Multicolour FISH and quantitative PCR can detect submicroscopic deletions in holoprosencephaly patients with a normal karyotype.

Holoprosencephaly (HPE) is the most common structural malformation of the developing forebrain. At birth, nearly 50% of children with HPE have cytogenetic anomalies. Approximately 20% of infants with normal chromosomes have sequence mutations in one of the four main HPE genes (SHH, ZIC2, SIX3, and TGIF). The other non-syndromic forms of HPE may be due to environmental factors or mutations in other genes, or potentially due to submicroscopic deletions of HPE genes. We used two complementary assays to test for HPE associated submicroscopic deletions. Firstly, we developed a multicolour fluorescent in situ hybridisation (FISH) assay using probes for the four major HPE genes and for two candidate genes (DISP1 and FOXA2). We analysed lymphoblastoid cell lines (LCL) from 103 patients who had CNS findings of HPE, normal karyotypes, and no point mutations, and found seven microdeletions. We subsequently applied quantitative PCR to 424 HPE DNA samples, including the 103 samples studied by FISH: 339 with CNS findings of HPE, and 85 with normal CNS and characteristic HPE facial findings. Microdeletions for either SHH, ZIC2, SIX3, or TGIF were found in 16 of the 339 severe HPE cases (that is, with CNS findings; 4.7%). In contrast, no microdeletion was found in the 85 patients at the mildest end of the HPE spectrum. Based on our data, microdeletion testing should be considered as part of an evaluation of holoprosencephaly, especially in severe HPE cases.

Two large Spanish pedigrees with nonsyndromic sensorineural deafness and the mtDNA mutation at nt 1555 in the 12s rRNA gene: evidence of heteroplasmy.

We describe two unrelated Spanish families with isolated sensorineural hearing loss. In both pedigrees, the deafness was transmitted maternally, which suggested a mitochondrial, DNA (mtDNA) defect. Within the same pedigree, some relatives showed aminoglycoside-induced deafness, whereas others were not exposed to aminoglycosides before the onset of hearing loss. Molecular genetic analysis in both families showed the A-to-G transition at nt 1555 (A1555G) in the mitochondrial 12S rRNA gene. In one pedigree, the mutation was homoplasmic; in the other, it was heteroplasmic. To assess the frequency of this mutation, we screened 42 patients of various ethnic backgrounds with isolated sensorineural hearing loss; none harbored the A1555G mutation. This is the first report of heteroplasmy in a family with isolated sensorineural deafness associated with the A1555G mutation.

MELAS point mutation with unusual clinical presentation.

Mitochondrial encephalomyopathy, lactic acidosis and stroke-like episodes (MELAS) is a multisystemic mitochondrial disorder (Pavlakis et al. Advances in Contemporary Neurology. Philadelphia: Davis, 1988: 95-133) and most patients with the typical MELAS phenotype have a point mutation in mitochondrial DNA, an A to G transition at nucleotide 3243 (Goto et al. Nature 1990; 348; 651-653; Koboyashi et al. Biochem Biophys Res Commun 1990; 173: 816-822; Ciafaloni et al. Ann Neurol 1992; 31: 391-398). A 9-yr-old boy presenting with chronic asthma and depression was found to have abnormal mitochondria, partial defects of respiratory chain enzymes, and the MELAS point mutation.

Philadelphia-negative chronic myelogenous leukemia in a patient with a unique complex translocation: 46,XY,t(9;12;15)(q34;12;q21).

Chronic myelogenous leukemia (CML) is associated with an acquired karyotypic abnormality, the Philadelphia (Ph) chromosome, in 95% of cases. The Ph chromosome is the product of a balanced translocation that results in a hybrid gene that is considered essential for the pathogenesis of this disease. We have found a complex translocation involving chromosomes 9, 12, and 15 in a 42-year-old Haitian male with the clinical findings of CML. Complex translocations have been shown to result in the masking of the Ph chromosome. We used a mixture of two BCR-specific DNA probes for Southern blot analysis in order to test this hypothesis in our patient. High-molecular weight DNA was digested with the restriction enzymes BglII, BamHI and HindIII. The BglII digestion revealed the presence of two abnormal fragments of 3.9 and 3.0 kb and the BamHI digestion an abnormal 15-kb fragment. These data suggest there is a breakpoint in region 2 of M-bcr. The identification of this breakpoint confirms our hypothesis that a rearrangement involving 22q11 has occurred in the leukemic cells of our patient. A secondary translocation involving chromosomes 12 and 15 has hidden the effects of this translocation. Combined cytogenetic and molecular analysis establishes the karyotype of our patient as 46,XY,t(9;12;15;22)(q34;q12;q21;q11).

The Marshall syndrome: report of a new family and review of the literature.

The Marshall syndrome is an autosomal dominant trait comprising ocular abnormalities, sensorineural hearing loss, craniofacial anomalies, and anhidrotic ectodermal dysplasia. To our knowledge, only seven additional multigenerational families have been reported since the initial description of the disorder by Marshall in 1958. We present a family in which six members in four generations are affected with apparent Marshall syndrome. We also review and compare similar disorders, such as Stickler, Weissenbacher-Zweimüller, and Wagner syndromes, and conclude that Marshall syndrome is a distinct entity.

