RESUMO
BACKGROUND: Familial adenomatous polyposis (FAP) is an autosomal dominant hereditary syndrome characterised by the development of hundreds to thousands of adenomatous colonic polyps during the second decade of life. FAP is caused by germ line mutations in the adenomatous polyposis coli (APC) gene located on chromosome 5q21-22. CASE PRESENTATION: A 36-year-old female was presented with 100-1000 adenomatous colonic polyps, typical of classic FAP symptoms. Genetic testing using massively parallel sequencing identified a 5-bp deletion (c.3927_3931delAAAGA) which causes frameshift (p.Glu1309Aspfs) and creates a premature stop codon, resulting in the replacement of the last 1535 amino acids of APC by five incorrect amino acids. Two of the proband's four siblings also exhibited classic FAP symptoms and carried the same 5-bp heterozygous deletion in the APC gene. One of the proband's two nephews also tested positive for this mutation but has not been examined by endoscopy due to his young age. CONCLUSIONS: We reported here for the first time the use of massively parallel sequencing (MPS)-based genetic testing to identify a germline mutation within a three-generation Vietnamese family. This mutation is most likely responsible for the development of FAP.
Assuntos
Proteína da Polipose Adenomatosa do Colo/genética , Polipose Adenomatosa do Colo/diagnóstico , Polipose Adenomatosa do Colo/genética , Mutação da Fase de Leitura , Heterozigoto , Polipose Adenomatosa do Colo/etnologia , Polipose Adenomatosa do Colo/cirurgia , Adulto , Povo Asiático , Pré-Escolar , Cromossomos Humanos Par 5/química , Colectomia/métodos , Feminino , Expressão Gênica , Testes Genéticos , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Masculino , Pessoa de Meia-Idade , Linhagem , Irmãos , VietnãRESUMO
OBJECTIVE: The most typical cytogenetic aberration in myelodysplastic syndromes is del(5q), which, when isolated, is associated with refractory anaemia and good prognosis. Based on high rates of erythroid response and transfusion independence, Lenalidomide (LEN) became the standard treatment. This multi-centre study was designed to supplement Italian Registry data on LEN by addressing prescription, administration appropriateness, haematological and cytogenetic responses and disease evolution. METHODS: MORE study was an observational, non-interventional, multi-centre, retrospective and prospective study. Cases were recruited from 45 Haematological Centres throughout Italy. Data were collected from the Italian National Registry for Lenalidomide administration and supplemented by a MORE data form. RESULTS: Data from 190/213 patients were analysed. In all, 149 had been diagnosed by conventional cytogenetics (GROUP A) and 41 only by FISH (GROUP B). Overall erythroid response was obtained in 92.8% of cases. Overall cytogenetic remission was achieved in 22.6% of cases. Disease progression occurred in 15.6% of cases. Clonal cytogenetic evolution characterised progression to AML but not to higher risk MDS. CONCLUSIONS: Erythroid response to Lenalidomide was similar in MDS with isolated del(5q) and with del(5q) plus one anomaly. Progression to AML or higher risk MDS showed different cytogenetic features.
