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We describe a chromosome rearrangement, ins(7;13)(q32q34;q32), which segregates in a three generation family, giving rise to three individuals with an unbalanced rearrangement. Two of the individuals, a sister and a brother, were investigated further in this study. They had minor facial dysmorphism and neuropsychiatric disorders including mental retardation, language delay and epilepsy. The sister had primary amenorrhea. Array CGH revealed a 12.2 Mb deletion at 7q34–q36.2 including more than 60 genes where CNTNAP2and NOBOXare of special interest. Comparison of the clinical and cytogenetic findings of our patients with previously reported patients, supports that haploinsuffiency of CNTNAP2can result in language delay and/or autism spectrum disorder. Furthermore, we report on the second women with a deletion involving NOBOXwho is affected by primary amenorrhea. © 2010 Wiley‐Liss, Inc.

Autosomal recessive primary microcephaly (MCPH) is characterized by reduced head circumference (≤4 SD) and mental retardation without any other neurological manifestation. Of the four identified MCPH genes, homozygous truncating mutations in ASPM(MCPH5) account for >50% of all reported families. In spite of the high frequency of MCPH in Pakistan only one case of compound heterozygosity for mutations in ASPMhas been reported yet. In this large MCPH study we ascertained 37 families including 319 persons (140 patients). Haplotype analysis of eight STS markers suggested linkage by homozygosity in 20 families, and re‐analysis of single sib ships in the remaining families demonstrated possible compound heterozygosity in two families. Direct sequencing indeed confirmed compound heterozygosity in two and homozygous mutations in 20 families, respectively, showing that up to 10% of families with MCPH caused by ASPM are compound heterozygous. In total we identified 16 different nonsense or frameshift mutations of which 12 were novel thereby increasing the number of mutations in ASPMsignificantly from 35 to 47. We found no correlation between the severity of the condition and the site of truncation. We suggest that the high frequency of compound heterozygosity observed in this study is taken into consideration as part of future genetic testing and counseling in Pakistani MCPH families. © 2009 Wiley‐Liss, Inc.

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Popliteal pterygium syndrome PPS and Van der Woude syndrome VWS are caused by mutations in the gene interferon regulatory factor 6 IRF6. Skeletal, genital malformations and involvement of the skin occur in PPS and orofacial clefting and lip pits occur in both. We report on a patient with unilateral cleft lip and palate, ankyloblepharon, paramedian lip pits, unilateral renal aplasia, and a coronal hypospadias. By sequencing IRF6, we detected a novel missense mutation Arg339Ile. The other family members were unaffected and had no IRF6mutations, including the patients brother who was also born with hypospadias. The patient and his brother were both conceived by in vitro fertilization IVF. It is discussed whether the renal malformation in the patient is related to the IVF procedure or to the IRF6mutation. © 2008 WileyLiss, Inc.

Cleft lip and/or palate (CL/P) is a common congenital malformation with a complex etiology, as many genes and environmental factors have been shown to play a role in craniofacial development. We used a genetic mapping approach to analyze a family with multiplex CL/P. A genome‐wide scan with a 10 kb single nucleotide polymorphism (SNP) chip followed by fine mapping with microsatellite markers in a CL/P multiplex family suggested linkage (maximum multipoint LOD score of 2.41) to a 6.5 Mb interval at 1q32.1‐q32.2. This interval was close to, but excluded IRF6. Mutations in the IRF6 (1q32.2) cause syndromic forms of CL/P, and several association studies have shown that polymorphisms in and around IRF6 are associated with non‐syndromic CL/P (NSCLP). However, in the family described here, IRF6 was excluded from the linkage interval. Sequencing of selected genes in the interval and comparative genome hybridization (CGH) did not reveal any mutations or genomic aberrations. Our data suggest that an unidentified CL/P gene, or a non‐coding IRF6 regulatory element in this linkage interval may have caused CL/P in this family. © 2007 Wiley‐Liss, Inc.

The detection of chromosomal abnormalities in patients with mental retardation (MR) and dysmorphic features increases with improvements of molecular cytogenetic methods. We report on six patients referred for detailed characterization of chromosomal abnormalities (four translocations, one inversion, one deletion) detected by conventional cytogenetics, in whom metaphase CGH revealed imbalances not involved in the initially detected rearrangements. The detected abnormalities were validated by real‐time PCR. Parents were investigated by CGH in four cases. The genomic screening revealed interstitial deletions of 2q33.2‐q34, 3p21, 4q12‐q13.1, 6q25, 13q22.2‐q31.1, and 14q12. The estimated minimum sizes of the deletions ranged from 2.65 to 9.27 Mb. The CGH assay did not reveal imbalances that colocalized with the breakpoints of the inversion or the translocations. The deletion of 6q included ESR1, in which polymorphisms are associated with variation of adult height. FOXG1B, known to be involved in cortical development, was located in the 14q deletion. The results illustrate that whole‐genome molecular cytogenetic analysis of phenotypically affected patients with abnormal conventional karyotypes may detect inapparent molecular cytogenetic abnormalities in patients with microscopic chromosomal abnormalities and that these data provide additional information of clinical importance. © 2006 Wiley‐Liss, Inc.