The other human genome.

In the past 13 years, a new chapter of human genetics, "mitochondrial genetics", has opened up and is becoming increasingly important in differential diagnosis. Although the clinical manifestations of disorders related to mitochondrial DNA (mtDNA) are extremely variable, recent advances in genetic testing aid in the identification of patients. Muscle morphology can give important clues for diagnosis, but histological features alone cannot define a specific disorder. Biochemical analysis may reveal a single enzyme defect, or when multiple activities are affected, suggest an mtDNA mutation. However, definitive diagnosis often requires DNA analysis and documentation of a specific mtDNA abnormality. Disorders associated with mtDNA mutations are associated with a wide variety of syndromes, and owing to the properties and characteristics of mtDNA, these are often transmitted by maternal inheritance. Although therapy for mitochondrial diseases is limited, identification of the molecular defect is important for genetic counseling.

A common mutation site in the beta-galactosidase gene originates in Puerto Rico.

Several mutation sites have been found in the beta-galactosidase gene of patients with GM1 gangliosidosis. In a previous report we found a common point mutation site in American patients with GM1 gangliosidosis resulting in a 208Arg --> Cys amino acid substitution. From the patients' family history, we suggested that this mutation may have come to South and North America via Puerto Rico. Four new patients with infantile GM1 gangliosidosis have been analyzed with allele-specific hybridization. Two siblings from Puerto Rico of Spanish ancestry are homozygous for this mutation. Another patient also from Puerto Rico is heterozygous for this allele, and another black patient does not have this mutation. These results support our initial hypothesis that this mutation has probably arisen in Puerto Rico.

Hemimaxillofacial dysplasia: a report of two new cases and further delineation of the disorder.

Miles, Lovas, and Cohen first described hemimaxillofacial dysplasia in two patients in 1987. This disorder consists of facial asymmetry, facial hypertrichosis, unilateral maxillary hyperplasia, and hypoplastic teeth. We report two additional cases with similar findings.

Natal molars in Pfeiffer syndrome type 3: a case report.

The following report is the first documented case of natal teeth associated with a recently described new entity, Pfeiffer syndrome type 3. The clinical manifestations consistent with the spectrum of this rare disorder are described with an emphasis on the concomitant natal teeth. Pfeiffer syndrome type 3 is one of the craniosynostosis syndromes and has been described in only two patients to date. Both mandibular incisors and maxillary molar natal teeth were found. Natal teeth are teeth, which are present in the oral cavity at birth. They are often associated with developmental abnormalities and recognized syndromes. Their incidence ranges from 1 in 2,000 to 3,500 births. The natal teeth found in this infant included both the mandibular primary incisors and maxillary primary first molars bilaterally. The clinical and histological considerations of natal teeth and their management are discussed. The presence of multiple natal teeth is extremely rare.

Two novel translocation breakpoints upstream of SOX9 define borders of the proximal and distal breakpoint cluster region in campomelic dysplasia.

The semilethal skeletal malformation syndrome campomelic dysplasia (CD) with or without XY sex reversal is caused by mutations within the SOX9 gene on 17q24.3 or by chromosomal aberrations (translocations, inversions or deletions) with breakpoints outside the SOX9 coding region. The previously published CD translocation breakpoints upstream of SOX9 fall into two clusters: a proximal cluster with breakpoints between 50-300 kb and a distal cluster with breakpoints between 899-932 kb. Here, we present clinical, cytogenetic and molecular data from two novel CD translocation cases. Case 1 with karyotype 46,XY,t(1;17)(q42.1;q24.3) has characteristic symptoms of CD, including mild tibial bowing, cryptorchidism and hypospadias. By standard fluorescence in situ hybridization (FISH) and by high-resolution fiber FISH, the 17q breakpoint was mapped 375 kb from SOX9, defining the centromeric border of the proximal breakpoint cluster region. Case 2 with karyotype 46,X,t(Y;17)(q11.2;q24.3) has the acampomelic form of CD and complete XY sex reversal. By FISH and somatic cell hybrid analysis, the 17q breakpoint was mapped 789 kb from SOX9, defining the telomeric border of the distal breakpoint cluster region. We discuss the structure of the 1 Mb cis-control region upstream of SOX9 and the correlation between the position of the 14 mapped translocation breakpoints with respect to disease severity and XY sex reversal.

A myeloproliferative disorder with eosinophilia associated with a unique translocation (3;5).

An association between eosinophilia and a structural chromosome abnormality has been noted in patients with acute non-lymphoblastic leukaemia (ANLL) and a deletion of the long arm of chromosome 16. There have been a number of other associations of specific chromosome abnormalities with neoplastic diseases involving the eosinophilic lineage; these include chromosome 12 short arm rearrangements, trisomy 8, t(8;21), t(5;14) and t(5;12). We report a patient with a myeloproliferative disorder characterized by chronic eosinophilic leukaemia complicated by autoimmune haemolytic anaemia and a previously unreported translocation (3;5)(p13;q13), and discuss the possible contribution of the RASA gene, localized to 5q13.3, to the development of the malignant phenotype.