Assuntos
Deleção Cromossômica , Cromossomos Humanos Par 5/química , Fatores Imunológicos/uso terapêutico , Leucemia Mieloide Aguda/tratamento farmacológico , Síndromes Mielodisplásicas/tratamento farmacológico , Sistema de Registros , Talidomida/análogos & derivados , Idoso , Progressão da Doença , Feminino , Humanos , Itália , Cariotipagem , Lenalidomida , Leucemia Mieloide Aguda/etiologia , Leucemia Mieloide Aguda/genética , Leucemia Mieloide Aguda/imunologia , Masculino , Pessoa de Meia-Idade , Síndromes Mielodisplásicas/complicações , Síndromes Mielodisplásicas/genética , Síndromes Mielodisplásicas/imunologia , Estudos Prospectivos , Indução de Remissão , Estudos Retrospectivos , Talidomida/uso terapêuticoRESUMO
Adult body height is a quantitative trait for which genome-wide association studies (GWAS) have identified numerous loci, primarily in European populations. These loci, comprising common variants, explain <10% of the phenotypic variance in height. We searched for novel associations between height and common (minor allele frequency, MAF ≥5%) or infrequent (0.5% < MAF < 5%) variants across the exome in African Americans. Using a reference panel of 1692 African Americans and 471 Europeans from the National Heart, Lung, and Blood Institute's (NHLBI) Exome Sequencing Project (ESP), we imputed whole-exome sequence data into 13 719 African Americans with existing array-based GWAS data (discovery). Variants achieving a height-association threshold of P < 5E-06 in the imputed dataset were followed up in an independent sample of 1989 African Americans with whole-exome sequence data (replication). We used P < 2.5E-07 (=0.05/196 779 variants) to define statistically significant associations in meta-analyses combining the discovery and replication sets (N = 15 708). We discovered and replicated three independent loci for association: 5p13.3/C5orf22/rs17410035 (MAF = 0.10, ß = 0.64 cm, P = 8.3E-08), 13q14.2/SPRYD7/rs114089985 (MAF = 0.03, ß = 1.46 cm, P = 4.8E-10) and 17q23.3/GH2/rs2006123 (MAF = 0.30; ß = 0.47 cm; P = 4.7E-09). Conditional analyses suggested 5p13.3 (C5orf22/rs17410035) and 13q14.2 (SPRYD7/rs114089985) may harbor novel height alleles independent of previous GWAS-identified variants (r(2) with GWAS loci <0.01); whereas 17q23.3/GH2/rs2006123 was correlated with GWAS-identified variants in European and African populations. Notably, 13q14.2/rs114089985 is infrequent in African Americans (MAF = 3%), extremely rare in European Americans (MAF = 0.03%), and monomorphic in Asian populations, suggesting it may be an African-American-specific height allele. Our findings demonstrate that whole-exome imputation of sequence variants can identify low-frequency variants and discover novel variants in non-European populations.
Assuntos
Alelos , Negro ou Afro-Americano , Estatura/genética , Exoma , Loci Gênicos , Característica Quantitativa Herdável , Adulto , Idoso , Cromossomos Humanos Par 13/química , Cromossomos Humanos Par 17/química , Cromossomos Humanos Par 5/química , Feminino , Frequência do Gene , Estudo de Associação Genômica Ampla , Humanos , Masculino , Pessoa de Meia-Idade , População BrancaRESUMO
Genome-wide association studies (GWAS) have mapped risk alleles for at least 10 distinct cancers to a small region of 63 000 bp on chromosome 5p15.33. This region harbors the TERT and CLPTM1L genes; the former encodes the catalytic subunit of telomerase reverse transcriptase and the latter may play a role in apoptosis. To investigate further the genetic architecture of common susceptibility alleles in this region, we conducted an agnostic subset-based meta-analysis (association analysis based on subsets) across six distinct cancers in 34 248 cases and 45 036 controls. Based on sequential conditional analysis, we identified as many as six independent risk loci marked by common single-nucleotide polymorphisms: five in the TERT gene (Region 1: rs7726159, P = 2.10 × 10(-39); Region 3: rs2853677, P = 3.30 × 10(-36) and PConditional = 2.36 × 10(-8); Region 4: rs2736098, P = 3.87 × 10(-12) and PConditional = 5.19 × 10(-6), Region 5: rs13172201, P = 0.041 and PConditional = 2.04 × 10(-6); and Region 6: rs10069690, P = 7.49 × 10(-15) and PConditional = 5.35 × 10(-7)) and one in the neighboring CLPTM1L gene (Region 2: rs451360; P = 1.90 × 10(-18) and PConditional = 7.06 × 10(-16)). Between three and five cancers mapped to each independent locus with both risk-enhancing and protective effects. Allele-specific effects on DNA methylation were seen for a subset of risk loci, indicating that methylation and subsequent effects on gene expression may contribute to the biology of risk variants on 5p15.33. Our results provide strong support for extensive pleiotropy across this region of 5p15.33, to an extent not previously observed in other cancer susceptibility loci.
