Human chromosome 9 pericentric homologies: implications for chromosome 9 heteromorphisms

Prenatal diagnosis of a familial 9p12 amplification inherited from a father carrier

OBJECTIVE

We present prenatal diagnosis of a familial 9p12 amplification inherited from a father carrier.

CASE REPORT

A 38-year-old, gravida 3, para 2, woman underwent amniocentesis at 17 weeks of gestation because of advanced maternal age. Amniocentesis revealed a heteromorphic variant of chromosome 9 with a 9p12 amplification on G-band preparations, but it was negative on C-band preparations. Cytogenetic analysis of the parents revealed that the phenotypically normal father carried the same euchromatic 9p + polymorphism. Array comparative genomic hybridization analysis on the DNA extracted from the father's blood revealed no genomic imbalance. At 37 weeks of gestation, a healthy 2760-g female baby was delivered with no phenotypic abnormality. She was doing well at age one year during follow-up.

CONCLUSION

Prenatal diagnosis of a 9p + variant can be a euchromatic chromosome variant of a familial 9p12 amplification without phenotypic consequences.

Establishment of human-embryonic-stem-cell line from mosaic trisomy 9 embryo

OBJECTIVE

Human-embryonic-stem-cell (hESC) lines derived from chromosomally or genetically abnormal embryos obtained following preimplantation genetic diagnosis are valuable in investigating genetic disorders.

MATERIALS AND METHODS

In this study, a new hESC line, Center of Clinical Reproductive Medicine 8 (CCRM8) was established by isolation, culture, and passaging of the inner cell mass of mosaic trisomy 9 embryos.

RESULTS

A karyotype analysis showed that the hESC line possessed a euploid (46 chromosomes). The undifferentiated hESCs exhibited long-term proliferation capacity and expressed typical markers of OCT4, TRA-1-60, and TRA-1-81. In vitro embryoid-body (EB) formation, differentiation, and in vivo teratoma production confirmed the pluripotency of the hESC line. The data represented here are the first detailed report on the characterization and differentiation of one Chinese hESC line generated from mosaic trisomy 9 embryos.

CONCLUSION

Our study showed that chromosomally aberrant embryos could generate a normal hESC line, which would be useful in investigating gene function and embryo development.

Extreme variant of enlarged heterochromatin region on chromosome 9Q in a normal child and multiple family members

Heteromorphisms of chromosome 9 are among the most common variations in the human karyotype. The pericentromeric polymorphisms of chromosome 9 include variations in the size of q-arm heterochromatin, pericentric inversions, and rarely, additional C-band-negative, G-band-positive material. The finding of a polymorphic variant, either in prenatal screening or in chromosomal analysis for phenotypic abnormalities, may cause parental anxiety and initiate genetic counselling. We report a case of a 39-year-old primigravida with unremarkable pregnancy, who had amniocentesis due to advanced maternal age. Chromosomal analysis demonstrated a long arm (q) variant of chromosome 9 with an enlarged heteromorphic area, approximately three times longer than known reported variants. Prenatal analysis demonstated an identical variant in the probands phenotypically normal father, uncle, and paternal grandmother, confirming an apparently "normal" variant.

Single nucleotide polymorphism-based genome-wide chromosome copy change, loss of heterozygosity, and aneuploidy in Barrett's esophagus neoplastic progression

