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Health Impact and Therapeutic Manipulation of the Gut Microbiome. 肠道微生物组对健康的影响和治疗操作。
Q2 Biochemistry, Genetics and Molecular Biology Pub Date : 2020-07-29 DOI: 10.3390/ht9030017
Eric Banan-Mwine Daliri, Fred Kwame Ofosu, Ramachandran Chelliah, Byong Hoon Lee, Deog-Hwan Oh

Recent advances in microbiome studies have revealed much information about how the gut virome, mycobiome, and gut bacteria influence health and disease. Over the years, many studies have reported associations between the gut microflora under different pathological conditions. However, information about the role of gut metabolites and the mechanisms by which the gut microbiota affect health and disease does not provide enough evidence. Recent advances in next-generation sequencing and metabolomics coupled with large, randomized clinical trials are helping scientists to understand whether gut dysbiosis precedes pathology or gut dysbiosis is secondary to pathology. In this review, we discuss our current knowledge on the impact of gut bacteria, virome, and mycobiome interactions with the host and how they could be manipulated to promote health.

微生物组研究的最新进展揭示了许多关于肠道病毒组、真菌组和肠道细菌如何影响健康和疾病的信息。多年来,许多研究报道了不同病理条件下肠道菌群之间的联系。然而,关于肠道代谢物的作用和肠道微生物群影响健康和疾病的机制的信息并没有提供足够的证据。新一代测序和代谢组学的最新进展,加上大型随机临床试验,正在帮助科学家了解肠道生态失调是先于病理还是继发于病理。在这篇综述中,我们讨论了我们目前对肠道细菌、病毒组和真菌组与宿主相互作用的影响以及如何控制它们以促进健康的了解。
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引用次数: 10
Influence of the Ovine Genital Tract Microbiota on the Species Artificial Insemination Outcome. A Pilot Study in Commercial Sheep Farms. 绵羊生殖道微生物群对种属人工授精结果的影响。商业羊场的试点研究。
Q2 Biochemistry, Genetics and Molecular Biology Pub Date : 2020-07-06 DOI: 10.3390/ht9030016
Malena Serrano, Eric Climent, Fernando Freire, Juan F Martínez-Blanch, Carmen González, Luis Reyes, M Carmen Solaz-Fuster, Jorge H Calvo, M Ángeles Jiménez, Francisco M Codoñer

To date, there is a lack of research into the vaginal and sperm microbiome and its bearing on artificial insemination (AI) success in the ovine species. Using hypervariable regions V3-V4 of the 16S rRNA, we describe, for the first time, the combined effect of the ovine microbiome of both females (50 ewes belonging to five herds) and males (five AI rams from an AI center) on AI outcome. Differences in microbiota abundance between pregnant and non-pregnant ewes and between ewes carrying progesterone-releasing intravaginal devices (PRID) with or without antibiotic were tested at different taxonomic levels. The antibiotic treatment applied with the PRID only altered Streptobacillus genus abundance, which was significantly lower in ewes carrying PRID with antibiotic. Mageebacillus, Histophilus, Actinobacilllus and Sneathia genera were significantly less abundant in pregnant ewes. In addition, these genera were more abundant in two farms with higher AI failure. Species of these genera such as Actinobacillus seminis and Histophilus somni have been associated with reproductive disorders in the ovine species. These genera were not present in the sperm samples of AI rams, but were found in the foreskin samples of rams belonging to herd 2 (with high AI failure rate) indicating that their presence in ewes' vagina could be due to prior transmission by natural mating with rams reared in the herd.

迄今为止,缺乏对阴道和精子微生物组及其对绵羊人工授精(AI)成功的影响的研究。利用16S rRNA的高变区V3-V4,我们首次描述了母羊(50只母羊,属于5个畜群)和公羊(5只来自人工智能中心的人工智能公羊)的微生物组对人工智能结果的综合影响。在不同的分类水平上测试了妊娠母羊和未妊娠母羊以及携带或不携带孕激素释放阴道装置(PRID)母羊之间微生物群丰度的差异。应用PRID的抗生素处理只改变了链球菌属丰度,在携带PRID的母羊中,抗生素显著降低了链球菌属丰度。妊娠母羊中Mageebacillus、Histophilus、放线菌bacillus和Sneathia属的数量明显减少。此外,这些属在AI失败率较高的两个养殖场中更为丰富。这些属的种,如放线菌精和梭尼组织杆菌与绵羊的生殖障碍有关。这些属不存在于人工智能公羊的精子样本中,但在属于2群的公羊的包皮样本中发现(人工智能失败率高),表明它们在母羊阴道中的存在可能是由于先前与该群中饲养的公羊自然交配而传播的。
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引用次数: 10
Dark Proteome Database: Studies on Disorder. Dark蛋白质组数据库:疾病研究。
Q2 Biochemistry, Genetics and Molecular Biology Pub Date : 2020-06-30 DOI: 10.3390/ht9030015
Nelson Perdigão, Pedro M C Pina, Cátia Rocha, João Manuel R S Tavares, Agostinho Rosa