Assuntos
Cromossomos Humanos Par 5/química , Regulação Neoplásica da Expressão Gênica , Loci Gênicos , Proteínas de Membrana/genética , Proteínas de Neoplasias/genética , Neoplasias/genética , Telomerase/genética , Alelos , Biologia Computacional , Metilação de DNA , Epigênese Genética , Feminino , Frequência do Gene , Predisposição Genética para Doença , Estudo de Associação Genômica Ampla , Humanos , Masculino , Neoplasias/patologia , Razão de Chances , Polimorfismo de Nucleotídeo Único , RiscoRESUMO
The aim of our study was to define if the type of primary chromosomal aberrations (CA) of the karyotype of patients with Acute myeloid leukemia (AML) and Myelodysplastic syndromes (MDS) determines the way and the rate of karyotype development. Conventional cytogenetic analysis was carried out on 248 AML and 105 MDS patients at diagnosis. Clonal evolution (CE) was found in 40% (51 of 128) of AML patients and in 47.5% (19 of 40) of MDS patients having CA in their karyotype. The first pattern we established was for the most frequent CA which initiate CE in 28 patients with a complex karyotype. These CA were non-balansed rearrangements in the following regions: 5q, 7q, 11q, 3q, monosomy 5, monosomy 7. The second pattern of CE was regarding the most frequent aneuploidias (+8, +11, +21, -Y, and the third pattern concerned balanced CA. We found significant difference in the distribution of karyotypes in different stages of progression between the first and the other two groups (p < 0.001). No statistical difference was found between the patterns in the second and the third group CA (p > 0.5).
Assuntos
Aberrações Cromossômicas , Evolução Clonal , Leucemia Mieloide Aguda/genética , Síndromes Mielodisplásicas/genética , Adolescente , Adulto , Idoso , Idoso de 80 Anos ou mais , Medula Óssea/metabolismo , Medula Óssea/patologia , Cromossomos Humanos Par 11/química , Cromossomos Humanos Par 21/química , Cromossomos Humanos Par 5/química , Cromossomos Humanos Par 7/química , Cromossomos Humanos Par 8/química , Cromossomos Humanos Y/química , Análise Citogenética , Humanos , Cariótipo , Leucemia Mieloide Aguda/diagnóstico , Leucemia Mieloide Aguda/patologia , Pessoa de Meia-Idade , Síndromes Mielodisplásicas/diagnóstico , Síndromes Mielodisplásicas/patologiaRESUMO
Fingerprints of the three-dimensional organization of genomes have emerged using advances in Hi-C and imaging techniques. However, genome dynamics is poorly understood. Here, we create the chromosome copolymer model (CCM) by representing chromosomes as a copolymer with two epigenetic loci types corresponding to euchromatin and heterochromatin. Using novel clustering techniques, we establish quantitatively that the simulated contact maps and topologically associating domains (TADs) for chromosomes 5 and 10 and those inferred from Hi-C experiments are in good agreement. Chromatin exhibits glassy dynamics with coherent motion on micron scale. The broad distribution of the diffusion exponents of the individual loci, which quantitatively agrees with experiments, is suggestive of highly heterogeneous dynamics. This is reflected in the cell-to-cell variations in the contact maps. Chromosome organization is hierarchical, involving the formation of chromosome droplets (CDs) on genomic scale, coinciding with the TAD size, followed by coalescence of the CDs, reminiscent of Ostwald ripening.
Assuntos
Cromossomos Humanos/química , Interfase , Simulação de Dinâmica Molecular , Conformação de Ácido Nucleico , Algoritmos , Cromossomos Humanos Par 10/química , Cromossomos Humanos Par 5/química , Análise por Conglomerados , Biologia Computacional , Simulação por Computador , Epigenômica , Eucromatina/química , Genoma , Heterocromatina/química , Humanos , Modelos GenéticosRESUMO
There have been several reports on 5q31.3 microdeletion syndrome. The overlapping deleted region includes purine-rich element binding protein A (PURA), which encodes transcriptional activator protein Pur-α. Patients with PURA mutations show moderate to severe neurodevelopmental delay and learning disability. Neonatal hypotonia, respiratory insufficiency, feeding difficulties, and seizures are often seen. Dysmorphic features including myopathic faces are helpful as clinical signs of the diagnosis. We report a patient with a novel PURA mutation detected by whole-exome sequencing. We suggest that PURA abnormality is a recognizable syndrome.
