deletion of the short arm of one chromosome 1 is a decisive step to anaplastic growth in meningiomas. Methods Statistical analyses were performed for the karyotypes of 661 meningiomas with respect to localization, progression, and recurrence of the tumor. A mathematical mixture model estimates typical pathogenetic routes in terms of the accumulation of somatic chromosome changes in tumor cells. The model generates a genetic progression score (GPS) that estimates the prognosis as related to the cytogenetic properties of a given tumor. Results In 53 patients, one or several recurrences were documented over the period of observation. This corresponds to a total rate of recurrence of 8.0% after macroscopically complete tumor extirpation. Higher GPS values were shown to be strongly correlated with tumor recurrence (P = 2.9 x 10(-7)). High-risk tumors, both in terms of histology and cytogenetics, are localized much more frequently at the brain surface than at the cranial base (P = 1.2 x 10(-5) for World Health Organization grade and P = 3.3 x 10(-12) for GPS categorization). Conclusion The tendency of cranial base meningiomas to recur seems to depend on surgical rather than biological reasons. As a quantitative measure, the GPS allows for a more precise assessment of the prognosis of meningiomas than the established categorical cytogenetic markers.

Diversification of a ZZ/ZW sex chromosome system in Characidium fish (Crenuchidae, Characiformes).

Abstract: Karyotype and other chromosomal markers of Characidium cf. gomesi were analyzed using conventional (Giemsa-staining, Ag-NOR and C-banding) and molecular (Fluorescent in situ hybridization (FISH) with 18S and 5S rDNA biotinylated probes) techniques. Both sexes had invariably diploid chromosome number 2n = 50 while karyotypes of males and females differed. That of male consisted of 32 metacentric + 18 submetacentric chromosomes and that of female consisted 31 metacentric + 18 submetacentric + 1 subtelocentric chromosomes. The Z chromosome was medium-sized metacentric, while W was highly heterochromatinized subtelocentric element. NORs as revealed by Ag-staining were situated at 2–7 telomeric regions while FISH with 18S probes showed consistently 10 signals at telomeric regions. FISH with 5S rDNA probe showed constantly signals at one metacentric pair. Distribution of centromeric heterochromatin was mostly in all chromosome pairs, besides some telomeric sites. The common origin of the sex chromosome system of ZZ/ZW type in the karyotypes of other representatives of the genus analyzed so far might be hypothesized based on biogeography and partial phylogeny of the group.

Integration of Cytogenetic and Genetic Linkage Maps Unveils the Physical Architecture of Tomato Chromosome 2

Abstract: We report the integration of the linkage map of tomato chromosome 2 with a high-density bacterial artificial chromosome fluorescence in situ hybridization (BAC–FISH)-based cytogenetic map. The euchromatic block of chromosome 2 resides between 13 and 142 cM and has a physical length of 48.12 μm, with 1 μm equivalent to 540 kb. BAC–FISH resolved a pair of loci that were 3.7–3.9 Mb apart and were not resolved on the linkage map. Most of the regions had crossover densities close to the mean of ∼200 kb/cM. Relatively hot and cold spots of recombination were unevenly distributed along the chromosome. The distribution of centimorgan/micrometer values was similar to the previously reported recombination nodule distribution along the pachytene chromosome. FISH-based physical maps will play an important role in advanced genomics research for tomato, including map-based cloning of agronomically important traits and whole-genome sequencing.

Deletion in chromosome region 22q11 in a child with CHARGE association.

Abstract: We present a female child with features of the CHARGE association, including iris coloboma, large ventricular septum defect (VSD), external ear abnormalities, severe growth retardation and moderate mental delay. A submicroscopic deletion in chromsome 22q11 was detected by means of fluorescence in situ hybridization (FISH) using probe DO832. The clinical features in this child compromise characteristics of both the velo-cardio-facial syndrome (VCFS) and the cat-eye syndrome. This may suggest the presence of a more complex rearrangement of 22q, with a deletion-duplication.

High rates of "unselected" aneuploidy and chromosome rearrangements in tel1 mec1 haploid yeast strains

Abstract: The yeast TEL1 and MEC1 genes (homologous to the mammalian ATM and ATR genes, respectively) serve partially redundant roles in the detection of DNA damage and in the regulation of telomere length. Haploid yeast tel1 mec1 strains were subcultured nonselectively for ∼200 cell divisions. The subcultured strains had very high rates of chromosome aberrations: duplications, deletions, and translocations. The breakpoints of the rearranged chromosomes were within retrotransposons (Ty or δ-repeats), and these chromosome aberrations nonrandomly involved chromosome III. In addition, we showed that strains with the hypomorphic mec1-21 allele often became disomic for chromosome VIII. This property of the mec1-21 strains is suppressed by a plasmid containing the DNA2 gene (located on chromosome VIII) that encodes an essential nuclease/helicase involved in DNA replication and DNA repair.

