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1.
Cell ; 187(6): 1547-1562.e13, 2024 Mar 14.
Artigo em Inglês | MEDLINE | ID: mdl-38428424

RESUMO

We sequenced and assembled using multiple long-read sequencing technologies the genomes of chimpanzee, bonobo, gorilla, orangutan, gibbon, macaque, owl monkey, and marmoset. We identified 1,338,997 lineage-specific fixed structural variants (SVs) disrupting 1,561 protein-coding genes and 136,932 regulatory elements, including the most complete set of human-specific fixed differences. We estimate that 819.47 Mbp or ∼27% of the genome has been affected by SVs across primate evolution. We identify 1,607 structurally divergent regions wherein recurrent structural variation contributes to creating SV hotspots where genes are recurrently lost (e.g., CARD, C4, and OLAH gene families) and additional lineage-specific genes are generated (e.g., CKAP2, VPS36, ACBD7, and NEK5 paralogs), becoming targets of rapid chromosomal diversification and positive selection (e.g., RGPD gene family). High-fidelity long-read sequencing has made these dynamic regions of the genome accessible for sequence-level analyses within and between primate species.


Assuntos
Genoma , Primatas , Animais , Humanos , Sequência de Bases , Primatas/classificação , Primatas/genética , Evolução Biológica , Análise de Sequência de DNA , Variação Estrutural do Genoma
2.
Nature ; 630(8016): 401-411, 2024 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-38811727

RESUMO

Apes possess two sex chromosomes-the male-specific Y chromosome and the X chromosome, which is present in both males and females. The Y chromosome is crucial for male reproduction, with deletions being linked to infertility1. The X chromosome is vital for reproduction and cognition2. Variation in mating patterns and brain function among apes suggests corresponding differences in their sex chromosomes. However, owing to their repetitive nature and incomplete reference assemblies, ape sex chromosomes have been challenging to study. Here, using the methodology developed for the telomere-to-telomere (T2T) human genome, we produced gapless assemblies of the X and Y chromosomes for five great apes (bonobo (Pan paniscus), chimpanzee (Pan troglodytes), western lowland gorilla (Gorilla gorilla gorilla), Bornean orangutan (Pongo pygmaeus) and Sumatran orangutan (Pongo abelii)) and a lesser ape (the siamang gibbon (Symphalangus syndactylus)), and untangled the intricacies of their evolution. Compared with the X chromosomes, the ape Y chromosomes vary greatly in size and have low alignability and high levels of structural rearrangements-owing to the accumulation of lineage-specific ampliconic regions, palindromes, transposable elements and satellites. Many Y chromosome genes expand in multi-copy families and some evolve under purifying selection. Thus, the Y chromosome exhibits dynamic evolution, whereas the X chromosome is more stable. Mapping short-read sequencing data to these assemblies revealed diversity and selection patterns on sex chromosomes of more than 100 individual great apes. These reference assemblies are expected to inform human evolution and conservation genetics of non-human apes, all of which are endangered species.


Assuntos
Hominidae , Cromossomo X , Cromossomo Y , Animais , Feminino , Masculino , Gorilla gorilla/genética , Hominidae/genética , Hominidae/classificação , Hylobatidae/genética , Pan paniscus/genética , Pan troglodytes/genética , Filogenia , Pongo abelii/genética , Pongo pygmaeus/genética , Telômero/genética , Cromossomo X/genética , Cromossomo Y/genética , Evolução Molecular , Variações do Número de Cópias de DNA/genética , Humanos , Espécies em Perigo de Extinção , Padrões de Referência
3.
Nature ; 617(7960): 325-334, 2023 05.
Artigo em Inglês | MEDLINE | ID: mdl-37165237

RESUMO

Single-nucleotide variants (SNVs) in segmental duplications (SDs) have not been systematically assessed because of the limitations of mapping short-read sequencing data1,2. Here we constructed 1:1 unambiguous alignments spanning high-identity SDs across 102 human haplotypes and compared the pattern of SNVs between unique and duplicated regions3,4. We find that human SNVs are elevated 60% in SDs compared to unique regions and estimate that at least 23% of this increase is due to interlocus gene conversion (IGC) with up to 4.3 megabase pairs of SD sequence converted on average per human haplotype. We develop a genome-wide map of IGC donors and acceptors, including 498 acceptor and 454 donor hotspots affecting the exons of about 800 protein-coding genes. These include 171 genes that have 'relocated' on average 1.61 megabase pairs in a subset of human haplotypes. Using a coalescent framework, we show that SD regions are slightly evolutionarily older when compared to unique sequences, probably owing to IGC. SNVs in SDs, however, show a distinct mutational spectrum: a 27.1% increase in transversions that convert cytosine to guanine or the reverse across all triplet contexts and a 7.6% reduction in the frequency of CpG-associated mutations when compared to unique DNA. We reason that these distinct mutational properties help to maintain an overall higher GC content of SD DNA compared to that of unique DNA, probably driven by GC-biased conversion between paralogous sequences5,6.