Assuntos
Deleção Cromossômica , Cromossomos Humanos Par 5/química , Proteínas de Ligação a DNA/genética , Deficiências do Desenvolvimento/genética , Deficiências da Aprendizagem/genética , Transtornos do Neurodesenvolvimento/genética , Fatores de Transcrição/genética , Sequência de Bases , Criança , Proteínas de Ligação a DNA/deficiência , Deficiências do Desenvolvimento/diagnóstico , Deficiências do Desenvolvimento/patologia , Fácies , Humanos , Deficiências da Aprendizagem/diagnóstico , Deficiências da Aprendizagem/patologia , Masculino , Transtornos do Neurodesenvolvimento/diagnóstico , Transtornos do Neurodesenvolvimento/patologia , Linhagem , Síndrome , Fatores de Transcrição/deficiência , Sequenciamento do ExomaRESUMO
Autosomal dominant North Carolina macular dystrophy (NCMD) is believed to represent a failure of macular development. The disorder has been linked to two loci, MCDR1 (chromosome 6q16) and MCDR3 (chromosome 5p15-p13). Recently, non-coding variants upstream of PRDM13 (MCDR1) and a duplication including IRX1 (MCDR3) have been identified. However, the underlying disease-causing mechanism remains uncertain. Through a combination of sequencing studies on eighteen NCMD families, we report two novel overlapping duplications at the MCDR3 locus, in a gene desert downstream of IRX1 and upstream of ADAMTS16. One duplication of 43 kb was identified in nine families (with evidence for a shared ancestral haplotype), and another one of 45 kb was found in a single family. Three families carry the previously reported V2 variant (MCDR1), while five remain unsolved. The MCDR3 locus is thus refined to a shared region of 39 kb that contains DNAse hypersensitive sites active at a restricted time window during retinal development. Publicly available data confirmed expression of IRX1 and ADAMTS16 in human fetal retina, with IRX1 preferentially expressed in fetal macula. These findings represent a major advance in our understanding of the molecular genetics of NCMD and provide insights into the genetic pathways involved in human macular development.
Assuntos
Proteínas ADAMTS/genética , Distrofias Hereditárias da Córnea/genética , Proteínas do Olho/genética , Loci Gênicos , Proteínas de Homeodomínio/genética , Fatores de Transcrição/genética , Proteínas ADAMTS/metabolismo , Adulto , Sequência de Bases , Duplicação Cromossômica , Cromossomos Humanos Par 5/química , Cromossomos Humanos Par 6/química , Distrofias Hereditárias da Córnea/diagnóstico por imagem , Distrofias Hereditárias da Córnea/patologia , Proteínas do Olho/metabolismo , Família , Feminino , Feto , Expressão Gênica , Haplótipos , Proteínas de Homeodomínio/metabolismo , Humanos , Masculino , Retina/metabolismo , Retina/patologia , Análise de Sequência de DNA , Tomografia de Coerência Óptica , Fatores de Transcrição/metabolismoRESUMO
Leukocyte telomere length (LTL) is a predictor of aging and a number of age-related diseases. We performed genome-wide association studies of mean LTL in 2632 individuals,with a two-stage replication in 3917 individuals from Chinese populations. To further validate our findings, we get the results of 696 samples from a cohort of European ancestry. We identified two loci associated with LTL that map in telomerase reverse transcriptase (TERT; rs2736100, Pâ=â1.93×10(-5)) on chromosome 5p15.33 and near keratin 80 (KRT80; rs17653722, Pâ=â6.96×10(-6)) on 12q13.13. In Chinese population each C allele of rs2736100 and T allele of rs17653722 was associated with a longer mean telomere length of 0.026 and 0.059 T/S, respectively, equivalent to about 3 and 7 years of average age-related telomere attrition. Our findings provide new insights into telomere regulatory mechanism and even pathogenesis of age-related diseases.
