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Philip D Cotter

Publications and source records attributed to Philip D Cotter.

At least 19 recordsLinked to original sources
PubMed2006

Molecular cytogenetic characterization of human papillomavirus16-transformed foreskin keratinocyte cell line 16-MT.

Anogenital cancers are closely associated with human papillomavirus (HPV), and HPV-infected individuals, particularly those with high-grade dysplasias, are at increased risk for cervical and anal cancers. Although genomic instability has been documented in HPV-infected keratinocytes, the full spectrum of genetic changes in HPV-associated lesions has not been fully defined. To address this, we examined an HPV16-transformed foreskin keratinocyte cell line, 16-MT, by GTG-banding, spectral karyotyping (SKY), and array comparative genomic hybridization (array CGH); these analyses revealed multiple numerical, complex, and cryptic chromosome rearrangements. Based on GTG-banding, the 16-MT karyotype was interpreted as 78-83,XXY,+add(1)(p36.3),+3,+4,+5,+5,+7,+8,+i(8)(q10)x2,+10,?der(12),der(13;14)(q10;q10),+15,+16,add(19)(q13.3),+21,+21,-22[cp20]. Multicolor analysis by SKY confirmed and further characterized the anomalies identified by GTG banding. The add(1) was identified as a der(1)(1qter-->1q25::1p36.1-->1qter), the add(19) as a dup(19), and the der(12) interpreted as a der(11) involving a duplication of chromosome 11 material and rearrangement with chromosome 19. In addition, previously unidentified der(9)t(9;22), der(3)t(3;19), and der(4)t(4;9) were noted. The 16-MT cell line showed losses and gains of DNA due to unbalanced translocations and complex rearrangements of regions containing known tumor suppressor genes. Chromosomal changes in these regions might explain the increased risk of cancer associated with HPV. Also, array CGH detected copy-number gains or amplifications of chromosomes 2, 8, 10, and 11 and deletions of chromosomes 3, 4, 11, and 15. These results provide the basis for the identification of candidate oncogenes responsible for cervical and anal cancer in amplified regions, and for putative tumor suppressor genes in commonly deleted regions like 11q22-23. Furthermore, these data represent the first full characterization of the HPV-positive cell line 16-MT.

Aneuploidy↗
PubMed2006

HRAS mutations in Costello syndrome: detection of constitutional activating mutations in codon 12 and 13 and loss of wild-type allele in malignancy.

Costello syndrome (CS) is a complex developmental disorder involving characteristic craniofacial features, failure to thrive, developmental delay, cardiac and skeletal anomalies, and a predisposition to develop neoplasia. Based on similarities with other cancer syndromes, we previously hypothesized that CS is likely due to activation of signal transduction through the Ras/MAPK pathway [Tartaglia et al., 2003]. In this study, the HRAS coding region was sequenced for mutations in a large, well-characterized cohort of 36 CS patients. Heterogeneous missense point mutations predicting an amino acid substitution were identified in 33/36 (92%) patients. The majority (91%) had a 34G --> A transition in codon 12. Less frequent mutations included 35G --> C (codon 12) and 37G --> T (codon 13). Parental samples did not have an HRAS mutation supporting the hypothesis of de novo heterogeneous mutations. There is phenotypic variability among patients with a 34G --> A transition. The most consistent features included characteristic facies and skin, failure to thrive, developmental delay, musculoskeletal abnormalities, visual impairment, cardiac abnormalities, and generalized hyperpigmentation. The two patients with 35G --> C had cardiac arrhythmias whereas one patient with a 37G --> T transversion had an enlarged aortic root. Of the patients with a clinical diagnosis of CS, neoplasia was the most consistent phenotypic feature for predicating an HRAS mutation. To gain an understanding of the relationship between constitutional HRAS mutations and malignancy, HRAS was sequenced in an advanced biphasic rhabdomyosarcoma/fibrosarcoma from an individual with a 34G --> A mutation. Loss of the wild-type HRAS allele was observed, suggesting tumorigenesis in CS patients is accompanied by additional somatic changes affecting HRAS. Finally, due to phenotypic overlap between CS and cardio-facio-cutaneous (CFC) syndromes, the HRAS coding region was sequenced in a well-characterized CFC cohort. No mutations were found which support a distinct genetic etiology between CS and CFC syndromes.

