High-resolution Chromosome Analysis Research Articles

Interstitial duplication of the short arm of chromosome 2: report of a new case and review.

An 18 month old girl was referred to us because of dysmorphic features and psychomotor and growth retardation. On physical examination, she was found to have microcephaly, open fontanelles, a...

Identification of a Duplication of Xq28 Associated with Bilateral Periventricular Nodular Heterotopia

Bilateral periventricular nodular heterotopia (BPNH) is a malformation of neuronal migration and is characterized by nodules of heterotopic gray matter lining the lateral ventricles of the brain. The majority of BPNH patients are female and have epilepsy as a sole clinical manifestation of their disease. Familial BPNH has been mapped to Xq28 by linkage analysis. A multiple congenital anomaly-mental retardation syndrome (BPNH/MR) was recently delineated in three unrelated boys with BPNH, cerebellar hypoplasia, severe mental retardation, epilepsy, and syndactyly. High-resolution chromosome analysis revealed a subtle abnormality of Xq28 in one of the boys with BPNH/MR syndrome. FISH with cosmids and YACs from Xq28 further characterized this abnormality as a 2.25-3.25-Mb inverted duplication. No abnormality of Xq28 was detected by G-banding or FISH in the other two boys. These data support the linkage assignment of BPNH to band Xq28 and narrow the critical region to the distal 2.25-3.25 Mb of Xq28.

Syndrome de Smith-Magenis

Background. — The main features of the Smith-Magenis syndrome include broad flat midface, brachycephaly, broad nasal bridge, brachydactyly, hoarse deep voice, speech and developmental delay, and behavioral anomalies. This syndrome is due to interstitial deletion of chromosome 17p11.2. Case report. — A 7-year-old girl was admitted for mental retardation. Clinical examination showed brachycephaly, broad flat midface, broad nasal bridge, malar hypoplasia, brachydactyly, decreased or absent deep tendon reflexes, and hoarse deep voice. She had a mild deafness, behavioral problems, and sleep disturbances. Chromosome analysis on lymphocytes identified a microdeletion of one chromosome subband 17p11.2. Molecular studies indicated loss of maternal allele. Conclusion. — The Smith-Magenis syndrome is probably underdiagnosed because of its usually mild clinical features. High-resolution chromosome analysis is needed for diagnosis.

Linkage and physical mapping of X-linked lissencephaly/SBH (XLIS): a gene causing neuronal migration defects in human brain.

While disorders of neuronal migration are associated with as much as 25% of recurrent childhood seizures, few of the genes required to establish neuronal position in cerebral cortex are known. Subcortical band heterotopia (SBH) and lissencephaly (LIS), two distinct neuronal migration disorders producing epilepsy and variable cognitive impairment, can be inherited alone or together in a single pedigree. Here we report a new genetic locus, XLIS, mapped by linkage analysis of five families and physical mapping of a balanced X;2 translocation in a girl with LIS. Linkage places the critical region in Xq21-q24, containing the breakpoint that maps to Xq22.3-q23 by high-resolution chromosome analysis. Markers used for somatic cell hybrid and fluorescence in situ hybridization analyses place the XLIS region within a 1 cM interval. These data suggest that SBH and X-linked lissencephaly are caused by mutation of a single gene, XLIS, that the milder SBH phenotype in females results from random X-inactivation (Lyonization), and that cloning of genes from the breakpoint region on X will yield XLIS.

Fragile X syndrome in two siblings with major congenital malformations

We report on 2 brothers with both fragile X and VACTERL-H syndrome. The first sibling, age 5, had bilateral cleft lip and palate, ventricular septal defect, and a hypoplastic thumb. The second sibling, age 2 1/2, had a trachesophageal fistula, esophageal atresia, and vertebral abnormality. High-resolution chromosome analysis showed a 46, XY chromosome constitution in both siblings. By PCR and Southern blot analysis, the siblings were found to have large triplet repeat expansions in the fragile X gene (FMR 1) and both had methylation mosaicism. Enzyme kinetic studies of iduronate sulfatase demonstrated a two-fold increase in activity in the first sib as compared to the second. Possible mechanisms through which the fragile X mutation can cause down-regulation of adjacent loci are discussed.