There is a misconception that intrinsic disorder in proteins is equivalent to darkness. The present study aims to establish, in the scope of the Swiss-Prot and Dark Proteome databases, the relationship between disorder and darkness. Three distinct predictors were used to calculate the disorder of Swiss-Prot proteins. The analysis of the results obtained with the used predictors and visualization paradigms resulted in the same conclusion that was reached before: disorder is mostly unrelated to darkness.

有一种误解认为蛋白质的内在紊乱等同于黑暗。本研究的目的是在Swiss-Prot和Dark蛋白质组数据库的范围内,建立紊乱和黑暗之间的关系。三个不同的预测因子被用来计算Swiss-Prot蛋白的紊乱。对所使用的预测因子和可视化范式所得到的结果进行分析,得出了与之前相同的结论:混乱与黑暗基本无关。
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引用次数: 1
Intra-Laboratory Evaluation of Luminescence Based High-Throughput Serum Bactericidal Assay (L-SBA) to Determine Bactericidal Activity of Human Sera against Shigella. 基于发光的高通量血清杀菌试验(L-SBA)测定人血清对志贺氏菌的杀菌活性的实验室内评价。
Q2 Biochemistry, Genetics and Molecular Biology Pub Date : 2020-06-08 DOI: 10.3390/ht9020014
Omar Rossi, Eleonora Molesti, Allan Saul, Carlo Giannelli, Francesca Micoli, Francesca Necchi

Despite the huge decrease in deaths caused by Shigella worldwide in recent decades, shigellosis still causes over 200,000 deaths every year. No vaccine is currently available, and the morbidity of the disease coupled with the rise of antimicrobial resistance renders the introduction of an effective vaccine extremely urgent. Although a clear immune correlate of protection against shigellosis has not yet been established, the demonstration of the bactericidal activity of antibodies induced upon vaccination may provide one means of the functionality of antibodies induced in protecting against Shigella. The method of choice to evaluate the complement-mediated functional activity of vaccine-induced antibodies is the Serum Bactericidal Assay (SBA). Here we present the development and intra-laboratory characterization of a high-throughput luminescence-based SBA (L-SBA) method, based on the detection of ATP as a proxy of surviving bacteria, to evaluate the complement-mediated killing of human sera. We demonstrated the high specificity of the assay against a homologous strain without any heterologous aspecificity detected against species-related and non-species-related strains. We assessed the linearity, repeatability and reproducibility of L-SBA on human sera. This work will guide the bactericidal activity assessment of clinical sera raised against S. sonnei. The method has the potential of being applicable with similar performances to determine the bactericidal activity of any non-clinical and clinical sera that rely on complement-mediated killing.

尽管近几十年来世界范围内由志贺氏菌引起的死亡人数大幅减少,但志贺氏菌病每年仍造成20多万人死亡。目前没有疫苗,该病的发病率加上抗菌素耐药性的上升,使得引进有效的疫苗极为紧迫。虽然对志贺氏菌病保护的明确免疫相关性尚未建立,但接种后诱导的抗体的杀菌活性的证明可能为诱导的抗体在保护志贺氏菌方面的功能提供了一种手段。评价补体介导的疫苗诱导抗体功能活性的选择方法是血清杀菌试验(SBA)。在这里,我们提出了一种基于高通量发光的SBA (L-SBA)方法的开发和实验室内表征,该方法基于检测ATP作为存活细菌的代理,以评估补体介导的人类血清杀伤。我们证明了该检测对同源菌株的高特异性,而对物种相关和非物种相关菌株没有检测到任何异源特异性。我们评估了L-SBA在人血清中的线性、重复性和再现性。本研究对临床血清sonnei链球菌的杀菌活性评价具有指导意义。该方法具有类似的应用潜力,可用于确定依赖补体介导杀伤的任何非临床和临床血清的杀菌活性。
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引用次数: 20
Genetic Counseling and NGS Screening for Recessive LGMD2A Families. 隐性LGMD2A家族的遗传咨询和NGS筛查。
Q2 Biochemistry, Genetics and Molecular Biology Pub Date : 2020-05-10 DOI: 10.3390/ht9020013
Claudia Strafella, Valerio Caputo, Giulia Campoli, Rosaria Maria Galota, Julia Mela, Stefania Zampatti, Giulietta Minozzi, Cristina Sancricca, Serenella Servidei, Emiliano Giardina, Raffaella Cascella

