Rare chromosome abnormalities, prevalence and prenatal diagnosis rates from population-based congenital anomaly registers in Europe.

The aim of this study is to quantify the prevalence and types of rare chromosome abnormalities (RCAs) in Europe for 2000-2006 inclusive, and to describe prenatal diagnosis rates and pregnancy outcome. Data held by the European Surveillance of Congenital Anomalies database were analysed on all the cases from 16 population-based registries in 11 European countries diagnosed prenatally or before 1 year of age, and delivered between 2000 and 2006. Cases were all unbalanced chromosome abnormalities and included live births, fetal deaths from 20 weeks gestation and terminations of pregnancy for fetal anomaly. There were 10,323 cases with a chromosome abnormality, giving a total birth prevalence rate of 43.8/10,000 births. Of these, 7335 cases had trisomy 21,18 or 13, giving individual prevalence rates of 23.0, 5.9 and 2.3/10,000 births, respectively (53, 13 and 5% of all reported chromosome errors, respectively). In all, 473 cases (5%) had a sex chromosome trisomy, and 778 (8%) had 45,X, giving prevalence rates of 2.0 and 3.3/10,000 births, respectively. There were 1,737 RCA cases (17%), giving a prevalence of 7.4/10,000 births. These included triploidy, other trisomies, marker chromosomes, unbalanced translocations, deletions and duplications. There was a wide variation between the registers in both the overall prenatal diagnosis rate of RCA, an average of 65% (range 5-92%) and the prevalence of RCA (range 2.4-12.9/10,000 births). In all, 49% were liveborn. The data provide the prevalence of families currently requiring specialised genetic counselling services in the perinatal period for these conditions and, for some, long-term care.

Sex chromosome translocation and speciation : a Drosophila genetic model

Although exceptions may be readily identified, two generalizations concerning genetic differences among species may be drawn from the available allozyme and chromosome data. First, structural gene differences among species vary widely. In many cases, species pairs do not differ more than intraspecific populations. This suggests that either very few or no gene substitutions are required to produce barriers to reproduction (Avise 1976). Second, chromosome form and/or number differs among even closely related species (White 1963; 1978; Fredga 1977; Wright 1970). Many of the observed chromosomal differences involve translocational rearrangements; these produce severe fitness depression in heterozygotes and were, thus, long considered unlikely candidates for the fixation required of genetic changes leading to speciation (Wright 1977). Nonetheless, the fact that species differences are frequently translocational argues convincingly for their fixation despite prejudices to the contrary. Haldane's rule states that in the F of interspecific crosses, the heterogametic sex is absent or sterile in the preponderance of cases (Haldane 1932). This rule definitely applies in the genus Dr°sophila (Ehrman 1962). Sex chromosome translocations do not impose a fitness depression as severe as that imposed by autosomal translocations, and X-Y translocations may account for Haldane's rule (Haldane 1932). Consequently a study of the fit ness parameters of an X·yL and a yS chromosome in Drosophila melanogaster populations was initiated by Tracey (1972). Preliminary results suggested that x.yL//YSmales enjoyed a mating advantage with X·yL//X·yL females, that this advantage was frequency dependent, that the translocation produced sexual isolation and that interactions between the yL, yS and a yellow marker contributed to the observed isolation (Tracey and Espinet 1976; Espinet and Tracey 1976). Encouraged by the results of these prelimimary studies, further experiments were performed to clarify the genetic nature of the observed sexual isolation, S the reality of the y frequency dependent fitness .and the behavioural changes, if any, produced by the translocation. The results of this work are reported herein. Although the marker genes used in earlier studies, sparkling poliert an d yellow have both been found to affect activity,but only yellow effects asymmetric sexual isolation. In addition yellow effects isolation through an interaction with the T(X-y) chromosomes, yS also effects isolation, and translocational strains are isolated from those of normal karyotype in the absence of marker gene differences. When yS chromosomes are in competition with y chromosomes on an X.yL background, yS males are at a distinct advantage only when their frequency is less than 97%. The sex chromosome translocation alters the normal courtship pattern by the incorporation of circling between vibration and licking in the male repertoire. Finally a model of speciation base on the fixation of this sex chromosome translocation in a geographically isolated gene pool is proposed.

