4.3-Mb triplication of 4q32.1-q32.2: report of a family through two generations.

Duplications of 4q31-qter have been rarely documented; moreover, triplications at this chromosomal region have never been described. Here we report a family through two generations (mother and three sons) with triplication of 4q32.1-q32.2. Their characteristic features include: macrocephaly, a long midface, hypoplastic zygoma, wide nasal bridge, short nose, downslanting and small palpebral fissures, and small, low-set and squared-off ears. Among the three sons, two had Hirschsprung disease, and one had constipation at birth. The phenotype of triplication of 4q32.1-q32.2 appeared to be distinct from duplications of 4q31-qter.

Interstitial deletion of 1p22.2p31.1 and medium-chain acyl-CoA dehydrogenase deficiency in a patient with global developmental delay.

We report on a 6-year-old girl who presented at 6 months of age with seizures, delayed psychomotor development and mild facial dysmorphism. A small muscular ventricular septal defect was documented on echocardiogram and brain MRI showed a frontal brain anomaly. Urine organic acid analysis revealed dicarboxylic aciduria, and plasma acylcarnitine analysis showed marked elevation of octanoyl (C8) and decanoyl (C10) carnitines with C8:C10 ratio of 9:1. These results were indicative of medium chain acyl-CoA dehydrogenase deficiency. ACADM gene sequencing showed an apparent homozygous c.166G > C (Ala31Pro) missense mutation in exon 3; however, only the mother was found to be a carrier of this novel missense mutation. This finding along with non-regressive developmental delay prompted further karyotype and genomic investigations. An interstitial deletion of chromosome 1 was detected by repeat G-banding: 46,XX,del(1)(p22.2p31.1). Parental karyotypes were normal. The deletion was characterized by array CGH analysis using a 1 Mb BAC/PAC array platform. Clones deleted extended from RP11-88B10 (1p31.1) to RP5-1007M22 (1p22.2), a 15.5 Mb deletion which includes the ACADM locus. Clinical review of 6/7 cases of interstitial deletions with breakpoints of 1p22 and 1p31/32, including the patient in this report, indicate a variable phenotype. Thus, although G-band breakpoints are similar, common breakpoints for these alterations are unlikely. This is the first report of a patient with fatty acid oxidation defect caused by a mutation in combination with an interstitial chromosomal deletion.

Late-appearing Philadelphia chromosome in childhood acute myeloid leukemia.

A 3-year-old female was diagnosed with acute myeloid leukemia (AML-M2). The disease was refractory to various chemotherapeutic agents. Cytogenetic analysis revealed a clone with trisomy 8 at diagnosis that was replaced by a clone containing a t(11;15) and del(20q) by the end of the second induction. A new clone, characterized by a Philadelphia chromosome, with the minor BCR/ABL p190 transcript, emerged 14 months after diagnosis and remained to the end of disease course. The late occurrence of the Philadelphia chromosome in AML has been documented rarely in adults.

Array-based genomic delineation of a familial duplication 11q14.1-q22.1 associated with recurrent depression.

Detection of abnormal karyotypes with associated clinical manifestations is an important tool for the identification of genes that confer susceptibility to genetic disorders. We present a family with a duplication 11q14.1-q22.1 resulting from an unbalanced familial insertion, associated with a mild dysmorphic phenotype and mood disorders, mainly major depression. This relatively large duplication of a segment from chromosome 11 is associated with a surprisingly little physical phenotypic effect in this family. The finding of mood disorders in adult members of the family who carry the insertion supports the view that the duplication may be important for the identification of contributing gene(s) to mood disorders. Major depression is considered to be a complex trait with multiple genetic alterations interacting with environmental factors. Array-based comparative genome hybridization (array CGH) analysis with a 1 Mb genomic array, defined the duplication region that extended over 16 Mb from 11q14.1 to 11q22.1. Brain-expressed genes that map within this 16 Mb region, are considered worthy of further investigation as gene(s) contributing to the etiology of major depression.

Speech and language impairment and oromotor dyspraxia due to deletion of 7q31 that involves FOXP2.

