Report and abstracts of the First International Workshop on Chromosome 9. Held at Girton College Cambridge, UK, 22-24 March, 1992

On the origin of crossover interference: A chromosome oscillatory movement (COM) model

BACKGROUND

It is now nearly a century since it was first discovered that crossovers between homologous parental chromosomes, originating at the Prophase stage of Meiosis I, are not randomly placed. In fact, the number and distribution of crossovers are strictly regulated with crossovers/chiasmata formed in optimal positions along the length of individual chromosomes, facilitating regular chromosome segregation at the first meiotic division. In spite of much research addressing this question, the underlying mechanism(s) for the phenomenon called crossover/chiasma interference is/are still unknown; and this constitutes an outstanding biological enigma.

RESULTS

The Chromosome Oscillatory Movement (COM) model for crossover/chiasma interference implies that, during Prophase of Meiosis I, oscillatory movements of the telomeres (attached to the nuclear membrane) and the kinetochores (within the centromeres) create waves along the length of chromosome pairs (bivalents) so that crossing-over and chiasma formation is facilitated by the proximity of parental homologs induced at the nodal regions of the waves thus created. This model adequately explains the salient features of crossover/chiasma interference, where (1) there is normally at least one crossover/chiasma per bivalent, (2) the number is correlated to bivalent length, (3) the positions are dependent on the number per bivalent, (4) interference distances are on average longer over the centromere than along chromosome arms, and (5) there are significant changes in carriers of structural chromosome rearrangements.

CONCLUSIONS

The crossover/chiasma frequency distribution in humans and mice with normal karyotypes as well as in carriers of structural chromosome rearrangements are those expected on the COM model. Further studies are underway to analyze mechanical/mathematical aspects of this model for the origin of crossover/chiasma interference, using string replicas of the homologous chromosomes at the Prophase stage of Meiosis I. The parameters to vary in this type of experiment will include: (1) the mitotic karyotype, i.e. ranked length and centromere index of the chromosomes involved, (2) the specific bivalent/multivalent length and flexibility, dependent on the way this structure is positioned within the nucleus and the size of the respective meiocyte nuclei, (3) the frequency characteristics of the oscillatory movements at respectively the telomeres and the kinetochores.

Characterization of human crossover interference

We present an analysis of crossover interference over the entire human genome, on the basis of genotype data from more than 8,000 polymorphisms in eight CEPH families. Overwhelming evidence was found for strong positive crossover interference, with average strength lying between the levels of interference implied by the Kosambi and Carter-Falconer map functions. Five mathematical models of interference were evaluated: the gamma model and four versions of the count-location model. The gamma model fit the data far better than did any of the other four models. Analysis of intercrossover distances was greatly superior to the analysis of crossover counts, in both demonstrating interference and distinguishing between the five models. In contrast to earlier suggestions, interference was found to continue uninterrupted across the centromeres. No convincing differences in the levels of interference were found between the sexes or among chromosomes; however, we did detect possible individual variation in interference among the eight mothers. Finally, we present an equation that provides the probability of the occurrence of a double crossover between two nonrecombinant, informative polymorphisms.

Four tumor suppressor loci on chromosome 9q in bladder cancer: evidence for two novel candidate regions at 9q22.3 and 9q31

