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Clinical and molecular cytogenetic studies of a large de novo interstitial deletion 16q11.2-16q21 including the putative transcription factor geneSALL1
  1. * Institut für Medizinische Genetik, Universitätsklinikum Charité, 10098 Berlin, Germany
  2. Institut für Pathologie, Universitätsklinikum Charité, 10098 Berlin, Germany
  3. Abteilung für Pränatale Diagnostik und Therapie, Universitätsklinikum Charité, 10098 Berlin, Germany
  4. § Institut für Humangenetik, Universität Göttingen, Heinrich-Düker-Weg, 37073 Göttingen, Germany
  1. Dr Knoblauch, hans.knoblauch{at}

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Editor—Interstitial deletions of the long arm of chromosome 16 share common clinical features including growth retardation, failure to thrive, microcephaly, high and prominent forehead, prominent metopic suture, large anterior fontanelle, hypertelorism, broad nasal bridge, low set and dysplastic ears, cleft palate, micrognathia, short neck, narrow thorax, broad first toes, mental retardation, muscular hypotonia, congenital heart defects, and gastrointestinal as well as renal anomalies.1 More than 26 patients with different interstitial long arm deletions of chromosome 16 have been reported.2-29 Recently, mutations in the transcription factor gene SALL1 on chromosome 16q12.130 were shown to result in Townes-Brocks syndrome, an autosomal dominantly inherited malformation syndrome characterised by malformations of the anus, hands, and ears as well as deafness.31 We describe a fetus with the 16q deletion syndrome and additional features, including unilateral radial aplasia, ulnar hypoplasia, preaxial hexadactyly, and segmentation defects of the vertebral column. Some of these features overlap with the malformations seen in Townes-Brocks syndrome. We therefore investigated the hypothesis that the SALL1 gene was included within the deletion.

The 31 year old, gravida 2, para 1 (her first child is a healthy boy) was referred at 24 weeks gestation because her fetus had cleft lip and palate detected by ultrasound screening. Biometry showed asymmetrical growth retardation with a thoraco-abdominal diameter of 43 mm (<5th centile) corresponding to 19 weeks' gestation, while the BPD (60 mm) and femur length (41 mm) were within normal limits. Careful examination by ultrasound showed multiple fetal abnormalities. Dilatation of the lateral ventricles, a dilated third ventricle, and a cavum septum pellucidum were noted. Aplasia of the right radius was suspected. The left kidney was absent. The right kidney was supplied by two arteries. The heart showed tetralogy of Fallot with absent pulmonary valve, agenesis of the ductus arteriosus, and a right sided aortic arch. The lungs were hypoplastic. Amniotic fluid, placenta, and umbilical vessels were normal. A fetal blood sample was taken for chromosome analysis. Necropsy examination after the parents opted for termination of the pregnancy in the 25th week of gestation showed a male fetus 31 cm in length and 690 g in weight (corresponding to the 24th/25th week of gestation). The fetus had a large neurocranium. Facial features included a prominent nasal bridge, a broad nose, hypertelorism, and upward slanting palpebral fissures. The ears were dysplastic, small, and deeply set with a single, left sided preauricular tag. The fetus had left sided cleft lip and palate. The chest was narrow. There was anal stenosis. In the upper extremities, the right radius was absent, while the ulna and thumb were hypoplastic. The left hand displayed preaxial hexadactyly with a finger-like thumb. Crowding of the toes was seen on both feet (figs 1 and 2).X rays confirmed the right radial aplasia and a shortened and thickened ulna. There was a single ossification centre (1 mm in diameter) within the hypoplastic right thumb, and a single ossification centre (1 mm in diameter) within the additional left thumb. The distal ossification centre of the additional left thumb was missing. The spine showed multiple segmentation defects (fusion of the third and fourth thoracic vertebral bodies, malformation of the eighth thoracic vertebral body, and aplasia of the third to fifth sacral vertebral bodies). Examination of the heart disclosed a perimembraneous ventricular septal defect (4 mm in diameter), aplasia of the semilunar pulmonary valve, agenesis of the ductus arteriosus, and overriding of the right descending aorta. The left kidney was absent.

