Brachydactyly type A3 is caused by a novel 13 bp HOXD13 frameshift deletion in a Chinese family

Brachydactyly type A (BDA) is defined as short middle phalanges of the affected digits and is subdivided into four types (BDA1‐4). To date, the molecular cause is unknown. However, there is some evidence that pathogenic variants of HOXD13 could be associated with BDA3 and BDA4. Here, we report a Chinese autosomal dominant BDA3 pedigree with a novel HOXD13 mutation. The affected individuals presented with an obviously shorter fifth middle phalanx. The radial side of the middle phalanx was shorter than the ulnar side, and the terminal phalanx of the fifth finger inclined radially and formed classical clinodactyly. Interestingly, the index finger was normal. The initial diagnosis was BDA3. However, the distal third and fourth middle phalanges were also slightly affected, resulting in mild radial clinodactyly. Both feet showed shortening of the middle phalanges, which were fused to the distal phalanges of the second to the fifth toes, as reported in BDA4. Therefore, this pedigree had combined BDA3 and atypical BDA4. By direct sequencing, a 13 bp deletion within exon 1 of HOXD13 (NM_000523.4: c.708_720del13; NP_000514.2: p.Gly237fs) was identified. The 13 bp deletion resulted in a frameshift and premature termination of HOXD13. This study provides further evidences that variants in HOXD13 cause BDA3‐BDA4 phenotypes.     

Molecular characterization of a novel, de novo, cryptic interstitial deletion on 19p13.3 in a child with a cutis aplasia and multiple congenital anomalies

We report on a de novo constitutional deletion within G-band region 19p13.3 in a girl with cutis aplasia of the scalp, facial anomalies, structural heart abnormalities, hypotonia, mild mental retardation and conductive hearing loss which we characterized with chromosomal microarray, fluorescence in situ hybridization (FISH), and SNP analyses. Initial microarray analysis revealed a 6-BAC-clone deletion covering an approximately 1.612?Mb region within 19p13.3. Subsequent BAC FISH studies delineated the proximal deletion breakpoint to within BAC clone RP11-125C3 and the distal deletion breakpoint to within BAC clone RP11-648B14. SNP analysis showed the deletion to be of paternal origin and further refined its distal breakpoint to within a 20?kb region between rs11666694 and novel SNP2 that we identified at g.2,924,845, and its proximal deletion breakpoint to within a 22?kb region between rs35280644 and rs262562. Accordingly, the size of the deletion was revised to 1.89-1.932?Mb in length. We identified many Alu, L1, and L2 repeats, as well as SINE and LINE sequences at both deletion breakpoints. We found the deletion to encompass 71 genes, two of which appear to be good candidates for the patient's observed craniofacial and cardiac anomalies: guanine nucleotide binding protein (G protein), alpha 11 (Gq class)(GNA11), and Transducin-like Enhancer of Split 2 (E(sp1) homolog, Drosophila)(TLE2).     

A subterminal deletion of the long arm of chromosome 10: a clinical report and review

We report on a girl with mental retardation, dysmorphic features, and behavioral problems. A small terminal deletion of the long arm of chromosome 10 was detected by subtelomeric fluorescence in situ hybridization (FISH) studies in all analyzed metaphases. The deletion was shown to be a de novo terminal deletion of approximately 6.1 Mb, with the deletion breakpoint localized at band 10q26.2, between BAC probes RP11-498K22 and RP11-42K2. A subterminal 10q deletion as found in the present patient has, to our knowledge, only been reported in 15 patients (including 8 familial cases). We review the clinical and behavioral phenotype of these patients with "pure" subterminal 10q deletion.     

A de novo 1.1-1.6 Mb subtelomeric deletion of chromosome 20q13.33 in a patient with learning difficulties but without obvious dysmorphic features

We report on a de novo submicroscopic deletion of 20q13.33 identified by subtelomeric fluorescence in situ hybridization (FISH) in a 4-year-old girl with learning difficulties, hyperlaxity and strabismus, but without obvious dysmorphic features. Further investigations by array-based comparative genomic hybridization (array-CGH) and FISH analysis allowed us to delineate the smallest reported subterminal deletion of chromosome 20q, spanning a 1.1-1.6 Mb with a breakpoint localized between BAC RP5-887L7 and RP11-261N11. The genes CHRNA4 and KCNQ2 implicated in autosomal dominant epilepsy are included in the deletion interval. Subterminal 20q deletions as found in the present patient have, to our knowledge, only been reported in three patients. We review the clinical and behavioral phenotype of such "pure" subterminal 20q deletions.     

