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Purpose: Copy number variants have emerged as a major cause of human disease such as autism and intellectual disabilities. Because copy number variants are common in normal individuals, determining the functional and clinical significance of rare copy number variants in patients remains challenging. The adoption of whole-genome chromosomal microarray analysis as a first-tier diagnostic test for individuals with unexplained developmental disabilities provides a unique opportunity to obtain large copy number variant datasets generated through routine patient care.Methods: A consortium of diagnostic laboratories was established (the International Standards for Cytogenomic Arrays consortium) to share copy number variant and phenotypic data in a central, public database. We present the largest copy number variant case-control study to date comprising 15,749 International Standards for Cytogenomic Arrays cases and 10,118 published controls, focusing our initial analysis on recurrent deletions and duplications involving 14 copy number variant regions.Results: Compared with controls, 14 deletions and seven duplications were significantly overrepresented in cases, providing a clinical diagnosis as pathogenic.Conclusion: Given the rapid expansion of clinical chromosomal microarray analysis testing, very large datasets will be available to determine the functional significance of increasingly rare copy number variants. This data will provide an evidence-based guide to clinicians across many disciplines involved in the diagnosis, management, and care of these patients and their families.

We describe a patient with striking generalized symmetrical enchondromatosis of the tubular bones and a de novo duplication of chromosome 12p11.23 to 12p11.22. The PTHLHgene within this region encodes a ligand for PTHR1: mutations in the gene encoding this receptor are associated with some cases of Ollier disease, several skeletal dysplasias including Blomstrand, Eiken, and Jansen and down‐regulation of PTHLHexpression in brachydactyly type E. Our findings suggest that abnormal PTHLH‐PTHR1signaling may underly this unusual form of enchondromatosis and indicate that unlike most cases of Ollier disease it is dominantly inherited. © 2010 Wiley‐Liss, Inc.

Monosomy 1p36 is the most common terminal deletion syndrome seen in humans, occurring in ∼1 in 5,000 live births. Common features include mental retardation, characteristic dysmorphic features, hypotonia, seizures, hearing loss, heart defects, cardiomyopathy, and behavior abnormalities. Similar phenotypes are seen among patients with a variety of deletion sizes, including terminal and interstitial deletions, complex rearrangements, and unbalanced translocations. Consequently, critical regions harboring causative genes for each of these features have been difficult to identify. Here we report on five individuals with 200–823 kb overlapping deletions of proximal 1p36.33, four of which are apparently de novo. They present with features of monosomy 1p36, including developmental delay and mental retardation, dysmorphic features, hypotonia, behavioral abnormalities including hyperphagia, and seizures. The smallest region of deletion overlap is 174 kb and contains five genes; these genes are likely candidates for some of the phenotypic features in monosomy 1p36. Other genes deleted in a subset of the patients likely play a contributory role in the phenotypes, including GABRDand seizures, PRKCZand neurologic features, and SKIand dysmorphic and neurologic features. Characterization of small deletions is important for narrowing critical intervals and for the identification of causative or candidate genes for features of monosomy 1p36 syndrome. © 2010 WileyLiss, Inc.

This study was an investigation of 90 patients referred to the Wessex Regional Genetics Laboratory for and negative by molecular cytogenetic analysis using array comparative genomic hybridization. This patient cohort represents typical referrals to a regional genetic centre. Methylation analysis was performed at 13 imprinted loci PLAGL1, IGF2R, MEST, GRB10, H19, IGF2 DMR2IGF2P0, KCNQ1OT1KvDMR, MEG3, SNRPN, PEG3, GNASGNASexon 1a and NESP55 and GNASAS. In total 690 6.67 were shown to have a methylation defect, 2 of which were associated with known imprinting disorders: 1 patient had isolated hypomethylation at IGF2P0, an atypical epigenotype associated with Russell–Silver syndrome, and 1 showed hypomethylation at KvDMRconsistent with a diagnosis of Beckwith–Wiedemann syndrome. A further 4 patients, 3 exhibiting complete hypermethylation, and 1 partial hypomethylation, had aberrations at IGF2R, the clinical significance of which remains unclear. This study demonstrates the potential utility of epigenetic investigation in routine diagnostic testing. © 2010 WileyLiss, Inc.