Duchenne muscular dystrophy in a girl identified by dystrophin deficiency.

We report an isolated case of a girl aged three years six months with Duchenne muscular dystrophy. Analysis of the patient's DNA with a probe covering the DNA gene revealed no deletion. Dystrophin, studied in biopsied muscle from the patient, using antidystrophin antibody in combination with immunofluorescence, was nearly completely absent. In this sporadic case of female muscular dystrophy, the identification of dystrophin-deficient muscle fibers made it possible to establish an accurate diagnosis of DMD affected female.

A large Alu-mediated deletion, identified by PCR, as the molecular basis for glycogen storage disease type II (GSDII).

Glycogen storage disease type II (GSDII) is an autosomal recessive disorder resulting from inherited deficiency of the enzyme lysosomal acid alpha-glucosidase. Over 40 different mutations have been described but no large deletions have been previously identified. We now describe a homozygous large (9-kb) deletion extending from IVS 15 to 4 kb downstream of the terminal exon (exon 20), detected by polymerase chain reaction (PCR)-based methods. The deletion was initially suspected because of failure to amplify a contiguous group of exons by PCR. We hypothesized an Alu/Alu recombination, based on our prior demonstration by Southern blotting of Alu elements in the regions potentially flanking the deletion. Additional sequence analysis of genomic fragments confirmed the presence of Alu elements and allowed the design of flanking primers for PCR amplification. Amplification resulted in a smaller than normal fragment (0.7 vs. 10 kb) in homozygosity in the proband and in heterozygosity in her parents. Cloning and sequencing of the smaller than normal 0.7-kb deletion fragment revealed an Alu/Alu deletion junction. In heterozygosity this deletion would not be detected by currently standard PCR mutation detection methods. Based on other Alu-mediated deletions, this deletion is likely to be recurrent and should be screened for in all non-consanguineous GSDII patients, particularly when only one mutation has been identified and none of the 12 single-nucleotide polymorphisms in the deleted region are heterozygous. These observations also suggest that initial characterization of genes at disease-causing loci should include a search for Alu and other repetitive elements to facilitate subsequent PCR-based mutation analysis.

Detection of an interstitial deletion of 2q21-22 by high resolution comparative genomic hybridization in a child with multiple congenital anomalies and an apparent balanced translocation.

Various molecular cytogenetic techniques are currently available to accurately characterize chromosome rearrangements in patients with multiple congenital anomalies. Among these is comparative genomic hybridization (CGH) whose main advantage is the ability to perform a whole genome scan without prior knowledge of the underlying chromosome abnormality. It has been used mostly in the area of cancer cytogenetics, but its role in clinical genetics is now expanding to even include preimplantation genetic diagnosis. We have used this method to reveal an interstitial deletion in a patient with multiple anomalies, who had for years been thought to have a de novo balanced translocation involving chromosomes 1 and 2. A review of published reports suggests that there is significant phenotypic and genetic heterogeneity in the small group of patients including our own with interstitial deletions of 2q21-q22.

Simultaneous occurrence of two supernumerary autosomal ring chromosomes r(1) and r(16) in twins.

Ring chromosomes are estimated to occur in 3/10000 newborns and the simultaneous occurrence of two autosomal rings must be a very rare event. Recently, the characterisation of these markers using fluorescence in situ hybridisation (FISH) has greatly enhanced cytogenetic-phenotypic correlations in patients with these marker chromosomes. This kind of analysis enabled us to clarify a unique karyotype containing a r(1) and a r(16) in identical twins born after a 26 week gestation with minimal somatic abnormalities. The origin of the rings was identified using a satellite and whole chromosome painting probes. FISH analysis showed the same abnormal female karyotype in both twins, 48,XX,+r(1)(p13q21),+r(16)(p11q11).ish r(1) (D1Z5+,wcpl+), r(16)(D16Z2+,wcp16+) in about two thirds of the cells. Each also had minor clones with a normal female karyotype or with one or the other supernumerary ring. Half of the r(1) contained CBG band negative material and the r(16) appeared to be totally CBG band positive. These twins represent the second report of the simultaneous occurrence of multiple autosomal rings. Their description may help to delineate a new chromosome disorder and shows the usefulness of FISH analysis.

Prenatal diagnosis of type 2 Pfeiffer syndrome.

Pfeiffer syndrome is an autosomal dominantly inherited disorder consisting of craniosynostosis, a flattened midface with a beaked nose and ocular proptosis, and broad and medially deviated thumbs and great toes. Recently, based on clinical findings, the disorder has been divided into three subtypes: type 1, characterized by mild expression; type 2, in which clover leaf skull deformity and multiple congenital anomalies are present at birth; and type 3, which is similar to type 2, but lacks the presence of the clover leaf skull at birth. We describe a fetus in whom sonographic findings of clover leaf skull deformity, ocular hypertelorism, and varus deformity of the great toe led to the prenatal diagnosis of Pfeiffer syndrome type 2. We believe this is the second prenatal diagnosis of Pfeiffer syndrome, and the first time type 2 has been definitely identified in the second trimester of pregnancy.