We report detailed clinical, cytogenetic, and molecular findings in a girl with a deletion of chromosome 7q31-q32. This child has a severe communication disorder with evidence of oromotor dyspraxia, dysmorphic features, and mild developmental delay. She is unable to cough, sneeze, or laugh spontaneously. Her deletion is on the paternally inherited chromosome and includes the FOXP2 gene, which has recently been associated with speech and language impairment and a similar form of oromotor dyspraxia in at least three other published cases. We hypothesize that our patient's communication disorder and oromotor deficiency are due to haploinsufficiency for FOXP2 and that her dysmorphism and developmental delay are a consequence of the absence of the other genes involved in the microdeletion. We propose that this patient, together with others reported in the literature, may define a new contiguous gene deletion syndrome encompassing the 7q31-FOXP2 region. Cytogenetic and molecular analysis of this region should be considered for other individuals displaying similar characteristics.

Association of the t(12;22)(q13;q12) EWS/ATF1 rearrangement with polyphenotypic round cell sarcoma of bone: a case report.

The t(12;22)(q13;q12) chromosomal rearrangement results in an EWS/ATF1 fusion transcript and is associated with clear cell sarcoma (CCS). CCS is an uncommon tumor arising in tendons and aponeuroses of the extremities and shows evidence of melanocytic differentiation at the light microscopic, immunohistochemical, and/or ultrastructural level. Only 5 cases have been reported to arise in bone, none of which had molecular confirmation of the diagnosis. The current report describes a 7-year-old girl with a primary round cell sarcoma of the left humerus showing polyphenotypic differentiation on immunohistochemical analysis. Antibodies directed at melanocytic antigens were negative, and there was no evidence of melanocytic differentiation by light microscopy or ultrastructural analysis. Cytogenetic analysis revealed rearrangement of the EWS locus within 22q12. RT-PCR and sequence analysis revealed the presence of a fusion transcript bringing together exon 7 of EWS with exon 5 of ATF1, consistent with a type 2 transcript reported in association with CCS. However, given the lack of morphologic features usually present in CCS, a diagnosis of polyphenotypic round cell sarcoma was made. This tumor thus expands the spectrum of neoplasms associated with the t(12;22)(q13;q12) rearrangement.

A der(19)t(12;19)(q12;p13.3) in a case of pediatric acute leukemia with unusual immunophenotype.

We describe a case of acute leukemia in a child with an unusual immunophenotype and a novel cytogenetic abnormality. The leukemia blasts expressed myeloid, natural killer and B-lineage associated antigens. Cytogenetics showed the presence of a novel unbalanced chromosomal translocation, der(19)t(12;19)(q12;p13.3). The patient achieved and maintained remission with myeloid-directed chemotherapy. The differential diagnosis of the immunophenotype and the potential fusion genes are discussed.

Intrascrotal lipoblastoma with a complex karyotype: a case report and review of the literature.

Lipoblastoma is a tumor of adipose tissue that usually occurs in young children. Most lipoblastomas occur on the extremities, trunk, and head and neck, and most have rearrangements of the 8q region. We describe a lipoblastoma in a 12-month-old boy who presented with a rapidly enlarging scrotal mass. Electron microscopy revealed features consistent with immature adipocytes, and cytogenetic analysis revealed the following karyotype: 57,XY,+4,+6,+7,der(8)t(8;12) (q22;q13), +der(8)t(8;12) (q22;q13), +9,+10,+12,-16,+17,+der(18)t(8;18)(q22;q23),+19,+20. Interestingly, the breakpoint on chromosome 12 (q13) is the same as that seen in lipoblastomas. To our knowledge, this is the first reported case of such a complex karyotype in lipoblastoma and adds to the expanding list of karyotypic abnormalities seen in such tumors.

Peripheral medulloepithelioma: an immunohistochemical, ultrastructural, and cytogenetic study of a rare, chemotherapy-sensitive, pediatric tumor.

A case of peripheral medulloepithelioma, a rapidly growing tumor involving the pelvic cavity of a 12-year-old girl, is presented. The diagnosis was supported by expression of vimentin, nestin, alpha-internexin, neurofilaments, and microtubule-associated protein 5 and by characteristic ultrastructure that included absence of cilia or microvilli. Trisomy of chromosomes 2 and 8 was the only detectable chromosomal abnormality. Combination chemotherapy resulted in complete remission. Because some of these rare tumors are sensitive to chemotherapy, their recognition and separation from other neuroectodermal tumors are advisable for better understanding of their biology and determination of optimal treatment.