The most common genetic alteration identified in transitional cell carcinoma (TCC) of the bladder is loss of heterozygosity (LOH) on chromosome 9. However, localization of tumor suppressor genes on 9q has been hampered by the low frequency of subchromosomal deletions. We have analysed 139 primary, initial low stage TCC of the bladder using a panel of 28 microsatellite markers spanning chromosome 9 at an average distance of 5 Mb, following a primer-extension preamplification (PEP) technique. Sixty-seven (48%) tumors showed LOH at one or more loci and partial deletions were detected in 62 (45%) tumors; apparent monosomy 9 was detected in only five (4%) tumors. Deletions were more frequent on 9q (44%) than on 9p (23%), the latter being mostly associated with 9q deletion, suggesting that alteration of genes on 9q may be an early event associated with superficial papillary tumors. Combined data from the cases with partial 9q deletions displayed four candidate regions for tumor suppressor loci, based on the frequency of deletion observed and tumors with unique deletions at these sites. In two tumors, the unique partial deletion comprised D9S12 at 9q22.3, a region encompassing loci for the Gorlin syndrome and multiple self-healing squamous epithelioma gene. In two other tumors, the single LOH was identified at the D9S172 locus at 9q31-32 where the dysautonia and Fukuyama-type congenital muscular dystrophy genes have been located. One tumor showed unique LOH at the GSN locus at 9q33, a region frequently deleted in other sporadic tumors while the fourth region of deletion was observed at 9q34 between ASS and ABL-1, in two tumors. This region is frequently deleted in tumors and encompasses the locus for the hereditary hemorrhagic telangiectasia gene. These findings suggest four target regions on 9q within which suppressor genes for TCC may reside.

An integrated map of chromosome 9

An integrated map of 211 loci on chromosome 9 is presented for which 198 loci have genetic locations. The results of the analysis indicate very strong interference for the chromosome and positional variations in recombination rates, most extreme in the male map where there is an excess of recombination near the p telomere and a marked suppression of recombination in a large region that includes the centromere.

La citogenetica e la genetica molecolare nella prognosi del carcinoma della vescica: Cytogenetics and molecular genetics in bladder carcinoma prognosis

The use of cytogenetics in the characterization of bladder tumours has made it possible to demonstrate that chromosomal alterations are correlated with stage and grade of the tumour and have a predictive value as regards both tumour recurrences and progression. In the last decade the chromosomes involved in the main aberrations have been identified, and a negative prognostic significance has been suggested for some chromosomal aberrations. The knowledge of cytogenetics has been deepened by the sophisticated methods of molecular genetics, that have discovered many oncogenes and suppressor genes probably involved in the development of bladder tumours. The most characteristic molecular alterations of these tumours are losses of genetic information on chromosomes 9, 11 and 17, as a consequence of deletions and/or mutations. Such alterations probably cause the loss and/or the inactivation of suppressor genes (partly hypothetic still) and could represent important predictive factors of tumour progression.

Genetic basis of susceptibility to melanoma

The search for candidate genes involved in the genesis of common cancers has traditionally been hampered by ambiguities in the process of determining by reliable, clinical criteria which persons harbor the genetic lesion that confers malignant susceptibility. In the case of cutaneous melanoma, the existence of genetic susceptibility has long been evident from its tendency to cluster in families, but it has been unclear until recently whether the genetic basis of familial melanoma derives from the concerted interaction of multiple genes or from a major locus with properties of a tumor suppressor gene. The original strategy used to circumvent difficulties in identifying those who harbor the genetic defect exploited a proposed melanoma precursor lesion, the dysplastic nevus, as the phenotypic marker from which the presence of the melanoma-associated genotype was inferred. That strategy in genetic linkage studies provided the first indication of a major gene for melanoma and assigned the locus to the short arm of chromosome 1. In part because the criteria for the dysplastic nevus have been neither well-defined nor generally agreed upon, multiple independent attempts to confirm the assignment of a gene to that location have failed. The probable map position of a major gene became clear when the most frequently deleted region of the human genome in melanoma tumors was localized to chromosome 9p. The significance of this assignment was established when genetic linkage studies of multiple melanoma kindreds subsequently evaluated the correlated inheritance between melanoma gene carriers, as assigned by a history of melanoma, and molecular markers for DNA polymorphisms near the 9p candidate region; this analysis provided strong statistical evidence of linkage to a melanoma susceptibility locus. Once this candidate tumor suppressor gene) as well as other relevant suppressor loci that may exist is actually cloned and characterized, rapid advances can be expected in our understanding of the pathophysiologic basis for development of melanoma. This will provide opportunities for exploring the mechanisms underlying defects in the gene and the molecular consequences of its loss of function. It will then be possible to identify precisely those persons with a genetic risk for melanoma; as a result, surveillance efforts can be more appropriately focused than has heretofore been possible.