Angelman syndrome in an inbred family.

Angelman syndrome (AS) is characterized by severe mental retardation, absent speech, puppet-like movements, inappropriate laughter, epilepsy, and abnormal electroencephalogram. The majority of AS patients (approximately 65%) have a maternal deficiency within chromosomal region 15q11-q13, caused by maternal deletion or paternal uniparental disomy (UPD). Approximately 35% of AS patients exhibit neither detectable deletion nor UPD, but a subset of these patients have abnormal methylation at several loci in the 15q11-q13 region. We describe here three patients with Angelman syndrome belonging to an extended inbred family. High resolution chromosome analysis combined with DNA analysis using 14 marker loci from the 15ql1-q13 region failed to detect a deletion in any of the three patients. Paternal UPD of chromosome 15 was detected in one case, while the other two patients have abnormal methylation at D15S9, D15S63, and SNRPN. Although the three patients are distantly related, the chromosome 15q11-q13 haplotypes are different, suggesting that independent mutations gave rise to AS in this family.

DNA Fluorescent Probes for Diagnosis of Velocardiofacial and Related Syndromes

To study the usefulness of fluorescent in situ hybridization (FISH) with the DNA probe D22S75 for detecting microdeletions in chromosome 22q11.2 in metaphases from patients with features of "CATCH 22" (cardiac anomalies, abnormal facies, thymic hypoplasia or aplasia, cleft palate, and hypocalcemia). High-resolution chromosome analysis and FISH were performed on metaphases from 10 control subjects, 42 patients with features of CATCH 22, and 6 parents of children with CATCH 22. Patients were screened for conotruncal heart defect, palatal abnormality, and facial features. We correlated the phenotype, karyotype, and deletion of a D22S75 locus. Specimens from nine patients with one or more features of CATCH 22 had a single hybridization signal for D22S75, indicating a deletion of chromosome 22q11.2. Four patients had all the major features of the syndrome and a chromosomal deletion. Thirteen patients had two CATCH 22 features, five of whom had a deletion. None of the 25 patients with a single CATCH 22 feature had a deletion. One patient with a deletion detected by FISH also had a deletion noted on high-resolution banding. All six parents who had blood samples studied by FISH had normal hybridization patterns. FISH is a useful adjunct to chromosome analysis for assessing patients with features of CATCH 22. Detecting a chromosomal deletion by FISH provides a definitive diagnosis and helps to ensure appropriate medical management and genetic counseling.

Fluorescent in situ hybridization for evaluation of prader‐willi and angelman syndromes

We have found fluorescence in situ hybridization (FISH) results more reliavle than high resolution chromosome analysis for the diagnosis of Prader-Willi (PWS) or Angelman syndromes (AS). Specifically, we have found success in the detection of 15q11q13 deletions among 55 cases. Our study suggests that FISH analysis using PWS/AS probes can facilitate diagnostic evaluation of these cases for deletions. 2 refs., 1 tab.

High resolution chromosome analysis and fluorescence in situ hybridization in patients referred for Prader‐Willi or Angelman syndrome

High resolution chromosome analysis and fluorescence in situ hybridization in patients referred for Prader‐Willi or Angelman syndrome

Diagnosis of Microdeletion Syndromes: High-Resolution Chromosome Analysis Versus Fluorescence In Situ Hybridization