Assuntos
Conversão Gênica , Mutação , Duplicações Segmentares Genômicas , Humanos , Conversão Gênica/genética , Genoma Humano/genética , Polimorfismo de Nucleotídeo Único/genética , Haplótipos/genética , Éxons/genética , Citosina/química , Guanina/química , Ilhas de CpG/genética
4.
Nature ; 621(7978): 355-364, 2023 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-37612510

RESUMO

The prevalence of highly repetitive sequences within the human Y chromosome has prevented its complete assembly to date1 and led to its systematic omission from genomic analyses. Here we present de novo assemblies of 43 Y chromosomes spanning 182,900 years of human evolution and report considerable diversity in size and structure. Half of the male-specific euchromatic region is subject to large inversions with a greater than twofold higher recurrence rate compared with all other chromosomes2. Ampliconic sequences associated with these inversions show differing mutation rates that are sequence context dependent, and some ampliconic genes exhibit evidence for concerted evolution with the acquisition and purging of lineage-specific pseudogenes. The largest heterochromatic region in the human genome, Yq12, is composed of alternating repeat arrays that show extensive variation in the number, size and distribution, but retain a 1:1 copy-number ratio. Finally, our data suggest that the boundary between the recombining pseudoautosomal region 1 and the non-recombining portions of the X and Y chromosomes lies 500 kb away from the currently established1 boundary. The availability of fully sequence-resolved Y chromosomes from multiple individuals provides a unique opportunity for identifying new associations of traits with specific Y-chromosomal variants and garnering insights into the evolution and function of complex regions of the human genome.


Assuntos
Cromossomos Humanos Y , Evolução Molecular , Humanos , Masculino , Cromossomos Humanos Y/genética , Genoma Humano/genética , Genômica , Taxa de Mutação , Fenótipo , Eucromatina/genética , Pseudogenes , Variação Genética/genética , Cromossomos Humanos X/genética , Regiões Pseudoautossômicas/genética
5.
Nature ; 621(7978): 344-354, 2023 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-37612512

RESUMO

The human Y chromosome has been notoriously difficult to sequence and assemble because of its complex repeat structure that includes long palindromes, tandem repeats and segmental duplications1-3. As a result, more than half of the Y chromosome is missing from the GRCh38 reference sequence and it remains the last human chromosome to be finished4,5. Here, the Telomere-to-Telomere (T2T) consortium presents the complete 62,460,029-base-pair sequence of a human Y chromosome from the HG002 genome (T2T-Y) that corrects multiple errors in GRCh38-Y and adds over 30 million base pairs of sequence to the reference, showing the complete ampliconic structures of gene families TSPY, DAZ and RBMY; 41 additional protein-coding genes, mostly from the TSPY family; and an alternating pattern of human satellite 1 and 3 blocks in the heterochromatic Yq12 region. We have combined T2T-Y with a previous assembly of the CHM13 genome4 and mapped available population variation, clinical variants and functional genomics data to produce a complete and comprehensive reference sequence for all 24 human chromosomes.


Assuntos
Cromossomos Humanos Y , Genômica , Análise de Sequência de DNA , Humanos , Sequência de Bases , Cromossomos Humanos Y/genética , DNA Satélite/genética , Variação Genética/genética , Genética Populacional , Genômica/métodos , Genômica/normas , Heterocromatina/genética , Família Multigênica/genética , Padrões de Referência , Duplicações Segmentares Genômicas/genética , Análise de Sequência de DNA/normas , Sequências de Repetição em Tandem/genética , Telômero/genética
6.
Mol Cell ; 78(5): 862-875.e8, 2020 06 04.
Artigo em Inglês | MEDLINE | ID: mdl-32348780

RESUMO

Nuclear RNA interference (RNAi) pathways work together with histone modifications to regulate gene expression and enact an adaptive response to transposable RNA elements. In the germline, nuclear RNAi can lead to trans-generational epigenetic inheritance (TEI) of gene silencing. We identified and characterized a family of nuclear Argonaute-interacting proteins (ENRIs) that control the strength and target specificity of nuclear RNAi in C. elegans, ensuring faithful inheritance of epigenetic memories. ENRI-1/2 prevent misloading of the nuclear Argonaute NRDE-3 with small RNAs that normally effect maternal piRNAs, which prevents precocious nuclear translocation of NRDE-3 in the early embryo. Additionally, they are negative regulators of nuclear RNAi triggered from exogenous sources. Loss of ENRI-3, an unstable protein expressed mostly in the male germline, misdirects the RNAi response to transposable elements and impairs TEI. The ENRIs determine the potency and specificity of nuclear RNAi responses by gating small RNAs into specific nuclear Argonautes.