Abnormalities, Multiple↗
PubMed2006

Duplication of distal 20q: clinical, cytogenetic and array CGH. Characterization of a new case.

Trisomy of the long arm of chromosome 20 is rare. We describe an 18-month-old male who was born at 36 weeks via Caesarian section after an uneventful pregnancy. During the newborn period he was found to have a right-sided cleft lip and cleft palate, hypertelorism, strabismus and mildly over-folded ears with cupping. Cardiovascular examination was consistent with the diagnosis of severe aortic coarctation, which was confirmed by echocardiogram. Additionally, hypothyroidism was diagnosed. Neurological evaluation at 18 months revealed a hypotonic infant with delayed acquisition of motor milestones. Cytogenetic analysis showed additional material on the long arm of chromosome 20, confirmed by fluorescence in situ hybridization (FISH) analysis as being of chromosome 20 origin. Because of the indistinct GTG-banding pattern it was not possible to distinguish between a proximal [dup(20)(q11.2q13.1)] or distal duplication [dup(20)(q13.1q13.3)]. To further define the duplication we used array comparative genomic hybridization (CGH) which demonstrated a 7.8 Mb interstitial duplication in distal 20q. Thus, the proband's karyotype was interpreted as 46,XY,dup(20)(q13.2q13.2). The proband is the first reported case of a pure duplication of this region. This case further highlights the utility of array CGH in characterizing aneusomies and, in particular, for accurate breakpoint designation and quantitation of ambiguous rearrangements.

Abnormalities, Multiple↗
PubMed2005

Ring chromosome 15: characterization by array CGH.

Ring chromosome 15 [r(15)] is an uncommon finding with less than 50 patients reported. Precise genotype-phenotype correlations are problematic because of the difficulties in determining the extent of euchromatic loss, the level of mosaicism, and the influence of the timing of ascertainment. We report two discordant examples of r(15) patients. In the first case, prenatal diagnosis of a de novo r(15) was made during the second trimester: mos 46,XX,r(15)(p11.2q26)[32]/45,XX,-15[13]/47,XX,r(15)(p11.2q26)x2[3]/46,XX,dic r(15)(p11.2q26p11.2q26[1]/46,XX[2]. Postnatal follow-up revealed extremely small stature, heart defects, and developmental delay. Patient 2 was a 31-year-old short-statured female who was living independently: 46,XX,r(15)(p11q26). Both cases showed loss of the 15q subtelomeric region by fluorescence in situ hybridization (FISH). To investigate the discordance in phenotypes between the two patients, we undertook array comparative genomic hybridization (array CGH) analyses to more fully characterize the deletions associated with these otherwise structurally indistinguishable r(15) chromosomes from conventional cytogenetic analyses and fluorescence in situ hybridization (FISH) studies. By array CGH, patient 1 showed deletion of multiple contiguous clones predicting an approximately 6 Mb deletion of distal 15q. In contrast, patient 2 showed loss of just the 15q subtelomeric clone and an interstitial clone by array CGH confirming that the severity of the phenotype correlated with the size of the deletion at the molecular level. These cases illustrate the utility of array CGH characterization for determining the size of the associated deletion in ring chromosomes and for facilitating phenotype-genotype correlations.

Adult↗
PubMed2005

Interstitial deletion of chromosome 12q: genotype-phenotype correlation of two patients utilizing array comparative genomic hybridization.