Small reciprocal insertion detected by spectral karyotyping (SKY) and delimited by array-CGH analysis

A 5.4-year-old male propositus is reported with mild dysmorphic features including hypoplasia of the radial part of both hands affecting thenar, thumb and fingers 2-3, incomplete syndactyly of fingers 3-4, single palmar creases, brachymesophalangia of toes 3-5, dissociated retardation of bone age, telecanthus, spina bifida occulta, cryptorchidism, muscular hypotonia, and borderline mental retardation. His karyotype was unbalanced, 46,XY,der(16)ins(4;16)(q26q28.1; q12.1q12.2)pat. In the propositus' father who had brachydactyly of fingers 2-5 and brachymesophalangia of toes 3-5 the insertion was reciprocal, 46,XY,rep ins(4;16)(q26q28.1;q12.1q12.2). Insertions are rare, reciprocal insertions most unusual. The characterization of the insertion in the propositus and the detection of its reciprocity in the father were achieved by the application of spectral karyotyping (SKY). Further examination of the propositus' unbalanced genome by array-CGH analysis delimited the chromosomal locations of the deletion/insertion rearrangement on a 0.5-2 Mb resolution level and allowed to design specific BAC FISH analyses that pinpointed the borders of the affected segments. The rearrangement involved a segment of 7.7 Mb between RP11-1030 g22 and RP11-52k8 at the chromosomal regions 4q26 and 4q28.1, respectively, and a segment of 2.8 Mb between RP11-242n20 at 16q12.1 and RP11-324d17 at 16q12.2. A simple molecular genetic explanation of the phenotype cannot be given. A relation to the Townes Brocks gene (SALL1) located 340 kb proximal of the 16q12 deletion/insertion is unlikely. Possibly more relevant is an overlap of the 16q12 deletion/insertion with a small deletion of the syntenic chromosomal region in the mouse that causes a developmental disorder of digits ("Fused toes").     

A novel microdeletion at chromosome 2q31.1-31.2 in a three-generation family presenting duplication of great toes with clinodactyly

HOXD gene cluster maps to chromosome 2q31 and plays a key role in embryonic limb morphogenesis. Mutations of the HOXD13 and HOXD10 genes have been found to be associated with digital and limb malformations. In addition, dysregulation of HOXD gene cluster has been proposed to account for the limb abnormalities in patients with chromosome 2q rearrangements. In this report, we investigated a three-generation family presenting clinical phenotypes of duplication of great toes, tapering fingers, and clinodactyly of the fifth finger in both hands, which were transmitted in a dominant fashion in this family. We identified and validated an interstitial microdeletion of ∼3.4 Mb at chromosome 2q31.1-31.2 by array-based comparative genomic hybridization, fluorescence in situ hybridization, and real-time quantitative polymerase chain reaction that cosegregates with the clinical phenotypes in this family. The microdeletion removes 30 labeled genes including the entire HOXD gene cluster, suggesting that the digital abnormalities of this family may be attributed to the haploinsufficiency of the HOXD gene cluster. The delineation of the microdeletion region may contribute to the genotype–phenotype correlation study in patients with genomic rearrangements of the long arm of chromosome 2 and helps to understand the pathogenesis of haploinsufficiency of the HOXD gene cluster.     

Distinct phenotype associated with a cryptic subtelomeric deletion of 19p13.3-pter

Telomeres are gene rich regions with a high recombination rate. Cryptic subtelomeric rearrangements are estimated to account for 5% of mental retardation/malformation syndromes. Here we present the first patient with a deletion of 19p13.3, identified by subtelomeric FISH analysis. His features included a distinctive facial appearance, cleft palate, hearing impairment, congenital heart malformation, keloid scarring, immune dysregulation, and mild learning difficulties. Subtelomeric FISH analysis identified a deletion of 19p13.3-pter. The deletion size was determined to be 1.2 Mb by FISH analysis. It extended from within the chromosomal region covered by BAC RP11-50C6 to 19pter. The deleted area encompassed approximately 60 genes. Fifteen possible candidate genes were considered with respect to the phenotype, including follistatin-related precursor 3 (FSTL3) and serine-threonine kinase 11 (STK-11).     

Three-dimensional CT image analysis of the digging system in the aardvark.

