Karyotype/phenotype controversy: genetic and molecular implications of alternative hypotheses

Five cases of supernumerary small ring chromosomes 1: Heterogeneity and genotype–phenotype correlation

Genetic counselling of patients with small supernumerary ring chromosomes (sSRCs) can be difficult, especially in prenatal testing, due to the complexity in establishing a karyotype-phenotype correlation. In fact, it has been estimated that about 10% of extra ring(1) chromosomes are associated with an unremarkable phenotype. We report on five new cases of extra ring chromosomes(1) manifesting different clinical outcome. One case was familial, segregating from a mother with mosaic karyotype, while the others were de novo. Ring chromosomes were characterised by FISH. In three subjects the involvement of the same euchromatic 1p region was demonstrated. Present observations corroborate previous results and provide some insight into the identification of the harmless ring(1) structures.

Molecular karyotyping of patients with MCA/MR: the blurred boundary between normal and pathogenic variation

Molecular karyotyping has revealed that microdeletions/duplications in the human genome are a major cause of multiple congenital anomalies associated with mental retardation (MCA/MR). The identification of a de novo chromosomal imbalance in a patient with MCA/MR is usually considered causal for the phenotype while a chromosomal imbalance inherited from a phenotypically normal parent is considered as a benign variation and not related to the disorder. Around 40% of imbalances in patients with MCA/MR in this series is inherited from a healthy parent and the majority of these appear to be (extremely) rare variants. As some of these contain known disease-causing genes and have also been found to be de novo in MCA/MR patients, this challenges the general view that such familial variants are innocent and of no major phenotypic consequence. Rather, we argue, that human genomes can be tolerant of genomic copy number variations depending on the genetic and environmental background and that different mechanisms play a role in determining whether these chromosomal imbalances manifest themselves.

Directly transmitted unbalanced chromosome abnormalities and euchromatic variants

In total, 200 families were reviewed with directly transmitted, cytogenetically visible unbalanced chromosome abnormalities (UBCAs) or euchromatic variants (EVs). Both the 130 UBCA and 70 EV families were divided into three groups depending on the presence or absence of an abnormal phenotype in parents and offspring. No detectable phenotypic effect was evident in 23/130 (18%) UBCA families ascertained mostly through prenatal diagnosis (group 1). In 30/130 (23%) families, the affected proband had the same UBCA as other phenotypically normal family members (group 2). In the remaining 77/130 (59%) families, UBCAs had consistently mild consequences (group 3). In the 70 families with established EVs of 8p23.1, 9p12, 9q12, 15q11.2, and 16p11.2, no phenotypic effect was apparent in 38/70 (54%). The same EV was found in affected probands and phenotypically normal family members in 30/70 families (43%) (group 2), and an EV co-segregated with mild phenotypic anomalies in only 2/70 (3%) families (group 3). Recent evidence indicates that EVs involve copy number variation of common paralogous gene and pseudogene sequences that are polymorphic in the normal population and only become visible at the cytogenetic level when copy number is high. The average size of the deletions and duplications in all three groups of UBCAs was close to 10 Mb, and these UBCAs and EVs form the "Chromosome Anomaly Collection" at http://www.ngrl.org.uk/Wessex/collection. The continuum of severity associated with UBCAs and the variability of the genome at the sub-cytogenetic level make further close collaboration between medical and laboratory staff essential to distinguish clinically silent variation from pathogenic rearrangement.

Limb deficiencies in infants with trisomy 13

In 1994, we published a case with trisomy 13 who presented with ectrodactyly [Urioste et al., 1994: Am J Med Genet 53:390-392]. Recently, Kuschel and Gillessen-Kaesbach [2000: Am J Med Genet 90:87-88] presented an infant with trisomy 13 who also had oligodactyly, and they considered their case as the second published with oligodactyly. Here, we present three cases with any type of limb deficiencies who, together with the one that was published previously [Urioste et al., 1994], correspond to the total of 75 cases with trisomy 13 identified in the Spanish Collaborative Study of Congenital Malformations (ECEMC). This gives us a minimum frequency of 5.33% (CI:1.45-13.65) for trisomy 13 cases having limb deficiencies whereas these defects have a frequency of 5.51 per 10,000 births in our population. Consequently, we think that limb deficiencies could be considered as one of the defects that constitute the spectrum of anomalies observed in infants with trisomy 13.

