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Biomedical subjects

Lisa G Shaffer

Publications and source records attributed to Lisa G Shaffer.

At least 55 records · Page 3Linked to original sources
PubMed2003

Genome architecture catalyzes nonrecurrent chromosomal rearrangements.

To investigate the potential involvement of genome architecture in nonrecurrent chromosome rearrangements, we analyzed the breakpoints of eight translocations and 18 unusual-sized deletions involving human proximal 17p. Surprisingly, we found that many deletion breakpoints occurred in low-copy repeats (LCRs); 13 were associated with novel large LCR17p structures, and 2 mapped within an LCR sequence (middle SMS-REP) within the Smith-Magenis syndrome (SMS) common deletion. Three translocation breakpoints involving 17p11 were found to be located within the centromeric alpha-satellite sequence D17Z1, three within a pericentromeric segment, and one at the distal SMS-REP. Remarkably, our analysis reveals that LCRs constitute >23% of the analyzed genome sequence in proximal 17p--an experimental observation two- to fourfold higher than predictions based on virtual analysis of the genome. Our data demonstrate that higher-order genomic architecture involving LCRs plays a significant role not only in recurrent chromosome rearrangements but also in translocations and unusual-sized deletions involving 17p.

Centromere↗
PubMed2003

Mosaicism in a patient with Down syndrome reveals post-fertilization formation of a Robertsonian translocation and isochromosome.

It has been estimated that a few hundred children are born each year in the United States with translocation Down syndrome. About 5% of the cases with Down syndrome carry a Robertsonian translocation involving chromosome 21. The case described here is a patient with Down syndrome who showed mosaicism for two cell lines. Each cell line contains a different, de novo acrocentric rearrangement. We constructed somatic cell hybrids from the patient's cells and determined the parental origins of the rearrangements by molecular and fluorescence in situ hybridization (FISH) analyses. The analysis showed that the rob(14q21q) formed between a paternally inherited chromosome 21 and a maternally inherited chromosome 14, indicating that this rearrangement formed post-zygotically. Further molecular analysis also determined that the rea(21q21q) is an isochromosome of paternal origin. The cell line containing the isochromosome is unbalanced, resulting in trisomy 21. Because the same paternal chromosome 21 was involved in both the isochromosome and the Robertsonian translocation, we speculate that an unstable chromosome 21 was stabilized either through formation of a rob(14q21q) or through formation of an isochromosome. The mechanism proposed for the formation of the rob(14q21q) in this case is different from that for most de novo rob(14q21q), but similar to a previously reported mosaic case of Down syndrome.

Cell Line↗
PubMed2003

Shuffling of genes within low-copy repeats on 22q11 (LCR22) by Alu-mediated recombination events during evolution.

Low-copy repeats, or segmental duplications, are highly dynamic regions in the genome. The low-copy repeats on chromosome 22q11.2 (LCR22) are a complex mosaic of genes and pseudogenes formed by duplication processes; they mediate chromosome rearrangements associated with velo-cardio-facial syndrome/DiGeorge syndrome, der(22) syndrome, and cat-eye syndrome. The ability to trace the substrates and products of recombination events provides a unique opportunity to identify the mechanisms responsible for shaping LCR22s. We examined the genomic sequence of known LCR22 genes and their duplicated derivatives. We found Alu (SINE) elements at the breakpoints in the substrates and at the junctions in the truncated products of recombination for USP18, GGT, and GGTLA, consistent with Alu-mediated unequal crossing-over events. In addition, we were able to trace a likely interchromosomal Alu-mediated fusion between IGSF3 on 1p13.1 and GGT on 22q11.2. Breakpoints occurred inside Alu elements as well as in the 5' or 3' ends of them. A possible stimulus for the 5' or 3' terminal rearrangements may be the high sequence similarities between different Alu elements, combined with a potential recombinogenic role of retrotransposon target-site duplications flanking the Alu element, containing potentially kinkable DNA sites. Such sites may represent focal points for recombination. Thus, genome shuffling by Alu-mediated rearrangements has contributed to genome architecture during primate evolution.

Alu Elements↗
PubMed2002

Obligate short-arm exchange in de novo Robertsonian translocation formation influences placement of crossovers in chromosome 21 nondisjunction.

