A complex chromosome rearrangement, der(6)ins(6)(p21.1q25.3q27)inv(6)(p25.3q27), in a child with cleidocranial dysplasia.

Complex chromosome rearrangements (CCRs) are structural abnormalities involving >2 chromosomes or >3 breakpoints. It has been suggested that the probability of imbalance increases as the number of breakpoints increase. Here we report a 7-month-old, Hispanic girl presenting with cleidocranial dysplasia (CCD) who was found to have a complex chromosome rearrangement of chromosome 6. Fluorescence in situ hybridization studies with bacterial artificial chromosome (BAC) clones showed that the rearrangement involved insertion of 6q into 6p disrupting the "Runt related transcription factor 2 (RUNX2)" gene at chromosome 6p21.1. In addition, a pericentric inversion of chromosome 6 was identified. Despite the complex nature of the rearrangement, no cryptic deletions or duplications could be detected by array comparative genomic hybridization.

Pericentric inversion, inv(14)(p11.2q22.3), in a 9-month old with features of Goldenhar syndrome.

Goldenhar syndrome, also called hemifacial microsomia or oculo-auriculo-verterbal dysplasia (OAVS) (MIM 164210), is a birth defect involving the first and second branchial arch derivatives with an incidence of 1/5000. The variable phenotype includes mostly unilateral deformity of the external ear and small ipsilateral half of the face with epibulbar dermoid and vertebral anomalies. A genome-wide search in one family suggested linkage to a region of 10.7 cM on chromosome 14q32; however, no candidate genes have been identified. We report on a 9-month old with OAVS and a pericentric inversion of chromosome 14 which he inherited from his phenotypically normal mother. Fluorescence in-situ hybridization analysis with bacterial artificial chromosome clones from chromosome 14 showed the breakpoint on 14q maps distal to 14q21.2, thus confirming the cytogenetic breakpoints. In light of previous linkage studies mapping OAVS to 14q, we propose that the long arm breakpoint in our proband disrupted a potential candidate gene for OAVS resulting in his clinical phenotype.

Molecular cytogenetic characterization of an interstitial de novo 13q deletion in a 3-month-old with severe pediatric gastroesophageal reflux.

Gastroesophageal reflux (GER) occurs when gastric contents travel back into the esophagus through the esophageal sphincter. GER is very common in infants with most growing out of it, but some continue to have chronic symptoms throughout childhood and adulthood. A gene for severe pediatric gastroesophageal reflux disease (GERD) was identified by linkage analysis and was mapped to chromosome 13. We report here a de novo interstitial deletion of chromosome 13 in a 3-month-old biracial male who presented to the emergency room with severe GER and failure to thrive. Chromosome analysis showed an interstitial deletion of chromosome 13, with the karyotype reported as 46, XY, del(13)(q12.3q14.1). BAC-FISH analysis demonstrated that the deletion encompasses 12.3 Mb and does involve the GERD1 locus. The GERD1 locus has been mapped to a 9-cM interval between the markers CAGR1 and D13S263, both of which are deleted in our patient. We propose that the GER phenotype in our patient is due to a haploinsufficiency of GERD1.

Molecular cytogenetic characterization of a unique and complex de novo 8p rearrangement.

Human chromosome 8p is prone to recurrent rearrangements with inv dup del(8p) being most common. Each of these recurrent rearrangements is associated with different clinical manifestations. Some of these recurrent rearrangements at 8p are mediated by an 8p submicroscopic paracentric inversion between the olfactory gene clusters present in one of the parents. However, recent reports have shown that some of the rearrangements are unique and complex and are mediated by other repetitive elements within 8p. Here, we report on a unique and complex 8p rearrangement with seizures as the major presenting feature in the patient. Extensive fluorescence in situ hybridization and microarray analyses with tiling path 8p array showed that the rearrangement is unique in that the 8p duplication is a direct tandem duplication and, unlike the more common inv dup del(8p), is not derived from parental submicroscopic inversion. Also unlike the inv dup del(8p), the phenotype in our case is milder with no central nervous system malformations or cardiac defects.

Do cytogenetic abnormalities precede morphologic abnormalities in a developing malignant condition?