Interstitial deletions of chromosome 12q are rare, with only 11 reported cases in the literature. We recently described two cases with cytogenetically identical interstitial deletions of the long arm of chromosome 12. Here, we report on a third patient, a 26-month-old male with a cytogenetically-identical interstitial deletion: 46,XY,del(12)(q21.2q22). Phenotypic features of this male proband included craniofacial and ectodermal anomalies, genitourinary anomalies, minor cardiac abnormalities, mild ventriculomegaly on brain MRI, hyperopia, and developmental delay. To further define the extent of the chromosomal aberration, microarray-based comparative genomic hybridization (array CGH) analysis was performed and the array data was compared to one of our previously reported cases. Although cytogenetic analysis of the two patients was concordant, molecular analysis by array CGH revealed that the patients had discordant distal breakpoints. The determination of molecular breakpoints and phenotypic analyses in these two patients, in conjunction with previously reported cases, leads us to propose a 12q deletion phenotype and a possible genetic locus for hyperkeratosis pilaris/ulerythema ophryogenes.

Child, Preschool↗
PubMed2005

Acquired inv(9): what is its significance?

Pericentric inversion of the heterochromatic region of chromosome 9 [inv(9)] is a common heteromorphism in the general population. It is presumed familial as there are no reports of de novo inv(9) chromosomes in constitutional karyotypes. We report 2 cases of acquired inv(9) chromosomes; 1 patient with acute myeloid leukemia, 46,XY,inv(9)(p11q13)[11]/46,XY[9], and a second with severe anemia, 46,XX,inv(9)(p11q13)[14]/46,XX[6]. The acquired nature of the inv(9) was confirmed by constitutional karyotyping and/or molecular analysis. The inv(9) in these patients may be a de novo inversion that cytogenetically mimics the constitutional inv(9) heteromorphism. Alternatively, it may be the result of neocentromere activation in 9q due to epigenetic events associated with the disease in these patients that results in a metacentric chromosome similarly mimicking the constitutional inv(9). One previous report of an acquired inv(9) was in a patient with essential thrombocythemia. The differences in clinical presentation may represent different underlying mechanisms generating the inv(9). The significance of an acquired inv(9) is unknown and will require reporting of additional cases.

Aged↗
PubMed2005

Xq chromosome duplication in males: clinical, cytogenetic and array CGH characterization of a new case and review.

Males with duplications within the long arm of the X chromosome are rare and most cases are inherited from a maternal heterozygote. We report a male with a de novo Xq duplication and review of the literature. The proband was ascertained prenatally after an abnormal expanded alpha-fetoprotein (AFP) screen and abnormal ultrasound findings. Chromosome analysis on amniocyte and subsequent peripheral blood lymphocyte cultures showed a male karyotype containing additional material on the long arm of the X chromosome. Fluorescence in situ hybridization with an X chromosome whole chromosome paint probe showed that the additional material was derived from the X chromosome, interpreted as a dup(X)(q13.3q24). Further characterization of the duplication by array CGH showed a duplication size between 30-44 Mb as determined by the map position of the flanking clones on the array, and refined the breakpoints of the duplicated region to Xq21.32 --> Xq25. At birth, the proband had multiple craniofacial abnormalities, musculoskeletal anomalies, bilateral cryptorchidism with scrotal hypoplasia, conductive hearing loss, and profound generalized hypotonia despite normal birthweight, length, and head circumference. Although data regarding Xq duplications in males are limited, a clear pattern of characteristic features can be discerned as illustrated in the present case and confirmed in our literature review. Mental, psychomotor and growth retardation, as well as, craniofacial anomalies, muscle hypotonia, hypoplastic genitalia, cryptorchidism, feeding difficulties, and endocrine dysfunction are all significant issues in these individuals.

Abnormalities, Multiple↗
PubMed2005

Prenatal diagnosis of minute supernumerary marker chromosomes.

