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Saitoh S, Buiting K, Cassidy SB, Conroy JM, Driscoll DJ, Gabriel JM, Gillessen-Kaesbach G, Glenn CC, Greenswag LR, Horsthemke B, Kondo I, Kuwajima K, Niikawa N, Rogan PK, Schwartz S, Seip J, Williams CA, Nicholls RD. Clinical spectrum and molecular diagnosis of Angelman and Prader-Willi syndrome patients with an imprinting mutation. AMERICAN JOURNAL OF MEDICAL GENETICS 1997; 68:195-206. [PMID: 9028458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Recent studies have identified a new class of Prader-Willi syndrome (PWS) and Angelman syndrome (AS) patients who have biparental inheritance, but neither the typical deletion nor uniparental disomy (UPD) or translocation. However, these patients have uniparental DNA methylation throughout 15q11-q13, and thus appear to have a mutation in the imprinting process for this region. Here we describe detailed clinical findings of five AS imprinting mutation patients (three families) and two PWS imprinting mutation patients (one new family). All these patients have essentially the classical clinical phenotype for the respective syndrome, except that the incidence of microcephaly is lower in imprinting mutation AS patients than in deletion AS patients. Furthermore, imprinting mutation AS and PWS patients do not typically have hypopigmentation, which is commonly found in patients with the usual large deletion. Molecular diagnosis of these cases is initially achieved by DNA methylation analyses of the DN34/ZNF127, PW71 (D15S63), and SNRPN loci. The latter two probes have clear advantages in the simple molecular diagnostic analysis of PWS and AS patients with an imprinting mutation, as has been found for typical deletion or UPD PWS and AS cases. With the recent finding of inherited microdeletions in PWS and AS imprinting mutation families, our studies define a new class of these two syndromes. The clinical and molecular identification of these PWS and AS patients has important genetic counseling consequences.
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Mowery-Rushton PA, Hanchett JM, Zipf WB, Rogan PK, Surti U. Identification of mosaicism in Prader-Willi syndrome using fluorescent in situ hybridization. AMERICAN JOURNAL OF MEDICAL GENETICS 1996; 66:403-12. [PMID: 8989457 DOI: 10.1002/(sici)1096-8628(19961230)66:4<403::aid-ajmg4>3.0.co;2-l] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
We report on our findings of 4 patients with mosaicism for a deletion of chromosome 15, most commonly associated with Prader-Willi syndrome (PWS). We examined a series of typical and atypical PWS patients in order to identify cytogenetically undetected deletions, using fluorescence in situ hybridization. In 4 of the patients analyzed we detected a deletion in 14-60% of peripheral blood leukocytes, using four commercially available probes. Our results indicate that mosaicism may play a role in the etiology of some PWS cases. These findings may be especially useful in patients who display discrepancies between clinical phenotype and established diagnostic criteria. Methylation and microsatellite polymorphism analyses of 2 patients with low-level mosaicism failed to identify the deletion. We propose that fluorescence in situ hybridization is the most effective method for detecting somatic mosaicism, since a large number of cells can be individually examined for the presence or absence of a specific deletion.
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Vgontzas AN, Bixler EO, Kales A, Centurione A, Rogan PK, Mascari M, Vela-Bueno A. Daytime sleepiness and REM abnormalities in Prader-Willi syndrome: evidence of generalized hypoarousal. Int J Neurosci 1996; 87:127-39. [PMID: 9003974 DOI: 10.3109/00207459609070832] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The aim of this study was to clarify the nature of the sleep abnormalities (excessive daytime sleepiness [EDS] and rapid eye movement [REM] sleep alterations) in Prader-Willi; Syndrome (PWS). Eight PWS patients, 15 normal, 16 narcoleptic, and 16 obese subjects were recorded in the sleep laboratory, both during daytime and nighttime. A principal-finding was that EDS in PWS was associated with an increased amount and depth of sleep. In PWS patients with EDS, compared to those PWS patients without EDS or the narcoleptic, obese, and normal groups, there were significant decreases in wakefulness and increases in percentage of sleep time (ST) and slow-wave sleep (SWS) both during daytime and nighttime testing. Also, in the adult PWS subjects (n = 6), in contrast to normal narcoleptic subjects, intensity of EDS was correlated with increased nocturnal percentage of ST and SWS and % SWS was positively correlated with % ST (both during daytime and nighttime testing). Another principal finding was that in PWS there is a unique alteration of the distribution of REM sleep in relation to controls. PWS patients with EDS or shortened nocturnal REM latencies showed a significantly increased number of REM periods, and a decreased average REM interval between REM periods compared to PWS patients with nonshortened nocturnal REM latencies or to the three control groups. Our data suggest that EDS and REM abnormalities in PWS are not manifestations of a narcoleptic-type syndrome or consequences of obesity. We propose that generalized 24-hour hypoarousal is the primary mechanism underlying the sleep abnormalities in PWS patients.