Trisomy and tetrasomy of distal chromosome 15q have rarely been reported. Although most of the described patients have some learning difficulties and are overgrown, the phenotype associated with distal trisomytetrasomy 15q is uncertain due to the small numbers of reported cases and the common cooccurrence of additional chromosome deletions in many patients with trisomy 15q. We present five individuals with overgrowth, learning difficulties and increased dosage of distal 15q. Partial trisomy 15q was identified in four of these cases. Two were generated through recombination of a parental pericentric inversion and two were generated through malsegregation of a maternal balanced 14;15 reciprocal translocation. In all four cases the trisomy can be considered “pure” as the 14p and 15p monosomies will exert no phenotypic effect. Partial tetrasomy 15q, as the result of an analphoid supernumerary chromosome derived from an inverted duplication of distal 15q, was identified in the fifth patient. In addition to the overgrowth and learning difficulties, all five had a characteristic facial appearance and three had renal anomalies. The gestalt consists of a long, thin face with a prominent chin and nose. Renal anomalies included renal agenesis, horseshoe kidney, and hydronephrosis. We provide further support for a distinct “15q overgrowth syndrome” caused by either trisomy or tetrasomy resulting in increased dosage of distal 15q. In addition we propose that renal anomalies and a distinctive facial appearance be considered major features of this condition. © 2009 WileyLiss, Inc.

We present a patient with a novel heterozygous deletion of 7q11.22–q11.23. Standard cytogenetic analysis using the ELNcosmid 82C and the ELNLIMK1cosmid 34B FISH probes suggested a diagnosis of Williams syndrome. Although he has supravalvular aortic stenosis and peripheral pulmonary artery stenosis, which are common in this condition, he does not have the clinical gestalt of Williams syndrome. 44k oligo array CGH analysis showed a 2.43 Mb deletion, encompassing the proximal 1.43 kb of the Williams syndrome critical region and extending approximately 1 Mb beyond it. The deletion of further genes outside the Williams syndrome critical region does not appear to be having a phenotypic effect at present. © 2008 WileyLiss, Inc.

Langer–Giedion syndrome results from a microdeletion at 8q24.1 encompassing the EXT1and the adjacent TRPS1gene. We report on a boy with an oligo arraycgh characterized small microdeletion involving EXT1alone but with some features of Langer–Giedion syndrome suggesting a functional disturbance of TRPS1. This boy, in addition to a mild Langer–Giedion like phenotype, also had some unusual features including prominent toe pads and fat pads on the soles of his feet similar to those described in Pierpont syndrome. © 2008 WileyLiss, Inc.

CONTEXT: Heterozygous, de novo mutations in the transcription factor SOX2 are associated with bilateral anophthalmia or severe microphthalmia and hypopituitarism. Variable additional abnormalities include defects of the corpus callosum and hippocampus. OBJECTIVE: We have ascertained a further three patients with severe eye defects and pituitary abnormalities who were screened for mutations in SOX2. To provide further evidence of a direct role for SOX2 in hypothalamo-pituitary development, we have studied the expression of the gene in human embryonic tissues. RESULTS: All three patients harbored heterozygous SOX2 mutations: a deletion encompassing the entire gene, an intragenic deletion (c.70_89del), and a novel nonsense mutation (p.Q61X) within the DNA binding domain that results in impaired transactivation. We also show that human SOX2 can inhibit β-catenin-driven reporter gene expression in vitro, whereas mutant SOX2 proteins are unable to repress efficiently this activity. Furthermore, we show that SOX2 is expressed throughout the human brain, including the developing hypothalamus, as well as Rathke’s pouch, the developing anterior pituitary, and the eye. CONCLUSIONS: Patients with SOX2 mutations often manifest the unusual phenotype of hypogonadotropic hypogonadism, with sparing of other pituitary hormones despite anterior pituitary hypoplasia. SOX2 expression patterns in human embryonic development support a direct involvement of the protein during development of tissues affected in these individuals. Given the critical role of Wnt-signaling in the development of most of these tissues, our data suggest that a failure to repress the Wnt-β-catenin pathway could be one of the underlying pathogenic mechanisms associated with loss-of-function mutations in SOX2.