Mosaic 22q11.2 microdeletion syndrome: diagnosis and clinical manifestations of two cases

Abstract: Chromosome 22q11.2 microdeletion syndrome is due to microdeletion of 22q11.2 region of chromosome 22. It is a common microdeletion syndrome however mosaic cases are very rare and reported only few previous occasions. In this report we describe two unrelated male children with clinical features consistent with 22q11.2 microdeletion syndrome characterized by cardiac defect, facial dysmorphism and developmental deficiency. One of the cases also had trigonocephaly. Interphase & metaphase FISH with 22q11.2 probe demonstrated mosaicism for hemizygous deletion of 22q11.2 region. Mosaicism is also observed in buccal cells as well as urine cells. Parents were without any deletion. These two cases represent rare cases of mosaic 22q11.2 microdeletion syndrome.

The origin of a "zebra" chromosome in wheat suggests nonhomologous recombination as a novel mechanism for new chromosome evolution and step changes in chromosome number.

Abstract: An alloplasmic wheat line, TA5536, with the “zebra” chromosome z5A was isolated from an Elymus trachycaulus/Triticum aestivum backcross derivative. This chromosome was named “zebra” because of its striped genomic in situ hybridization pattern. Its origin was traced to nonhomologous chromosome 5A of wheat and 1Ht of Elymus; four chromatin segments were derived from chromosome 1Ht and five chromatin segments including the centromere from 5A. In this study, our objective was to determine the mechanism of origin of chromosome z5A, whether by nonhomologous recombination or by multiple translocation events. Different crossing schemes were used to recover recombinants containing various Elymus chromatin segments of the z5A chromosome. In addition, one z5AL telocentric chromosome and three z5AL isochromosomes were recovered. The dissection of the Elymus segments into different stocks allowed us to determine the chromosomal origin of the different chromosome fragments on the basis of the order of the RFLP markers employed and suggested that the zebra chromosome originated from nonhomologous recombination. We present a model of possible mechanism(s) of chromosome evolution and step changes in chromosome number applicable to a wide range of organisms.

A familial interstitial deletion of the long arm of chromosome 21.

Abstract: A mother and daughter with an interstitial deletion of the chromosome segment 21q11 to 21q21.3 have similar minor dysmorphism and mild mental retardation. These two patients are compared to others in the literature with deletion of the same region of chromosome 21. Molecular analysis of DNA from our patients localizes the DNA segments D21S1, D21S11, D21S8, and D21S22 within the deleted region.

Trisomy of the short arm of chromosome 8: Association with translocation between chromosomes 8 and 22 46,XY,22−,t(8p22q)+

Abstract: The case of a retarded child with trisomy of the short arm of chromosome 8 associated with translocation between the short arm of chromosome 8 and the long arm of chromosome 22 is reported. Balanced translocation involving the same chromosomes was present in the mother and brother of the propositus. The specific chromosomes involved in the abnormality in this family were identified by use of fluorescence microscopy with quinacrine mustard staining, autoradiography and Giemsa banding. This appears to be the first case report of this anomaly, although trisomy of the short arm of chromosome 9 has been reported previously.

Thymus deficiency in an infant with a chromosome t(18;22)(q12.2;p11.2)pat rearrangement.

Abstract: The finding of an unbalanced t(18;22)pat chromosome rearrangement in a boy with multiple anomalies including apparent absence of the thymus is described. The observation is of interest because of the reported association of chromosome 22 rearrangements with the DiGeorge sequence. In contrast to previous reports of this association, the deletion involving chromosome 22 is confined to the short arm.

Ring chromosome 22 and neurofibromatosis.

Abstract: Variable constitutional mosaicism, mos45,XY,-22/46,XY,-22,+mar/46,XY,-22,+r(22)/47,XY,-22,+r(22)+mar/ 47, XY,-22,+r(22)*2, was found in PHA-stimulated peripheral blood, in a lymphoblastoid cell line and in cultured skin fibroblasts from a mentally retarded patient with neurofibromatosis. Both the ring chromosome and the small extra marker chromosome stained positively by in situ hybridization with a chromosome 14/22-specific alphoid repeat probe. DNA dosage analysis showed constitutional loss of one copy of the arylsulfatase A gene (ARSA), consistent with its terminal location on 22q. There was no evidence of constitutional loss of D22S1 or D22S28 which flank the neurofibromatosis type 2 (NF2) locus. Analysis of two DNA samples from a skin neurofibroma indicated retainment of two copies of D22S1, whereas the results were ambiguous with respect to tumor-specific loss of one copy of D22S28. It is suggested that the development of neurofibromatosis of unclear type in two r(22) carriers might be associated with somatic mutation of the NF2 locus due to instability of the ring chromosome(s), and in analogy, that somatic mutation of either NF1 or NF2 may account for some cases of neurofibromatosis which do not meet the criteria of either NF1 or NF2. The occurrence of seminoma in the proband may be fortuitous, but could also be due to the presence of a seminoma-associated locus on chromosome 22.