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Floros J, DiAngelo S, Koptides M, Karinch AM, Rogan PK, Nielsen H, Spragg RG, Watterberg K, Deiter G. Human SP-A locus: allele frequencies and linkage disequilibrium between the two surfactant protein A genes. Am J Respir Cell Mol Biol 1996; 15:489-98. [PMID: 8879183 DOI: 10.1165/ajrcmb.15.4.8879183] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Two surfactant protein A (SP-A) genes and several alleles for each SP-A locus have been previously described. In this report we investigate the potential usefulness of the SP-A loci as markers for genetic studies. We establish conditions that allow the identification of alleles with very similar sequences; We also determine the degree of polymorphism for each SP-A locus: The heterozygosity and polymorphism information content (PIC) values for the SP-A1 locus are 0.63 and 0.55, respectively, and for the SP-A2 locus are 0.50 and 0.56. In the course of these studies, we identify one new SP-A2 allele and show that the SP-A1 and SP-A2 loci are in linkage disequilibrium (P < 0.000001). We also identify 19 of the 20 possible haplotypes in a population of n = 239. Nine of the observed haplotypes reach statistical significance (P < 0.01) in this population, and the segregation of two haplotypes (6A2/1A0 and 6A4/1A) without recombination is verified in a family pedigree. These data together indicate that both SP-A loci are sufficiently polymorphic to be good markers for use in genetic studies. Furthermore, the finding of one novel allele suggests that additional unknown SP-A alleles are yet to be found.
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Vgontzas AN, Kales A, Seip J, Mascari MJ, Bixler EO, Myers DC, Vela-Bueno AV, Rogan PK. Relationship of sleep abnormalities to patient genotypes in Prader-Willi syndrome. AMERICAN JOURNAL OF MEDICAL GENETICS 1996; 67:478-82. [PMID: 8886165 DOI: 10.1002/(sici)1096-8628(19960920)67:5<478::aid-ajmg7>3.0.co;2-g] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
To assess whether sleep abnormalities are related to the genetic abnormalities in Prader-Willi Syndrome (PWS), we performed polysomnographic studies (nighttime and daytime) and determined the chromosome 15 genotypes in eight patients with PWS. Four patients demonstrated sleep onset REM periods (SOREM), and five met the objective polysomnographic criteria for severe or moderate excessive daytime sleepiness (EDS). Three of the four patients with SOREM displayed a paternally derived deletion of chromosome 15q11-q13, whereas the fourth exhibited maternal uniparental heterodisomy in this chromosomal region (UPD). Two of the four patients that did not display SOREM carried paternally derived deletions; the remaining two demonstrated UPD. Four of the five patients with EDS displayed paternal deletions, and the fifth exhibited UPD. One of three patients without evidence of EDS demonstrated paternal deletion; the remaining two showed UPD. Although neither EDS nor SOREM was not consistently associated with a specific genetic abnormality, these phenotypes may be more common in patients with paternal deletions than in those UPD. Sleep abnormalities in PWS cannot be explained by a single genetic model.