The Down syndrome critical region

Since the early 1970's numerous attempts have been made to learn whether specific segments of chromosome 21, when triplicated, are responsible for the clinical condition Down syndrome (DS). Studies were reported in which positive or negative clinical diagnoses of DS were made in the presence of partial trisomy of one or another segment of the chromosome. The distal half of the long arm of 21 (21q22) possesses most of the gene transcribing sites of the chromosome. It was this region that was thought to contain loci essential to production of the clinical syndrome. Subsequent studies identified subregions of this band as "minimal" or "critical" sites necessary and sufficient to produce the clinical condition. A major problem with these assignments was that different investigators defined different critical/minimal regions. In 1994 evidence was presented in which regions of most of the long arm of chromosome 21 were said to contribute to the DS phenotype. Soon after, a report described a child with DS and partial tetrasomy of the short arm and proximal long arm of 21, segments clearly distinct from the previously identified critical areas. Thus the clinical diagnosis of DS can be made in the presence of partial aneuploidy of nearly all segments of chromosome 21. It must be concluded that no evidence exists that individual loci on 21 are singularly responsible for specific phenotypic abnormalities in DS. Without exception, each of the clinical findings associated with DS is a multifactorial trait. The analysis of each trait in DS should thus be similar to analyses of the same traits in the general population with a focus on the way aneuploidy affects expression of multifactorial characteristics.

Interstitial tandem duplication of 6p: a case with partial trisomy (6)(p12p21.3)

A de novo interstitial tandem duplication of 6p12p21.3 was observed in a 7-month-old boy with growth retardation, psychomotor delay and craniofacial, brain, limb, and genital anomalies. Fluorescent in situ hybridization using a chromosome 6 paint probe demonstrated that the extra material belonged to chromosome 6. Although it has been suggested that 6p25 is the critical band involved in the expression of the phenotype of 6p duplication, comparison of the clinical findings of this case with those from the literature cases showed strong similarities.

Mild "duplication 6q syndrome": a case with partial trisomy (6)(q23.3q25.3)

We report on a female infant with partial 6q trisomy (46,XX,dir dup(6)(q23.3q25.3)) and phenotypic characteristics of the "duplication 6q syndrome," including intrauterine growth retardation, dolichocephaly, depressed nasal bridge, almond-shaped palpebral fissures, short neck, flexion-contractures of the wrists, and mild generalized hypertonia. Although clearly belonging to the described "duplication 6q syndrome," her features were milder than those found in the literature. Comparison of the phenotype of this child with other published reports indicates that specific phenotypic components of the duplication 6q syndrome cannot be attributed to duplication of a specific band or bands on 6q.

A case of duplication of 13q32-->qter and deletion of 18p11.32-->pter with mild phenotype: Patau syndrome and duplications of 13q revisited

A mild clinical phenotype is described in a patient with duplication of 13q32-->qter and a small deletion of 18p11.32-->pter. The 8 year old white male presented with psychomotor retardation, tethered cord, soft, fleshy ears, and normal facial features except for thin lips. The karyotype was found to be 46, XY, der(18)t(13;18) (q32;p11.32) pat confirmed by fluorescence in situ hybridisation (FISH). A review of earlier studies showed that features of trisomy 13 are found in cases of duplication of bands 13q14 to qter. None of the cardinal features of trisomy 13 was seen in this patient. The absence of polydactyly, hernias, urogenital abnormalities, and haemangiomas contrast this condition with both trisomy 13 and duplication of 13q14-22-->qter. Possible explanations for lack of Patau syndrome in this patient could include restriction of the critical region for Patau syndrome to duplication 13q14-->13q32 with variable expression, gene interactions, or interchromosomal effects.

Impact of rearrangements on function and position of chromosomes in the interphase nucleus and on human genetic disorders

A synthesis of numerous published data and my own observations reveal that chromatin structure in interphase is functional, dynamic and complex. I hypothesize that: (1) chromosome regions organize nuclear structures and thus their own environment (address themselves in sites and condensation patterns most appropriate for their functional state in the particular cell); (2) chromosome rearrangement could alter nuclear architecture and thus function; and (3) these ideas can explain the contribution of chromosome rearrangements, even in a balanced form, to human pathologic conditions.

Ear length: a potential sonographic marker for Down syndrome

OBJECTIVES

The purpose of this study was to determine if antenatal sonographic determination of fetal ear length is a useful screening method for identification of fetuses with Down syndrome.

METHODS

Ear length measurements were recorded in 418 fetuses undergoing ultrasound scanning between 20 and 28 weeks of gestation. Four trisomy 21 and six trisomy 18 fetuses were identified by karyotyping. The relationship between ear length and gestational age in the normal population was determined by linear regression analysis: expected ear length = -6.000 + 1.075 gestational age. The ability of measured-to-expected ear length cut-off ratios to discriminate between affected and non-affected fetuses was assessed.

RESULTS

The mean ear length and measured-to-expected ear length ratios were significantly lower in the affected group as compared to the normal one. A measured-to-expected ear length ratio of less than 0.8 was 75.0% sensitive and 98.8% specific in detecting Down syndrome fetuses, and resulted in an 8.5% positive predictive value in the general population.