We examined the bone movement in the forepaw and hind paw in the aardvark (Orycteropus afer) by using three-dimensional (3D)-computed tomography (CT) techniques and osteometrical methods to confirm the functional adaptation of the extremities as a digging system. The four metacarpal bones could be strongly bent from the distal carpal bones. The distal end of the second and third metacarpal bones possessed enlarged smooth articulation surfaces that allowed the proximal phalanx to bend at a sharp angle. However, the articulation surface was not well-developed in the distal end of the fourth and fifth metacarpal bones and the proximal phalanx could bend at smaller angle in these two lateral digits. The proximal phalanges sharply crook from the metatarsal in the first, second, third and fourth digits in the hind paw. We suggest that the medial two digits in the forepaw directly contribute to the crushing, when these proximal phalanges crook in the phase of power stroke. In contrast the lateral third and fourth digits may act as sweeper of the crushed soil. These suggestions regarding the different functional adaptation between medial two digits and lateral two digits are consistent with the anatomical data of the forearm musculature. In the hind paw, we suggest that the second, third and fourth digits are functionally similar and that the hind paw may not act as a crushing apparatus but as a running motor or soil-sweeper similarly using these main three digits.     

Cryptic 17q22 deletion in a boy with a t(10;17)(p15.3;q22) translocation, multiple synostosis syndrome 1, and hypogonadotropic hypogonadism

We report on a boy who had multiple synostosis syndrome 1, an autosomal dominant disorder characterized by progressive symphalangism, multiple joint fusions, conductive deafness, and mild facial dysmorphism. In addition the boy developed delay of puberty, bone age, and closure of the epiphyseal lines of long bones with tall stature. These findings and decreased plasma LH and FSH levels at age 19 years were compatible with hypogonadotropic hypogonadism. G-banded chromosomes showed a balanced translocation t(10;17)(p15.3;q22). Chromosomal FISH analysis, using a series of BAC clones surrounding the translocation breakpoints, detected a 2.2-3.9 Mb deletion at 17q22. The deletion encompassed NOG, a gene responsible for multiple synostosis syndrome 1. It was assumed that a gene for pituitary secretion of gonoadotropic hormones was deleted at the 17q22 segment.     

De novo complete trisomy 5p: clinical and neuroradiological findings

A Thai mother and son with distal symphalangism and other associated abnormalities are reported. Distal and middle phalanges of fingers and toes 2-5 were either aplastic/hypoplastic or fused between the corresponding digits. The second fingers and fourth fingernails were most severely affected in both patients. The mother's hands were less severely affected; the middle and distal phalanges of her hands were malformed and fused. Besides the absence of fusion lines, the shape of the fused middle and distal phalanges was quite different from that of other types of fusion, i.e., fused bones in both patients did not maintain the normal configuration of bone, referring to as "middle-distal phalangeal complex". Distal symphalangism was observed in toes 2-5 of the mother and in toe 3 of the son. Both patients had additional clinical manifestations such as narrowing of the zygomatic arch, dental pulp stone, microdontia of a mandibular permanent central incisor, cone-shaped epiphyses of middle phalanges of fingers, and absence of scaphoid, trapezium, trapezoid, and pisiform bones. Mutation analysis of NOG and ROR2, the genes responsible for proximal symphalangism and brachydactyly type B, respectively, was negative.     

The hand profile in de Lange syndrome: Diagnostic criteria

The hand pattern profiles of 18 previously published and 10 new cases of de Lange syndrome were compared to those of cases referred as suspects, but judged clinically and by numerical taxonomic methods not to have de Lange syndrome (non-de Lange). Based on a Poznanski metacarpophalangel profile of the 2 groups of patients, a simple scoring system using 11 measurements was devised using the 16 most marked differences within and between metacarpals and phalanges. Of the metacarpals, the first is shorter than the second, third, fourth, or fifth; and the second fifth are shorter than the third or fourth. Of the middle phalanges, the third and fourth are shorter than the respective metacarpal and than the second and fifth middle phalanx. Of the distal phalanges, the fifth is shorter than the second. The mean Z score for these 11 measurements is further below normal in the de Lange group than in the non-de Lange group. All 11 non-de Lange patients had a score less than 17, and all 28 de Lange patients had a score of 18 or more.     

The hand profile on de Lange syndrome: diagnostic criteria.