Chromosome copy gain, loss, and loss of heterozygosity (LOH) involving most chromosomes have been reported in many cancers; however, less is known about chromosome instability in premalignant conditions. 17p LOH and DNA content abnormalities have been previously reported to predict progression from Barrett's esophagus (BE) to esophageal adenocarcinoma (EA). Here, we evaluated genome-wide chromosomal instability in multiple stages of BE and EA in whole biopsies. Forty-two patients were selected to represent different stages of progression from BE to EA. Whole BE or EA biopsies were minced, and aliquots were processed for flow cytometry and genotyped with a paired constitutive control for each patient using 33,423 single nucleotide polymorphisms (SNP). Copy gains, losses, and LOH increased in frequency and size between early- and late-stage BE (P < 0.001), with SNP abnormalities increasing from <2% to >30% in early and late stages, respectively. A set of statistically significant events was unique to either early or late, or both, stages, including previously reported and novel abnormalities. The total number of SNP alterations was highly correlated with DNA content aneuploidy and was sensitive and specific to identify patients with concurrent EA (empirical receiver operating characteristic area under the curve = 0.91). With the exception of 9p LOH, most copy gains, losses, and LOH detected in early stages of BE were smaller than those detected in later stages, and few chromosomal events were common in all stages of progression. Measures of chromosomal instability can be quantified in whole biopsies using SNP-based genotyping and have potential to be an integrated platform for cancer risk stratification in BE.

Structural variation of the human genome

There is growing appreciation that the human genome contains significant numbers of structural rearrangements, such as insertions, deletions, inversions, and large tandem repeats. Recent studies have defined approximately 5% of the human genome as structurally variant in the normal population, involving more than 800 independent genes. We present a detailed review of the various structural rearrangements identified to date in humans, with particular reference to their influence on human phenotypic variation. Our current knowledge of the extent of human structural variation shows that the human genome is a highly dynamic structure that shows significant large-scale variation from the currently published genome reference sequence.

The variant inv(2)(p11.2q13) is a genuinely recurrent rearrangement but displays some breakpoint heterogeneity

Human chromosome 2 contains large blocks of segmental duplications (SDs), both within and between proximal 2p and proximal 2q, and these may contribute to the frequency of the common variant inversion inv(2)(p11.2q13). Despite their being cytogenetically homogeneous, we have identified four different breakpoint combinations by fluorescence in situ hybridization mapping of 40 cases of inv(2)(p11.2q13) of European origin. For the vast majority of inversions (35/40), the breakpoints fell within the same spanning BACs, which hybridized to both 2p11.2 and 2q13 on the normal and inverted homologues. Sequence analysis revealed that these BACs contain a significant proportion of intrachromosomal SDs with sequence homology to the reciprocal breakpoint region. In contrast, BACs spanning the rare breakpoint combinations contain fewer SDs and with sequence homology only to the same chromosome arm. Using haplotype analysis, we identified a number of related family subgroups with identical or very closely related haplotypes. However, the majority of cases were not related, demonstrating for the first time that the inv(2)(p11.2q13) is a truly recurrent rearrangement. Therefore, there are three explanations to account for the frequent observation of the inv(2)(p11.2q13): the majority have arisen independently in different ancestors, while a minority either have been transmitted from a common founder or have different breakpoints at the molecular cytogenetic level.

Large-scale polymorphism of heterochromatic repeats in the DNA of Arabidopsis thaliana

BACKGROUND

The composition of the individual eukaryote's genome and its variation within a species remain poorly defined. Even for a sequenced genome such as that of the model plant Arabidopsis thaliana accession Col-0, the large arrays of heterochromatic repeats are incompletely sequenced, with gaps of uncertain size persisting in them.

RESULTS

Using geographically separate populations of A. thaliana, we assayed variation in the heterochromatic repeat arrays using two independent methods and identified significant polymorphism among them, with variation by as much as a factor of two in the centromeric 180 bp repeat, in the 45S rDNA arrays and in the Athila retroelements. In the accession with highest genome size as measured by flow cytometry, Loh-0, we found more than a two-fold increase in 5S RNA gene copies relative to Col-0; results from fluorescence in situ hybridization with 5S probes were consistent with the existence of size polymorphism between Loh-0 and Col-0 at the 5S loci. Comparative genomic hybridization results of Loh-0 and Col-0 did not support contiguous variation in copy number of protein-coding genes on the scale needed to explain their observed genome size difference. We developed a computational data model to test whether the variation we measured in the repeat fractions could account for the different genome sizes determined with flow cytometry, and found that this proposed relationship could account for about 50% of the variance in genome size among the accessions.