A 7 Mb duplication at 22q13 in a girl with bipolar disorder and hippocampal malformation.

Abstract: We identified a duplication of 22q13.1-q13.2 in a 10-year-old girl and demonstrated that this duplication was the recombinant product of a maternal intrachromosomal insertion. Phenotypic characteristics included prominent forehead, small low-set ears, hypertelorism, epicanthal folds, small palpebral fissures, short philtrum, and syndactyly. MRI of the brain revealed high signal abnormalities in the periventricular white matter, a hypoplastic corpus callosum, under-rotated hippocampus on the left and atrophic hippocampus on the right. Since age 5, the child's behavior has shown cyclic maniacal episodes with severely disorganized mood and behavior. Psychiatric and cognitive assessment led to a diagnosis of bipolar disorder not otherwise specified, manic episodes, attention deficit hyperactivity disorder and moderate mental retardation. Array-CGH revealed an interstitial duplication of 6.9 Mb at chromosome 22q: dup(22)(q13.1q13.2). FISH using BAC clones confirmed the array-CGH results and demonstrated that the duplication was inverted. G-banding analysis in the proposita's mother revealed a banding pattern suggestive of an intrachromosomal insertion, as demonstrated by dual-color FISH with BACs that were duplicated in the proposita and multicolor-banding (MCB) based on microdissection derived region-specific libraries for chromosome 22. Our findings suggest that in both seemingly de novo deletions and duplications, the parent transmitting the imbalance should be investigated for possible balanced rearrangements. This report reinforces previous evidence that chromosome imbalances, and thus gene dosage effects, may be at the basis of some psychiatric disorders. Stringent correlations between submicroscopic imbalances, specific behavioral phenotypes and brain imaging will possibly help in dissecting complex behavioral traits. © 2008 Wiley-Liss, Inc.

Linkage of transcobalamin II (TC2) to the P blood group system and assignment to chromosome 22.

Abstract: The linkage relationships of transcobalamin II (TC2) against 64 other marker systems are studied in a Danish family material (families 604-1505). A strong indication of linkage between TC2 and the blood group system P was discovered (z = 7.91 at theta = 0.14 for males and theta = 0.20 for females combined). Accordingly, TC2 could be assigned to chromosome 22 (since blood group P has earlier been assigned to this chromosome).

An extra small metacentric chromosome identified as a deleted chromosome no. 17.

Abstract: In an 11-year-old girl with multiple congenital abnormalities and mental retardation, an extra, small, metacentric chromosome was identified by banding methods as a deleted chromosome No. 17. This represents the first reported case of partial trisomy 17.

46,XY, t(3;22)(p2;q13) resuIting in partial trisomy for the short arm of chromosome 3

Abstract: A familial translocation involving the short arm of chromosome 3 and the long, arm of chromosome 22 is reported, along with an infant with multiple congenital anomalies, which are probably the result of partial trisomy for the short arm of chromosome 3.

High definition cytogenetics and oligonucleotide aCGH analyses of cisplatin‐resistant ovarian cancer cells

Abstract: Array comparative genomic hybridization (aCGH) is a key platform to assess cancer genomic profiles. Many structural genomic aberrations cannot be detected by aCGH alone. We have applied molecular cytogenetic analyses including spectral karyotyping, multicolor banding, and fluorescence in situ hybridization with aCGH to comprehensively investigate the genomic aberrations associated with cisplatin resistance in A2780 ovarian cancer cells. A2780 is a well-established model of chemotherapeutic resistance with distinct karyotypic abnormalities in the parental and cisplatin-resistant cells. Cytogenetic analysis revealed that two unbalanced translocations, der(8)t(1;8) and der(X)t(X;1), and loss of chromosome 13 were present only in the resistant line. Our aCGH analyses detected imbalances affecting an additional 10.59% of the genome in the cisplatin-resistant cells compared with the parental. DNA copy number changes included deletions at 1p10-p22.1, 8p23.3, and Xq13.1-pter, and a duplication of 8q11.22-q23. Cryptic genomic aberrations associated with concurrent localized changes of specific gene expression included a homozygous deletion of 0.38 Mb at 1p21.3 adjacent to SNX7, and an insertional transposition of 0.85 Mb from 13q12.12 into chromosome 22. This latter rearrangement led to an overexpression of four contiguous genes that flanked one of the breakpoint regions in chromosome 13. Furthermore, 17 genes showed differential expression correlating with genomic gain or loss between the resistant and parent lines, validated by a second expression array platform. These results highlight the integration of comprehensive profiling to determine relationships of genomic aberrations and genes associated with an in vitro drug resistance model in ovarian cancer. This article contains Supplementary Material available at http://www.interscience.wiley.com/jpages/1045-2257/suppmat.