Contiguous gene syndromes are characterized by deletions or duplications of specific chromosomal segments involving clusters of single genes. Although these syndromes are associated with distinct clinical phenotypes, these features are difficult to distinguish in the newborn and early childhood periods. In such cases, demonstration of chromosomal involvement through cytogenetic studies is of vital importance in arriving at an accurate diagnosis. In this article results of microdeletion analysis of 31 cases comprising 16 cases of Prader-Willi syndrome, 3 of Angelman syndrome, 7 of Miller-Dieker syndrome, and 5 of DiGeorge syndrome are reported. All patients were studied with both high-resolution chromosome analysis and fluorescence in situ hybridization. In the majority of cases there is 100% concordance between the two techniques. However, in one patient suspected of having DiGeorge syndrome with a normal karyotype at the 750 band level, fluorescence in situ hybridization identified a deletion within the critical region. Without fluorescence in situ hybridization studies on this patient, it would not have been possible to confirm the diagnosis of DiGeorge syndrome cytogenetically. Based on these results and other studies reported in the literature, it is recommended that all suspected cases of microdeletion syndromes should be studied using fluorescence in situ hybridization, irrespective of high-resolution chromosome results. However, because of the difficulties associated with clinical diagnosis of these syndromes, fluorescence in situ hybridization should not replace standard chromosome analysis.

The link between cytogenetics and mendelism

High resolution chromosome analysis, molecular cytogenetics, and study of the association between specific chromosome rearrangements and single gene disorders have provided a chromosomal basis to a number of mendelian diseases. Deletions and duplications of small regions, usually less than 3 Mb in size, result in an alteration of normal gene dosage of a number of unrelated genes physically close to each other and are responsible for contiguous gene syndromes. For example, haploinsufficiency is implicated for del 8q24.1 in Langer-Giedion syndrome, del 17p13.3 in Miller-Dieker syndrome, and del 22q11.2 in DiGeorge and Velo-cardiofacial syndromes. Another chromosomal mechanism causing mendelian phenotypes is translocation, which may eventually interrupt a disease gene. It is assumed that translocation breakpoints are running through a relevant gene, hindering the production of the gene product. An example is breakage 16p13.3 associated with Rubinstein-Taybi syndrome. Females with X/autosome translocations have an almost exclusive inactivation of the normal X. Interruption of a disease gene in the translocated X causes the expression of a mendelian phenotype in the presence of an allelic recessive mutation onto the nonrearranged X. Finally, if a human gene shows exclusive expression from a single parental homologue, ie, it is imprinted, deletion of the chromosomal segment containing the active allele results in structural monosomy and functional nullisomy. This situation is illustrated by Prader-Willi and Angelman syndromes. Over seventy human genes have been precisely assigned to chromosomal regions using a cytogenetic approach. Chromosome techniques combined with molecular methods have proved to have powerful and sensitive diagnostic capabilities.

Absence of chromosome fragility at 19q13.3 in patients with myotonic dystrophy

Myotonic dystrophy (DM) is an autosomal dominant disorder characterized by a trinucleotide (AGC) amplification at 19q13.3. The degree of trinucleotide amplification may increase in successive generations and generally correlates with severity of the disorder. Because amplification of a trinucleotide repeat is also associated with the observation of a fra(X)(q27.3) in the fragile X syndrome, we investigated whether chromosome fragility at 19q13.3 might be inducible in patients with DM. Using 3 different culture stress systems (medium 199, RPMI 1640 with excess TdR, and RPMI 1640 with FudR) and high resolution chromosome analyses, we studied 6 individuals with DM and 5 unaffected relatives representing two unrelated families. Molecular studies were done on two of the most affected patients and showed AGC repeat sequences of 970 and 1,260 at 19q13.3. The normal range of AGC repeat is 5 to 30. We found no indication of fragility at 19q13.3 in any of these individuals.

Detection of a cryptic paracentric inversion within band 11p13 in familial aniridia by fluorescence in situ hybridization.

