Molecular cytogenetics.

In the past decade, clinical cytogenetics has undergone remarkable advancement as molecular biology techniques have been applied to conventional chromosome analysis. The limitations of conventional banding analysis in the accurate diagnosis and interpretation of certain chromosome abnormalities have largely been overcome by these new technologies, which include fluorescence in situ hybridization (FISH), comparative genomic hybridization (CGH), and multicolor FISH (M-FISH, SKY, and Rx-FISH). Clinical applications include diagnosis of microdeletion and microduplication syndromes, detection of subtelomeric rearrangements in idiopathic mental retardation, identification of marker and derivative chromosomes, prenatal diagnosis of trisomy syndromes, and gene rearrangements and gene amplification in tumors. Molecular cytogenetic methods have expanded the possibilities for precise genetic diagnoses, which are extremely important for clinical management of patients and appropriate counseling of their families.

Survey of the fragile X syndrome CGG repeat and the short-tandem-repeat and single-nucleotide-polymorphism haplotypes in an African American population.

Previous studies have shown that specific short-tandem-repeat (STR) and single-nucleotide-polymorphism (SNP)-based haplotypes within and among unaffected and fragile X white populations are found to be associated with specific CGG-repeat patterns. It has been hypothesized that these associations result from different mutational mechanisms, possibly influenced by the CGG structure and/or cis-acting factors. Alternatively, haplotype associations may result from the long mutational history of increasing instability. To understand the basis of the mutational process, we examined the CGG-repeat size, three flanking STR markers (DXS548-FRAXAC1-FRAXAC2), and one SNP (ATL1) spanning 150 kb around the CGG repeat in unaffected (n=637) and fragile X (n=63) African American populations and compared them with unaffected (n=721) and fragile X (n=102) white populations. Several important differences were found between the two ethnic groups. First, in contrast to that seen in the white population, no associations were observed among the African American intermediate or "predisposed" alleles (41-60 repeats). Second, two previously undescribed haplotypes accounted for the majority of the African American fragile X population. Third, a putative "protective" haplotype was not found among African Americans, whereas it was found among whites. Fourth, in contrast to that seen in whites, the SNP ATL1 was in linkage equilibrium among African Americans, and it did not add new information to the STR haplotypes. These data indicate that the STR- and SNP-based haplotype associations identified in whites probably reflect the mutational history of the expansion, rather than a mutational mechanism or pathway.

X-linked mental retardation syndrome with characteristic "coarse" facial appearance, brachydactyly, and short stature maps to proximal Xq.

We describe a three-generation family in which X-linked mental retardation (XLMR) is associated with minor facial anomalies and brachydactyly. Two brothers and four nephews have "coarse" facial appearance, brachydactyly with widening of the distal phalanges, short stature, and moderate mental retardation. The three obligate carrier women have normal intelligence and normal physical findings. The results of linkage analysis carried out in 1988 using restriction fragment length polymorphisms (RFLPs) were suggestive of linkage to DXYS1 and DXS101 in proximal Xq (Zmax = 1.63 at straight thetamax = 0.0) [Carpenter et al., 1988: Am J Med Genet 43:A139]. The family was restudied with 16 microsatellite loci from Xp11.4 through Xq24. Linkage analysis demonstrated significant linkage to DXS1003, ALAS2, AR, DXS986, DXS990, DXS454, DXS1106, DXS1105, and DXS1220 from Xp11.3 to Xq23 (Zmax = 2.53 at straight thetamax = 0.0). Recombinations detected between MAOB and DXS1055 and between DXS1220 and DXS1001 place the disease locus between Xp11.3 and Xq23. Among the genes known to map to this region is the XNP gene for the alpha-thalassemia/mental retardation syndrome (ATR-X). This fact, along with the phenotypic similarity between our patients and ATR-X males, led us to consider XNP as a candidate gene for this family. X-inactivation studies provided further evidence for the involvement of XNP by showing completely skewed X-inactivation patterns in the three obligate carrier females, a pattern characteristic of carriers of XNP mutations.

Regional localization of a nonspecific X-linked mental retardation gene (MRX59) to Xp21.2-p22.2.

Linkage analysis was performed on a four-generation family with nonspecific mental retardation (MRX59). The five affected males, ranging in age from 2 years to 52 years, have a normal facial appearance and mild to severe mental impairment. Four obligate carriers are physically normal and not retarded. A maximum LOD score of 2.41 at straight theta = 0.00 was observed with the microsatellite markers, DMD45 in Xp21.2, DXS989 in Xp22.1, and DXS207 in Xp22.2. Recombinations were detected within the dystrophin gene (DMD) in one of the affected males and between DXS207 and DXS987 in Xp22.2 in one of the carriers. These recombinants define the proximal and distal boundaries of a candidate gene region. Genetic localization of this familial condition made prenatal diagnosis informative for one of the obligate carriers.

