Jill K. Northup

Position Effects Due to Chromosome Breakpoints that Map ∼900 Kb Upstream and ∼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 ∼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 ∼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.

Molecular cytogenetic characterization of a familial der(1)del(1)(p36.33)dup(1)(p36.33p36.22) with variable phenotype.

Chromosome deletions involving 1p36 are the most common known terminal rearrangements occurring at a frequency of ∼1 in 5,000 live births. In contrast, duplications of the same region have been reported rarely. We describe a familial rearrangement der(1)del(1)(p36.33)dup(1)(p36.33p36.22) identified in a mother, daughter, and son. These individuals help define a syndrome with variable mental disability, attention deficit‐hyperactivity disorder, and a distinctive facial appearance with wide palpebral fissures, broad nasal root, macrostomia, ear malformations, and prominent incisors. Based on our results we suggest that the complex rearrangement seen in our family could be the result of the breakage‐fusion‐bridge (BFB) cycles model of formation.

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.

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.

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‐Hodgkins 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 Burkitts 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 patients 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.

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.

Role of chromosome 1 pericentric heterochromatin (1q) in pathogenesis of myelodysplastic syndromes: report of 2 new cases.

Chromosome 1 pericentromeric heterochromatin (1q) has been shown to play an important role in the pathogenesis of non-Hodgkin lymphoma and multiple myeloma. Myelodysplastic syndrome (MDS) results from marrow failure in two or more cell lineages. Although trisomy 1q has been reported in MDS, it is usually present with additional common abnormalities such as trisomy 8, monosomy 5 or monosomy 7, leading to speculation that 1q abnormalities are mostly secondary events representing clonal evolution. We report two cases of MDS in which consistent involvement of 1q heterochromatin is seen as the primary clonal abnormality. Both patients presented with fatigue and pancytopenia. Based on the published reports and our cases, we propose that the 1q heterochromatin plays a vital role in the pathophysiology of MDS. Abnormalities involving 1q result in aberrant heterochromatin/euchromatin junctions, leading to gene dosage abnormalities. Further studies of 1q abnormalities in MDS might provide specific insights as to the exact role of the excess 1q heterochromatin in the etiology of MDS.

First report of an interstitial deletion, del(5)(q33.1q35.1) in a girl with primary amenorrhea, seizures, and severe behavioral and developmental deficiencies†

Constitutional interstitial deletions of the long arm of chromosome 5 are extremely rare with only 36 cases reported [Courtens et al., 1998]. Deletions distal to 5q33 have been reported only in 10 patients [Joseph et al., 1990; Kleczkowska et al., 1993; Stratton et al., 1994; Giltay et al., 1997; Gibbons et al., 1999; Krammer et al., 1999; Pauli et al., 1999; Spranger et al., 2000; Schafer et al., 2001; Schiffer et al., 2003]. To our knowledge, there are no reports of constitutional interstitial deletion, del(5)(q33q35) in adolescents. Here, we report on a 17-year-old Caucasian female with del(5)(q33.1q35.1) presenting with primary amenorrhea, seizures, and severe behavioral and mental deficiencies. A 17-year-old, Caucasian girl was referred to genetics clinic because of failure to thrive and primary amenorrhea. She had a history of mental retardation, cerebral palsy and seizures. On physical examination, her weight was 34.7 kg (<5th centile), height was 150 cm (<5th centile), and head circumference was 52 cm (<5th centile). She had minor dysmorphic features including narrow face, deepset eyes, low-set ears, deviated nasal bridge, higharched palate, triangular face, and poor dentition. She also had clinodactyly of the 5th digit and flexion contractures of digits on the hands. She had Tanner III stage breast development. There were no other major organ malformations. However, she displayed very unusual behaviors, such as aggressive sexual behavior towards males and acting like a dog or cat by barking at people and licking her hands repeatedly. She could walk, but was very wobbly, and was not able to talk, write, or distinguish colors. She had a history of chronic diarrhea and constipation. Despite an enormous appetite, she had lost 9.1 kg within a span of 3 months secondary to diarrhea. Laboratory investigations included chromosome analysis, FISHstudies, serumaminoacidsandhormone levels. Serum amino acid screen showed high serum levels of threonine (24.8; normal 9.0–18.8 mmol/dl), glutamine (104.4; normal 21.5–82.5 mmol/dl), glycine (85.1; normal 17.2–41.0 mmol/dl), alanine (84.0; normal 22.7–53.7 mmol/dl), citrulline (4.5; normal 1.9–4.3 mmol/dl), alpha-amino-N-butyric acid (2.3; normal 1.0–2.2 mmol/dl); cystine (14.8; normal 3.4– 12.0mmol/dl), cystathionine (0.2mmol/dl), lysine (22.5; normal9.7–18.7mmol/dl), 1-CH3-histidine (2.2;normal 0–0.9 mmol/dl) and low serum levels of aspartic acid (1.2; normal 1.4–7.2 mmol/dl), and tyrosine (4.3; normal 4.4–10.6 mmol/dl). These results are suggestive of hepatic dysfunction although liver function tests were normal. Serum FSH and LH levels were normal while the estradiol was very low (8 pg/ml). Chromosome analysis from cultured peripheral blood lymphocytes showed an unbalanced structural rearrangement in all 20 cells analyzed. Based on