GAD2 on chromosome 10p12 is a candidate gene for human obesity

The gene GAD2 encoding the glutamic acid decarboxylase enzyme (GAD65) is a positional candidate gene for obesity on Chromosome 10p11–12, a susceptibility locus for morbid obesity in four independent ethnic populations. GAD65 catalyzes the formation of γ-aminobutyric acid (GABA), which interacts with neuropeptide Y in the paraventricular nucleus to contribute to stimulate food intake. A case-control study (575 morbidly obese and 646 control subjects) analyzing GAD2 variants identified both a protective haplotype, including the most frequent alleles of single nucleotide polymorphisms (SNPs) +61450 C>A and +83897 T>A (OR = 0.81, 95% CI [0.681–0.972], p = 0.0049) and an at-risk SNP (−243 A>G) for morbid obesity (OR = 1.3, 95% CI [1.053–1.585], p = 0.014). Furthermore, familial-based analyses confirmed the association with the obesity of SNP +61450 C>A and +83897 T>A haplotype (χ2 = 7.637, p = 0.02). In the murine insulinoma cell line βTC3, the G at-risk allele of SNP −243 A>G increased six times GAD2 promoter activity (p < 0.0001) and induced a 6-fold higher affinity for nuclear extracts. The −243 A>G SNP was associated with higher hunger scores (p = 0.007) and disinhibition scores (p = 0.028), as assessed by the Stunkard Three-Factor Eating Questionnaire. As GAD2 is highly expressed in pancreatic β cells, we analyzed GAD65 antibody level as a marker of β-cell activity and of insulin secretion. In the control group, −243 A>G, +61450 C>A, and +83897 T>A SNPs were associated with lower GAD65 autoantibody levels (p values of 0.003, 0.047, and 0.006, respectively). SNP +83897 T>A was associated with lower fasting insulin and insulin secretion, as assessed by the HOMA-B% homeostasis model of β-cell function (p = 0.009 and 0.01, respectively). These data support the hypothesis of the orexigenic effect of GABA in humans and of a contribution of genes involved in GABA metabolism in the modulation of food intake and in the development of morbid obesity.

Development of Y-chromosome-Specific SCAR Markers Conserved in Taurine, Zebu and Bubaline Cattle

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

X-chromosome genetic variation in São Paulo State (Brazil) population

As data on X-chromosomal short tandem repeats (X-STRs) for the Brazilian population are scarse, the aim of this study was to determine the allele frequencies of five X-STRs (DXS6854, DXS7424, DXS101, DXS6808 and DXS7132) in the São Paulo State, Brazil. No deviations from the Hardy-Weinberg equilibrium were observed, with the exception of DXS101. The forensic efficiency parameters demonstrated that DXS101 was the most informative marker. Population comparisons revealed that the X-STR profile sampled in the state of São Paulo was more similar to European and African populations than Asiatic populations reported in this work.

DNA gains at 8q23.2: a potential early marker in head and neck carcinomas

Gains or amplifications involving chromosome arm 8q are one of the most recurrent chromosomal alterations in head and neck tumors. To characterize previously reported gains, we performed fluorescence in situ hybridization (FISH) using the sequences BAC RP1179E1 and 8-centromere PMJ 128 as probes. Gains and/or amplifications were detected in all 19 cases evaluated by FISH. The FISH analysis, but not G-banding, revealed homogeneously staining region in three cases. We conclude that gains of one or more genes on chromosome arm 8q may be important for the early stages of head and neck carcinomas. (C) 2003 Elsevier B.V. All rights reserved.

Genomic organization and comparative chromosome mapping of the U1 snRNA gene in cichlid fish, with an emphasis in Oreochromis niloticus

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

LHX6 is a sensitive methylation marker in head and neck carcinomas

Head and neck cancer remains a morbid and often fatal disease and at the present time few effective molecular markers have been identified. The purpose of the present work was to identify new molecular markers for head and neck squamous cell carcinoma (HNSCC). We applied methylation-sensitive arbitrarily primed PCR (MS/APPCR) to isolate sequences differentially methylated in HNSCC. The most frequently hypermethylated fragment we found maps close to a cytosine guanine dinucleotide (CpG) island on chromosome 9q33.2, and hypermethylation of this CpG island was associated with transcriptional silencing of an alternative transcript of the LHX6 gene. Using combined bisulfite restriction analysis (COBRA), hypermethylation of this fragment was detected in 13 of 14 (92.8%) HNSCC cell lines studied and 21 of 32 (65.6%) primary tumors, whereas little or no methylation was seen in 10 normal oral mucosa samples. We extended this investigation to other cancer cell lines and methylation was found in those derived from colon, breast, leukemia and lung, and methylation was also found in 12/14 primary colon tumors. These findings suggest that differentially methylated (DIME)-6 hypermethylation is a good cancer marker in HNSCC as well as in other kinds of neoplasias and confirm the importance of searching for markers of epigenetic dysregulation in cancer.

Preliminary radiation hybrid map for river buffalo chromosome 6 and comparison to bovine chromosome 3

We present the first radiation hybrid (RH) map of river buffalo (Bubalus bubalis) chromosome 6 (BBU6) developed with a recently constructed river buffalo whole-genome RH panel (BBURH5000). The preliminary map contains 33 cattle-derived markers, including 12 microsatellites, 19 coding genes and two ESTs, distributed across two linkage groups. Retention frequencies for markers ranged from 14.4% to 40.0%. Most of the marker orders within the linkage groups on BBU6 were consistent with the cattle genome sequence and RH maps. This preliminary RH map is the starting point for comparing gene order between river buffalo and cattle, presenting an opportunity for the examination of micro-rearrangements of these chromosomes. Also, resources for positional candidate cloning in river buffalo are enhanced.