Fine mapping of the locus for nevoid basal cell carcinoma syndrome on chromosome 9q

The nevoid basal cell carcinoma syndrome is an autosomal dominant disorder characterized primarily by multiple basal cell carcinomas, odontogenic keratocysts, and pits of the palms and soles. Tumor deletion studies and linkage analysis in Caucasians have revealed that the gene is on chromosome 9q. To further refine the location of the nevoid basal cell carcinoma syndrome locus, we tested linkage to this region in three families. Evaluation of recombinants suggested that the nevoid basal cell carcinoma syndrome locus lies in the interval defined distally by D9S127. Our data, together with existing published data defining D9S12 as a proximal flanking marker, refine the location of nevoid basal cell carcinoma syndrome to an 8.3-cM interval. Two of the families studied were African-American and show a notable variation in phenotypic expression in which affected individuals developed few skin cancers. However, despite clinical heterogeneity, our data are consistent with the hypothesis that the same locus is involved in these African-American families.

Mapping studies of the distal imprinting region of mouse chromosome 2

The known limits of the distal imprinting region of mouse Chromosome (Chr) 2 are defined by the breakpoints of the translocations T(2;8)2Wa, (T2Wa), and T(2;16)28H, (T28H), in distal H3, and proximal H4 respectively. We have shown that T2Wa and T(2;4)1Go, (T1Go), which has a breakpoint in central H3 map close to a, non-agouti. Ada, adenosine deaminase, lies very near the proximal boundary and Ra, ragged, maps very close to the distal boundary, and is less than 0.2 cM from wasted, wst. From the current data Ada can be taken as the proximal, and Ra as the distal gene marker of the imprinting region on the linkage map. From consensus maps twenty three other markers, including fourteen genes, lie between Ada and Ra, some of which may be useful in investigations of imprinting. Of the markers included in the study reported here, four, Ada, ls, lethal spotting, Ra and wst lie or probably lie within the region but none display any evidence of imprinting. We suggest that recombination frequency is elevated in distal Chr 2, because in none of the crosses could the most closely linked marker be ordered in relation to the translocation breakpoint due to the high frequency of double crossovers.

Genomic cloning and localization by FISH and linkage analysis of the human gene encoding the primary subunit NMDAR1 (GRIN1) of the NMDA receptor channel

A cDNA clone of the NMDAR1 (isoform E) has been used to screen both lambda and cosmid genomic libraries. A genomic phage clone was identified and sequenced and was found to contain some of the 3' coding regions of the GRIN1 gene. This clone was used to localize the gene using fluorescent in situ hybridization (FISH) to normal chromosomes, and also to a lymphoblastoid cell line containing a translocation involving chromosomes 9 and 15. FISH localized the gene to chromosome 9q34.3. The clone was used to screen a panel of genomic DNAs cut with 20 restriction enzymes. A VNTR sequence 5' to the gene, which was polymorphic for a number of restriction enzymes, was detected. A PvuII fragment of the genomic clone was found to detect the VNTR on Southern hybridization. The polymorphic VNTR marker was mapped against chromosome 9q34 markers using linkage analysis in the CEPH families. The GRIN1 gene was linked to D9S7 with a maximum lod score of 20.09 at zero recombination fraction in males and 0.03% recombination in females.