Assuntos
Proteínas de Caenorhabditis elegans/genética , Proteínas de Caenorhabditis elegans/metabolismo , Inativação Gênica/fisiologia , Animais , Proteínas Argonautas/genética , Proteínas Argonautas/metabolismo , Caenorhabditis elegans/genética , Caenorhabditis elegans/metabolismo , Núcleo Celular/metabolismo , Células Germinativas/metabolismo , Proteínas Nucleares/metabolismo , Interferência de RNA/fisiologia , RNA de Cadeia Dupla/metabolismo , RNA Nuclear/metabolismo , RNA Interferente Pequeno/genética , Proteínas de Ligação a RNA/genética
7.
Nature ; 593(7857): 101-107, 2021 05.
Artigo em Inglês | MEDLINE | ID: mdl-33828295

RESUMO

The complete assembly of each human chromosome is essential for understanding human biology and evolution1,2. Here we use complementary long-read sequencing technologies to complete the linear assembly of human chromosome 8. Our assembly resolves the sequence of five previously long-standing gaps, including a 2.08-Mb centromeric α-satellite array, a 644-kb copy number polymorphism in the ß-defensin gene cluster that is important for disease risk, and an 863-kb variable number tandem repeat at chromosome 8q21.2 that can function as a neocentromere. We show that the centromeric α-satellite array is generally methylated except for a 73-kb hypomethylated region of diverse higher-order α-satellites enriched with CENP-A nucleosomes, consistent with the location of the kinetochore. In addition, we confirm the overall organization and methylation pattern of the centromere in a diploid human genome. Using a dual long-read sequencing approach, we complete high-quality draft assemblies of the orthologous centromere from chromosome 8 in chimpanzee, orangutan and macaque to reconstruct its evolutionary history. Comparative and phylogenetic analyses show that the higher-order α-satellite structure evolved in the great ape ancestor with a layered symmetry, in which more ancient higher-order repeats locate peripherally to monomeric α-satellites. We estimate that the mutation rate of centromeric satellite DNA is accelerated by more than 2.2-fold compared to the unique portions of the genome, and this acceleration extends into the flanking sequence.


Assuntos
Cromossomos Humanos Par 8/química , Cromossomos Humanos Par 8/genética , Evolução Molecular , Animais , Linhagem Celular , Centrômero/química , Centrômero/genética , Centrômero/metabolismo , Cromossomos Humanos Par 8/fisiologia , Metilação de DNA , DNA Satélite/genética , Epigênese Genética , Feminino , Humanos , Macaca mulatta/genética , Masculino , Repetições Minissatélites/genética , Pan troglodytes/genética , Filogenia , Pongo abelii/genética , Telômero/química , Telômero/genética , Telômero/metabolismo
8.
Nature ; 594(7861): 77-81, 2021 06.
Artigo em Inglês | MEDLINE | ID: mdl-33953399

RESUMO

The divergence of chimpanzee and bonobo provides one of the few examples of recent hominid speciation1,2. Here we describe a fully annotated, high-quality bonobo genome assembly, which was constructed without guidance from reference genomes by applying a multiplatform genomics approach. We generate a bonobo genome assembly in which more than 98% of genes are completely annotated and 99% of the gaps are closed, including the resolution of about half of the segmental duplications and almost all of the full-length mobile elements. We compare the bonobo genome to those of other great apes1,3-5 and identify more than 5,569 fixed structural variants that specifically distinguish the bonobo and chimpanzee lineages. We focus on genes that have been lost, changed in structure or expanded in the last few million years of bonobo evolution. We produce a high-resolution map of incomplete lineage sorting and estimate that around 5.1% of the human genome is genetically closer to chimpanzee or bonobo and that more than 36.5% of the genome shows incomplete lineage sorting if we consider a deeper phylogeny including gorilla and orangutan. We also show that 26% of the segments of incomplete lineage sorting between human and chimpanzee or human and bonobo are non-randomly distributed and that genes within these clustered segments show significant excess of amino acid replacement compared to the rest of the genome.