Figure 1

Postmortem picture of the fetus presented. Note the left sided cleft lip/cleft palate, right sided radial aplasia, and a narrow chest.

Figure 2

Lateral view of the fetal head. Note the dysplastic, small, and deeply set ears with a single left sided preauricular appendage, and retrognathia.

Chromosome analysis of fetal lymphocytes showed a large interstitial deletion of the long arm of chromosome 16 in all metaphases analysed. The result was confirmed by chromosome analysis of fetal fibroblasts. The karyotypes of the parents were normal. To define the exact site of the deletion, comparative genomic hybridisation (CGH) and fluorescence in situ hybridisation (FISH) analysis were performed. CGH was performed with fetal DNA as described elsewhere.32CGH analysis defined the deletion to encompass bands 16q11.2 to 16q21 (fig 3). FISH analysis was performed using YACs from within and outside the deletion. YACs 922f01 (D16S415), 965g04 (D16S514/ D16S739), and 957h03 (D16S400/D16S3129) residing in 16q12-16q21 were shown to give only one signal on the normal chromosome 16, but none from the deleted chromosome 16. The STS numbers mapped to the corresponding YAC clones are given in parentheses. YAC 821g09 (D13S3021) located in 16q22 was not deleted. In addition, FISH using a PAC clone (reference: LLNLP704M031126Q4) including the SALL1gene33 showed heterozygous deletion ofSALL1 (fig 4). DAPI banding confirmed the loss of the whole heterochromatin of chromosome 16 harbouring the deletion. The resulting fetal karyotype was defined as 46,XY,del(16)(q11.2;q21) according to ISCN.34

Figure 3

G banded chromosomes of fetal fibroblasts and CGH (comparative genomic hybridisation) analysis using fetal DNA showing an interstitial deletion 16q11.2-q21 according to ICSN34 as illustrated by the ideogram. Fifteen metaphases were used for CGH analysis. The bar located on the left of the ideogram indicates the deleted region.

Figure 4

Two colour FISH analysis of fetal metaphase spreads (fibroblasts) using a PAC clone including SALL1.33 The signal from the PAC clone, mapping to 16q12.1, gives only one signal on one chromosome 16, while the YAC clone (CEPH 765b06) located on the short arm of chromosome 16 (16p13) shows signals on both chromosomes.

The phenotype of the 16q deletion syndrome was attributed to the deletion of critical bands at 16q11.2-q13,9 12 2516q21,11 16 19 21 24 and 16q22.1.14Specific features, such as congenital cataract20 and iris coloboma,28 result from more distal deletions of 16q22.3 and 16q23.1-24.2. Some of the features documented in patients with proximal deletions of chromosome 16q are also seen in Townes-Brocks syndrome.31 35 36 The clinical presentation of TBS is highly variable37 within and between affected families. Characteristic features of TBS are anorectal abnormalities (imperforate anus, ectopic anus), abnormalities of the hands (preaxial polydactyly, triphalangeal thumbs, hypoplastic thumbs), abnormalities of the feet (syndactyly, club foot), deformities of the outer ear (“lop ears”) and preauricular tags, and deafness.38 Renal malformations include agenesis as well as hypoplastic or polycystic kidneys and may lead to renal failure.39 The frequency of cardiac defects in TBS is high in those patients evaluated for cardiac defects by echocardiography.40 Mental retardation has rarely been reported.41 42