Molecular and cytogenetic analysis of chromosome 9 deletions in 75 malignant gliomas

A deletion mapping analysis of chromosome 9 has been performed on a series of 75 samples derived from malignant gliomas. A total of 27 tumors displayed different deletions for the loci studied (D9S1, NRASLI, D9S18, IFNA, and IFNBI). In most instances, losses involving the markers located on the short arm of chromosome 9 were observed, and only two samples were characterized by losses of the short and long arms. Either partial or complete homozygous deletions of IFN genes were observed in 15 cases, and 12 other samples showed hemizygous deletions for these genes. The results show that the 9p abnormalities are not exclusive to high-grade astrocytic tumors, as some low-grade samples (two astrocytoma grade II and six oligodendrogliomas) displayed this anomaly which, in a few instances, was the sole abnormality detected.

Linkage mapping of the Aldo-2, Pax-5, Ambp, and D4h9S3E loci on mouse chromosome 4 in the region of homology with human chromosome 9

The genes for aldolase-B (ALDOB), the alpha 1-microglobulin/bikunin precursor (AMBP), the paired box gene PAX5, and the anonymous DNA marker D9S3 map to human chromosome 9 (HSA9). We have set out to map the mouse homologues of each of these genes. The mouse genes for Pax-5 and Ambp previously have been shown to map to MMU4. We have used an interspecific backcross to confirm these localizations and to map the mouse homologues of ALDOB (Aldo-2) and D9S3 (D4H9S3E) to the same chromosome. These genes were mapped with respect to the four anchor loci for MMU4. In addition, the panel of backcross DNAs had previously been typed for delta-amino levulinate dehydratase (Lv), orosomucoid-1 (Orm-1), and hexabrachion (Hxb), the human homologues of which map to HSA9q. The recombination distances +/- the standard error between each pair of loci are D4Nds4-1.6 +/- 1.1-D4H9S3E-4.0 +/- 1.7-Galt-0.8 +/- 0.8-Pax-5-4.8 +/- 1.9-Aldo-2-6.3 +/- 2.2-(Lv, Orm-1, Ambp)-1.6 +/- 1.1-Hxb-4.0 +/- 1.7-Tyrp-1-4.8 +/- 1.9-Ifa. The data from this study have extended the known region of conserved synteny between human chromosome 9 and mouse chromosome 4.

Translocation of BCR to chromosome 9: a new cytogenetic variant detected by FISH in two Ph-negative, BCR-positive patients with chronic myeloid leukemia

Leukemic cells from two patients with Philadelphia-negative chronic myeloid leukemia (CML) were investigated: 1) Cytogenetics showed a normal 46,XY karyotype in both cases, 2) molecular studies revealed rearrangement of the M-BCR region and formation of BCR-ABL fusion mRNA with b2a2 (patient 1) or b3a2 (patient 2) configuration, and 3) fluorescence in situ hybridization (FISH) demonstrated relocation of the 5' BCR sequences from one chromosome 22 to one chromosome 9. The ABL probe hybridized to both chromosomes 9 at band q34, while two other probes which map centromeric and telomeric of BCR on 22q11 hybridized solely with chromosome 22. For the first time, a BCR-ABL rearrangement is shown to take place on 9q34 instead of in the usual location on 22q11. A rearrangement in the latter site is found in all Ph-positive CML and in almost all investigated CML with variant Ph or Ph-negative, BCR-positive cases. The few aberrant chromosomal localizations of BCR-ABL recombinant genes found previously were apparently the result of complex and successive changes. Furthermore in patient 2, both chromosomes 9 showed positive FISH signals with both ABL and BCR probes. Restriction fragment length polymorphism (RFLP) analysis indicated that mitotic recombination had occurred on the long arm of chromosome 9 and that the rearranged chromosome 9 was of paternal origin. The leukemic cells of this patient showed a duplication of the BCR-ABL gene, analogous to duplication of the Ph chromosome in classic CML. In addition they had lost the maternal alleles of the 9q34 chromosomal region.(ABSTRACT TRUNCATED AT 250 WORDS)

Localization of the retinoid X receptor alpha gene (RXRA) to chromosome 9q34

The retinoid X receptor alpha is one of a number of retinoic acid receptors which are members of the steroid/thyroid hormone superfamily. Localization of RXRA was achieved using the polymerase chain reaction on a panel of somatic cell hybrids. A cosmid clone was isolated using the RXRA PCR product, and this was used to further localize the gene by fluorescence in situ hybridization to chromosome 9q34 distal to the dopamine beta hydroxylase gene (DBH). This mapping position was confirmed by PCR on a panel of translocation hybrids.