CONCLUSIONS

This preliminary study suggests that antenatal ear length measurements might be a promising sonographic screening method for the detection of Down syndrome in the second trimester of pregnancy.

Three cases of dup(10p)/del(10q) syndrome resulting from maternal pericentric inversion

Two families and 3 patients with dup(10p)/del(10q) syndrome segregating from a maternal pericentric inversion are described, including a stillborn female with Potter sequence and multicystic renal dysplasia. Comparison of 32 dup(10p) patients to 11 del(10)(q25) patients emphasized dolichocephaly, wide sutures, frontal bossing, micrognathia, and renal defects as distinguishing characteristics of the dup(10p) syndrome. The 3 new and 6 previously reported dup(10p)/del(10q) patients had several manifestations in common with the dup(10p) and del(10q) syndromes, but were more typical of dup(10p) syndrome with respect to all 5 distinguishing characters.

Chromosomal and genetic forms of growth failure

This chapter does not deal with single diseases, but gives a general account of chromosomal and genetically caused disturbances of growth; even a complete list and description of the various disorders would, in view of the large number of syndromes involving short stature, exceed its scope. Many chromosomal aberrations are non-viable disturbances of growth that lead to intrauterine amniotic death. Following a brief account of the normal development of the germ cell (gametogenesis, embryogenesis, phenogenesis) to the newborn, the incidence of the various chromosomal disturbances in the different stages of development and the effects on growth are discussed. In the case of chromosomal aberrations, particular attention is paid to the significance of mosaic formation. In addition, the new phenomena of genomic imprinting and uniparental disomy, exemplified by the Prader-Willi syndrome, are dealt with. Uniparental disomy, which was first demonstrated with the aid of molecular genetics, may provide an explanation for the sporadic appearance of many syndromes involving short stature. Many genes and environmental influences are involved in the individual shaping of body size so that a systematic classification of the various syndromes involving short stature is not possible. Finally, attention is drawn to the increased rate of formation of malignant tumours in certain syndromes involving disturbances of growth.

Karyotype/phenotype correlation in females with short stature

We studied 60 females who presented with short stature. The main aim was to determine the effect of karyotype variation on phenotype. A somatic feature score was calculated for each case depending on the presence of 17 clinical somatic changes known to occur in Turner syndrome. Karyotype studies showed the following results: 45,X (n = 22): 46,XX (n = 11); 45,X/46,XX (n = 10); 46,XX/46,Xi(Xq) (n = 4); 46,XX/46,XXq- (n = 3); 46,XX/46,XXp- (n = 2); 46,Xi(Xq) (n = 2); 45,X/46,Xi(Xq) (n = 2); 46,XXp- (n = 1); 46,XX/47,XXX (n = 1); 46,XXq- (n = 1); 45,X/46,X(ry) (n = 1). Karyotype/phenotype correlation showed the gradation of severity of clinical phenotype to be related to the number of X chromosomes. The highest somatic scores and the most severe clinical manifestations were noted in cases of pure 45,X Turner and the mildest in 46,XX/46,XX(str) mosaics or pure 46,XX, including hypergonadotrophic hypogonadism. Our findings revealed a dosage effect of the X chromosome on phenotype, thus confirming that partial X chromosome inactivation modifies somatic and pubertal development. Our results also support both the additive and interactive hypotheses of karyotype/phenotype correlation.

Genomics of human dysmorphogenesis

A survey of Mendelian Inheritance in Man emphasizes the large Mendelian contribution to human dysmorphogenesis and contrasts single gene conditions with chromosomal disorders. There were 1761 conditions that involved altered morphogenesis (49% of disease entries), including 1040 multiple defect syndromes and 721 inherited single birth defects. Premature death (36-57%), mental retardation (20-59%), and growth retardation (37-59%) are more frequent in autosomal recessive or X-linked syndromes, while predisposition to tumorigenesis was more common in dominant (16%) than recessive (3.4%) syndromes. Comparison of the Mendelian conditions with 100 chromosomal disorders showed a strikingly similar spectrum of malformation, with skeletal, craniofacial, eye, epidermal, and neuromuscular systems being most frequently affected. Chromosomal syndromes average 10.6 systems affected per disorder, in contrast to 3.55 for Mendelian syndromes, and pleiotropy does correlate weakly with aneuploid segment length. Genomic understanding of these relationships is still primitive, with 74 of 1609 (4.6%) autosomal conditions and 43 of 152 (29%) X-linked conditions mapped to specific chromosomal regions. The societal toll of human dysmorphogenesis and the evident progress with X-linked disorders provide a powerful rationale for the Human Genome Project.