Robertsonian translocations (ROBs) involving chromosome 21 are found in approximately 5% of patients with Down syndrome (DS). The most common nonhomologous ROB in DS is rob(14q21q). Aberrant recombination is associated with nondisjunction (NDJ) leading to trisomy 21. Haplotype analysis of 23 patients with DS and de novo rob(14q21q) showed that all translocations and all nondisjoined chromosomes 21 were maternally derived. Meiosis II NDJ occurred in 21 of 23 families. For these, a ROB DS chromosome 21 genetic map was constructed and compared to a normal female map and a published trisomy 21 map derived from meiosis II NDJ. The location of exchanges differed significantly from both maps, with a significant shift to a more distal interval in the ROB DS map. The shift may perturb segregation, leading to the meiosis II NDJ in this study, and is further evidence for crossover interference. More importantly, because the event in the short arms that forms the de novo ROB influences the placement of chiasmata in the long arm, it is most likely that the translocation formation occurs through a recombination pathway in meiosis. Additionally, we have demonstrated that events that occur in meiosis I can influence events, such as chromatid segregation in meiosis II, many decades later.

Chromosome Aberrations↗
PubMed2002

Parental origin and timing of de novo Robertsonian translocation formation.

Robertsonian translocations (ROBs) are the most common chromosomal rearrangements in humans. ROBs are whole-arm rearrangements between the acrocentric chromosomes 13-15, 21, and 22. ROBs can be classified into two groups depending on their frequency of occurrence, common (rob(13q14q) and rob(14q21q)), and rare (all remaining possible nonhomologous combinations). Herein, we have studied 29 case subjects of common and rare de novo ROBs to determine their parental origins and timing of formation. We compared these case subjects to 35 published case subjects of common ROBs and found that most common ROBs apparently have the same breakpoints and arise mainly during oogenesis (50/54). These probably form through a common mechanism and have been termed "class 1." Collectively, rare ROBs also occur mostly during oogenesis (7/10) but probably arise through a more "random" mechanism or a variety of mechanisms and have been termed "class 2." Thus, we demonstrate that although both classes of ROBs occur predominantly during meiosis, the common, class 1 ROBs occur primarily during oogenesis and likely form through a mechanism distinct from that forming class 2 ROBs.

Chromosome Breakage↗
PubMed2002

Genomic rearrangements resulting in PLP1 deletion occur by nonhomologous end joining and cause different dysmyelinating phenotypes in males and females.

In the majority of patients with Pelizaeus-Merzbacher disease, duplication of the proteolipid protein gene PLP1 is responsible, whereas deletion of PLP1 is infrequent. Genomic mechanisms for these submicroscopic chromosomal rearrangements remain unknown. We identified three families with PLP1 deletions (including one family described elsewhere) that arose by three distinct processes. In one family, PLP1 deletion resulted from a maternal balanced submicroscopic insertional translocation of the entire PLP1 gene to the telomere of chromosome 19. PLP1 on the 19qtel is probably inactive by virtue of a position effect, because a healthy male sibling carries the same der(19) chromosome along with a normal X chromosome. Genomic mapping of the deleted segments revealed that the deletions are smaller than most of the PLP1 duplications and involve only two other genes. We hypothesize that the deletion is infrequent, because only the smaller deletions can avoid causing either infertility or lethality. Analyses of the DNA sequence flanking the deletion breakpoints revealed Alu-Alu recombination in the family with translocation. In the other two families, no homologous sequence flanking the breakpoints was found, but the distal breakpoints were embedded in novel low-copy repeats, suggesting the potential involvement of genome architecture in stimulating these rearrangements. In one family, junction sequences revealed a complex recombination event. Our data suggest that PLP1 deletions are likely caused by nonhomologous end joining.

Base Sequence↗
PubMed2002

Subtelomeric FISH uncovers trisomy 14q32: lessons for imprinted regions, cryptic rearrangements and variant acrocentric short arms.