The identification of supernumerary marker chromosomes (SMC) at prenatal diagnosis is problematic, particularly for the prediction of phenotype. The assessment of phenotypic risk is based on the size, morphology and origin of the SMC. Fluorescence in situ hybridization (FISH) characterization and family studies are also employed to aid in determining the significance of a prenatally ascertained SMC. Generally, SMC containing euchromatin are more likely to be associated with abnormal phenotypes and SMC without euchromatin are more likely to result in normal phenotypes. The smallest of SMC, minute SMC (minSMC) appear as dot-like or centric fragments and are particularly difficult to identify and characterize. Previous empirical observations suggested that the risk of phenotypic abnormality in prenatally ascertained minSMC was < or = 5%. We identified minSMC in chorionic villus samples (CVS) or amniocytes from 11 unrelated pregnancies. The chromosomal origin of each minSMC was identified by sequential FISH analysis with chromosome-specific centromere probes. Further FISH analysis with whole chromosome paint probes was undertaken to assess each minSMC for the presence or absence of euchromatin, since the presence of euchromatin may be associated with a higher risk of abnormality. Two minSMC were shown to have euchromatin. The first, a minSMC(12) was found in CVS but not confirmed in amniocytes, indicating confined placental mosaicism. The second, a minSMC derived from chromosome 19, was associated with ultrasound abnormalities. Apart from a case with mild speech delay, the remaining minSMC cases without detectable euchromatin had a normal outcome at birth and/or on longer term follow-up. Additional FISH analyses with a telomeric repeat probe showed no signal on any of the minSMC tested, suggesting that they were ring chromosomes in structure. These data further support the concept that minSMC containing euchromatin are more likely to be associated with an abnormal phenotype, although as more data are collected, this may vary by chromosome of origin. The absence of detectable euchromatin, while not guaranteeing a normal result, is most likely to have a normal outcome. The present report and previous studies do not yet allow any significant adjustment of the empirical < or = 5% risk estimate for minSMC identified at prenatal diagnosis. However, reporting of additional cases with characterization of the minSMC and particularly with long-term follow-up will, in time, allow for more accurate risk estimates and provide prognostic information.

Adult↗
PubMed2005

Transformation of follicular lymphoma to Burkitt-like lymphoma within a single lymph node.

Aberrant expression of bcl-2 , caused by a t(14;18) translocation, is most commonly associated with follicular lymphoma. In a subset of these tumors, additional acquisition of a translocation involving c-myc leads to transformation to a high-grade lymphoma. We report a case of follicular lymphoma containing a t(14;18) translocation transforming into a Burkitt-like lymphoma containing the original t(14;18) as well as an additional t(8;14). The latter translocation resulted in the phenotype of Burkitt-like lymphoma, and the transformation from follicular lymphoma to Burkitt-like lymphoma was demonstrable within a single lymph node. To the best of our knowledge, this is the first report of a case documenting direct transformation of follicular lymphoma into Burkitt-like lymphoma in the same lymph node. This case illustrates the dramatic oncogenic stimulus that results from the inhibition of apoptosis by bcl-2 combined with the deregulation of cell growth by c-myc .

Burkitt Lymphoma↗
PubMed2005

Case report: Y;6 translocation with deletion of 6p.

Translocations between the Y chromosome and an autosome are rare. We report a phenotypic male with a translocation between the Y chromosome and chromosome 6p, leading to partial 6p monosomy and XX male syndrome. He is the second child to be reported with this karyotype. Phenotypic findings included growth retardation, severe developmental delay, a Dandy-Walker malformation, cardiac and urogenital abnormalities, bilateral hearing loss, cleft palate, severe kyphoscoliosis, minor digital anomalies, and a hypoplastic phallus. Craniofacial dysmorphism consisted of dolichocephaly, hypertelorism, down-slanting palpebral fissures, depressed nasal bridge and a tented upper lip. Cytogenetic analysis showed the karyotype 46,XX,der(6)t(Y;6)(p11.2;p23).ish der(6)(SRY+,6pTEL48-). The effects of partial monosomy 6p are discussed and compared to other patients with interstitial and terminal 6p deletions.

Abnormalities, Multiple↗
PubMed2003

Rapid prenatal diagnosis in translocation carriers by interphase FISH with chromosome-specific subtelomere probes.