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Belchis DA, Meece CA, Benko FA, Rogan PK, Williams RA, Gocke CD. Loss of heterozygosity and microsatellite instability at the retinoblastoma locus in osteosarcomas. DIAGNOSTIC MOLECULAR PATHOLOGY : THE AMERICAN JOURNAL OF SURGICAL PATHOLOGY, PART B 1996; 5:214-9. [PMID: 8866236 DOI: 10.1097/00019606-199609000-00011] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Studies of osteosarcoma cell lines or frozen tissue have detected loss of heterozygosity (LOH) at the retinoblastoma (RB) locus by Southern blot analysis or restriction fragment length polymorphism. Most archived clinical specimens cannot be analyzed by these techniques. We analyzed formalin-fixed, paraffin-embedded samples from 19 cases of osteosarcoma for molecular changes at the RB locus using polymerase chain reaction amplification of polymorphic short tandem repeat sequences (microsatellite repeats). Four repeat sequences, two within and two flanking the RB gene, were analyzed. Fourteen of 18 informative cases (78%) showed molecular changes at the RB locus. LOH was identified in 13 cases (72%). Unexpectedly, microsatellite instability (MI) was found in eight cases (44%). All of the cases of MI involved alterations of more than one repeat unit, and six of eight were associated with LOH. LOH was identified at three unlinked loci in one case and at a single locus in another Microsatellite analysis of archival tissue yields prevalence rates of LOH comparable to those found by other methods and has the added advantage of showing MI. The ability to use formalin-fixed, paraffin-embedded tissue extends genetic analysis to routinely processed surgical material and may permit molecular confirmation of challenging cases of osteosarcoma.
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White LM, Rogan PK, Nicholls RD, Wu BL, Korf B, Knoll JH. Allele-specific replication of 15q11-q13 loci: a diagnostic test for detection of uniparental disomy. Am J Hum Genet 1996; 59:423-30. [PMID: 8755930 PMCID: PMC1914739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Allele-specific replication differences have been observed in imprinted chromosomal regions. We have exploited this characteristic of an imprinted region by using FISH at D15S9 and SNRPN (small nuclear ribonucleo protein N) on interphase nuclei to distinguish between Angelman and Prader-Willi syndrome patient samples with uniparental disomy of chromosome 15q11-q13 (n = 11) from those with biparental inheritance (n = 13). The familial recurrence risks are low when the child has de novo uniparental disomy and may be as high as 50% when the child has biparental inheritance. The frequency of interphase cells with asynchronous replication was significantly lower in patients with uniparental disomy than in patients with biparental inheritance. Within the sample population of patients with biparental inheritance, those with altered methylation and presumably imprinting center mutations could not be distinguished from those with no currently detectable mutation. This test is cost effective because it is performed on interphase cells from the same hybridized cytological preparation in which a deletion is excluded, and additional specimens are not required to determine the parental origin of chromosome 15.
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Saitoh S, Buiting K, Rogan PK, Buxton JL, Driscoll DJ, Arnemann J, König R, Malcolm S, Horsthemke B, Nicholls RD. Minimal definition of the imprinting center and fixation of chromosome 15q11-q13 epigenotype by imprinting mutations. Proc Natl Acad Sci U S A 1996; 93:7811-5. [PMID: 8755558 PMCID: PMC38830 DOI: 10.1073/pnas.93.15.7811] [Citation(s) in RCA: 123] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Patients with disorders involving imprinted genes such as Angelman syndrome (AS) and Prader-Willi syndrome (PWS) can have a mutation in the imprinting mechanism. Previously, we identified an imprinting center (IC) within chromosome 15q11-ql3 and proposed that IC mutations block resetting of the imprint, fixing on that chromosome the parental imprint (epigenotype) on which the mutation arose. We now describe four new microdeletions of the IC, the smallest (6 kb) of which currently defines the minimal region sufficient to confer an AS imprinting mutation. The AS deletions all overlap this minimal region, centromeric to the PWS microdeletions, which include the first exon of the SNRPN gene. None of five genes or transcripts in the 1.0 Mb vicinity of the IC (ZNF127, SNRPN, PAR-5, IPW, and PAR-1), each normally expressed only from the paternal allele, was expressed in cells from PWS imprinting mutation patients. In contrast, AS imprinting mutation patients show biparental expression of SNRPN and IPW but must lack expression of the putative AS gene 250-1000 kb distal of the IC. These data strongly support a model in which the paternal chromosome of these PWS patients carries an ancestral maternal epigenotype, and the maternal chromosome of these AS patients carries an ancestral paternal epigenotype. The IC therefore functions to reset the maternal and paternal imprints throughout a 2-Mb imprinted domain within human chromosome 15q11-q13 during gametogenesis.