The recent development of a set of chromosome-specific, subtelomeric probes has proved useful in diagnosis and recurrence risk counseling of patients and families with mental retardation and in further characterization of known chromosomal abnormalities. Cases of cryptic, subtelomeric rearrangements may account for up to 7.5% of cases of idiopathic moderate-severe mental retardation. We present the molecular cytogenetic studies of trisomy 14q detected by subtelomeric fluorescence in situ hybridization (FISH). Our patient is a 3-year-old girl with growth and developmental delay, myelomeningocele, partial agenesis of the corpus callosum, hypertelorism, tented mouth, simple ears, small mandible, and congenital heart disease (atrial and ventricular septal defects with subaortic conus). G-banded chromosome analysis was apparently normal. A set of FISH-based, subtelomeric, region-specific probes revealed trisomy for 14q in the child. Parental FISH studies established that the mother is a balanced carrier for a half-cryptic translocation between the distal long arm of chromosome 14 and the short arm of chromosome 22. FISH analysis using two BAC clones that contain the imprinted genes MEG3 and DLK1, which localize to 14q32, established that our patient has two maternal copies of these genes. Because the child does not have features of the maternal UPD 14 syndrome, this case suggests that it is absence of expression of a paternally expressed gene, rather than overexpression of a maternally expressed gene, that is responsible for the maternal UPD 14 phenotype.

Abnormalities, Multiple↗
PubMed2002

Poly(ADP-ribose) polymerase 2 localizes to mammalian active centromeres and interacts with PARP-1, Cenpa, Cenpb and Bub3, but not Cenpc.

Poly(ADP-ribose) polymerase 2 (PARP-2) is a newly discovered member of the PARP family. We report the association of PARP-2 with mammalian centromeres in a cell-cycle-dependent manner, accumulating at centromeres during prometaphase and metaphase, disassociating during anaphase, and disappearing from the centromeres by telophase. Analysis of a pseudodicentric chromosome and a human neocentromere indicates that PARP-2 binding occurs only at active centromeres in a sequence-independent manner. Centromere binding peaks at the outer centromere region, and is significantly enhanced upon treatment with microtubule-inhibiting drugs. Co-immunoprecipitation assay demonstrates interaction between PARP-2 and its functional homolog PARP-1, constitutive centromere proteins Cenpa and Cenpb, and spindle checkpoint protein Bub3, but not with a third constitutive centromere protein Cenpc. These results, together with our previous demonstration that PARP-1 displays an identical binding pattern with Cenpa, Cenpb and Bub3, but not Cenpc, and that all three proteins undergo significant poly(ADP-ribosyl)ation upon gamma-irradiation of cells, point to possible diverse roles of PARP-2 and PARP-1 in modulating the structure and checkpoint functions of the mammalian centromere, in particular during radiation-induced DNA damage.

Animals↗
PubMed2002

Identification of uniparental disomy in phenotypically abnormal carriers of isochromosomes or Robertsonian translocations.

Carriers of either homologous or non-homologous acrocentric rearrangements are at an increased risk for aneuploidy, and, thus, for uniparental disomy (UPD). Abnormal phenotypes due to genomic imprinting are associated with UPD for the acrocentric chromosomes 14 and 15. The purpose of this study was to determine the prevalence of UPD in a population with acrocentric rearrangements (either an isochromosome or a Robertsonian translocation) and abnormal phenotypes. Fifty individuals were studied. Of the 50 rearrangements, two were homologous rearrangements and both showed UPD. Forty-eight were non-homologous Robertsonian translocations, of which two showed UPD. This study demonstrates that UPD explains the abnormal phenotypes in some balanced carriers of acrocentric rearrangements. Our results and the large number of case reports in the literature suggest that patients with abnormal phenotypes and acrocentric rearrangements of chromosomes 14 or 15 should be tested for UPD.

Abnormalities, Multiple↗
PubMed2002

Familial complex chromosomal rearrangement resulting in a recombinant chromosome.

Familial complex chromosomal rearrangements (CCRs) are rare and tend to involve fewer breakpoints and fewer chromosomes than CCRs that are de novo in origin. We report on a CCR identified in a child with congenital heart disease and dysmorphic features. Initially, the child's karyotype was thought to involve a straightforward three-way translocation between chromosomes 3, 8, and 16. However, after analyzing the mother's chromosomes, the mother was found to have a more complex rearrangement that resulted in a recombinant chromosome in the child. The mother's karyotype included an inverted chromosome 2 and multiple translocations involving chromosomes 3, 5, 8, and 16. No evidence of deletion or duplication that could account for the clinical findings in the child was identified.

Chromosome Aberrations↗
PubMed2002

Refinement of the genomic structure of STX1A and mutation analysis in nondeletion Williams syndrome patients.