Assuntos
Evolução Molecular , Genoma/genética , Genômica , Pan paniscus/genética , Filogenia , Animais , Fator de Iniciação 4A em Eucariotos/genética , Feminino , Genes , Gorilla gorilla/genética , Anotação de Sequência Molecular/normas , Pan troglodytes/genética , Pongo/genética , Duplicações Segmentares Genômicas , Análise de Sequência de DNA
9.
Am J Hum Genet ; 109(4): 631-646, 2022 04 07.
Artigo em Inglês | MEDLINE | ID: mdl-35290762

RESUMO

Studies of de novo mutation (DNM) have typically excluded some of the most repetitive and complex regions of the genome because these regions cannot be unambiguously mapped with short-read sequencing data. To better understand the genome-wide pattern of DNM, we generated long-read sequence data from an autism parent-child quad with an affected female where no pathogenic variant had been discovered in short-read Illumina sequence data. We deeply sequenced all four individuals by using three sequencing platforms (Illumina, Oxford Nanopore, and Pacific Biosciences) and three complementary technologies (Strand-seq, optical mapping, and 10X Genomics). Using long-read sequencing, we initially discovered and validated 171 DNMs across two children-a 20% increase in the number of de novo single-nucleotide variants (SNVs) and indels when compared to short-read callsets. The number of DNMs further increased by 5% when considering a more complete human reference (T2T-CHM13) because of the recovery of events in regions absent from GRCh38 (e.g., three DNMs in heterochromatic satellites). In total, we validated 195 de novo germline mutations and 23 potential post-zygotic mosaic mutations across both children; the overall true substitution rate based on this integrated callset is at least 1.41 × 10-8 substitutions per nucleotide per generation. We also identified six de novo insertions and deletions in tandem repeats, two of which represent structural variants. We demonstrate that long-read sequencing and assembly, especially when combined with a more complete reference genome, increases the number of DNMs by >25% compared to previous studies, providing a more complete catalog of DNM compared to short-read data alone.


Assuntos
Genômica , Sequenciamento de Nucleotídeos em Larga Escala , Feminino , Humanos , Mutação/genética , Nucleotídeos , Análise de Sequência de DNA , Software
10.
Am J Hum Genet ; 108(8): 1436-1449, 2021 08 05.
Artigo em Inglês | MEDLINE | ID: mdl-34216551

RESUMO

Despite widespread clinical genetic testing, many individuals with suspected genetic conditions lack a precise diagnosis, limiting their opportunity to take advantage of state-of-the-art treatments. In some cases, testing reveals difficult-to-evaluate structural differences, candidate variants that do not fully explain the phenotype, single pathogenic variants in recessive disorders, or no variants in genes of interest. Thus, there is a need for better tools to identify a precise genetic diagnosis in individuals when conventional testing approaches have been exhausted. We performed targeted long-read sequencing (T-LRS) using adaptive sampling on the Oxford Nanopore platform on 40 individuals, 10 of whom lacked a complete molecular diagnosis. We computationally targeted up to 151 Mbp of sequence per individual and searched for pathogenic substitutions, structural variants, and methylation differences using a single data source. We detected all genomic aberrations-including single-nucleotide variants, copy number changes, repeat expansions, and methylation differences-identified by prior clinical testing. In 8/8 individuals with complex structural rearrangements, T-LRS enabled more precise resolution of the mutation, leading to changes in clinical management in one case. In ten individuals with suspected Mendelian conditions lacking a precise genetic diagnosis, T-LRS identified pathogenic or likely pathogenic variants in six and variants of uncertain significance in two others. T-LRS accurately identifies pathogenic structural variants, resolves complex rearrangements, and identifies Mendelian variants not detected by other technologies. T-LRS represents an efficient and cost-effective strategy to evaluate high-priority genes and regions or complex clinical testing results.