Fine mapping of chromosomal deletions and genotype–phenotype comparisons of clinically well‐defined patients can be used to confirm or reveal loci and genes associated with human disorders. Eleven patients with cytogenetically visible deletions involving the terminal region of chromosome 5q have been described, but the extent of the deletion was determined only in one case. In this study we describe a 15‐year‐old boy with Ebstein anomaly, atrial septal defect (ASD), atrioventricular (AV) conduction defect, and microcephaly. He had an apparently balanced paracentric inversion of chromosome 5, with the karyotype 46, XY,inv(5)(q13q35) de novo. Further mapping of the chromosome breakpoints using fluorescence in situ hybridization (FISH) revealed a 2.2 Mb microdeletion at the 5q35 breakpoint, which spans 16 genes, including the cardiac homeobox transcription factor gene NKX2‐5. The current data suggest that haploinsufficiency of NKX2‐5 cause Ebstein anomaly and support previous results showing that NKX2‐5 mutations cause ASD and AV conduction defect. Furthermore, we suggest presence of a new microcephaly locus within a 2.2 Mb region at 5q35.1–q35.2. © 2006 Wiley‐Liss, Inc.

A phenotype–genotype correlation was previously described for carriers of different sized of polyalanine expansions in HOXD13. We report on a detailed comparison of 55 members (∼220 limbs) from 4 Danish families with duplications of 21 or 27 bp, expanding the polyalanine repeat from 15 to 22 and 24 residues, respectively. Two of these were previously described by Danish pioneers of human genetics, Tage Kemp and Oluf Thomsen. A clinical score was assigned to each limb based on manifestations assumed to represent different degrees of a duplication defect in hand rays 3–4 and foot rays 4–5. The length of metacarpals and phalangeal bones in rays 1, 2, and 5 was measured on hand radiographs and converted to Z‐scores. The relative difference between corresponding right and left bones and directional, total, and fluctuating asymmetry was calculated for each individual. All of these parameters were compared between carriers of the +9 alanine expansion, the +7 alanine expansion, and non‐mutation carriers with affected parents from the two families. Upper limb scores and the rate of abnormal bones (>2SD) were significantly higher in the first group than in the others. The first metacarpal and the middle phalanx of the little finger were significantly shorter, and the proximal phalanx of the index finger was significantly longer in this group than in the others. An increased level of total and fluctuating asymmetry was observed in long expansion carriers. Thus, our data have added evidence to the phenotype–genotype correlation previously reported, which was further extended to include lesser involvement of bones in ray 1, 2, and 5. © 2005 Wiley‐Liss, Inc.

We report on a father and a son with nasal and limb defects characteristic of Laurin–Sandrow syndrome (LSS) excluding for the first time X‐linked inheritance in this rare condition. Based on a search for genes expressed late during nose formation and early in limb formation we identified retinoic acid receptor B (RARB) and retinoic acid receptor G (RARG) as possible candidate genes and sequenced bidirectionally including all exons and intron–exon bounders. We identified a single nucleotide substitution in intron 2 of RARB, which is conserved in human, chimp, dog, mouse, rat, and chicken. However, it was located 83 bp from exon 2, suggesting it is a rare polymorphism which does not account for the phenotype. No other mutations were found. This suggests that another yet unknown gene is responsible for the condition. © 2005 Wiley‐Liss, Inc.

Oculo–dento–digital dysplasia (ODDD) [OMIM 164200] is a rare autosomal dominant pleiotropic disorder comprising ocular, craniofacial, and digital anomalies, caused by mutations in the gap junction alpha-1 gene (GJA1 or Connexin 43 (CX43)) [Paznekas et al., 2003]. In a Danish family affected over five generations, we found a novel mutation, 286G → A, resulting in Val96Met. We provide an easy method for mutation detection by use of the restriction enzyme Nde1 and discuss possible pathogenetic mechanisms, arguing that loss of function cannot be excluded. This is the second article reporting ODDD mutations. © 2004 Wiley-Liss, Inc.

The phenotype of Gorlin–Goltz syndrome or basal cell nevus syndrome (BCNS, #109400, OMIM), a Mendelian trait due to PTCH mutations has been reported in a few cases of interstitial deletion of chromosome 9q. We present an 11-year-old girl with clinical features consistent with BCNS including bridging of sella turcica, biparietal bossing, downward slanting palpebral fissures, mandible prognathism, pectus excavatum, thumb abnormalities, occult spina bifida at L5-S4, numerous basal cell nevi, and single basal cell carcinoma. Cytogenetic analysis using high-resolution banding techniques and fluorescence in situ hybridization (FISH) revealed interstitial chromosome deletion 9q22.32-q33.2 involving the PTCH gene as a secondary breakage event to a chromosome translocation t(9;17)(q34.1;p11.2)mat. Further FISH studies showed the translocation breakpoint on 9q34.11 maps proximal to ABL, between the BAC clone RP11-88G17 and the LMX1B gene. The latter gene encodes a transcription factor, in which loss of function mutations are responsible for the nail-patella syndrome (NPS, #161200 OMIM). Interestingly, some features of our proband (e.g., bilateral patellar dysplasia and abnormal clavicular shape), as well as her healthy sister who carries the same translocation, are also found in patients with NPS. The chromosome 17p11.2 breakpoint maps in the Smith-Magenis syndrome common deletion region, within two overlapping BAC clones, CTD-2354J3 and RP11-311F12. © 2003 Wiley-Liss, Inc.

In 1927, Oluf Thomsen, in a classic paper, described a seven-generation family with autosomal dominant axial synpolydactyly (SPD)—the Vordingborgtyp of axis duplication and dysostosis. Expansion of a polyalanine tract in the HOXD13 gene is known to cause synpolydactyly. We have rediscovered part of the family described by Thomsen, and detected a 9 triplet polyalanine expansion within HOXD13segregating with the disorder. The phenotypic spectrum in mutation carriers ranged from severe to inapparent bone malformations. In the latter case, only dermatoglyphics revealed the genetic status. © 2002 Wiley-Liss, Inc.

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