Williams syndrome (WS) is a contiguous gene deletion disorder in which the commonly deleted region contains at least 17 genes. One of these genes, Syntaxin 1A (STX1A), codes for a protein that is highly expressed in the nervous system and is essential for the docking of synaptic vesicles with the presynaptic plasma membrane. In this study, we refine the complete genomic structure of the human STX1A gene by direct sequencing and primer walking of bacterial artificial chromosome (BAC) clones and show that STX1A contains at least 10 exons and 9 introns. The length of exons range from 27 bp to 138 bp and all splice sites conform to the GT-AG rule. Investigation of the STX1A gene sequence in five WS patients without detectable deletions did not identify any point mutations. Although the regulatory elements that control STX1A transcription were not examined, these results do not support a role for STX1A in the WS phenotype.

Adolescent↗
PubMed2002

Haploinsufficiency of PAX9 is associated with autosomal dominant hypodontia.

We recently identified a frame-shift mutation in the PAX9 gene as the underlying cause for hypodontia involving permanent molar teeth segregating in an autosomal dominant pattern in a single large family (Stockton et al. 2000). Here we report a small nuclear family in which a father and his daughter are affected with severe hypodontia, involving agenesis of all primary and permanent molars, evidently caused by deletion of the entire PAX9 gene. Hemizygosity at the PAX9 locus in the two affected individuals was initially discovered when an informative single nucleotide polymorphism, identified while sequencing the gene for mutations, appeared to demonstrate non-Mendelian inheritance. Fluorescence in situ hybridization (FISH) analysis with a cosmid containing the PAX9 gene yielded a signal on only one chromosome 14 homologue and confirmed the presence of a deletion encompassing the PAX9 locus. Analysis of microsatellite loci in the vicinity of PAX9 delineated one breakpoint of the deletion. These data, in concert with FISH analysis with cosmids encompassing a 199 kb region, indicated that the deletion is between approximately 44 kb and 100 kb. PAX9 is one of two genes, and the only odontogenic gene within the deletion interval, thus supporting the model of haploinsufficiency for PAX9 as the underlying basis for hypodontia.

Anodontia↗
PubMed2002

A case of segmental paternal isodisomy of chromosome 14.

Uniparental disomy of chromosome 14 (UPD 14) results in one of two distinct abnormal phenotypes, depending upon the parent of origin. This discordance may result from the reciprocal over-expression and/or under-expression of one or more imprinted genes. We report a case of segmental paternal isodisomy for chromosome 14 with features similar to those reported in other paternal disomy 14 cases. Microsatellite marker analysis revealed an apparent somatic recombination event in 14q12 leading to proximal biparental inheritance, but segmental paternal uniparental isodisomy distal to this site. Analysis of monochromosomal somatic cell hybrids containing either the paternally inherited or the maternally inherited chromosome 14 revealed no deletion of the maternally inherited chromosome 14 and demonstrated the presence of paternal sequences from D14S121 to the telomere on both chromosomes 14. Thus, the patient has paternal isodisomy for 14q12-14qter. Because the patient shows most of the features associated with paternal disomy 14, this supports the presence of the imprinted domain(s) distal to 14q12 and suggests that the proximal region of chromosome 14 does not contain imprinted genes that contribute significantly to the paternal UPD 14 phenotype.

Abnormalities, Multiple↗
PubMed2002

Craniofacial anomalies, deafness, brachydactyly, short stature, and moderate mental retardation due to a cryptic 6p;11q translocation.

Monozygotic twin brothers are described who share clinical features which include: moderate mental retardation, short stature, macrocephaly, frontal bossing, ptosis, low-set ears, brachydactyly, 5th fingers clinodactyly, single palmar creases, cryptorchidism, and prelingual sensorineural deafness. One of the twins presented with mild cardiac dilatation and died at age 3(1/2) from cardiac arrest during an episode of acute respiratory infection. While chromosome analyses performed for both twins on peripheral blood showed apparently normal karyotypes, screening for all telomeric regions on the surviving propositus revealed a combination of partial 6p trisomy and partial 11q monosomy. A balanced reciprocal translocation was found in the father. The phenotype of the twins is most likely related to this cryptic chromosomal rearrangement. The fact that the phenotype in this family partially overlaps with some previously reported phenotypes is discussed.