Assuntos
Povo Asiático , Loci Gênicos , Telomerase/genética , Homeostase do Telômero , Telômero , Fatores Etários , Alelos , Cromossomos Humanos Par 5/química , Estudo de Associação Genômica Ampla , Humanos , Queratinas/genética , Leucócitos/citologia , Leucócitos/metabolismo , População BrancaRESUMO
A number of loci related to the immune response are located on human chromosomal region 5q31-33, and polymorphisms in this region have been reported to be associated with autoimmune and infectious diseases. In Southeast Asian populations, no systematic survey with dense SNP markers has been performed for the 5q31-33 region. In this study, the LD and haplotype structures for a 472-kb region on 5q31 were investigated in a Thai population to provide useful information for association studies. In addition, the LD structure in Thais was compared with that of the CHB and JPT HapMap populations (CHB + JPT) to evaluate the transferability of tagging SNPs from CHB + JPT for Thais. We show that the minor allele frequency, pattern of LD block, and genetic structure in the 5q31-33 region were highly concordant between Thais and CHB + JPT. A high transferability of tagging SNPs from CHB + JPT for Thais was observed. Our results suggest that tagging SNPs from CHB + JPT (Northeast Asians) can efficiently capture common variants in Southeast Asians, and that the HapMap data are useful for association studies in Southeast Asian populations.
Assuntos
Cromossomos Humanos Par 5 , Desequilíbrio de Ligação , Polimorfismo de Nucleotídeo Único , Mapeamento Cromossômico , Cromossomos Humanos Par 5/química , Bases de Dados Genéticas , Frequência do Gene , Genética Populacional , Humanos , Sitios de Sequências Rotuladas , TailândiaRESUMO
In contrast to those of metaphase chromosomes, the shape, length, and architecture of human interphase chromosomes are not well understood. This is mainly due to technical problems in the visualization of interphase chromosomes in total and of their substructures. We analyzed the structure of chromosomes in interphase nuclei through use of high-resolution multicolor banding (MCB), which paints the total shape of chromosomes and creates a DNA-mediated, chromosome-region-specific, pseudocolored banding pattern at high resolution. A microdissection-derived human chromosome 5-specific MCB probe mixture was hybridized to human lymphocyte interphase nuclei harvested for routine chromosome analysis, as well as to interphase nuclei from HeLa cells arrested at different phases of the cell cycle. The length of the axis of interphase chromosome 5 was determined, and the shape and MCB pattern were compared with those of metaphase chromosomes. We show that, in lymphocytes, the length of the axis of interphase chromosome 5 is comparable to that of a metaphase chromosome at 600-band resolution. Consequently, the concept of chromosome condensation during mitosis has to be reassessed. In addition, chromosome 5 in interphase is not as straight as metaphase chromosomes, being bent and/or folded. The shape and banding pattern of interphase chromosome 5 of lymphocytes and HeLa cells are similar to those of the corresponding metaphase chromosomes at all stages of the cell cycle. The MCB pattern also allows the detection and characterization of chromosome aberrations. This may be of fundamental importance in establishing chromosome analyses in nondividing cells.
Assuntos
Cromossomos Humanos Par 5 , Interfase/genética , Ciclo Celular , Aberrações Cromossômicas , Coloração Cromossômica , Cromossomos Humanos Par 5/química , DNA/química , Células HeLa , Humanos , Hibridização in Situ Fluorescente , Masculino , Metáfase/genéticaRESUMO
The genes for IL-3, IL-4, IL-5, IL-9, IL-13, and granulocyte-macrophage colony-stimulating factor (GM-CSF) are known to be clustered on human chromosome 5q and on mouse chromosome 11. IL-2 and interferon gamma (IFN-gamma) genes are located on separate chromosomes. It is well known that upon stimulation by antigen presentation, TH1 and TH2 subsets of T helper cells start to transcribe distinct sets of cytokine genes. Thus mechanisms should exist that transmit extracellular signals into the nucleus, thereby coordinately turning on transcriptional machinery in cell type-specific manners. Several different mechanisms exist in which specific as well as coordinated expression of cytokines are regulated at the transcriptional level. These include (1) regulation by proximal cis-elements, to which specific transcription factors bind, (2) regulation by distal cis-elements, such as enhancers or locus controlling elements, especially those located several kilobases away from the target gene, and (3) enhancement of transcription by viral trans-activators in a pathologic state. In this article, we review the recent studies on the above issues, with particular emphasis on our own results that support the presence of different modes of control mechanisms. We also discuss the possible approaches to the thorough understanding of the coordinated and specific regulation of cytokines.