The hand pattern profiles of 18 previously published and 10 new cases of de Lange syndrome were compared to those of cases referred as suspects, but judged clinically and by numerical taxonomic methods not to have de Lange syndrome (non-de Lange). Based on a Poznanski metacarpophalangeal profile of the 2 groups of patients, a simple scoring system using 11 measurements was devised using the 16 most marked differences within and between metacarpals and phalanges. Of the metacarpals, the first is shorter than the second, third, fourth, or fifth; and the second and fifth are shorter than the third or fourth. Of the middle phalanges, the third and fourth are shorter than the respective metacarpal and than the second and fifth middle phalanx. Of the distal phalanges, the fifth is shorter than the second. The mean Z score for these 11 measurements is further below normal in the de Lange group than in the non-de Lange group. All 11 non-de Lange patients had a score less than 17, and all 28 de Lange patients had a score of 18 or more.     

Mesoaxial complete syndactyly and synostosis with hypoplastic thumbs: an unusual combination or homozygous expression of syndactyly type I?

Syndactyly type I is an autosomal dominant condition with complete or partial webbing between the third and fourth fingers or the second and third toes or both. We report here a previously undescribed phenotype of severe mesoaxial syndactyly and synostosis in patients born to affected parents. The characteristic features of these severe cases are (1) complete syndactyly and synostosis of the third and fourth fingers; (2) severe bone reduction in the proximal phalanges of the same fingers; (3) hypoplasia of the thumbs and halluces; (4) aplasia/hypoplasia of the middle phalanges of the second and fifth fingers; and (5) complete or partial soft tissue syndactyly of the toes. We report on three offspring with this phenotype from two different branches of a syndactyly type I family, suggesting that they may be homozygous for this condition. SSCP and linkage analysis indicated that neither HOXD13 nor other relevant genes in the chromosome 2q31 region was responsible for this phenotype.     

A de novo subterminal trisomy 10p and monosomy 18q in a girl with MCA/MR: case report and review

We report on a 3-year-old girl with psychomotor retardation, cardiopathy, strabismus, umbilical hernia, and facial dysmorphism in whom a de novo unbalanced submicroscopic translocation (10p;18q) was found by MLPA (Multiplex Ligation dependent Probe Amplification) and FISH analyses. Additional FISH studies with locus specific RP11 BAC probes and analyses with microsatellites revealed that the translocation resulted in a deletion estimated between 6 and 9 Mb on the maternal chromosome 18 and a subtelomeric 10p duplication of approximately 6.9 Mb. The proband's karyotype is 46,XX.ish der(18) t(10;18)(18pter-->18q23:10p15 --> 10pter). A subterminal duplication of 10p, as well as a subterminal deletion of 18q have been rarely reported so far. The clinical phenotype of this patient is reviewed and discussed.     

Pure proximal deletion of chromosome 21 and kyphosis

We report on two unrelated patients with a proximal deletion of the long arm of chromosome 21. The deletion encompassed 14.5 Mb of DNA. Molecular studies showed that the two telomeric breakpoints were within the same DNA clone (BAC RP11-56D12). The centromeric breakpoints, however, were separated by only 250 kb of DNA (BAC RP11-645E14 and RP11-324B9). The phenotype observed in the two patients was very different, as patient 2, who had the largest deletion, had severe kyphosis not observed in patient 1. Previous studies have identified a 6 Mb region of chromosome 21 associated with severe kyphosis. Interestingly, this region overlaps the 250 kb segment deleted in patient 2. We suggest that one gene (NT011512.4) located in this small overlapping region might be responsible for severe kyphosis.     

De novo complete trisomy 5p: Clinical and neuroradiological findings

A Thai mother and son with distal symphalangism and other associated abnormalities are reported. Distal and middle phalanges of fingers and toes 2–5 were either aplastic/hypoplastic or fused between the corresponding digits. The second fingers and fourth fingernails were most severely affected in both patients. The mother's hands were less severely affected; the middle and distal phalanges of her hands were malformed and fused. Besides the absence of fusion lines, the shape of the fused middle and distal phalanges was quite different from that of other types of fusion, i.e., fused bones in both patients did not maintain the normal configuration of bone, referring to as “middle‐distal phalangeal complex”. Distal symphalangism was observed in toes 2–5 of the mother and in toe 3 of the son. Both patients had additional clinical manifestations such as narrowing of the zygomatic arch, dental pulp stone, microdontia of a mandibular permanent central incisor, cone‐shaped epiphyses of middle phalanges of fingers, and absence of scaphoid, trapezium, trapezoid, and pisiform bones. Mutation analysis of NOG and ROR2, the genes responsible for proximal symphalangism and brachydactyly type B, respectively, was negative. © 2002 Wiley‐Liss, Inc.     