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Veletza SV, Rogan PK, TenHave T, Olowe SA, Floros J. Racial differences in allelic distribution at the human pulmonary surfactant protein B gene locus (SP-B). Exp Lung Res 1996; 22:489-94. [PMID: 8872090 DOI: 10.3109/01902149609046037] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Variable numbers of composite repetitive motifs are found in different individuals within intron 4 of the surfactant protein B (SP-B) gene (Biochem J. 1995;305:583). This study tests the hypothesis that the distribution of SP-B alleles differs among racial/ethnic groups. A total of 412 SP-B alleles were analyzed: 206 from Caucasian, 68 from African-American, and 138 from Nigerian individuals. Twelve groups of alleles (A-L) carrying 3 to 18 motifs were found. The distribution of the 12 alleles in the Caucasian group differs from that found in the Nigerian (p < .001) and African-American (p < .001) populations. The overall distribution of alleles between the African-American and the Nigerian populations were not statistically different. Specific alleles were also present in different proportions among the groups studied. For example, the most common allele (allele E) in all three populations is present at a significantly higher frequency in Caucasians than in the other two populations, but its frequency does not differ from the Nigerian and African-American groups. A less frequent allele, H, also differs significantly when Caucasians are compared with each of the other two populations, but the frequency of this allele is comparable between the African-American and Nigerian populations. To assess the importance of having comparable racial composition between the control and the case groups, a group of African-Americans with respiratory distress syndrome (RDS) (n = 40) was compared with the African American and the Caucasian groups studied above. No significant difference was observed between the racially matched groups but a significant difference (p = .006) was observed between the racially mixed groups. The results indicate that the distribution of SP-B alleles differs between the racial groups but not between the ethnic groups studied. Thus, racial composition of the groups under study is important when considering whether particular alleles at this locus predispose to inherited disorders.
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Consevage MW, Seip JR, Belchis DA, Davis AT, Baylen BG, Rogan PK. Association of a mosaic chromosomal 22q11 deletion with hypoplastic left heart syndrome. Am J Cardiol 1996; 77:1023-5. [PMID: 8644631 DOI: 10.1016/s0002-9149(97)89165-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The atypical presentation of CATCH 22 raises several important concerns. First, in this patient, as in others, the heart defects were found in association with subtle facial abnormalities but with few of the other criteria normally seen in CATCH 22. This association alone may be sufficient to raise suspicion that an interstitial 22q11 deletion may be present. Second, the incidence of chromosome 22 deletions in parents of children with a 22q11 deletion (25%) suggests that siblings or subsequent fetuses may also be at risk. Parents with subtle or unusual manifestations of CATCH 22 may be unaware of their potential carrier status. Finally, the recognition of chromosomal mosaicism in this patient may have been fortuitous, as cytogenetic studies of leukocytes from other individuals with a mosaic karyotype may sometimes fail to reveal a 22q11 deletion that is present in cardiac tissues. Molecular cytogenetic analysis of cardiac specimens that are removed during routine surgical procedures may be warranted in appropriate clinical situations.
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Nicholls RD, Jong MT, Glenn CC, Gabriel J, Rogan PK, Driscoll DJ, Saitoh S. Multiple imprinted genes associated with Prader-Willi syndrome and location of an imprinting control element. ACTA GENETICAE MEDICAE ET GEMELLOLOGIAE 1996; 45:87-9. [PMID: 8872016 DOI: 10.1017/s000156600000115x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Our studies aim to identify the mechanisms and genes involved in genomic imprinting in mammalian development and human disease. Imprinting refers to an epigenetic modification of DNA that results in parent-of-origin specific expression during embryogenesis and in the adult. This imprint is reset at each generation, depending on the sex of the parental gametogenesis. Prader-Willi (PWS) and Angelman (AS) syndromes are excellent models for the study of genomic imprinting in humans, since these distinct neurobehavioural disorders are both associated with genetic abnormalities (large deletions, uniparental disomy, and imprinting mutations) of inheritance in chromosome 15q11-q13, dependent on the parental origin (reviewed in ref. 1). Some AS patients have biparental inheritance, consistent with a single imprinted gene (active on the maternal chromosome), whereas similar PWS patients are not found suggesting that at least two imprinted genes (active on the paternal allele) may be necessary for classical PWS. We have previously shown that the small ribonucleoprotein associated protein SmN gene (SNRPN), located in the PWS critical region [2], is only expressed from the paternal allele and is differentially methylated on parental alleles [3]. Therefore, SNRPN may have a role in PWS. Methylation imprints have also been found at two other loci in 15q11-q13, PW71 [4] and D15S9 [5], which map 120 kb and 1.5 Mb proximal to SNRPN, respectively. We have now characterized in detail the gene structure and expression from two imprinted loci within 15q11-q13, SNRPN and D15S9, which suggests that both loci are surprisingly complex, with important implications for the pathogenesis of PWS.