A series of 125 patients referred primarily with aniridia classified as either sporadic (74), familial (24), or in association with WAGR syndrome (14) or other malformations (13) was analysed for mutations, initially by karyotyping and targeted FISH analysis of chromosome 11p13. These methods identified mutations in a significant proportion of patients, 34/125 (27%). Two cases had chromosome rearrangements involving 11p13, 16 cases had visible deletions, and 16 cases had cryptic deletions identified by FISH. The frequency of cryptic deletions in familial aniridia was 27% and in sporadic isolated aniridia was 22%. Of the 14 cases referred with WAGR syndrome, 10 (71%) had chromosomal deletions, 2 cryptic and 8 visible. Of the 13 cases with aniridia and other malformations, 5 (38%) had a chromosomal rearrangement or deletion. In 37 cases with no karyotypic or cryptic chromosome abnormality, sequence analysis of the PAX6 gene was performed. Mutations were identified in 33 cases; 22 with sporadic aniridia, 10 with familial aniridia and 1 with aniridia and other non‐WAGR syndrome associated anomalies. Overall, 67 of 71 cases (94%) undergoing full mutation analysis had a mutation in the PAX6 genomic region. © 2008 Wiley‐Liss, Inc.

Trisomy 6 is seen in early miscarriages in association with an intact, empty amniotic sac or as a pseudomosaic in amniotic fluid cultures. We report the finding of mosaic trisomy 6 in a 23‐week‐gestation pregnancy terminated because of intrauterine death. The post‐mortem showed a well formed macerated male fetus with an atrioventricular septal defect and an exomphalos. By conventional cytogenetics, trisomy 6 was found in 12 out of 25 (48%) fibroblast colonies from fetal skin and 21 out of 32 (66%) colonies derived from amnion, while the remaining metaphases showed an apparently normal male karyotype. Molecular genetic studies on DNA from uncultured fetal skin and cord samples using polymorphic microsatellite repeat sequences showed no evidence of trisomy 6, but demonstrated that both chromosome 6 homologs were of maternal origin consistent with maternal uniparental disomy (UPD). © 2006 Wiley‐Liss, Inc.

We report on a 30‐month‐old baby girl with typical clinical features of WAGR syndrome. In addition, the patient showed bilateral preaxial polydactyly of the feet. Cytogenetic and fluorescent in situ hybridization (FISH) analyses identified a deletion, del(11)(p13p14.1), extending from 6.1 to 21.7 Mb in size. Although the simultaneous appearance of WAGR and polydactyly has been already described, to our knowledge this is the first case in which the characterization at the cytogenetic molecular level of a patient with these phenotypes is reported. These observations indicate that preaxial polydactyly may be another feature of the WAGR syndrome and suggest the existence of a related gene in the WAGR critical region or in its proximity. © 2005 Wiley‐Liss, Inc.

We reascertained a family in which first cousins were affected by Angelman syndrome and Prader–Willi syndrome. A paracentric inversion of 15q11-q15 had previously been reported in this family but we show, using fluorescence in situ hybridization (FISH), that the rearrangement segregating in this family is not a paracentric inversion but an inverted intrachromosomal insertion, inv ins(15)(q15q13q11.2). We also describe a further recombinant resulting in a maternal duplication of the Prader–Willi/Angelman critical region. This family illustrates the importance of distinguishing paracentric inversions from intrachromosomal insertions. © 2004 Wiley-Liss, Inc.