We report the first familial case of dominantly inherited aniridia with a cryptic inversion within band 11p13. High-resolution chromosome analysis gave a suspicion of a tiny constitutional aberration around band 11p13 and fluorescence in situ hybridization using 11p cosmids successfully confirmed that the aniridia patients of this family have an inversion within band 11p13. The distal breakpoint of the inversion is telomeric to a candidate aniridia gene (AN2) and suggests that more genes might be involved in the etiology of aniridia. In situ hybridization is a powerful tool to detect cryptic rearrangements in sporadic or familial patients with aniridia. This family indicated the importance of careful observation of the 11p13 region of aniridia patients, even if the aniridia was autosomal dominantly inherited.

Further evidence for dominant inheritance at the chromosome 15q11-13 locus in familial Angelman syndrome.

Eleven patients with Angelman syndrome (AS) and their parents from 5 families have been studied with high resolution chromosome analysis and molecular probes from region 15q11-13 in an attempt to elucidate the mode of inheritance in familial AS. No deletions were detected. All families were informative with a combination of different short arm cytogenetic markers. All sets of sibs inherited the same maternal chromosome 15, but in 3 families sibs inherited different paternal 15s. Analysis of 6 polymorphic DNA markers supported the conclusion that AS sibs inherit the same maternal 15, but often different paternal 15s. These data make autosomal recessive inheritance at a 15q11-13 locus very unlikely and support the hypothesis that familial AS is due to maternal transmission of a mutation within 15q11-13.

Expression of the ETS2 and transferrin receptor genes in Philadelphia-positive chronic myeloid leukemia patients with a reciprocal t(3;21).

The translocation t(3;21)(q26;q22) is a rare recurring clonal abnormality, either preceding or associated with blast crisis in Philadelphia chromosome-positive chronic myeloid leukemia (CML) patients. We previously localized the chromosomal breakpoints at 3q26.2 and 21q22.2, using high resolution chromosomal analysis. Two genes of interest are localized near the breakpoints, the transferrin receptor gene and the ETS2 proto-oncogene. Their chromosomal localizations, determined by in situ hybridization on normal metaphase cells, were 3q29 and 21q22.3, respectively. They underwent a reciprocal translocation in patients with t(3;21). Their structures were not altered by the translocation, and both were expressed to varying levels in t(3;21) patients. Southern blotting investigations showed that the structure of other single-copy genes, including FIM3, localized near the breakpoints, were not affected by the translocation. An analysis of ETS2 expression performed on CML patients without t(3;21) showed the presence of the transcript in 100% of the blast crises, but only in 20% of the chronic-phase patients. Thus ETS2 expression may either be linked to or play a role in CML progression.

Tumor cell heterogeneity: an overview

Tumors, particularly malignant tumors, whether primary or metastatic, exhibit considerable heterogeneity in their cellular composition, a phenomenon that has been known for decades. In the past, evidence of cellular heterogeneity was primarily found in the wide variation in morphologic appearance of cells of any given tumor type upon routine histologic examination. During the past lo-15 years, functional and biologic heterogeneity in human or animal neoplasms has been studied extensively through a variety of new and evolving biotechnologies. Among the techniques that have seen wide application recently are: monoclonal antibodies employed in histochemical or flow cytometric systems to detect soluble or surface tumor antigens; DNA/RNA probes used in conjunction with in-situ or in-liquid hybridization assays with or without PCR amplification of key DNA sequences using the polymerase chain reaction (PCR), and high resolution chromosome analyses. Heterogeneity is now recognized as an important aspect of cancer biology with signi~~ant implications for diagnosis and treatment. Neoplasms are known to be composed of cell populations which are heterogeneous with respect to a variety of characteristics e.g. genetic, biochemical, immunologic and other functional properties. Cell diversity is fundamentally an acquired property so that, by the time tumors become clinically overt, their constituent cells are already endowed with diverse biologic characteristics. The origin and significance of such diversity have been the subject of extensive scientific inquiry [1,2]. Experimental and clinical evidence strongly suggest that most neoplasms are clonal in origin i.e. they derive from single cells that have undergone malignant transformation. One might surmise, therefore, that the progeny of such malignant cells might all be alike. This assumption has proven incorrect. A number of