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Rogan PK, Seip JR, Driscoll DJ, Papenhausen PR, Johnson VP, Raskin S, Woodward AL, Butler MG. Distinct 15q genotypes in Russell-Silver and ring 15 syndromes. AMERICAN JOURNAL OF MEDICAL GENETICS 1996; 62:10-5. [PMID: 8779316 PMCID: PMC5986579 DOI: 10.1002/(sici)1096-8628(19960301)62:1<10::aid-ajmg3>3.0.co;2-#] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Individuals with a ring 15 chromosome [r(15)] and those with Russell-Silver syndrome have short stature, developmental delay, triangular face, and clinodactyly. To assess whether the apparent phenotypic overlap of these conditions reflects a common genetic cause, the extent of deletions in chromosome 15q was determined in 5 patients with r(15), 1 patient with del 15q26.1-qter, and 5 patients with Russell-Silver syndrome. All patients with Russell-Silver syndrome were diploid for genetic markers in distal 15q, indicating that Russell-Silver syndrome in these individuals was unlikely to be related to the expression of single alleles at these or linked genetic loci. At least 3 distinct sites of chromosome breakage close to the telomere were found in the r(15) and del 15q25.1-qter patients, with 1 r(15) patient having both a terminal and an interstitial deletion. Although the patient with del 15q25.1-qter exhibited the largest deletion and the most profound growth retardation, the degree of growth impairment among the r(15) patients was not correlated with the size of the deleted interval. Rather, the parental origin of the ring chromosome in several patients was associated with phenotypes that are also seen in patients with either Prader-Willi (PWS) or Angelman (AS) syndromes, conditions that result from uniparental expression of genes on chromosome 15. In fact, unequal representation of chromosome 15 alleles in 1 patient with r(15) suggests the possibility that a mosaic karyotype composed of the constitutional cell line and cell line(s) possibly deficient in the ring chromosome might be present. The PWS-like or AS-like phenotypes could be explained by postzygotic loss of the ring chromosome, leading to uniparental inheritance of the intact chromosome in some tissues of r(15) patients.
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Hess EJ, Rogan PK, Domoto M, Tinker DE, Ladda RL, Ramer JC. Absence of linkage of apparently single gene mediated ADHD with the human syntenic region of the mouse mutant Coloboma. AMERICAN JOURNAL OF MEDICAL GENETICS 1995; 60:573-9. [PMID: 8825900 DOI: 10.1002/ajmg.1320600619] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Attention deficit disorder (ADHD) is a complex biobehavioral phenotype which affects up to 8% of the general population and often impairs social, academic, and job performance. Its origins are heterogeneous, but a significant genetic component is suggested by family and twin studies. The murine strain, coloboma, displays a spontaneously hyperactive phenotype that is responsive to dextroamphetamine and has been proposed as a genetic model for ADHD. Coloboma is a semi-dominant mutation that is caused by a hemizygous deletion of the SNAP-25 and other genes on mouse chromosome 2q. To test the possibility that the human homolog of the mouse coloboma gene(s) could be responsible for ADHD, we have carried out linkage studies with polymorphic markers in the region syntenic to coloboma (20p11-p12). Five families in which the pattern of inheritance of ADHD appears to be autosomal dominant were studied. Segregation analysis of the traits studied suggested that the best fitting model was a sex-influenced, single gene, Mendelian pattern. Several genetic models were evaluated based on estimates of penetrance, phenocopy rate, and allele frequency derived from our patient population and those of other investigators. No significant linkage was detected between the disease locus and markers spanning this chromosome 20 interval.