CONCLUSION

Our analyses are consistent with substantial repeat number polymorphism for 5S and 45S ribosomal genes among accession of A. thaliana. Differences are also suggested for centromeric and pericentromeric repeats. Our analysis also points to the difficulties in measuring the repeated fraction of the genome and suggests that independent validation of genome size should be sought in addition to flow cytometric measurements.

Novel deletion variants of 9q13–q21.12 and classical euchromatic variants of 9q12/qh involve deletion, duplication and triplication of large tracts of segmentally duplicated pericentromeric euchromatin

Large-scale copy number variation that is cytogenetically visible in normal individuals has been described as euchromatic variation but needs to be distinguished from pathogenic euchromatic deletion or duplication. Here, we report eight patients (three families and two individuals) with interstitial deletions of 9q13-q21.12. Fluorescence in situ hybridisation with a large panel of BACs showed that all the deleted clones were from extensive tracts of segmentally duplicated euchromatin, copies of which map to both the long and short arms of chromosome 9. The variety of reasons for which these patients were ascertained, and the phenotypically normal parents, indicates that this is a novel euchromatic variant with no phenotypic effect. Further, four patients with classical euchromatic variants of 9q12/qh or 9p12 were also shown to have duplications or triplications of this segmentally duplicated material common to both 9p and 9q. The cytogenetic boundaries between the segmentally duplicated regions and flanking unique sequences were mapped to 9p13.1 in the short arm (BAC RP11-402N8 at 38.7 Mb) and to 9q21.12 in the long arm (BAC RP11-88I18 at 70.3 Mb). The BACs identified in this study should in future make it possible to differentiate between clinically significant deletions or duplications and euchromatic variants with no established phenotypic consequences.

A set of duplicons on human chromosome 9 is involved in the origin of a supernumerary marker chromosome

Human chromosome 9 is involved in a number of recurrent structural rearrangements; moreover, its pericentromeric region exhibits a remarkable evolutionary plasticity. In this study we present the molecular characterization of a constitutional rearrangement, involving the 9p21.1q13 region, which led to the formation of a supernumerary marker chromosome (SMC). We defined the sequence of the breakpoints and identified a new set of duplicons on human chromosome 9, named LCR9s (chromosome 9 low-copy repeats). Two of these duplicons were shown to be involved in a somatic exchange leading to the formation of the SMC. High-resolution FISH coupled to database search demonstrated that a total number of 35 LCR9 paralogs are present in the human genome. These newly described chromosome 9 duplicons have features that may be crucial in driving structural chromosome rearrangements in germinal and somatic cells.

The euchromatic 9p+ polymorphism is a locus-specific amplification caused by repeated copies of a small DNA segment mapping within 9p12

A large duplication involving the proximal euchromatic region of chromosome 9p was detected by conventional cytogenetics in a healthy 33-year-old woman and in two unrelated foetuses; both of them received the rearrangement from their healthy father. The duplicated segment was R(RBG) and C(CBG)-negative and G(GTG)-positive and was also positive for a 9-specific painting probe. It was preliminarily interpreted as a pathological quantitative change of the genome in the foetuses. FISH analyses allowed us to characterise the chromosome boundaries of this polymorphism, being identified by the RP11-15E1 BAC clone, proximally, and by the RP11-402N8 clone, distally, both probes falling within the 9p12 region. The contiguous, distally, RP11-916H19 probe was not included in the amplification, and may represent the discriminating genetic locus between chromosome polymorphism and chromosome mutation. The 9p12 amplification was approximately 12, 7 and 8 Mb in the three different families and was stable through generations. Our observations confirm the already provided evidence that proximal 9p duplications represent a benign euchromatic polymorphism. However, we demonstrated that these variants are not a simple duplication of the region 9p11.2-p13.1, as already suggested, but that they result from a many-fold amplification of a segment mapping within 9p12. These results provide important insights both in the genetic counselling and in the prenatal diagnosis of rare euchromatic chromosome variants and in understanding the architecture of the human genome.