We report on a man with mental retardation and a complex karyotype with cells containing up to three morphologically distinct supernumerary marker chromosomes (SMCs) in most metaphases. Fluorescence in situ hybridisation studies using chromosome 15-specific probes characterised the presence of seven SMCs all derived from chromosome 15. The results suggest that the patient originally had a large inv dup(15) containing two copies of the Prader-Willi/Angelman critical region which became mitotically unstable, and by a process of dynamic mosaicism various morphologically distinct SMCs arose. © 2001 Wiley-Liss, Inc.

Germ cells in female mammals become committed to meiosis and enter its prophase sequentially in fetal life and, according to the Production Line Hypothesis, the oocytes thus generated are released after puberty as mature ova in the same sequence as that of meiotic entry in fetu. This hypothesis in its original and complete form has a subordinate proposition that concerns chiasma (Xma) frequency; it postulates that Xma number would decrease with fetal age. Consequently, univalents would increase, leading to errors of chromosome disjunction at the first meiotic division (MI), and thus to maternal age-dependent numerical chromosome anomalies. By using an in vitro/in vivo approach, we radioactively labelled the DNA of germ cells at premeiotic synthesis as they sequentially entered meiosis, while the fetal ovaries were in culture. At the end of this in vitro phase, pachytene/diplotene (P/D) stages were studied to determine their labelled fraction. The ovaries were then transplanted to spayed females and, after the in vivo phase, mature ova were harvested and the proportion of labelled first and second meiotic metaphases (MI/MII) determined. By marking the germ cells with label while in vitro during periods equivalent to early and late gestation, and by comparing the observed proportions of labelled MI/MII with those of oocytes labelled at P/D, we concluded that, in the mouse, ova do not mature at random for release, but are formed according to a production line system in which the time of release after puberty is related to the time of entry into meiosis in fetu.

OBJECTIVES:To assess the incidence of microdeletions of chromosomal region 22q11 in a population of infants coming to a regional pediatric cardiac center with selected abnormalities of the ventricular outflow tracts and aortic arch and, further, to provide phenotypic/genetic correlations to determine whether patients with 22q11 deletions can be clinically recognized in infancy. BACKGROUND:DiGeorge syndrome and velocardiofacial syndrome are frequently associated with malformations of the ventricular outflow tracts and aortic arch. Both are usually caused by microdeletions of chromosomal region 22q11. The overall importance of such deletions as a cause of these cardiac malformations remains to be established. STUDY DESIGN:All infants with the candidate cardiac phenotypes during a 34-month period were studied. Dysmorphic features, type of cardiac defect, serum calcium concentration, and thymic status were recorded. Cytogenetic studies, including high-resolution karyotyping and fluorescence in situ hybridization using cosmids (cEO or cH748) from the DiGeorge critical region, were performed after clinical assessment. RESULTS:Fifty infants (including 36 with tetralogy of Fallot with or without pulmonary atresia) were seen during the study period. Twenty-six infants (52%) were dysmorphic, including 19 who were considered to have a phenotypic appearance consistent with 22q11 deletion. Genetic analysis confirmed hemizygosity for 22q11 in 8 of these 19 cases. Results of fluorescence in situ hybridization studies were normal in 22 infants without dysmorphic features and in 5 infants with dysmorphic features not suggestive of a 22q11 deletion. CONCLUSIONS:Microdeletions of chromosomal region 22q11 are an important cause of selected malformations of the ventricular outflow tracts and aortic arch and account for about 15% to 20% of cases. These deletions may be clinically recognized in early infancy and can be rapidly confirmed by fluorescence in situ hybridization. (J PEDIATR1996;129:26-32)