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Kauffman EJ, Gestl EE, Kim DJ, Walker C, Hite JM, Yan G, Rogan PK, Johnson SL, Cheng KC. Microsatellite-centromere mapping in the zebrafish (Danio rerio). Genomics 1995; 30:337-41. [PMID: 8586435 DOI: 10.1006/geno.1995.9869] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Ten (CA)n microsatellite simple sequence repeat (SSR) markers, 1, 2, 12, 14, 16, 18, 20, 22, 26, and 29, were used to show high chiasma interference and to determine centromere-marker map distances in the zebrafish (Danio rerio). Of these, SSR 12 exhibited no recombinant tetratypes among 175 half-tetrad embryos, placing this marker within 1 cM of the centromere of Linkage Group XVII. Fractions of heterozygous half-tetrads for the remaining nine markers ranged from 0.64 to 0.89. Of these, six recombinant fractions were more than 0.67 (P < 0.05), indicating strong chiasma interference during female meiosis in the zebrafish. Consistent with previous mapping data, SSRs 2 and 20 of Linkage Group VI were tightly linked. Half-tetrad analysis will allow the mapping of the remaining centromeres and may be useful in the mapping of new genes and mutations in the zebrafish.
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Rogan PK, Close P, Blouin JL, Seip JR, Gannutz L, Ladda RL, Antonarakis SE. Duplication and loss of chromosome 21 in two children with Down syndrome and acute leukemia. AMERICAN JOURNAL OF MEDICAL GENETICS 1995; 59:174-81. [PMID: 8588582 DOI: 10.1002/ajmg.1320590212] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Acute leukemia in Down syndrome (DS) is often associated with additional changes in the number or structure of chromosome 21. We present two DS patients whose leukemic karyotypes were associated with changes in chromosome 21 ploidy. Patient 1 developed acute lymphocytic leukemia (type L1); disomy for chromosome 21 was evident in all blast cells examined. Loss of the paternal chromosome in the leukemic clone produced maternal uniparental disomy with isodisomy over a 25-cM interval. The second patient had acute monoblastic leukemia (type M5) with tetrasomy 21 in all leukemic cells. DNA polymorphism analysis showed duplicate paternal chromosomes in the constitutional genotype. The maternal chromosome was subsequently duplicated in the leukemic clone. The distinct inheritance patterns of chromosome 21 in the blast cells of these patients would appear to indicate that leukemogenesis occurred by different genetic mechanisms in each individual.
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Orr GA, Rogan PK. Development of a directory of genetic probes as a shared institutional resource. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 1995; 46:35-39. [PMID: 7743779 DOI: 10.1016/0169-2607(94)01596-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
This report describes design and implementation of a genetic probe directory database for use by researchers in a medical school. The purpose of the database is to allow researchers to exchange descriptive information concerning probes available in their laboratories in order to facilitate collaboration. The Genetic Probe Database Browser (GPDB) allows multi-field constraints and wildcard searchers of the database, e-mail upload and download of data, and provides simple database administrator tools. The GPDB is implemented in C under the UNIX operating system, and uses the 'Curses' character terminal package to provide access to users unable to use modern graphical user interfaces. Currently, 10 researchers have contributed approximately 250 genetic probes, and several research collaborations have been started because of this resources.
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Rogan PK, Schneider TD. Using information content and base frequencies to distinguish mutations from genetic polymorphisms in splice junction recognition sites. Hum Mutat 1995; 6:74-6. [PMID: 7550236 DOI: 10.1002/humu.1380060114] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Predicting the effects of nucleotide substitutions in human splice sites has been based on analysis of consensus sequences. We used a graphic representation of sequence conservation and base frequency, the sequence logo, to demonstrate that a change in a splice acceptor of hMSH2 (a gene associated with familial nonpolyposis colon cancer) probably does not reduce splicing efficiency. This confirms a population genetic study that suggested that this substitution is a genetic polymorphism. The information theory-based sequence logo is quantitative and more sensitive than the corresponding splice acceptor consensus sequence for detection of true mutations. Information analysis may potentially be used to distinguish polymorphisms from mutations in other types of transcriptional, translational, or protein-coding motifs.
