Análisis de variación del número de copias y de patrones de metilación en la región 15q11-q13 / Variation analysis of the number of copies and methylene patterns in region 15q11-q13

La región q11-q13 del cromosoma 15 humano es proclive a sufrir alteraciones genéticas. Algunos genes de la región presentan expresión parental diferencial monoalélica, regulada por imprinting (EI). Errores en la regulación del EI, disomías uniparentales (DSU), así como también el cambio en el número de copias genómicas (CNV) producidos por sitios susceptibles de quiebre cromosómico (BP), producen alteraciones en esta región. Las enfermedades más frecuentes asociadas son el síndrome de Prader-Willi, el síndrome de Angelman y el síndrome de microduplicación 15q11-q13. En el presente trabajo analizamos la región 15q11-q13 por Methyl specific-multiplex ligation-dependent probe amplification (MS-MLPA) en 181 muestras de ADN derivadas a nuestro servicio de análisis genético molecular. En este trabajo mostramos que, de las 181 muestras, 39 presentaron alteraciones detectables por MS-MLPA. El 61.5% (24/39) de esas alteraciones detectadas fueron deleciones, el 5.1% (2/39) duplicaciones y el 33.3%(13/39) DSU/EI. Los CNV fueron 4 veces más frecuentes que las DSU/EI (OR = 4; IC 95%: 1.56-10.25) consistente con la literatura. Entre los CNV, dos casos atípicos permiten postular posibles sitios BP que no han sido informados en la literatura previamente.

Human chromosome 15q11-q13 region is prone to suffer genetic alterations. Some genes of this region have a differential monoallelic imprinting-regulated expression pattern. Defects in imprinting regulation (IE), uniparental disomy (UPD) or copy number variation (CNV) due to chromosomal breakpoints (BP) in 15q11-q13 region, are associated with several diseases. The most frequent are Prader-Willi syndrome, Angelman syndrome and 15q11-q13 microduplication syndrome. In this work, we analyzed DNA samples from 181 patients with phenotypes which were compatible with the above-mentioned diseases, using Methyl specific-multiplex ligation-dependent probe amplification (MS-MLPA). We show that, of the 181 samples, 39 presented alterations detectable by MS-MLPA. Of those alterations, 61.5% (24/39) were deletions, 5.1% (2/39) duplications and 33.3% (13/39) UPD/IE. The CNV cases were 4 times more frequent than UPD/IE (OR= 4; IC 95%: 1.56-10.25), consistent with the literature. Among the CNVs, two atypical cases allow to postulate new possible BP sites that have not been reported previously in the literature.

Combined Genome-Wide Linkage and Association Analyses of Fasting Glucose Level in Healthy Twins and Families of Korea

This study was undertaken to identify genetic polymorphisms that are associated with the risk of an elevated fasting glucose (FG) level using genome-wide analyses. We explored a quantitative trait locus (QTL) for FG level in a genome-wide study from a Korean twin-family cohort (the Healthy Twin Study) using a combined linkage and family-based association analysis approach. We investigated 1,754 individuals, which included 432 families and 219 pairs of monozygotic twins. Regions of chromosomes 2q23.3-2q31.1, 15q26.1-15q26.3, 16p12.1, and 20p13-20p12.2, were found to show evidence of linkage with FG level, and several markers in these regions were found to be significantly associated with FG level using family-based or general association tests. In particular, a single-nucleotide polymorphism (rs6138953) on the PTPRA gene in the 20p13 region (combined P = 1.8 x 10(-6)) was found to be associated with FG level, and the PRKCB1 gene (in 16p12.1) to be possibly associated with FG level. In conclusion, multiple regions of chromosomes 2q23.3-2q31.1, 15q26.1-15q26.3, 16p12.1, and 20p13-20p12.2 are associated with FG level in our Korean twin-family cohort. The combined approach of genome-wide linkage and family-based association analysis is useful to identify novel or known genetic regions concerning FG level in a family cohort study.