TBS is caused by mutations of the SALL1putative transcription factor gene located on chromosome 16q12.1.30 All mutations so far identified in TBS patients33 are predicted to result in a prematurely terminated SALL1 protein lacking all double zinc finger domains thought to be essential forSALL1 gene function. Therefore, TBS is strongly suspected to result from haploinsufficiency forSALL1. This hypothesis is strengthened by the observation of a chromosomal translocation and a pericentric inversion in TBS patients, both involving a common breakpoint at 16q12.1.43 44 The features of the fetus reported here show overlap with TBS. Our FISH studies prove that one allele ofSALL1 is indeed deleted. Therefore, we suggest that the ear anomalies, hand anomalies (preaxial polydactyly, hypoplastic thumb), anal stenosis, and the renal agenesis observed in the fetus result from heterozygous deletion ofSALL1. The cardiac defects might also result from the SALL1 deletion, since two TBS patients with tetralogy of Fallot have been described previously.45 46 The anomalies of the radius and ulna seen in the fetus most likely result from the deletion of a contiguous gene in the deleted region. Vertebral segmentation defects have only recently been reported in a TBS patient.47 However, aSALL1 mutation has not been found in these patients.

Hoo et al 17 presented two mentally retarded sisters with a deletion of 16q12.1. Features described in these sisters included dysplastic ears with abnormal folding of the helices, proximally placed thumbs, and bilateral, symmetrically small kidneys. Twins with a deletion of 16q12.2-13 showed ectopic anus, congenital heart defects, and dysplastic ears.12 A 10 year old boy with a de novo interstitial deletion 16q12.1q13 presented with micrognathia, a median cleft, low set dysplastic ears, a preauricular appendage, fusion of the third and fourth and the fifth and sixth vertebrae of the neck, hypospadias, hydrocephalus, sensorineural hearing deficits, and additional dysmorphic features.25 Further clinical features described in patients with deletions of the proximal long arm of chromosome 16 are summarised in table 1. Whether or notSALL1 is deleted in those patients reported with features similar to TBS and with deletions including 16q13 but not 16q12.1 remains to be elucidated.11 16 19 Some families have been reported in which affected subjects show features typical of both TBS and Goldenhar syndrome/oculoauriculovertebral spectrum.48 49 One family was described with hemifacial microsomia and radial ray defects.50 The affected members of this family displayed abnormal ears, multiple preauricular tags and pits, and unilateral micrognathia. In addition, triphalangeal thumbs, unilateral preaxial polydactyly, and a slightly anteriorly placed anus were present. Autosomal dominant inheritance was suggested in this family. Unilateral microphthalmia and facial asymmetry were observed in a family with anteriorly placed anus, irregular toes, and a digitalised thumb.51 Gabrielli et al 48 described an infant with facial asymmetry, abnormal ears, preauricular tags, and anteriorly placed anus without triphalangeal thumbs or vertebral anomalies. Recently, aSALL1 mutation was detected in the patient described by Gabrielli et al,48showing that SALL1 mutations can also result in a Goldenhar-like phenotype.33 It remains to be seen if the affected subjects in the families reported by Johnsonet al 49 and Moeschleret al 50 also carry mutations inSALL1.

Table 1

Clinical characteristics of patients with a deletion of the long arm of chromosome 16 including 16q12.1 or 16q13

In summary, our results suggest that haploinsufficiency forSALL1 might contribute to TBS-like features seen in the fetus presented here. In addition, certain clinical features in patients with proximal deletions of 16q including q12.1 are likely to result from haploid SALL1deletions. Nevertheless, the interstitial deletion in this fetus probably includes several hundred genes, arguing against a simplistic additive genetic model to explain the observed phenotype. Moreover, additional features of the 16q deletion syndrome, which are not part of the phenotypic spectrum of TBS, are likely to be caused by the deletion of additional genes located within the deletion. Some clinical features might be non-specific and cannot be attributed to the deletion of a single gene. FISH studies should indicate whetherSALL1 is deleted in those patients reported with features similar to TBS but with deletions including 16q13 but not 16q12.1. If a SALL1 deletion cannot be confirmed in these patients, a TBS-like phenotype in these patients might still result from a position effect influencingSALL1 gene expression.


Reference address for YACs:;∼ctyogen/CHRM16.HTM. We would like to thank Karin Lehmann and Gundula Leschick for expert technical assistance. Dr Friedrich C Luft helped us with the text. This work was funded in part by a grant from the Wilhelm-Sander-Stiftung to JK.