Discontinuities and unsynapsed regions in meiotic chromosomes have a cis effect on meiotic recombination patterns in normal human males

During meiosis, homologous chromosome pairing is essential for subsequent meiotic recombination (crossover). Discontinuous chromosome regions (gaps) or unsynapsed chromosome regions (splits) in the synaptonemal complex (SC) indicate anomalies in chromosome synapsis. Recently developed immunofluorescence techniques (using antibodies against SC proteins and the crossover-associated MLH1 protein) were combined with fluorescence in situ hybridization (using centromere-specific DNA probes) to identify bivalents with gaps/splits and to examine the effect of gaps/splits on meiotic recombination patterns during the pachytene stage of meiotic prophase from three normal human males. Gaps were observed only in the heterochromatic regions of chromosomes 9 and 1, with 9q gaps accounting for 90% of these events. Most splits were also found in chromosomes 9 and 1, with 58% of splits occurring on 9q. Gaps and splits significantly altered the distribution of MLH1 foci on the SC. On gapped SC 9q, the frequency of MLH1 foci was decreased compared with controls, and single 9q crossovers tended toward a more distal distribution. Furthermore, the larger the gap the more distal the location of the MLH1 focus closest to the q arm's telomere. MLH1 foci on split SC 9 had distributions similar to those of gapped SC 9; however, splits did not change the frequencies of MLH1 foci on SC 9. This is the first demonstration that gaps and splits have an effect on meiotic recombination in humans.

Acquired inv(9): what is its significance?

Pericentric inversion of the heterochromatic region of chromosome 9 [inv(9)] is a common heteromorphism in the general population. It is presumed familial as there are no reports of de novo inv(9) chromosomes in constitutional karyotypes. We report 2 cases of acquired inv(9) chromosomes; 1 patient with acute myeloid leukemia, 46,XY,inv(9)(p11q13)[11]/46,XY[9], and a second with severe anemia, 46,XX,inv(9)(p11q13)[14]/46,XX[6]. The acquired nature of the inv(9) was confirmed by constitutional karyotyping and/or molecular analysis. The inv(9) in these patients may be a de novo inversion that cytogenetically mimics the constitutional inv(9) heteromorphism. Alternatively, it may be the result of neocentromere activation in 9q due to epigenetic events associated with the disease in these patients that results in a metacentric chromosome similarly mimicking the constitutional inv(9). One previous report of an acquired inv(9) was in a patient with essential thrombocythemia. The differences in clinical presentation may represent different underlying mechanisms generating the inv(9). The significance of an acquired inv(9) is unknown and will require reporting of additional cases.

Evolution versus constitution: differences in chromosomal inversion

We compared the chromosomal breakpoints of evolutionary conserved and constitutional inversions. Multicolor banding and human-specific bacterial artificial chromosomes were applied to map the breakpoints of constitutional pericentric inversions on human chromosomes 2 and 9. For the first time, we present a high-resolution analysis of the breakpoint regions, which are characterized by gene destitution, co-localization with fragile sites, multitude repeats as well as pseudogenes and, remarkably, a large sequence homology to the opposite breakpoint. In contrast, evolutionary inversion breakpoints lack such extensive cross-hybridizing regions and are often associated with fragile sites of the genome and low-copy repeats. These molecular characteristics gave evidence for different types of inversion formation and indicate that evolutionary inversions cannot originate from constitutional inversions like those of chromosomes 2 and 9. Finally, the constitutional inversion breakpoints were investigated on three different great ape species and on four test persons each bearing the same cytogenetically determined inversion on chromosomes 2 and 9, respectively. Our data indicate the existence of different molecular breakpoints for the two variant chromosomes.