Age-related language characteristics of children and adolescents with fragile X syndrome.

In addition to moderate-to-severe mental retardation (MR), the fragile X [fra(X)] mutation produces significant impediments in speech and language. Severe delays in speech and language have been demonstrated in both adult males and young individuals with the fra(X) mutation. Having observed longitudinal declines in IQ scores in young males with fra(X) and given the relationship between cognitive ability and language skill, we wanted to determine whether speech-language deficits in young males with fra(X) were age-related in ways comparable with those observed in cognitive deficits. We examined a small sample (n = 16) of children and adolescents, ages 6-17 years, using the Clinical Evaluation of Language Fundamental-Preschool (CELF-P). The CELF-P is used to evaluate language deficits in preschool children and assesses receptive and expressive language ability. It is standardized for children ages 3-7 years and provides age-normed standard scores. To evaluate changes in language scores, we converted raw scores into age-equivalents. Results indicate that males with fra(X) have significantly lower age equivalent scores compared with females. A cross-sectional analysis of males' age-equivalent scores reveals that a plateau is reached at approximately 48 months. Our findings suggest that, as with IQ and adaptive behavior scores, language development in young, fully mutated fra(X) individuals appears to reach a plateau as they age.

Longitudinal assessment of adaptive and maladaptive behaviors in fragile X males: growth, development, and profiles.

As young fully mutated fragile X [fra(X)] males age, cognitive levels (IQ scores) and adaptive behavior levels (DQ scores) decline. Given the variable behavioral profiles reported previously, we wondered whether changes in specific attributes of adaptive behavior are related to declines in composite adaptive behavior levels. We also examined maladaptive behavior to determine if changes are related to age. Therefore, we evaluated three areas of adaptive behavior, as well as maladaptive behavior, in 28 fully mutated fra(X) males, ages 4-14 years. To develop a profile of adaptive behavior, we analyzed nine subscale scores from the Vine-land Adaptive Behavior Scale (VABS). To assess maladaptive behavior, we graded part I of the VABS Maladaptive Behavior Scale. Subjects were sorted into three age cohorts, according to their initial test age: younger than 6 years; 6 to 9 years; older than 9 years. Results indicate that, in all age groups, the communications domain is the most severely impacted compared with either the socialization domain or daily living skills and that, in all age groups, the socialization domain is a relative strength compared with either the communications domain or daily living skills. The youngest cohort manifested significant increases in age-equivalent community living skills. Significant differences in age-equivalent scores between cohorts were observed in written language and play skills. Maladaptive behavior scores were available from cross-sectional data only. Twenty males (74%) showed significantly higher maladaptive scores than expected from other children their age. Our data analysis also revealed a moderate and significant negative correlation between maladaptive behavior levels and age (r = -0.54; P < 0.01). Curiously, adaptive and maladaptive behaviors did not correlate with each other.

Clinical applications of primed in situ labelling (PRINS) rapid identification of a marker chromosome in a fetus.

Marker chromosomes pose a serious problem in clinical cytogenetic diagnosis since the conventional banding analyses are often not useful in identifying their origin or composition. In the absence of information, counseling as to the clinical significance and prognosis is difficult, especially in prenatal diagnosis. With the introduction of fluorescence in situ hybridization (FISH) marker identification has became feasible. However, FISH is relatively time-consuming and expensive. In an effort to overcome these disadvantages, we have used primed in situ labelling (PRINS) technique as an alternative. Presented here is one case in which PRINS was useful in rapidly identifying the origin of a marker chromosome detected on amniotic fluid chromosome analysis. Based on our experience with this case and others, we propose that PRINS can become a viable and cost effective alternative to FISH and is as reliable as FISH in terms of accuracy, specificity, and sensitivity.

Technical pitfalls encountered in PCR quantification using microsatellites.

Quantitative PCR has proved useful for different purposes, including the detection of particular genetic changes, such as deletions and duplications in several inherited disorders. Using patients with the known duplication mutation for Charcot-Marie-Tooth disease Type 1A as examples, the importance of selecting informative microsatellite loci and proper electrophoretic conditions so as to eliminate potential sources of error in quantitative PCR studies is discussed.

Charcot-Marie-Tooth disease type 1A: a family study with microsatellites.