Abnormalities, Multiple↗
PubMed2002

Low or absent unconjugated estriol in pregnancy: an indicator for steroid sulfatase deficiency detectable by fluorescence in situ hybridization and biochemical analysis.

It has been previously reported that a low or absent maternal serum unconjugated estriol (uE3) level is associated with placental steroid sulfatase (STS) deficiency. Here we report a correlation between patients who present with a very low or absent maternal serum uE3 and a deletion of the STS gene as assessed by fluorescence in situ hybridization (FISH). We studied nine prenatal cases that presented to the clinical laboratory with an abnormal triple screen, specifically low or absent maternal serum uE3 and a 46,XY karyotype. FISH analysis showed complete deletion of a probe containing the STS gene in six cases and one case had a partial deletion (reduced but not absent signal). The remaining two cases were not deleted for the STS probe. All mothers tested whose fetus showed a deletion were shown to be STS deletion carriers using FISH. Biochemical analysis was performed on 7/9 prenatal specimens. All fetuses deleted for the STS probe were also found to be deficient for STS by biochemical analysis of cultured amniotic fluid (5/5). Of the two fetuses not deleted for the STS probe, one was deficient for STS activity, while the other had a normal result. The abnormal result of enzyme deficiency by biochemical analysis in a non-deletion case likely represents a mutation in the STS gene, not detectable by this FISH assay. Postnatal FISH confirmation of the STS deletion was performed in 1/7 cases. Clinical follow-up was available for 4/9 cases following birth.

Adult↗
PubMed2002

Robertsonian translocations: mechanisms of formation, aneuploidy, and uniparental disomy and diagnostic considerations.

Robertsonian translocations (ROBs) are rearrangements of the acrocentric chromosomes 13-15 and 21-22. Cytologically, ROBs between homologous chromosomes cannot be distinguished from isochromosomes that originate through duplication of a single homologue. Both types of rearrangements can be involved in aneuploidy. A conceptus with a trisomy or a monosomy can be rescued, and in a proportion of cases, a uniparental disomy (UPD) would result. If there are regions of genome imprinting on a uniparental chromosome pair, phenotypic consequences can result. Chromosomes 14 and 15 are imprinted, and UPD of these are known to result in abnormalities. Thus, prenatal testing should be considered in all pregnancies when one of the parents is a balanced carrier of a ROB because of the risk for aneuploidy, and UPD testing should be considered in fetuses found to carry a balanced ROB or isochromosome that involves chromosomes 14 or 15. Additionally, infants or children with congenital anomalies who carry a ROB should also be considered for UPD testing.

Aneuploidy↗
PubMed2002

Genes in a refined Smith-Magenis syndrome critical deletion interval on chromosome 17p11.2 and the syntenic region of the mouse.

Smith-Magenis syndrome (SMS) is a multiple congenital anomaly/mental retardation syndrome associated with behavioral abnormalities and sleep disturbance. Most patients have the same approximately 4 Mb interstitial genomic deletion within chromosome 17p11.2. To investigate the molecular bases of the SMS phenotype, we constructed BAC/PAC contigs covering the SMS common deletion interval and its syntenic region on mouse chromosome 11. Comparative genome analysis reveals the absence of all three approximately 200-kb SMS-REP low-copy repeats in the mouse and indicates that the evolution of SMS-REPs was accompanied by transposition of adjacent genes. Physical and genetic map comparisons in humans reveal reduced recombination in both sexes. Moreover, by examining the deleted regions in SMS patients with unusual-sized deletions, we refined the minimal Smith-Magenis critical region (SMCR) to an approximately 1.1-Mb genomic interval that is syntenic to an approxiamtely 1.0-Mb region in the mouse. Genes within the SMCR and its mouse syntenic region were identified by homology searches and by gene prediction programs, and their gene structures and expression profiles were characterized. In addition to 12 genes previously mapped, we identified 8 new genes and 10 predicted genes in the SMCR. In the mouse syntenic region of the human SMCR, 16 genes and 6 predicted genes were identified. The SMCR is highly conserved between humans and mice, including 19 genes with the same gene order and orientation. Our findings will facilitate both the identification of gene(s) responsible for the SMS phenotype and the engineering of an SMS mouse model.

Abnormalities, Multiple↗