Relative order and location of DNA sequences on chromosome 21 linked to familial Alzheimer disease

Recently, a gene causing familial Alzheimer disease (FAD) was linked to DNA probes on chromosome 21 by genetic analysis. To investigate the precise physical location of these DNA probes, we have constructed a physical map of this region of chromosome 21 by using quantitative Southern blot analysis of cell lines aneuploid for parts of chromosome 21. The following DNA sequences were investigated: D21S16, D21S13, FB68L (cDNA probe for the amyloid protein precursor [APP] gene), and D21S1. We find that all DNA probes are located in the same region of chromosome 21, in q11.2-q21.05. We further show that D21S16 must be centromeric to D21S13, because D21S16, but not D21S13 is present in one copy in a cell line with deletion of the region 21pter-21q 11.2. High resolution chromosome analysis is presented to define this breakpoint. This new panel of aneuploid cell lines will allow the rapid mapping of new DNA probes in the vicinity of the FAD gene.

Isodicentric X chromosome in a patient with Turner syndrome ? implications for localization of the X-inactivation center

Cytogenetic analyses have previously shown that the region Xq11.2-q21 is retained in all structurally abnormal X chromosomes. From these observations the conclusion has been drawn that this "critical region" on the proximal long arm of the X chromosome contains the locus controlling X-inactivation. Structurally abnormal X chromosomes without the X-inactivation center would allow nullisomy, disomy, or trisomy for genes on the X chromosome, and this condition is presumed nonviable. We studied a 28-year-old woman with primary amenorrhea and features of Turner syndrome who had an unusual isodicentric chromosome of the short arm of X. This patient provided us with the opportunity to more closely define the location of the X-inactivation center. High resolution chromosome analysis showed a 46,X,idic(X)(pter----q13.2::q13.2----pter) chromosome pattern in 94% of her cells and a 45,X complement in 6%. Replication studies showed this derivative X chromosome to be late-replicating (inactive) in all cells analyzed. DNA analysis confirmed the breakpoint of the isodicentric chromosome to be proximal to PGK1. Based on these results, the locus for the X-inactivation center can be refined to be within Xq11.2-q13.2.

Greig syndrome associated with an interstitial deletion of 7p: confirmation of the localization of Greig syndrome to 7p13

An 11-month-old infant with Greig cephalopolysyndactyly syndrome and mild developmental delay is described. High-resolution chromosomal analysis showed a de novo interstitial deletion of chromosome 7p with breakpoints located at p13 and p14. Cytogenetic analysis of polymorphisms of the heterochromatin in the pericentromeric region suggested the deleted chromosome was of paternal origin. This case confirms the localization of Greig syndrome to 7p13 and emphasizes the importance of performing cytogenetic studies on patients with Mendelian disorders who have unusual findings or cognitive abnormalities in a disorder usually associated with normal intellect. Review of clinical features in published reports of patients with a deletion involving 7p13 showed a number to have features overlapping with Greig syndrome. Because of this, we suggest that cytogenetic aberrations, particularly chromosomal microdeletions, may represent a significant etiology for Greig syndrome.

`Typus Edinburgensis' Explained

In 1974, an Edinburgh family was described in which five infants from three generations had a consistently abnormal facial appearance, retarded motor and mental development, and failure to thrive. All died in the first months of life. The eponym "Typus Edinburgensis" was used to label these infants.1 Although at that time no chromosomal abnormality was detected, it was predicted that the advancement of cytogenetic technology might eventually reveal an associated chromosomal abnormality. High-resolution chromosome analysis has now identified a familial reciprocal and apparently balanced translocation between chromosomes 1 and 2 in three members of this family, following detection of an unbalanced karyotype in a neonate with an abnormal phenotype similar to that previously described.