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Gabriel J, Gottlieb W, Garcia A, Rogan PK, Saitoh S, Nicholls RD. A common insertion/deletion polymorphism in the Prader-Willi syndrome minimal critical region. Hum Mol Genet 1994; 3:1912. [PMID: 7849727 DOI: 10.1093/hmg/3.10.1912] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
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Woodage T, Prasad M, Dixon JW, Selby RE, Romain DR, Columbano-Green LM, Graham D, Rogan PK, Seip JR, Smith A. Bloom syndrome and maternal uniparental disomy for chromosome 15. Am J Hum Genet 1994; 55:74-80. [PMID: 7912890 PMCID: PMC1918231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Bloom syndrome (BS) is an autosomal recessive disorder characterized by increases in the frequency of sister-chromatid exchange and in the incidence of malignancy. Chromosome-transfer studies have shown the BS locus to map to chromosome 15q. This report describes a subject with features of both BS and Prader-Willi syndrome (PWS). Molecular analysis showed maternal uniparental disomy for chromosome 15. Meiotic recombination between the two disomic chromosomes 15 has resulted in heterodisomy for proximal 15q and isodisomy for distal 15q. In this individual BS is probably due to homozygosity for a gene that is telomeric to D15S95 (15q25), rather than to genetic imprinting, the mechanism responsible for the development of PWS. This report represents the first application of disomy analysis to the regional localization of a disease gene. This strategy promises to be useful in the genetic mapping of other uncommon autosomal recessive conditions.
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Consevage MW, Salada GC, Baylen BG, Ladda RL, Rogan PK. A new missense mutation, Arg719Gln, in the beta-cardiac heavy chain myosin gene of patients with familial hypertrophic cardiomyopathy. Hum Mol Genet 1994; 3:1025-6. [PMID: 7848441 DOI: 10.1093/hmg/3.6.1025] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
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Krizkova L, Sakthivel R, Olowe SA, Rogan PK, Floros J. Human SP-A: genotype and single-strand conformation polymorphism analysis. THE AMERICAN JOURNAL OF PHYSIOLOGY 1994; 266:L519-27. [PMID: 8203545 DOI: 10.1152/ajplung.1994.266.5.l519] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
We have previously characterized two surfactant protein A (SP-A) cDNAs termed 1A and 6A, as well as a 6A allelic variant termed 6A1. These sequences are quite heterogeneous at the 3' untranslated region (3'UT). Differences between 6A and 6A1 alleles include an 11-bp insertion/deletion 407 bases downstream from the start of the translation termination codon and a base pair polymorphism (C or G) in exon 1 (position 1,193; White, Damm, Miller, Spratt, Schilling, Hawgood, Benson, and Cordell. Nature Lond. 317: 361-363, 1985). The 11-bp (GCCCACTGCCT) segment is present in 6A1 and absent in 6A. The 6A/6A genotype, in a small number of specimens, showed a trend toward a higher frequency in the black Nigerian population compared with Caucasians. In this report, we examine the frequency of the 6A genotype in a larger number of samples from Caucasians and black Nigerians as well as the meiotic stability of the 3'UT heterogeneity. Slot-blot analysis and allele-specific oligonucleotide probes have confirmed that the 6A/6A genotype is more frequent in the Nigerian population. Single-strand conformation polymorphisms in the 3'UT appear to be stably inherited by members of a three-generation family, suggesting that these nucleotide variants represent natural polymorphisms in the population.
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Ladda RL, Zonana J, Ramer JC, Mascari MJ, Rogan PK. Congenital contractures, ectodermal dysplasia, cleft lip/palate, and developmental impairment: a distinct syndrome. AMERICAN JOURNAL OF MEDICAL GENETICS 1993; 47:550-5. [PMID: 7504881 DOI: 10.1002/ajmg.1320470422] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Brothers were affected with severe congenital contractures, multiple cutaneous manifestations of ectodermal dysplasia, cleft lip/palate, and psychomotor and growth impairment. High resolution prometaphase chromosomes were normal. Molecular studies of DNA markers, closely flanking the X-linked hypohidrotic ectodermal dysplasia locus, did not show evidence of a submicroscopic deletion from the Xq12-q13 region. The parents and a normal sister exhibited none of these findings. This constellation of anomalies appears to represent a unique AR or XLR syndrome.