Numerical chromosome polymorphism in Mikania cordifolia Willd. (Asteraceae)

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Myelodysplastic syndrome in childhood: report of two cases with deletion of chromosome 4 and the Philadelphia chromosome

We report two pediatric patients with unclassified myelodysplastic syndrome (MDS) by the French-American-British (FAB) group. Both cases had clinical and hematological peculiarities, which had not been described yet. The cytogenetic alterations were 4q deletion and the Philadelphia (Ph) chromosome which appeared at different moments of the disease. One patient showed the Ph chromosome at disease transformation and the other at diagnosis. The different breakpoints at 4q and the presence of Ph could be a marker of this form of MDS. The association of clinical and hematological findings suggests the possibility of a new group of pediatric MDS. (C) 2002 Elsevier B.V. Ltd. All rights reserved.

A new locus for autosomal dominant amelogenesis imperfecta on chromosome 8q24.3

Amelogenesis imperfecta (AI) is a collective term used to describe phenotypically diverse forms of defective tooth enamel development. AI has been reported to exhibit a variety of inheritance patterns, and several loci have been identified that are associated with AI. We have performed a genome-wide scan in a large Brazilian family segregating an autosomal dominant form of AI and mapped a novel locus to 8q24.3. A maximum multipoint LOD score of 7.5 was obtained at marker D8S2334 (146,101,309 bp). The disease locus lies in a 1.9 cM (2.1 Mb) region according to the Rutgers Combined Linkage-Physical map, between a VNTR marker (at 143,988,705 bp) and the telomere (146,274,826 bp). Ten candidate genes were identified based on gene ontology and microarray-facilitated gene selection using the expression of murine orthologues in dental tissue, and examined for the presence of a mutation. However, no causative mutation was identified.

Use of primers derived from a new sequence of the bovine Y chromosome for sexing Bos taurus and Bos indicus embryos

A bovine male-specific marker was identified in our laboratory through random amplified polymorphic DNA (RAPD) analysis. This fragment of 3216 bp was cloned, sequenced and mapped by fluorescent in situ hybridization (FISH) on the taurine Yq. Primers derived from this sequence were initially screened by polymerase chain reaction (PCR) for their ability to detect Y-specific segments in zebu and taurine genomic DNA. Two of these primers amplified a 655 bp Y-specific sequence present in taurine and zebu male genomic DNA. These primers were then used for detecting the 655 bp male sequence in DNA from 173 zebu and 30 taurine embryos, which had been previously sexed using primers for the sequence BC 1.2. The results revealed an accuracy of 100%. (C) 2002 Elsevier B.V. All rights reserved.

A radiation hybrid map of bovine X Chromosome (BTAX)

We present a comprehensive radiation hybrid map of the bovine X chromosome (Chr) containing 20 new markers, including both microsatellites and expressed genes. This study was conducted with a 5000-rad whole genome RH cell panel consisting of 90 hybrid cell lines. Retention frequencies of individual markers range from 7.8% for XIST to 31.1% for TGLA325. Statistical analysis with RHMAPPER placed all the loci into five linkage groups under a LOD score criterion of 6.0. These groups could be oriented relative to each other because they included multiple microsatellite loci from the consensus linkage map of the X Chr. Markers included in both this RH map and the bovine cytogenetic map were in a consistent order. The comparative bovine-human map thus generated consists of five blocks of genes, the order of which is conserved, although in the opposite direction when presented as ideograms with p and q arms. Inversions of three blocks account for the difference in gene order across the entirety of the two X Chrs.

Chromosome localization of the ribosomal genes 18S and 5S in four stocks of rainbow trout (Oncorhynchus mykiss) from cultivated and naturalized stocks in Brazil

In the present study, fluorescence in situ hybridization (FISH) was employed to determine the chromosomal location of genes 18S rDNA and 5S rDNA in four rainbow trout stocks. In specimens from the stocks of Núcleo Experimental de Salmonicultura de Campos do Jordão and Gavião river, 18S genes were located at a subterminal position in the long arms of two submetacentric chromosomes, whereas in specimens from stocks of Mount Shasta and Teresópolis they were found in the short arms. In all analyzed stocks, 5S genes were located in two chromosome pairs. In a subtelocentric pair, 5S genes were present in the short arms and, in the other submetacentric pair, 5S genes were at an interstitial position. In the latter, 18S and 5S genes were contiguous. Taking into account that both 18S and 5S rDNA genes have been localized in the short arm of a submetacentric chromosome in almost all rainbow trout samples so far studied, the presence of such genes in the long arm, as seen in the samples from Núcleo Experimental de Salmonicultura de Campos do Jordão and Gavião river, supports the hypothesis of a pericentric inversion involving this chromosome segment in the ancestor line of these stocks. The observed polymorphism allowed the identification of a very useful genomic marker, and may therefore constitute an important tool in the genetic management of rainbow trout stocks.