Assuntos
Aberrações Cromossômicas , Análise Citogenética/métodos , Doenças Genéticas Inatas/diagnóstico , Doenças Genéticas Inatas/genética , Predisposição Genética para Doença , Genoma Humano , Mutação , Variações do Número de Cópias de DNA , Feminino , Testes Genéticos , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Cariotipagem , Masculino , Análise de Sequência de DNA
11.
J Soc Work End Life Palliat Care ; 18(2): 146-159, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-35282796

RESUMO

Research has demonstrated a lack of support for hospice caregivers and a higher than average level of self-reported anxiety and depression. While online support groups are gaining popularity, few protocols have been published, little research has demonstrated the skills required to facilitate, and virtually no data has explored the clinical outcomes affiliated with participation in such groups. This paper presents the preliminary experience and results of a clinical trial testing the use of online support groups designed to both educate and provide social support to caregivers of hospice cancer patients. A detailed protocol outlines educational strategies, discussion questions, and a blueprint outlining ways to engage participants. A review of field notes completed by the interventionist reveal specific facilitation skills and strategies used to engage participants. Finally, preliminary analysis of 78 participants shows the group is having a statistically significant impact on the caregiver depression.


Assuntos
Cuidados Paliativos na Terminalidade da Vida , Hospitais para Doentes Terminais , Neoplasias , Mídias Sociais , Cuidadores , Humanos , Neoplasias/terapia , Literatura de Revisão como Assunto , Grupos de Autoajuda
12.
Psychopathology ; 54(3): 159-168, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-33975316

RESUMO

INTRODUCTION: Over time, there have been different views regarding the verbal auditory hallucinations (VAHs) reported by borderline personality disorder (BPD) and schizophrenia patients. More recently, their similarity has been emphasized, a view that undoubtedly has significant implications in terms of differential diagnosis and management. To explore this important issue, we undertook a detailed phenomenological assessment of persistent VAH reported by BPD and schizophrenia DSM-IV participants. METHODS: The Psychotic Symptoms Rating Scale (PSYRATS), the Revised Beliefs About Voices Questionnaire (BAVQ-R), the Multidimensional Scale for Hallucinations (MSH), and a detailed clinical interview were administered to 11 BPD and 10 schizophrenia DSM-IV participants. RESULTS: The VAHs of both groups were similar regarding intensity, reported as located inside or outside the head, and frequency in which they were described as a third-person phenomenon. However, the patients' stance towards their VAH was clearly different. Whilst BPD patients identified them in a clear way in terms of gender and age and disliked them, schizophrenia patients identified them more vaguely, reported them both as more disruptive but at the same time engaged with them more positively; schizophrenia patients also integrated their VAH more into delusions. DISCUSSION: Whilst reporting similar intensity of their VAH, the 2 groups' stance towards them were strikingly different in that BPD participants regarded them as identifiable and unequivocally unpleasant whilst schizophrenia participants regarded them in a rather vague and ambiguous manner. Methodologically, this preliminary study suggests that in-depth phenomenological assessment can help to elucidate the differential diagnosis of VAH in these, possibly other, clinical groups. Further research is warranted to establish whether these preliminary findings are replicated on a bigger clinical sample.


Assuntos
Transtorno da Personalidade Borderline/complicações , Transtorno da Personalidade Borderline/psicologia , Alucinações/diagnóstico , Esquizofrenia/complicações , Adolescente , Adulto , Idoso , Manual Diagnóstico e Estatístico de Transtornos Mentais , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Inquéritos e Questionários , Adulto Jovem
13.
Br J Anaesth ; 124(3): 251-260, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-32007241

RESUMO

Immunotherapy has revolutionised the treatment of oncologic malignancies. Immune checkpoint inhibitors represent a new class of immunotherapy drugs. Although these drugs show promise, they are associated with immune-related adverse reactions. An increasing number of patients who undergo surgery will have had treatment with immune checkpoint inhibitors. In this narrative review article, we discuss their mechanism of action, therapeutic effects, pertinent toxicities, and address specific perioperative considerations for patients treated with immune checkpoint inhibitors.


Assuntos
Anestesiologistas , Antineoplásicos Imunológicos/efeitos adversos , Imunoterapia/efeitos adversos , Neoplasias/tratamento farmacológico , Assistência Perioperatória/métodos , Papel do Médico , Anticorpos Monoclonais/efeitos adversos , Anticorpos Monoclonais/uso terapêutico , Antineoplásicos Imunológicos/uso terapêutico , Antígeno CTLA-4/antagonistas & inibidores , Humanos , Imunoterapia/métodos , Complicações Intraoperatórias/induzido quimicamente , Complicações Intraoperatórias/prevenção & controle , Neoplasias/imunologia , Complicações Pós-Operatórias/induzido quimicamente , Complicações Pós-Operatórias/prevenção & controle
14.
Health Promot Int ; 35(6): 1312-1319, 2020 Dec 01.
Artigo em Inglês | MEDLINE | ID: mdl-31986195