Detection of PML/RARA Rearrangement by Reverse Transcriptase-PCR and Sequencing in a Case of Microgranular Acute Promyelocytic Leukemia Lacking t(15;17) on Karyotype and FISH / 대한진단검사의학회지

We report a case of morphologically microgranular acute promyelocytic leukemia with PML/RARA fusion transcripts demonstrated by reverse transcriptase-PCR and cDNA sequencing, and no PML/RARA fusion detected by karyotype and FISH analyses. Karyotype was 47,XX,+8[19]/46,XX[1]. Although the newer FISH probes provide more accurate detections of t(15;17), it would be necessary to perform other molecular tests to further identify the masked PML/RARA fusions.

Molecular markers for diagnosis of Prader-Willi syndrome in thai patients by fish.

Paternal microdeletion of chromosome 15 at q11-q13 has been reported in 75% of Prader-Willi syndrome (PWS) patients in western countries. Diagnosis of PWS in Thailand is mainly based on clinical observation and, in some cases, confirmed by conventional cytogenetic analysis. Loss of a tiny segment in this region (microdeletion) has made it difficult to discriminate from the normal karyotype. An attempt to solve this problem has been made by using a high resolution chromosome culture. However, this method is a tedious and time-consuming technique which is suitable for only experienced cytogeneticists. We report molecular cytogenetic analysis for PWS in Thai patients using FISH in addition to standard GTG- banding chromosome analysis. Nine Thai patients clinically diagnosed or with a suspicion of PWS were investigated. The FISH probes consist of the region-specific probes (SNRPN or D15S10 probe) and two chromosome 15-specific control probes (D15Z1 centromeric and PML chromosome 15 long arm probe). Bright field and FISH programs of an automatic karyotyper were applied to facilitate the efficiency of the chromosome analysis. We found that 2 out of 9 patients showed a deletion at 15q11-q13 region by standard GTG chromosome analysis while 4 out of 9 patients showed a delation in this region by FISH. Consistent losing of SNRPN and D15S10 signals in FISH was observed in these patients. This forty-four per cent deletion is considerably lower than those reported from western countries. We propose that DNA methylation at SNRPN promoter as well as structural abnormalities in other chromosome regions might also play a role in the etiology of this disorder in Thais, which should be investigated further.

Cytogenetics and fluorescence in-situ hybridization in detection of hematological malignancies.

BACKGROUND: The technique of Fluorescence In-Situ Hybridization (FISH), a hybrid of cytogenetics and molecular biology has increased the resolution and application of cytogenetics in various neoplastic processes. In various types of leukemias, primary investigation by conventional cytogenetic [CC] technique followed by FISH has increased our understanding of the abnormal clonal formation involving different gene region. AIMS: Present study is aimed to use different kinds of in-house FISH probes in various hematological malignancies and its correlation with conventional cytogenetic finding. MATERIAL AND METHODS: Cytogenetic study was carried out in 360 patients either from peripheral blood or from bone marrow cells suspected for various types of leukemias. Four of 360 cases were further selected for FISH study by using different types of in-house probes, such as BAC [Bacterial Artificial Chromosome], PAC [Phague Artificial Chromosome], alphoid, PCP [Partial Chromosome Paint] and WCP [Whole Chromosome paint]. RESULTS: The results confirmed breakpoints of inversion 16 and del 16 in case 2 and 3 respectively. Whereas, case 1 did not confirm the cytogenetic findings of t(15;17) by PML/RARa fusion signals as multiple cell lines were involved in the patients. PCP and WCP were helpful in the identification of the marker chromosome in case 1. Telomeric and centromeric probes confirmed the cytogenetic findings of t(5;7) in case 4. CONCLUSION: We observe from this study that, in addition to the conventional cytogenetic study, FISH study provide further confirmation of chromosomal rearrangements. This facilitates our understanding of the neoplastic process more precisely for the better prognostication of the patient.