Localization of the gene for familial dysautonomia on chromosome 9 and definition of DNA markers for genetic diagnosis

Familial dysautonomia (DYS), the Riley-Day syndrome, is an autosomal recessive disorder characterized by developmental loss of neurons from the sensory and autonomic nervous system. It is limited to the Ashkenazi Jewish population, where the carrier frequency is 1 in 30. We have mapped the DYS gene to chromosome 9q31-q33 by linkage with ten DNA markers in 26 families. The maximum lod score of 21.1 with no recombinants was achieved with D9S58. This marker also showed strong linkage disequilibrium with DYS, with one allele present on 73% of affected chromosomes compared to 5.4% of controls (chi 2 = 3142, 15 d.f. p < 0.0001). D9S53 and D9S105 represent the closest flanking markers for the disease gene. This localization will permit prenatal diagnosis of DYS in affected families and aid the isolation of the disease gene.

Linkage analysis of infantile pyloric stenosis and markers from chromosome 9q11-q33: no evidence for a major gene in this candidate region

A genetic component in the aetiology of infantile pyloric stenosis (PS) is well established. Segregation analysis is compatible with a multifactorial sex modified threshold model of inheritance but a major gene of low penetrance has not been excluded. PS has been reported to occur in 57% (four of seven) of cases with duplication of chromosome 9q11-q33. Twenty families with PS were studied using genetic markers at loci D9S55, D9S111, D9S15, D9S12, D9S56, D9S59, and ASS from this region of chromosome 9. Pairwise lod scores of -2 were obtained with all these markers at recombination fractions greater or equal to 0.04 under both autosomal dominant and autosomal recessive models of inheritance. This provides evidence against the existence of a major locus predisposing to PS within chromosome 9q11-q33.

Chromosome bands--flavours to savour

The mammalian chromosome is longitudinally heterogeneous in structure and function and this is the basis for the specific banding patterns produced by various chromosome staining techniques. The two most frequently used techniques are G, or Giemsa banding and R, or reverse banding. Each type of stained band is characterised by variations in gene density, time of replication, base composition, density of repeat sequences, and chromatin packaging. It is increasingly apparent that R and G bands, which are complementary to each other, represent separate compartments of the euchromatic human genome, with R bands containing the vast majority of genes. R bands are also more GC-rich, contain a higher density of Alu repeats, and replicate earlier in S phase, than G bands. These properties may be interdependent and may have coevolved.

Identification of markers flanking the tuberous sclerosis locus on chromosome 9 (TSC1)

Analysis of a large tuberous sclerosis pedigree confirmed linkage to a locus on the long arm of chromosome 9, with recombination events placing the disease gene distal to gelsolin and proximal to dopamine beta-hydroxylase.

Linkage of an important gene locus for tuberous sclerosis to a chromosome 16 marker for polycystic kidney disease

Tuberous sclerosis complex (TSC) is an autosomal dominant disorder of unknown aetiology that affects numerous body systems including skin, brain and kidneys. Some TSC has been linked to chromosome 9, additional TSC genes on chromosomes 11 and 12 have been proposed, but the majority of TSC families remain unlinked. Using TSC families in which data had excluded linkage to chromosome 9, we failed to detect linkage with loci on chromosomes 11, 12 and others. One marker examined was D16S283, the closest locus on the proximal side of the polycystic kidney disease type 1 (PKD1) gene. Linkage between TSC and D16S283 demonstrated a lod score of 9.50 at theta = 0.02 with one family independently presenting a lod score of 4.44 at theta = 0.05. These data reveal an important TSC locus near the region of PKD1 on chromosome 16p13.