Unique insertional translocation in a childhood Wilms' tumor survivor detected when his daughter developed bilateral retinoblastoma.

Retinoblastoma and Wilms' tumor are rare childhood embryonic tumors associated with loss or inactivation of tumor suppressor genes, RB1 located within 13q14, and WT1 located within 11p13. Interchromosomal insertional translocations occur rarely, and such rearrangements within RB1 or WT1, even rarer. We report a unique family in which an insertional translocation of a chromosomal segment that included band 13q14 inserted into 11p13 caused childhood Wilms' tumor in the father, and whose child developed bilateral retinoblastoma. This is the first case of an insertional translocation that caused both tumors. This insertional translocation had significant consequences for genetic counseling and in utero diagnosis. The estimated risk for an offspring of this father to develop Wilms' tumor is up to 50%, to develop retinoblastoma up to 25%, to have neither tumor 25%, and to have both tumors 0%.

Malignant hematological disorders in children with Wolf-Hirschhorn syndrome.

Wolf-Hirschhorn syndrome (WHS) is a rare chromosomal disorder attributable to a deletion at the short arm of chromosome 4. This syndrome is associated with characteristic facial appearance, multiple congenital abnormalities, mental retardation, feeding difficulties and failure to thrive. We report two girls with WHS who developed myelodysplastic syndrome (MDS). According to the "Category, Cytology, Cytogenetic (CCC)"classification of childhood MDS, patient 1 had refractory cytopenia with ring sideroblasts at the age of 6 years, while patient 2 had refractory cytopenia with dysplasia at the age of 5-1/2 years. Patient 1 progressed to refractory cytopenia with excess blasts within a year, while patient 2 progressed to acute lymphoblastic leukemia within 1 month of presentation. It is possible that allelic loss of a tumor suppressor gene such as WHSC1 and/or FGFR3 from the deleted segment 4p16.3 plays a critical role in the process of malignant transformation. To our knowledge, this is the first report of severe hematological complications like MDS and leukemia in children with WHS and may be an important genetic model for understanding malignant hematological transformation. This report also underscores the importance of evaluating children with WHS for hematopoietic dysfunction.

Human chromosome 7: DNA sequence and biology.

DNA sequence and annotation of the entire human chromosome 7, encompassing nearly 158 million nucleotides of DNA and 1917 gene structures, are presented. To generate a higher order description, additional structural features such as imprinted genes, fragile sites, and segmental duplications were integrated at the level of the DNA sequence with medical genetic data, including 440 chromosome rearrangement breakpoints associated with disease. This approach enabled the discovery of candidate genes for developmental diseases including autism.

An active ring X and haploinsufficiency of SHOX contribute to short stature, congenital anomalies, and developmental delay in a female.

We report on a female infant with short stature and mesomelic limb shortening, multiple congenital abnormalities, developmental delay, and Rieger anomaly. Cytogenetic analysis revealed a complex rearrangement of the sex chromosomes in this patient. In addition to a normal X chromosome, a derivative Y [der(Y)] chromosome composed of X and Y material and a ring X [r(X)] were present. Consistent with the fact that this infant had normal female genitalia, the SRY gene was not detected in the Y chromosome portion of the der(Y). By fluorescence in situ hybridization (FISH), XIST was present on the normal X and the r(X), but not on the der(Y). The normal X was late replicating (inactive) and the r(X) early replicating (active) in all lymphocyte metaphases examined. As the X chromosome material on the der(Y) cannot be inactivated, the unusual skew of activation toward the r(X) presumably resulted in the least amount of functional disomy of X-linked genes in the cells of this patient. Deletion of one copy of the SHOX gene was detected in this patient. Haploinsufficiency of this gene is known to be correlated with short stature and mesomelic limb shortening.

Genetic analysis of patients with the Saethre-Chotzen phenotype.