In a cytogenetic, molecular, and clinical study of patients with autosomal supernumerary marker chromosomes (SMC), 6 out of 72 (8.3%) were shown by fluorescence in situ hybridisation (FISH) to be derived from chromosome 22. PCR microsatellite analysis and FISH using primers and cosmids from proximal 22q showed 3 of the 6 to contain euchromatin. The first, a de novo nonmosaic bisatellited, dicentric SMC, was acsertained in a patient with cat eye syndrome and Duane anomaly. Microsatellite analysis showed the SMC was maternal in origin with euchromatin extending to D22S427, i.e., proximal to the DiGeorge syndrome critical region (DGSCR). The second, a nonmosaic bisatellited, dicentric marker, was found in a child with severe hypotonia and developmental delay and had been inherited from the patient's phenotypically normal father. FISH showed the SMC to contain euchromatin extending into the DGSCR. The third, a de novo SMC, was ascertained antenatally and was shown to contain 22q euchromatin extending distal to the DGSCR. The 19-week terminated fetus was phenotypically normal at autopsy. Two of the three SMC(22)s not containing detectable proximal 22q euchromatin were ascertained coincidentally in phenotypically normal individuals, whereas the third, the only mosaic with a minority euploid cell line, was found in a patient with mild developmental delay. These results suggest that SMC(22)s devoid of proximal 22q euchromatin are not associated with adverse phenotypic effects whereas SMC(22)s containing euchromatin may be found in individuals with phenotypes ranging from cat eye syndrome to normal. Am. J. Med. Genet. 72:440–447, 1997. © 1997 Wiley-Liss, Inc.

A spontaneous abortion with an unbalanced translocation involving chromosomes 3, 4 and 14 is described. The mother and grandmother of the abortus were balanced carriers of the condition. A marker 9 was also segregating in the family.

Submicroscopic deletions of chromosome 22q11 have been reported in a multiple anomaly syndrome variously labelled as velocardiofacial syndrome, conotruncal anomaly face syndrome, and Di George syndrome. Most 22q11 microdeletions occur sporadically, although in some cases the deletion may be transmitted. We describe two affected sibs with confirmed 22q11 deletions from unaffected parents who are not deleted. Haplotype analysis demonstrates that the deletion in the affected sibs has occurred on the same maternal chromosome 22. Furthermore, an unaffected sib was found to have inherited the same maternal haplotype at 22q11 in an undeleted form. This is the first molecular demonstration of germ line mosaicism for a microdeletion at chromosome 22q11 and highlights the need for caution in estimation of recurrence risks, even when constitutional deletions have been excluded on parental analysis. Am. J. Med. Genet. 78:103–106, 1998. © 1998 Wiley-Liss, Inc.

Using fluorescence in situ hybridization (FISH), supernumerary marker chromosomes (SMC) from all the human autosomes except chromosome 5, have now been described, most being derived from the acrocentric autosomes. This review summarizes the results of 168 cases of autosomal SMC excluding those from chromosome 15 where FISH has been used to define the chromosomal origin of the SMC and from which phenotypic information is available. Although the number of reported cases from some of the chromosomal SMC groups remains small, the pooled data suggest that the risk of an abnormal phenotype associated with a randomly ascertained de novo SMC derived from the acrocentric autosomes (excluding 15s) is ~7% compared with ~28% for SMCs derived from the nonacrocentric autosomes. Am. J. Med. Genet. 75:367-381, 1998. © 1998 Wiley-Liss, Inc.

The chromosomal origins and in some cases the molecular composition of 26 autosomal supernumerary marker chromosomes (SMC) were identified using combined fluorescence in situ hybridization (FISH) and polymerase chain reaction (PCR) techniques. Fifteen were de novo, 4 maternally and 2 paternally transmitted and in 5 cases the parental origin is not known. Eleven cases were non-mosaic and fifteen cases had SMC cell lines ranging from 8–87%. Ten cases were ascertained prenatally, nine postnatally with abnormal phenotypes, three with poor reproductive histories and four co-incidentally. Five SMC were small rings from chromosomes 3, 6 (2 cases), 20 and 21; 8 were bisatellited from chromosomes 13/21 (4 cases), 14 (3 cases) and 14/22 (1 case). The remaining 13 appeared to be minutes comprising centromeric material only from chromosomes 1, 4, 12, 13/21 (2 cases), 14 (3 cases), 16 (2 cases), 19; 5/19, and a centric fusion involving 13 or 21 and 14. Euchromatin was detected in 9 out of 18 SMC tested with paints and/or PCR, and abnormal phenotypes were most commonly observed in patients with small ring shaped SMCs containing euchromatic sequences. Uniparental paternal isodisomy (UPD) for chromosome 6 was detected in one patient but was the only example of UPD for the normal homologues in association with an autosomal SMC in an overall total of 30 cases examined. Am. J. Med. Genet. 75:355-366, 1998. © 1998 Wiley-Liss, Inc.