Variation in meiotic recombination frequencies among human males

Meiotic recombination is essential for the segregation of homologous chromosomes and the formation of normal haploid gametes. Little is known about patterns of meiotic recombination in human germ cells or the mechanisms that control these patterns. Here, newly developed immunofluorescence techniques, based on the detection of MLH1 (a DNA mismatch repair protein) foci on synaptonemal complexes (SCs) at prophase I of meiosis, were used to examine recombination in human spermatocytes. The mean number of MLH1 foci per cell in all donors was 48.0 with range from 21 to 65. Remarkable variation in the recombination frequency was noted among 11 normal individuals: the mean frequencies of chromosomal recombination foci ranged from a low of 42.5 to a high of 55.0 exchanges. Donor age did not contribute to this variation. There was no correlation between this variation and the frequency of gaps (discontinuities) or splits (unpaired chromosome regions) in the SCs. The mean percentage of cells with gaps was 35% (range: 20% to 58%) and with splits was 7% (range: 0% to 37%). Bivalents without a recombination focus were rare, with a frequency of only 0.3%. Thus, achiasmate chromosomes appear to be rare in human male meiosis.

DNA sequence and analysis of human chromosome 9

Chromosome 9 is highly structurally polymorphic. It contains the largest autosomal block of heterochromatin, which is heteromorphic in 6-8% of humans, whereas pericentric inversions occur in more than 1% of the population. The finished euchromatic sequence of chromosome 9 comprises 109,044,351 base pairs and represents >99.6% of the region. Analysis of the sequence reveals many intra- and interchromosomal duplications, including segmental duplications adjacent to both the centromere and the large heterochromatic block. We have annotated 1,149 genes, including genes implicated in male-to-female sex reversal, cancer and neurodegenerative disease, and 426 pseudogenes. The chromosome contains the largest interferon gene cluster in the human genome. There is also a region of exceptionally high gene and G + C content including genes paralogous to those in the major histocompatibility complex. We have also detected recently duplicated genes that exhibit different rates of sequence divergence, presumably reflecting natural selection.

Homologous sequences at human chromosome 9 bands p12 and q13-21.1 are involved in different patterns of pericentric rearrangements

A thorough study of the heterochromatin organisation in the pericentromeric region and the proximal long (q) and short (p) arms of human chromosome 9 (HSA 9) revealed homology between 9p12 and 9q13-21.1, two regions that are usually not distinguishable by molecular cytogenetic techniques. Furthermore, the chromosomal regions 9p12 and 9q13-21.1 showed some level of homology with the short arms of the human acrocentric chromosomes. We studied five normal controls and 51 clinical cases: 48 with chromosome 9 heteromorphisms, one with an exceptionally large inversion and two with an additional derivative chromosome 9. Using fluorescence in situ hybridisation (FISH) with three differentially labelled chromosome 9-specific probes we were able to distinguish 12 heteromorphic patterns in addition to the most frequent pattern (defined as normal). In addition, we studied one inversion 9 case with the recently described multicolour banding (MCB) technique. Our results, and previously published findings, suggest several hotspots for recombination in the pericentromeric heterochromatin of HSA 9. They also demonstrate that constitutional inversions affecting the pericentromeric region of chromosome 9 carry breakpoints located preferentially in 9p12 or 9q13-21.1 and less frequently in 9q12.

Molecular mechanisms for constitutional chromosomal rearrangements in humans

Cytogenetic imbalance in the newborn is a frequent cause of mental retardation and birth defects. Although aneuploidy accounts for the majority of imbalance, structural aberrations contribute to a significant fraction of recognized chromosomal anomalies. This review describes the major classes of constitutional, structural cytogenetic abnormalities and recent studies that explore the molecular mechanisms that bring about their de novo occurrence. Genomic features flanking the sites of recombination may result in susceptibility to chromosomal rearrangement. One such substrate for recombination is low-copy region-specific repeats. The identification of genome architectural features conferring susceptibility to rearrangements has been accomplished using methods that enable investigation of regions of the genome that are too small to be visualized by traditional cytogenetics and too large to be resolved by conventional gel electrophoresis. These investigations resulted in the identification of previously unrecognized structural cytogenetic anomalies, which are associated with genetic syndromes and allowed for the molecular basis of some chromosomal rearrangements to be delineated.