RESUMO

Increasingly life is lived online, yet little is known about the actual nature and extent of online content that people view due to the difficulty of recording real time exposure. This includes people's exposure to harmful commodity marketing. This study aimed to develop a methodology to assess the nature and extent of exposure to, and engagement with, unhealthy commodity marketing and other public health harms online, particularly children's exposure. A convenience sample of 16 young adult participants (aged 21-29) recorded their device usage for 2 days using Zoom software. Data were coded and analysed to assess the nature and extent of marketing for alcohol, gambling, junk food and smoking products. Four focus groups were conducted with participants to explore their data collection and coding experiences, and results assessed using thematic analysis. The study found that, with some modifications, this method was feasible for gathering real-time objective data from the online world that can be analysed for a range of public health harms, including marketing of unhealthy commodities. Larger studies are recommended to build global evidence for public health action in the online world.


Assuntos
Jogo de Azar , Marketing , Criança , Grupos Focais , Humanos , Saúde Pública , Fumar , Adulto Jovem
15.
Genet Med ; 21(4): 913-922, 2019 04.
Artigo em Inglês | MEDLINE | ID: mdl-30254378

RESUMO

PURPOSE: The identification of carriers of hereditary breast and ovarian cancer (HBOC) gene variants through family cancer history alone is suboptimal, and most population-based genetic testing studies have been limited to founder mutations in high-risk populations. Here, we determine the clinical utility of identifying actionable variants in a healthy cohort of women. METHODS: Germline DNA from a subset of healthy Australian women participating in the lifepool project was screened using an 11-gene custom sequencing panel. Women with clinically actionable results were invited to attend a familial cancer clinic (FCC) for post-test genetic counseling and confirmatory testing. Outcomes measured included the prevalence of pathogenic variants, and the uptake rate of genetic counseling, risk reduction surgery, and cascade testing. RESULTS: Thirty-eight of 5908 women (0.64%) carried a clinically actionable pathogenic variant. Forty-two percent of pathogenic variant carriers did not have a first-degree relative with breast or ovarian cancer and 89% pursued referral to an FCC. Forty-six percent (6/13) of eligible women pursued risk reduction surgery, and the uptake rate of cascade testing averaged 3.3 family members per index case. CONCLUSION: Within our cohort, HBOC genetic testing was well accepted, and the majority of high-risk gene carriers identified would not meet eligibility criteria for genetic testing based on their existing family history.


Assuntos
Neoplasias da Mama/genética , Predisposição Genética para Doença , Síndrome Hereditária de Câncer de Mama e Ovário/genética , Neoplasias Ovarianas/genética , Idoso , Austrália , Neoplasias da Mama/patologia , Feminino , Aconselhamento Genético , Genética Populacional , Mutação em Linhagem Germinativa/genética , Síndrome Hereditária de Câncer de Mama e Ovário/patologia , Heterozigoto , Humanos , Pessoa de Meia-Idade , Mutação , Neoplasias Ovarianas/patologia
16.
Nature ; 500(7461): 207-11, 2013 Aug 08.
Artigo em Inglês | MEDLINE | ID: mdl-23925245

RESUMO

The HeLa cell line was established in 1951 from cervical cancer cells taken from a patient, Henrietta Lacks. This was the first successful attempt to immortalize human-derived cells in vitro. The robust growth and unrestricted distribution of HeLa cells resulted in its broad adoption--both intentionally and through widespread cross-contamination--and for the past 60 years it has served a role analogous to that of a model organism. The cumulative impact of the HeLa cell line on research is demonstrated by its occurrence in more than 74,000 PubMed abstracts (approximately 0.3%). The genomic architecture of HeLa remains largely unexplored beyond its karyotype, partly because like many cancers, its extensive aneuploidy renders such analyses challenging. We carried out haplotype-resolved whole-genome sequencing of the HeLa CCL-2 strain, examined point- and indel-mutation variations, mapped copy-number variations and loss of heterozygosity regions, and phased variants across full chromosome arms. We also investigated variation and copy-number profiles for HeLa S3 and eight additional strains. We find that HeLa is relatively stable in terms of point variation, with few new mutations accumulating after early passaging. Haplotype resolution facilitated reconstruction of an amplified, highly rearranged region of chromosome 8q24.21 at which integration of the human papilloma virus type 18 (HPV-18) genome occurred and that is likely to be the event that initiated tumorigenesis. We combined these maps with RNA-seq and ENCODE Project data sets to phase the HeLa epigenome. This revealed strong, haplotype-specific activation of the proto-oncogene MYC by the integrated HPV-18 genome approximately 500 kilobases upstream, and enabled global analyses of the relationship between gene dosage and expression. These data provide an extensively phased, high-quality reference genome for past and future experiments relying on HeLa, and demonstrate the value of haplotype resolution for characterizing cancer genomes and epigenomes.