Seventeen patients presenting with either de novo or familial supernumerary marker (mar) 15 chromosomes were shown by fluorescent in situ hybridization techniques (FISH) to have markers derived from and composed entirely of chromosome 15 material. Using a combination of conventional cytogenetics, FISH, Southern blotting and multiplex polymerase chain reaction (PCR) methods, it was possible to sub-classify the 17 mar(15)s into six distinct morphological and molecular groups. Analysis of DNA and metaphase spreads from the probands and their parents using probes and primers from the pericentromeric and Prader-Willi/Angelman syndromes critical regions (PWS/AS), clearly differentiated between marker 15 s which included the PWS/AS critical regions and those which did not. A direct correlation between the presence of the PWS/AS region in the mar(15) and severe mental retardation was observed. Based on these results, a system of classification of supernumerary marker 15 chromosomes is proposed.

Incontinentia pigmenti (IP) is a rare X-linked disease with marked female-to-female transmission and a dominant pattern of inheritance. Reports of six unrelated females with IP and X-autosomal translocations, all with the X breakpoint at Xp11, and an additional report of a female with IP and a 45,X/46,X,r(X) karyotype suggests that this may be the locus for the IP gene. When four of these cases, including the r(X), were re-examined with a non-isotopic in situ hybridization technique and an X centromere-specific probe (pSV2X5), the Xp11 breakpoint was confirmed. However, results from a fifth reported case, t(X;17), showed that the X breakpoint was within the centromeric alphoid repetitive sequences recognized by the probe pSV2X5. As the clinical presentation of this patient was consitent with the IP phenotype and diagnosis, the centromeric position of the X-chromosome breakpoint raises several questions with respect to the homogeneity of the Xp11 locus for IP.

Homozygous mutant curly tail mouse embryos developing spinal neural tube defects (NTD) exhibit a celltype-specific abnormality of cell proliferation that affects the gut endoderm and notochord but not the neuroepithelium. We suggested that spinal NTD in these embryos may result from the imbalance of cell proliferation rates between affected and unaffected cell types. In order to test this hypothesis, curly tail embryos were subjected to influences that retard growth in vivo and in vitro. The expectation was that growth of unaffected rapidly growing cell types would be reduced to a greater extent than affected slowly growing cell types, thus counteracting the genetically determined imbalance of cell proliferation rates and leading to normalization of spinal neurulation. Food deprivation of pregnant females for 48 h prior to the stage of posterior neuropore closure reduced the overall incidence of spinal NTD and almost completely prevented open spina bifida, the most severe form of spinal NTD in curly tail mice. Analysis of embryos earlier in gestation showed that growth retardation acts by reducing the incidence of delayed neuropore closure. Culture of embryos at 40-5°C for 15-23 h from day 1(1 of gestation, like food deprivation in vivo, also produced growth retardation and led to normalization of posterior neuropore closure. Labelling of embryos in vitro with [3H]thymidine for 1 h at the end of the culture period showed that the labelling index is reduced to a greater extent in the neuroepithelium than in other cell types in growth-retarded embryos compared with controls cultured at 38°C. Moreover, the incidence of cell death is increased in the neuroepithelium to a greater extent than in other cell types. These results are consistent with the hypothesis that spinal NTD in curly tail embryos result from a genetically determined growth imbalance between neuroepithelium and gut endoderm/notochord.