Identification of Tumor Suppressor Loci on the Long Arm of Chromosome 15 in Primary Small Cell Lung Cancer

Small cell lung cancer (SCLC) frequently shows a loss of heterozygosity (LOH) on chromosome 15q. In order to define the commonly affected region on chromosome 15q, we tested 23 primary SCLCs by microsatellite analysis. By analyzing 43 polymorphic microsatellite markers located on chromosome 15q, we found that 14 (60.8%) of 23 tumors exhibited a LOH in at least one of the tested microsatellite markers. Two (14.3%) of the 14 tumors were found to have more than a 50% LOH on chromosome 15q. LOH was observed in five commonly deleted regions on 15q. Of those regions, LOH from D15S1012 to D15S1016 was the most frequent (47.8%). LOH was also observed in more than 20-30% of tumors at four other regions, from D15S1031 to D15S1007, from D15S643 to D15S980, from D15S979 to D15S202, and from D15S652 to D15S642. Four of the 23 tumors exhibited shifted bands in at least one of the tested microsatellite markers. Shifted bands occurred in 3.2% (29 of 914) of the loci tested. Our data suggests the presence of at least five tumor suppressor loci on chromosome 15q in SCLC, and further that these may play an important role in SCLC tumorigenesis.

Real-time PCR analysis of the apoptosis related genes in ATRA treated APL t(15;17) patients

All-trans retinoic acid (ATRA) treatment of the acute promyelocytic leukemia (APL) have subsequently resulted in cell apoptosis, but the molecular mechanism of this effect remains elusive. In order to understand a possible involvement of genes regulating apoptotic signal pathways, expression levels of bcl2, bax, dapk1, myc, bad, wt1, and mcl genes were analyzed during ATRA treatment in five APL patients with t (15;17) using Real- time PCR (LightCycler). Two samples from each patient were compared to each other: primary diagnostic sample and a sample taken at remission. Effect of the ATRA treatment was demonstrated by the concomitant induction of cd14 and il1beta genes in four patients. Also other apoptosis related genes were found down-regulated in general but especially the down regulated levels of wt1 and bax attract attention. Result suggested that ATRA dependent apoptosis of APL was under the control of both internal and external pathways without relationships to the amount of the blast populations. Ratio of bcl2 to bax may be more important for this regulation than the ratio of bcl2 to bad. Either bcl2 family or less known apoptosis related genes as wt1 will still be required to further studies in this setting.

Acute promyelocytic leukemia: the study of t(15; 17) translocation by fluorescent in situ hybridization, reverse transcriptase-polymerase chain reaction and cytogenetic techniques

Acute promyelocytic leukemia (AML M3) is a well-defined subtype of leukemia with specific and peculiar characteristics. Immediate identification of t(15;17) or the PML/RARA gene rearrangement is fundamental for treatment. The objective of the present study was to compare fluorescent in situ hybridization (FISH), reverse transcriptase-polymerase chain reaction (RT-PCR) and karyotyping in 18 samples (12 at diagnosis and 6 after treatment) from 13 AML M3 patients. Bone marrow samples were submitted to karyotype G-banding, FISH and RT-PCR. At diagnosis, cytogenetics was successful in 10 of 12 samples, 8 with t(15;17) and 2 without. FISH was positive in 11/12 cases (one had no cells for analysis) and positivity varied from 25 to 93 per cent (mean: 56 per cent). RT-PCR was done in 6/12 cases and all were positive. Four of 8 patients with t(15;17) presented positive RT-PCR as well as 2 without metaphases. The lack of RT-PCR results in the other samples was due to poor quality RNA. When the three tests were compared at diagnosis, karyotyping presented the translocation in 80 per cent of the tested samples while FISH and RT-PCR showed the PML/RARA rearrangement in 100 per cent of them. Of 6 samples evaluated after treatment, 3 showed a normal karyotype, 1 persistence of an abnormal clone and 2 no metaphases. FISH was negative in 4 samples studied and 2 had no material for analysis. RT-PCR was positive in 4 (2 of which showed negative FISH, indicating residual disease) and negative in 2. When the three tests were compared after treatment, they showed concordance in 2 of 6 samples or, when there were not enough cells for all tests, concordance between karyotype and RT-PCR in one. At remission, RT-PCR was the most sensitive test in detecting residual disease, as expected (positive in 4/6 samples). An incidence of about 40 per cent of 5' breaks and 60 per cent of 3' breaks, i.e., bcr3 and bcr1/bcr2, respectively, was observed.