Interphase fluorescence in situ hybridization (FISH) analysis can provide rapid preliminary analysis of chromosome aneuploidy from direct amniocyte and chorionic villus sample (CVS) preparations. Typically, interphase FISH is used in screening for numerical abnormalities of chromosomes X, Y, 13, 18, and 21. More recently, FISH probe sets became available for the subtelomeric region of each chromosome, allowing screening for terminal chromosome rearrangements. The purpose of the current study was to evaluate the use of dual-color interphase FISH analysis with chromosome-specific subtelomere probes for rapid prenatal diagnosis in 14 pregnancies from 12 different translocation carriers. Interphase FISH analysis was performed on direct CVS or amniocyte preparations from 12 reciprocal translocation and two Robertsonian translocation pregnancies with the appropriate chromosome-specific subtelomere probes for each chromosome involved in the translocation. Analysis of the interphase FISH probe signals predicted balanced or normal segregants in each case, thus rapidly excluding a chromosomally unbalanced segregant. Subsequent metaphase analysis showed normal karyotypes in seven fetuses and balanced translocations in the remaining seven. This series illustrates the utility of interphase FISH analysis with chromosome-specific subtelomere probes for rapid prenatal diagnosis in cases of parental reciprocal translocations and Robertsonian translocations.

Amniocentesis↗
PubMed2003

Ring 21 chromosome and a satellited 1p in the same patient: novel origin for an ectopic NOR.

Nucleolus organizer regions (NORs) are present on the satellite stalks located on the short arms of the acrocentric chromosomes. NORs present on non-acrocentric chromosomes (ectopic NORs) are rare and were reported in both phenotypically normal and abnormal individuals. We describe a patient, ascertained prenatally, with an ectopic NOR on 1p and a ring 21 chromosomes. Amniocentesis was performed at 27-weeks gestation on a 19-year-old woman after identification of intrauterine growth retardation (IUGR) by ultrasound. Cytogenetic analysis of amniocytes from the fetus showed a mos 46,XX,1ps,r(21) (p11.2q22.3)[44]/45,XX,1ps,-21[6] karyotype. Parental karyotypes were normal, indicating a de novo origin for these rearrangements in the fetus. Molecular cytogenetic characterization of the 1ps showed no loss of euchromatin and retention of the telomeric repeats. Characterization of the r(21) using array comparative genomic hybridization (CGH) identified that the deletion was approximately 5 Mb encompassing most of chromosome band 21q22.3. The ectopic NOR (1ps) was most likely derived from the acentric 21p fragment generated by the chromosome breakage event that lead to formation of the r(21) chromosome. This represents a novel mechanism for the origin of ectopic NORs. In addition, this study illustrates the importance of FISH analysis with telomeric and subtelomeric probes for characterization of chromosomes with ectopic NORs.

Chromosomes, Human, Pair 1↗
PubMed2003

A promoter mutation in the erythroid-specific 5-aminolevulinate synthase (ALAS2) gene causes X-linked sideroblastic anemia.

X-linked sideroblastic anemia (XLSA) is caused by mutations in the erythroid-specific 5-aminolevulinate synthase gene (ALAS2). XLSA was diagnosed in a 32-year-old woman with a mild phenotype and moderately late onset. Pyridoxine therapy had no effect in the proband, but in her affected son engendered a modest increase in hemoglobin concentration and a 4-fold reduction in ferritin iron. Molecular analysis identified a C to G transversion at nucleotide -206 from the transcription start site, as defined by primer extension, in the proximal promoter region of ALAS2. No other mutations were found in the promoter region, the flanking intronic sequences, the exons, or the 3' genomic region. The same mutation was found in her affected son but not in any other of her unaffected relatives. The mutation resulted in a 94% loss of activity relative to the wild-type sequence for a luciferase reporter construct containing the proximal 293 nucleotides (nt's) of the ALAS2 promoter when transfected into human erythroid K562 cells. Confirming the mutation's deleterious effect, the ALAS2 mRNA level in the proband's erythroid precursors was reduced 87%. The mutation occurred in or near 3 different putative transcription factor binding sites of unknown erythroid importance. The dramatic decreases in reporter activity and mRNA level suggest that the region of the mutation may bind a novel and important erythroid regulatory element.

5-Aminolevulinate Synthetase↗