Assuntos
Cromossomos Humanos Par 5/fisiologia , Citocinas/genética , Genes/imunologia , Família Multigênica/imunologia , Sequências Reguladoras de Ácido Nucleico/imunologia , Animais , Cromossomos Humanos Par 5/química , Humanos , CamundongosRESUMO
The primed in situ (PRINS) labeling technique allows a rapid and specific labeling of human chromosomes in situ. This method is based on annealing of specific oligonucleotide primers and subsequent primer extension by a Taq DNA polymerase. We have developed a PRINS protocole for the cytogenetic analysis of somatic hybrid cell lines. Painting of human chromosomes is performed using Alu specific primers. Individual human chromosomes are identified using chromosome-specific alpha-satellite primers. The method was successfully tested to 3 different human-hamster hybrid cell lines. This approach provides an interesting alternative to classical cytogenetic and in situ hybridization techniques for the characterization of the human content of hybrid cell lines.
Assuntos
Cromossomos/química , Primers do DNA , Células Híbridas/química , Animais , Linhagem Celular , Cromossomos Humanos Par 5/química , Cricetinae , Humanos , Hibridização in Situ Fluorescente , Sequências Repetitivas de Ácido NucleicoRESUMO
We describe a microfabricated hybrid device that consists of a microfabricated chip containing multiple twin-T injectors attached to an array of capillaries that serve as the separation channels. A new fabrication process was employed to create two differently sized round channels in a chip. Twin-T injectors were formed by the smaller round channels that match the bore of the separation capillaries and separation capillaries were incorporated to the injectors through the larger round channels that match the outer diameter of the capillaries. This allows for a minimum dead volume and provides a robust chip/capillary interface. This hybrid design takes full advantage, such as sample stacking and purification and uniform signal intensity profile, of the unique chip injection scheme for DNA sequencing while employing long straight capillaries for the separations. In essence, the separation channel length is optimized for both speed and resolution since it is unconstrained by chip size. To demonstrate the reliability and practicality of this hybrid device, we sequenced over 1000 real-world samples from Human Chromosome 5 and Ciona intestinalis, prepared at Joint Genome Institute. We achieved average Phred20 read of 675 bases in about 70 min with a success rate of 91%. For the similar type of samples on MegaBACE 1000, the average Phred20 read is about 550-600 bases in 120 min separation time with a success rate of about 80-90%.
Assuntos
Mapeamento Cromossômico , Cromossomos Humanos Par 5/química , DNA/química , Animais , Sequência de Bases , Ciona intestinalis , DNA/genética , Eletroforese Capilar/instrumentação , Eletroforese Capilar/métodos , Desenho de Equipamento , Humanos , Miniaturização/instrumentação , Miniaturização/métodos , Dados de Sequência Molecular , Análise de Sequência com Séries de OligonucleotídeosRESUMO
OBJECTIVE: To demonstrate that cellular preparations requiring color analysis of different domains stained by molecular cytogenetic methods (fluorescence in situ hybridization) can be processed by spectral analysis of fluorescent emissions by either factor analysis of medical image sequences (FAMIS) or a META confocal configuration to isolate fluorescent probes. STUDY DESIGN: Three-dimensional sequences of images obtained by spectral analysis in a META confocal microscope (Carl Zeiss SAS, Jena, Germany) were analyzed by META processing and the FAMIS algorithm, which provides factor curves. META and factor images were then the result of image-processing methods that cover emission spectra. RESULTS: Factor curves and factor or META images can help to analyze targets inside nuclei. CONCLUSION: It is possible to process preparations containing numerous spots on different colors to differentiate stained targets and to improve visualization and detection.