Assuntos
Epigenômica , Genoma Humano/genética , Aneuploidia , Variações do Número de Cópias de DNA , Feminino , Genes myc/genética , Haplótipos , Células HeLa , Papillomavirus Humano 18/genética , Papillomavirus Humano 18/fisiologia , Humanos , Dados de Sequência Molecular , Mutação , Proto-Oncogene Mas , Análise de Sequência de DNA , Ativação Transcricional/genética , Neoplasias do Colo do Útero/genética , Neoplasias do Colo do Útero/patologia , Neoplasias do Colo do Útero/virologia
17.
Radiology ; 289(2): 564-567, 2018 11.
Artigo em Inglês | MEDLINE | ID: mdl-30106351

RESUMO

Pembrolizumab is a programmed cell death protein 1, or PD-1, inhibitor therapy immunotherapy for patients with advanced melanoma. This report discusses a series of documented cases of sarcoid-like reactions associated with this therapy. Three patients with malignant melanoma developed metastatic disease and were treated with pembrolizumab immunotherapy. Subsequent imaging showed lymphadenopathy in the mediastinum and hilar regions that was confirmed to represent a sarcoid-like reaction at histologic examination. Radiologists should be aware of the association between pembrolizumab and the development of sarcoid-like reactions to avoid inaccurately ascribing these imaging findings to metastatic disease. Clinical presentation, biopsy, radiographic evidence of bilateral hilar lymphadenopathy (with paratracheal lymphadenopathy), and elevated serum angiotensin-converting enzyme levels aid in the diagnosis of sarcoid-like reactions and help avoid these reactions being mistaken for recurrent or metastatic disease.


Assuntos
Anticorpos Monoclonais Humanizados/efeitos adversos , Antineoplásicos Imunológicos/efeitos adversos , Linfadenopatia/induzido quimicamente , Melanoma/tratamento farmacológico , Anticorpos Monoclonais Humanizados/uso terapêutico , Antineoplásicos Imunológicos/uso terapêutico , Biópsia , Feminino , Glucocorticoides/uso terapêutico , Humanos , Linfonodos/diagnóstico por imagem , Linfonodos/patologia , Linfadenopatia/diagnóstico , Linfadenopatia/tratamento farmacológico , Masculino , Mediastino , Melanoma/secundário , Pessoa de Meia-Idade , Tomografia por Emissão de Pósitrons combinada à Tomografia Computadorizada , Prednisolona/uso terapêutico
18.
BMC Psychiatry ; 18(1): 281, 2018 09 04.
Artigo em Inglês | MEDLINE | ID: mdl-30180832

RESUMO

BACKGROUND: Around 25% of prisoners meet diagnostic criteria for attention-deficit/hyperactivity disorder (ADHD). Because ADHD is associated with increased recidivism and other functional and behavioural problems, appropriate diagnosis and treatment can be a critical intervention to improve outcomes. While ADHD is a treatable condition, best managed by a combination of medication and psychological treatments, among individuals in the criminal justice system ADHD remains both mis- and under-diagnosed and consequently inadequately treated. We aimed to identify barriers within the prison system that prevent appropriate intervention, and provide a practical approach to identify and treat incarcerated offenders with ADHD. METHODS: The United Kingdom ADHD Partnership hosted a consensus meeting to discuss practical interventions for youth (< 18 years) and adult (≥18 years) offenders with ADHD. Experts at the meeting addressed prisoners' needs for effective identification, treatment, and multiagency liaison, and considered the requirement of different approaches based on age or gender. RESULTS: The authors developed a consensus statement that offers practical advice to anyone working with prison populations. We identified specific barriers within the prison and criminal justice system such as the lack of adequate: staff and offender awareness of ADHD symptoms and treatments; trained mental health staff; use of appropriate screening and diagnostic tools; appropriate multimodal interventions; care management; supportive services; multiagency liaison; and preparation for prison release. Through discussion, a consensus was reached regarding prisoners' needs, effective identification, treatment and multiagency liaison and considered how this may differ for age and gender. CONCLUSIONS: This practical approach based upon expert consensus will inform effective identification and treatment of offenders with ADHD. Appropriate intervention is expected to have a positive impact on the offender and society and lead to increased productivity, decreased resource utilization, and most importantly reduced rates of re-offending. Research is still needed, however, to identify optimal clinical operating models and to monitor their implementation and measure their success. Furthermore, government support will likely be required to effect change in criminal justice and mental health service policies.