Cytogenetic evaluation of bone marrow and neoplastic tissues plays a critical role in determining patient management and prognosis. Here, we highlight two cases in which the cytogenetic studies challenge the common practice of using hematologic and morphologic changes as key factors in malignant disease management. The first case is that of a lymph node sample from a 40-yr-old non-Hodgkin's lymphoma (NHL) patient sent for determination of disease progress. Hematologic studies showed no evidence of transformation to high-grade NHL (>15% blasts with rare mitotic figures). Cytogenetic studies of lymph node showed multiple clonal abnormalities, most notably a der(18) from a t(14;18) which is associated with high-grade NHL. After two cycles of chemotherapy with fludarabine, the patient did not show any clinical response, suggesting possible progression to high-grade lymphoma. The second case is of a patient with a history of human immunodeficiency virus and blastic natural killer leukemia/lymphoma. Hematologic studies of ascitic fluid classified the patient as having pleural effusion lymphoma whereas bone marrow analysis showed no malignancy. Bone marrow cytogenetic studies showed multiple clonal abnormalities including a t(8;14), which is commonly associated with Burkitt's lymphoma (BL). To our knowledge, this is the first case wherein a morphologically normal bone marrow showed presence of clonal abnormalities consistent with BL or Pleural effusion lymphoma. After two cycles of CHOP (cyclophosphamide, doxorubicin, vincristine and prednisone) chemotherapy, the patient's general condition and ascitis improved and she was discharged. These studies clearly demonstrate that genetic changes often precede morphologic changes in a developing malignant condition. Therefore, the critical information needed for care of patients with malignant disorders may be incomplete or inaccurate if cytogenetic evaluation is overlooked.

Interphase FISH screening for the LCR-mediated common rearrangement of isochromosome 17q in primary myelofibrosis.

Non-allelic homologous recombination (NAHR) between low-copy repeats (LCRs) has been implicated recently in somatic rearrangements including isochromosome i(17q), which is associated with hematologic malignancies as well as solid tumors. In hematological malignancies, the most common i(17q) breakpoint results from LCR-mediated NAHR, which creates a dicentric chromosome, idic(17)(p11.2). We report an elderly patient who presented with primary myelofibrosis (MF) with myeloid metaplasia (MMM), associated with idic(17)(p11.2) as the sole chromosomal abnormality, making this the first idic(17)(p11.2) myeloproliferative case reported in which the breakpoints are mapped to the breakpoint cluster region in proximal 17p. The rearrangement breakpoint maps to the previously defined LCR cluster, further suggesting that the genomic architecture of proximal 17p may be responsible for the formation of the majority of i(17q) cases. We describe our development of a rapid screening test using interphase FISH to detect idic(17)(p11.2), discuss the potential prognostic value of this molecular diagnostic test, and examine the relevance of LCR-mediated NAHR to common rearrangements in neoplasms.

Position effects due to chromosome breakpoints that map approximately 900 Kb upstream and approximately 1.3 Mb downstream of SOX9 in two patients with campomelic dysplasia.

Campomelic dysplasia (CD) is a semilethal skeletal malformation syndrome with or without XY sex reversal. In addition to the multiple mutations found within the sex-determining region Y-related high-mobility group box gene (SOX9) on 17q24.3, several chromosome anomalies (translocations, inversions, and deletions) with breakpoints scattered over 1 Mb upstream of SOX9 have been described. Here, we present a balanced translocation, t(4;17)(q28.3;q24.3), segregating in a family with a mild acampomelic CD with Robin sequence. Both chromosome breakpoints have been identified by fluorescence in situ hybridization and have been sequenced using a somatic cell hybrid. The 17q24.3 breakpoint maps approximately 900 kb upstream of SOX9, which is within the same bacterial artificial chromosome clone as the breakpoints of two other reported patients with mild CD. We also report a prenatal identification of acampomelic CD with male-to-female sex reversal in a fetus with a de novo balanced complex karyotype, 46,XY,t(4;7;8;17)(4qter-->4p15.1::17q25.1-->17qter;7qter-->7p15.3::4p15.1-->4pter;8pter-->8q12.1::7p15.3-->7pter;17pter-->17q25.1::8q12.1-->8qter). Surprisingly, the 17q breakpoint maps approximately 1.3 Mb downstream of SOX9, making this the longest-range position effect found in the field of human genetics and the first report of a patient with CD with the chromosome breakpoint mapping 3' of SOX9. By using the Regulatory Potential score in conjunction with analysis of the rearrangement breakpoints, we identified a candidate upstream cis-regulatory element, SOX9cre1. We provide evidence that this 1.1-kb evolutionarily conserved element and the downstream breakpoint region colocalize with SOX9 in the interphase nucleus, despite being located 1.1 Mb upstream and 1.3 Mb downstream of it, respectively. The potential molecular mechanism responsible for the position effect is discussed.