Saethre-Chotzen syndrome is a common craniosynostosis syndrome characterized by craniofacial and limb anomalies. Intragenic mutations of the TWIST gene within 7p21 have been identified as a cause of this disorder. There is phenotypic overlap with other craniosynostosis syndromes, and intragenic mutations in FGFR2 (fibroblast growth factor receptor 2) and FGFR3 (fibroblast growth factor receptor 3) have been demonstrated in the other conditions. Furthermore, complete gene deletions of TWIST have also been found in a significant proportion of patients with Saethre-Chotzen syndrome. We investigated 11 patients clinically identified as having the Saethre-Chotzen phenotype and 4 patients with craniosynostosis but without a clear diagnosis. Of the patients with the Saethre-Chotzen phenotype, four were found to carry the FGFR3 P250R mutation, three were found to be heterozygous for three different novel mutations in the coding region of TWIST, and two were found to have a deletion of one copy of the entire TWIST gene. Developmental delay was a distinguishing feature of the patients with deletions, compared to patients with intragenic mutations of TWIST, in agreement with the results of Johnson et al. [1998: Am J Hum Genet 63:1282-1293]. No mutations were found for the four patients with craniosynostosis without a clear diagnosis. Therefore, 9 of our 11 patients (82%) with the Saethre-Chotzen phenotype had detectable genetic changes in FGFR3 or TWIST. We propose that initial screening for the FGFR3 P250R mutation, followed by sequencing of TWIST and then fluorescence in situ hybridization (FISH) for deletion detection of TWIST, is sufficient to detect mutations in > 80% of patients with the Saethre-Chotzen phenotype.

Molecular genetic studies of human chromosome 7 in Russell-Silver syndrome.

Russell-Silver syndrome (RSS) is a form of congenital short stature characterized by severe growth retardation and variable dysmorphic features. In some RSS individuals, alterations in imprinted genes may be involved because approximately 7% of sporadic patients have been observed to have maternal uniparental disomy (mUPD) of chromosome 7. RSS patients with structural abnormalities of chromosome 7 have also been described. In these individuals the chromosome rearrangement could disrupt the balance of imprinted genes, contribute to a recessive form of RSS, or lead to haploinsufficiency of a crucial developmental gene product. Because the mechanism and molecular defects on chromosome 7 causing RSS are still unknown, we tested our collection of 77 RSS families for mUPD7 and were able to identify three new cases. We also characterized two RSS patients with de novo cytogenetic abnormalities involving the short arm of chromosome 7. One had a partial duplication [46, XX, dup(7)(p12 p14)] and the second contained a paracentric inversion [46, XY, inv(7)(p14 p21)]. Fluorescence in situ hybridization (FISH) mapping revealed that the breakpoints on 7p14 were localized to the same novel gene, C7orf10, which encompasses >700 kb of DNA. We also identified other transcription units from this immediate region, but all seem to be biallelically expressed when using a somatic cell hybrid assay.

Detecting rearrangements in children using subtelomeric FISH and SKY.

The etiology of mental retardation (MR), often presenting as developmental delay in childhood, is unknown in approximately one-half of cases. G-banding is the standard method for investigating those suspected of having a chromosomal etiology; however, detection of structural abnormalities is limited by the size and pattern of the G-bands involved. Rearrangements involving subtelomeric regions have been shown to cause MR and this has generated interest in investigating the prevalence of these rearrangements using telomere-specific probes. In addition, because cryptic interchromosomal rearrangements may not be small or confined to chromosomal ends, spectral karyotyping (SKY) using chromosome-specific painting probes may be of value. We report here a study using these two FISH-based techniques in 50 children with idiopathic MR or developmental delay and normal GTG-banded karyotypes. Our objective was to assess the prevalence of cryptic rearrangements in this population using subtelomeric FISH and SKY. Three rearrangements were detected by subtelomeric FISH: a derivative 5 from a maternal t(5;21); a recombinant 11 from a paternal pericentric inversion; and a 2q deletion that was also present in the mother. Only the derivative 5 was detected by SKY. SKY did not detect any interstitial interchromosomal rearrangement. The prevalence of clinically significant cryptic rearrangements by subtelomeric FISH and SKY was thus 4% (95% confidence interval 0.5-13.7) and 2% (95% CI 0.05-10.7), respectively. This study supports the view that G-banding does not detect all clinically significant chromosomal abnormalities and that subtelomeric FISH and SKY can detect some of these abnormalities.