Charcot-Marie-Tooth (CMT) disease (also called Hereditary Motor and Sensory Neuropathy) is an inherited peripheral neuropathy with a prevalence rate of 1 in 2,500. Charcot-Marie-Tooth disease type 1A (CMT1A), the most common autosomal dominant form of the disease, is associated with a duplication of a segment of chromosome 17 (17p11.2). In this report we present a three-generation family with CMT1A where simple sequence repeats (di- or tri-nucleotide repeats, also called microsatellites) were used in conjunction with polymerase chain reaction (PCR) to identify the duplication. The presence of three alleles or the presence of two alleles with a dosage ratio of 1:2 for the markers D17S839 and D17S921 indicates the presence of the duplicated segment in affected family members, whereas two alleles with a ratio of 1:1 indicate absence of the duplication. Several markers outside the duplication region which have two alleles with a dosage ratio of 1:1 were used as controls. Seven CMT1A patients in this family carry the CMT1A duplication. One 12-year-old boy who has not exhibited any clinical symptoms does not have the CMT1A duplication. We believe that this is a simple, rapid, and effective method to identify the CMT1A duplication in most patients suspected of having CMT1A.

Familial deletion of chromosome 18 (p11.2).

Familial transmission of del (18p) syndrome from a mother to her daughter is rare and has been reported only once before. We report a female patient referred to us at age 18 years because of mental retardation associated with short stature. Similar clinical features are also seen in her mother. Chromosome analysis revealed a 46,XX, del (18) (p11.2) karyotype in both the proposita and her mother. Fluorescence in situ hybridization with whole chromosome paint for chromosome 18 showed no evidence of translocation. Because of the familial transmission of del (18p), this case has wider implications in genetic counseling.

Partial trisomy 13q identified by sequential fluorescence in situ hybridization.

We report on a 19-month-old boy with partial trisomy 13q resulting from a probable balanced translocation involving chromosomes 1 and 13. The infant presented with omphalocele, malrotation, microcephaly with overriding skull bones, micrognathia, apparently low-set ears, rocker-bottom feet, and congenital heart disease, findings suggestive of trisomy 13. Karyotypic studies from peripheral blood lymphocytes documented an unbalanced karyotype 46,XY,-1,+der(1). The mother's chromosomes were normal, and the father was not available. Conventional cytogenetic techniques were unable to identify the extra material on the terminal 1q. Using fluorescence in situ hybridization (FISH) on the GTL-banded metaphases, the extra material on 1q was identified as the terminal long arm of 13, thus resulting in partial trisomy 13 (q32-qter).

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.

Genetic anticipation. Expanding tandem repeats.

The recent discovery that expanding trinucleotide repeats are a form of mutation is a radical departure from the traditional genetic principles of inheritance based on the stable transmission of DNA sequences. The concept that a gene may be altered from tissue to tissue in a single individual or from one generation to the next and that it may confer increasing mutability on itself has provided some insight into the phenomenon of anticipation as manifested by increasing severity, declining age of onset, and increasing penetrance in several inherited disorders. This concept raises the question of how common this mutational mechanism may be in the causes of genetic disease. For example, expansions of trinucleotide repeats may be the underlying mechanism for other disorders that show features suggestive of anticipation such as schizophrenia, bipolar affective disorder, autism and other hereditary ataxias. Expressed genes with trinucleotide repeats have been observed in fetal and adult brains. A recent approach to identifying expanded repeats may simplify the process of finding candidate genes. It is intriguing to speculate how often observations such as intrafamilial variation and even new mutations may be due to such a mechanism. Systematic studies of families with disorders found to be associated with such repeats will be necessary. The implications in genetic counseling for prediction of postnatal outcome as well as risks of recurrence are truly staggering. Meanwhile, the immediate benefit of the knowledge of trinucleotide repeat expansions concerning the six disorders discussed will be the application of direct methods of diagnosis avoiding linkage analysis. The long-term benefits may very well be the discovery of more effective treatment modalities based on correction of the gene defects. Exciting times for human genetics appear to be at hand.

Maternal serum free beta hCG screening: results of studies including 480 cases of Down syndrome.

The median maternal serum free beta human chorionic gonadotropin (hCG) multiple of the median (MOM) of 480 Down syndrome cases in the second trimester was 2.64, significantly greater than the reported median MOM of intact hCG (p < 0.0001). In 234 of these cases from retrospective and prospective studies, the effectiveness of maternal serum free beta hCG was evaluated in combination with alpha-fetoprotein (AFP) and maternal age in second-trimester Down syndrome screening. Down syndrome detection in the gestational age range of 14-16 weeks was 82 per cent. In all gestational weeks (14-22), a 77.7 per cent Down syndrome detection rate was achieved. In prospective screening of 44,272 patients under the age of 35 years, 69 per cent of Down syndrome cases were detected (73 per cent in gestational weeks 14-16). The false-positive rate for the prospective study was 3.8 per cent. The use of free beta hCG combined with maternal serum AFP and maternal age-related risk for Down syndrome in a screening population (i.e., women under 35 years) yields an improved detection efficiency over other protocols.