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Mowrey PN, Chorney MJ, Venditti CP, Latif F, Modi WS, Lerman MI, Zbar B, Robins DB, Rogan PK, Ladda RL. Clinical and molecular analyses of deletion 3p25-pter syndrome. AMERICAN JOURNAL OF MEDICAL GENETICS 1993; 46:623-9. [PMID: 8103286 DOI: 10.1002/ajmg.1320460604] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Hemizygous deletion of 3p25-pter is associated with a phenotype of profound growth failure, microcephaly, characteristic facial changes, and mental retardation. Since the severity may be quite variable, we have studied 3 cases of del 3p25-pter to define the clinical manifestations and the critical chromosome region for phenotypic expression. The patient we now report died at age 6 months and provided an opportunity for a detailed necropsy analysis for only the second time in a del(3p) patient. He had marked hypoplasia of all organs, hypomyelination of white matter, and multiple renal cortical microcysts. Ordered genomic markers from the distal regions of chromosome 3p aided in determining the parent of origin of each deletion and in defining the boundaries of the deleted chromosomal segments. The deleted markers distal to the RAF1 oncogene in 2 of the 3 patients were consistently hemizygous. One patient had an interstitial deletion based on evidence of diploid inheritance of one of the most distal loci (D3S17). Available genetic linkage maps suggest that the deletion spans at least 19 centimorgans (cM).
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Ramer JC, Eggli K, Rogan PK, Ladda RL. Identical twins with Weissenbacher-Zweymüller syndrome and neural tube defect. AMERICAN JOURNAL OF MEDICAL GENETICS 1993; 45:614-8. [PMID: 8456835 DOI: 10.1002/ajmg.1320450520] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Neurologic abnormalities have been described only once previously in a child with Weissenbacher-Zweymüller syndrome (WZS), a rare skeletal dysplasia, evident neonatally. We report on identical twin male infants with skeletal findings typical of WZS, including small size at birth, proximal limb shortness, mid face hypoplasia, and myopia. In addition, twin B had a parieto occipital encephalocele while twin A had a meningocele at the same location. Twin B has had significant delays in development and hearing loss.
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Mascari MJ, Gottlieb W, Rogan PK, Butler MG, Waller DA, Armour JA, Jeffreys AJ, Ladda RL, Nicholls RD. The frequency of uniparental disomy in Prader-Willi syndrome. Implications for molecular diagnosis. N Engl J Med 1992; 326:1599-607. [PMID: 1584261 PMCID: PMC7556354 DOI: 10.1056/nejm199206113262404] [Citation(s) in RCA: 203] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
BACKGROUND Prader-Willi syndrome is a genetic disorder characterized by infantile hypotonia, obesity, hypogonadism, and mental retardation, but it is difficult to diagnose clinically in infants and young children. In about two thirds of patients, a cytogenetically visible deletion can be detected in the paternally derived chromosome 15 (15q11q13). Recently, patients with Prader-Willi syndrome have been described who do not have the cytogenetic deletion but instead have two copies of the 15q11q13 region that are inherited from the mother (with none inherited from the father). This unusual form of inheritance is known as maternal uniparental disomy. Using molecular genetic techniques, we sought to determine the frequency of uniparental disomy in Prader-Willi syndrome. METHODS We performed molecular analyses using DNA markers within 15q11q13 and elsewhere on chromosome 15 in 30 patients with Prader-Willi syndrome who had no cytogenetically visible deletion. We also studied their parents. Three patients with Prader-Willi syndrome who had a cytogenetic deletion served as controls. RESULTS In 18 of the 30 patients without a cytogenetic deletion (60 percent), we demonstrated the presence of maternal uniparental disomy for chromosome 15 and its association with advanced maternal age. In another eight patients (27 percent), we identified large molecular deletions. The remaining four patients (13 percent) had evidence of normal biparental inheritance for chromosome 15; three of these patients were the only ones in the study who had some atypical clinical features. CONCLUSIONS In about 20 percent of all cases, Prader-Willi syndrome results from the inheritance of both copies of chromosome 15 from the mother (maternal uniparental disomy). With the combined use of cytogenetic and molecular techniques, the genetic basis of Prader-Willi syndrome can be identified in up to 95 percent of patients.
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