Assuntos
Transtorno do Deficit de Atenção com Hiperatividade/psicologia , Transtorno do Deficit de Atenção com Hiperatividade/terapia , Consenso , Prova Pericial/métodos , Prisioneiros/psicologia , Prisões , Adolescente , Adulto , Transtorno do Deficit de Atenção com Hiperatividade/diagnóstico , Direito Penal/métodos , Criminosos/psicologia , Feminino , Humanos , Masculino , Serviços de Saúde Mental , Resultado do Tratamento , Reino Unido/epidemiologia
19.
Genes Chromosomes Cancer ; 55(3): 278-87, 2016 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-26650888

RESUMO

Investigation of the genetic lesions underlying classical Hodgkin lymphoma (CHL) has been challenging due to the rarity of Hodgkin and Reed-Sternberg (HRS) cells, the pathognomonic neoplastic cells of CHL. In an effort to catalog more comprehensively recurrent copy number alterations occurring during oncogenesis, we investigated somatic alterations involved in CHL using whole-genome sequencing-mediated copy number analysis of purified HRS cells. We performed low-coverage sequencing of small numbers of intact HRS cells and paired non-neoplastic B lymphocytes isolated by flow cytometric cell sorting from 19 primary cases, as well as two commonly used HRS-derived cell lines (KM-H2 and L1236). We found that HRS cells contain strikingly fewer copy number abnormalities than CHL cell lines. A subset of cases displayed nonintegral chromosomal copy number states, suggesting internal heterogeneity within the HRS cell population. Recurrent somatic copy number alterations involving known factors in CHL pathogenesis were identified (REL, the PD-1 pathway, and TNFAIP3). In eight cases (42%) we observed recurrent copy number loss of chr1:2,352,236-4,574,271, a region containing the candidate tumor suppressor TNFRSF14. Using flow cytometry, we demonstrated reduced TNFRSF14 expression in HRS cells from 5 of 22 additional cases (23%) and in two of three CHL cell lines. These studies suggest that TNFRSF14 dysregulation may contribute to the pathobiology of CHL in a subset of cases.


Assuntos
Doença de Hodgkin/genética , Membro 14 de Receptores do Fator de Necrose Tumoral/genética , Linhagem Celular Tumoral , Separação Celular , Citometria de Fluxo , Doença de Hodgkin/metabolismo , Humanos , Análise de Sequência com Séries de Oligonucleotídeos , Membro 14 de Receptores do Fator de Necrose Tumoral/biossíntese , Membro 14 de Receptores do Fator de Necrose Tumoral/deficiência , Células de Reed-Sternberg
20.
Am J Hum Genet ; 92(1): 99-106, 2013 Jan 10.
Artigo em Inglês | MEDLINE | ID: mdl-23261302

RESUMO

Primary ciliary dyskinesia (PCD) is a genetically heterogeneous, autosomal-recessive disorder, characterized by oto-sino-pulmonary disease and situs abnormalities. PCD-causing mutations have been identified in 14 genes, but they collectively account for only ~60% of all PCD. To identify mutations that cause PCD, we performed exome sequencing on six unrelated probands with ciliary outer dynein arm (ODA) defects. Mutations in CCDC114, an ortholog of the Chlamydomonas reinhardtii motility gene DCC2, were identified in a family with two affected siblings. Sanger sequencing of 67 additional individuals with PCD with ODA defects from 58 families revealed CCDC114 mutations in 4 individuals in 3 families. All 6 individuals with CCDC114 mutations had characteristic oto-sino-pulmonary disease, but none had situs abnormalities. In the remaining 5 individuals with PCD who underwent exome sequencing, we identified mutations in two genes (DNAI2, DNAH5) known to cause PCD, including an Ashkenazi Jewish founder mutation in DNAI2. These results revealed that mutations in CCDC114 are a cause of ciliary dysmotility and PCD and further demonstrate the utility of exome sequencing to identify genetic causes in heterogeneous recessive disorders.


Assuntos
Síndrome de Kartagener/genética , Proteínas Associadas aos Microtúbulos/genética , Mutação , Adulto , Pré-Escolar , Exoma , Feminino , Genes Recessivos , Humanos , Masculino , Pessoa de Meia-Idade , Linhagem , Isoformas de Proteínas , Análise de Sequência de DNA
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