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The fluorescence in situ hybridisation (FISH) technique was tested for its ability to detect somatic mosaicism in mothers of isolated deletion cases of Duchenne/ Becker muscular dystrophy. A control female with known germline and somatic mosaicism was examined, and both the normal cell line and the carrier cell line were detected. Subsequent FISH analysis of three other mothers of boys with apparent de novo dystrophin gene deletions revealed a second patient with a high level of somatic mosaicism, suggesting that a proportion of de novo dystrophin gene deletions occur as mitotic errors early in development rather than as meiotic errors during gametogenesis.

Three families in which a satellited Y chromosome (Yqs) was segregating without apparent phenotypic effect were re-investigated with non-isotopic in situ hybridization methods. Active nucleolus organizer regions were seen in the distal long arm region of all Yqs chromosomes studied and in situ hybridization with the probe D15Z1 showed that, in all three families, the Yqs was the result of a 15p;Yq translocation. In one case, an additional focus of D15Z1 hybridization was seen on 21p.

We report a case of Albright hereditary osteodystrophy (AHO) in a three-year-old girl with a microduplication at 17q11.2. The child developed obesity within the first 6 months of life. A diagnosis of Albright was made at age 2 years when biochemical evidence of parathyroid resistance was found. No mutations were identified in guanine nucleotide-binding protein G (s) subunit alpha (GNAS1). Subsequent investigations revealed methylation disturbance at GNAS1A, neuroendocrine secretory protein antisense (NESPAS) and neuroendocrine secretory protein 55 (NESP55) confirming a diagnosis of pseudohypothyroidism type 1B. A deletion of NESP55 and uniparental disomy chromosome 20 were excluded which suggested that the features of AHO arose through a purely epigenetic mechanism. Further investigation revealed a de novo microduplication at 17q11.2 encompassing the neurofibromatosis type 1 (NF1) gene. The combination of two rare de novo events in the same child raises the possibility that duplication of a gene within the 17q11.2 region may have triggered abnormal methylation in the GNAS cluster region on chromosome 20.

Microdeletions of 22q11 are a well recognised cause of DiGeorge Syndrome, Velocardiofacial syndrome and familial conotruncal heart disease. We sought to clarify the importance of 22q11 microdeletions and other identifiable cytogenetic abnormalities in the etiology of conotruncal malformations and to establish clinical-genetic correlations. From 6/92-8/94 we prospectively studied 39 consecutive infants presenting to a regional pediatric cardiac centre with a conotruncal malformation. Diagnoses were: tetralogy (21), pulmonary atresia NSD (8), DORV (3). type B IAA (3), truncus (2). absent pulmonary valve syndrome (1) and isolated right aortic arch (1). 17 (44%) were considered dysmorphic by a clinical geneticist. In 5 cases the dysmorphic features were major. but no firm diagnosis was established on clinical grounds. One of these patients was shown to have an unbalanced translocation involving chromosomes 4 & 16. Twelve patients had subtler dysmorphic features. Nine of these cases were prospectively considered to have phenotypic appearances consistent with microdeletion of 22q11. In 7/9 the diagnosis was confirmed using fluorescence in situ hybridisation (FISH); 7 cases were confirmed using the cosmid EO and in one case with an equivocal result with cEO, hemizygosity of the 22q1 1 region was confirmed with use of a second cosmid for the TUPLE-1 gene region (cH487). FISH on samples from 19 infants considered free of phenotypic appearances of 22q1 1 microdeletions were all negative. Amongst the deleted patients. thymic aplasia was demonstrated at the time of cardiac surgery in 3. In the other 4 deleted patients no thymic shadow was evident on neonatal CXR. T cell studies were perfordeleted patients & were normal in 3 cases. Serious infection arose in only 1 patient with 22q11 deletion but with normal T cell studies. Transient symptomatic hypocalcemia developed in 2 patients. both deleted for 22q1 1. We conclude that 22q11 microdeletions are clinically recognisable in early infancy and constitute one of the commonest identifiable genetic causes of congenital head disease. Thymic aplasia is common in deleted patients, though serious infections are rare. These observations have important implications for transfusion management. long term follow-up and for genetic counselling.