Autism and mental retardation: the genetic relationship and contribution

Autism, a neurodevelopmental disorder first described in 1943, is reviewed. The signs and symptoms of the disorder are described together with the etiological factors. The evidence for a genetic etiology of autism and its association with other genetic disorders are discussed. Possible candidate genes for autism are described

Impronta genómica en el síndrome de Prader-Willi y en el síndrome de Angelman / Genetic imprinting in the Prader-Willi and Angelman syndromes

Los síndromes de Angelman y Prader-Willi son desórdenes del neurocomportamiento con manifestaciones clínicas diferentes y constituyen el mejor ejemplo del concepto de impronta genómica. Se encuentran asociados con deficiencias maternas y paternas de una misma región en el cromosoma 15q11-q13, respectivamente. Los pacientes con síndrome de Prader-Willi presentan hipotonía muscular al nacimiento, obesidad, talla baja, retraso psicomotor e hipogonadismo; la facies es peculiar. El síndrome de Angelman se caracteriza por microbraquicefalia, pelo delgado y claro, hipoplasia maxilar, ojos hundidos, boca grande con protrusión lingual y prognatismo; el retraso psicomotor es severo, neurológicamente presentan ataxia, movimientos como ®marioneta¼ y ausencia del lenguaje; la mayoría de los pacientes presenta convulsiones, electroencefalograma anormal y paroxismos de risa. El pronóstico de ambas enfermedades es bueno si se evitan las complicaciones

Estudo clínico, citogenético e molecular nas síndromes de Prader-Willi e Angelman / Clinical, cytogenetical and molecular studies in Prader-Willi and Angelman syndromes

A Síndrome de Prader-Willi (SPW) e a Síndrome de Angelman (SA) säo doenças neurogenéticas consideradas como exemplos do fenômeno de impressäo genômica, em seres humano, estando relacionadas com alteraçöes envolvendo a regiäo cromossômica 15q11-13. As alteraçöes genéticas predominantes, na SPW, säo deleçöes na regiäo 15q11-13, de origem paterna e dissomia uniparental materna e, na SA, encontram-se deleçöes na regiäo 15q11-13 materna e dissomia uniparental paterna. Estudamos 5 pacientes com suspeita clínica de SPW e 4 pacientes com suspeita clínica de SA, atendidos no Setor de Genética Médica do Hospital das Clínicas da FMRP-USP, com o objetivo de estabelecer o diagnóstico clínico e etiológico nessa amostra. Para isso, utilizamos citogenética convencional, estudo de metilaçäo por Southern blotting com a sonda KB17 (ilha CpG do gene SNRPN), após digestäo com as enzimas de restriçäo Xba I e Not I, e análise de polimorfismos de repetiçäo (CA)n por PCR, usando os primers 196 e IR4-3R. Dos 9 pacientes avaliados, todos tiveram avaliaçäo citogenética convencional normal. Foram confirmados molecularmente 1 caso de SPW por deleçäo nova, 1 caso de SPW por dissomia uniparenteal materna e 1 caso de SPW em que a causa genética näo pode ser esclarecida pela análise de polimorfismo com os primers usados. Foram confirmados, molecularmente, 2 casos de SA, ambos por deleçäo nova na regiäo 15q11-13 e, 1 caso de SA, cuja clínica é extremamente sugestiva, teve resultado molecular normal, podendo-se sugerir uma mutaçäo de ponto no gene responsável pela SA.

Maternal inheritance of a 10/15 translocation in a female with a history of obstetric problems

O cariótipo 46,XX, -10, -15, t(10;15) (p15;q22) foi observado em uma cultura de linfócitos de uma mulher indiana com múltiplos abortos. Anormalidades cromossômicas similares estavam presentes em sua mäe, um irmäo e três irmäs. Ascite, cianose e problemas hepato-renais presentes nas três filhas talvez sejam decorrentes de tais rearranjos cromossômicos.