Molecular cytogenetic analysis of five 2q37 deletions: refining the brachydactyly candidate region

Deletions of the 2q37 region are associated with a recognizable pattern of MCA/MR so-called the AHO-like syndrome. Brachydactyly is a variable but characteristic feature of this clinical entity. Here we report on five cases of cytogenetically visible de novo deletions of this 2q37 chromosome region. Using FISH, we characterized at the molecular level the breakpoints of these deletions using a set of 15 BACs, PACs and YACs. In four patients, terminal deletions of variable size ranged between 6.2 and 10 Mb. The fifth patient had an interstitial deletion with an AHO-like phenotype including brachydactyly. These findings when compared to previous observations allowed us to narrow down the brachydactyly critical region between BACs RP11-585E12 and RP11-351E10. It contains HDAC4 and STK25 candidate genes loci.     

Array-CGH analysis and clinical description of 2q37.3 de novo subtelomeric deletion

We report on a 13-year-old girl with normal karyotype and a de novo cryptic terminal deletion of chromosome 2q, detected by subtelomeric FISH analysis. Further investigation with array-CGH analysis using the 1Mb resolution Spectral Chip 2600 (Spectral Genomics) confirmed the deletion and also showed a deletion of four additional clones. No other abnormalities were detected by array-CGH. FISH studies using 8 BAC-probes were performed for fine mapping of the deletion and confirmed the array results. FISH analysis showed that the deletion breakpoint lies between clones RP11-84G18 and RP11-83N2 (physical distance between clones 0.36Mb) and extends to the telomere. The size of the deletion was estimated to be about 6.4-6.7Mb. Clinical findings include: developmental delay, severe behavioural disturbances, growth-pubertal retardation, congenital conductive mild hearing loss, growth hormone deficiency, compensate hypothyroidism, dysmorphic facial features, excessive joint hypermobility, brachymetaphalangy, abnormal dermatoglyphics and a history of neonatal laryngomalacia, hypotonia and umbilical hernia. The phenotype of our patient is in keeping with those of the literature, with the exception of cardiovascular, urogenital, neurological anomalies and eczema, which were not observed. The report of the clinical and molecular presentation of similar cases will allow accurate phenotype-genotype correlation and proper genetic counseling of the family.     

Cytogenetic and molecular cytogenetic findings in 43 aneurysmal bone cysts: aberrations of 17p mapped to 17p13.2 by fluorescence in situ hybridization.

Aneurysmal bone cyst is a benign, cystic lesion of bone composed of blood-filled spaces separated by fibrous septa. Relatively few cases of aneurysmal bone cyst have been cytogenetically characterized, yet abnormalities of the short arm of chromosome 17 appear to be recurrent. In this study, conventional cytogenetic analysis of 43 aneurysmal bone cyst specimens from 38 patients over a 12-year period revealed clonal chromosomal abnormalities in 12 specimens. Karyotypic anomalies of 17p, including a complex translocation and inversion, were identified in eight of these 12 specimens. In an effort to further define the aberrant 17p breakpoint, fluorescence in situ hybridization (FISH) analyses were performed using a series of probe combinations spanning a 5.1 Mb region between the TP53 (17p13.1) and Miller-Dieker lissencephaly syndrome (17p13.3) gene loci. These studies revealed the critical breakpoint locus at 17p13.2, flanked proximally by an RP11-46I8, RP11-333E1, and RP11-457I18 bacterial artificial chromosome (BAC) probe cocktail and distally by an RP11-198F11 and RP11-115H24 BAC and RP5-1050D4 P1 artificial chromosome (PAC) probe cocktail. Overall, abnormalities of the 17p13.2 locus were identified by metaphase and/or interphase cell FISH analysis in 22 of 35 (63%) aneurysmal bone cyst specimens examined including 26 karyotypically normal specimens. These cytogenetic and molecular cytogenetic findings expand our knowledge of chromosomal alterations in aneurysmal bone cyst, further localize the critically involved 17p breakpoint, and provide an alternative approach (ie FISH) for detecting 17p abnormalities in nondividing cells of aneurysmal bone cysts. The latter could potentially be utilized as an adjunct in diagnostically challenging cases.