: Genetic counseling applied to limb-girdle muscular dystrophies (LGMDs) can be very challenging due to their clinical and genetic heterogeneity and the availability of different molecular assays. Genetic counseling should therefore be addressed to select the most suitable approach to increase the diagnostic rate and provide an accurate estimation of recurrence risk. This is particularly true for families with a positive history for recessive LGMD, in which the presence of a known pathogenetic mutation segregating within the family may not be enough to exclude the risk of having affected children without exploring the genetic background of phenotypically unaffected partners. In this work, we presented a family with a positive history for LGMD2A (OMIM #253600, also known as calpainopathy) characterized by compound heterozygosity for two CAPN3 mutations. The genetic specialist suggested the segregation analysis of both mutations within the family as a first-level analysis. Sequentially, next-generation sequencing (NGS) analysis was performed in the partners of healthy carriers to provide an accurate recurrence/reproductive risk estimation considering the genetic background of the couple. Finally, this work highlighted the importance of providing a genetic counseling/testing service even in unaffected individuals with a carrier partner. This approach can support genetic counselors in estimating the reproductive/recurrence risk and eventually, suggesting prenatal testing, early diagnosis or other medical surveillance strategies.

由于肢体肌营养不良症的临床和遗传异质性以及不同分子检测方法的可用性,遗传咨询应用于肢体肌营养不良症(LGMDs)可能非常具有挑战性。因此,遗传咨询应致力于选择最合适的方法来提高诊断率,并提供准确的复发风险估计。对于有隐性LGMD阳性病史的家庭尤其如此,在这种情况下,如果不探索未受表型影响的伴侣的遗传背景,家庭中存在已知的致病突变隔离可能不足以排除患病儿童的风险。在这项工作中,我们提出了一个具有LGMD2A阳性病史(OMIM #253600,也称为calpainopathy)的家庭,其特征是两个CAPN3突变的复合杂合性。遗传专家建议将家族内两个突变的分离分析作为一级分析。随后,对健康携带者的伴侣进行下一代测序(NGS)分析,以提供准确的复发/生殖风险估计,考虑到这对夫妇的遗传背景。最后,这项工作强调了提供遗传咨询/测试服务的重要性,即使是在未受影响的个体与携带者的伴侣。这种方法可以帮助遗传咨询师估计生殖/复发风险,并最终建议产前检查、早期诊断或其他医疗监测策略。
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引用次数: 1
Microbiota and Human Reproduction: The Case of Female Infertility. 微生物群与人类生殖:女性不育的案例。
Q2 Biochemistry, Genetics and Molecular Biology Pub Date : 2020-05-03 DOI: 10.3390/ht9020012
Rossella Tomaiuolo, Iolanda Veneruso, Federica Cariati, Valeria D'Argenio

During the last decade, the availability of next-generation sequencing-based approaches has revealed the presence of microbial communities in almost all the human body, including the reproductive tract. As for other body sites, this resident microbiota has been involved in the maintenance of a healthy status. As a consequence, alterations due to internal or external factors may lead to microbial dysbiosis and to the development of pathologies. Female reproductive microbiota has also been suggested to affect infertility, and it may play a key role in the success of assisted reproductive technologies, such as embryo implantation and pregnancy care. While the vaginal microbiota is well described, the uterine microbiota is underexplored. This could be due to technical issues, as the uterus is a low biomass environment. Here, we review the state of the art regarding the role of the female reproductive system microbiota in women's health and human reproduction, highlighting its contribution to infertility.

在过去的十年中,基于新一代测序方法的可用性揭示了几乎所有人体(包括生殖道)中微生物群落的存在。至于身体其他部位,这种常驻微生物群参与了健康状态的维持。因此,由于内部或外部因素的改变可能导致微生物生态失调和病理的发展。女性生殖微生物群也被认为影响不孕症,它可能在胚胎植入和妊娠护理等辅助生殖技术的成功中发挥关键作用。虽然阴道微生物群被很好地描述,但子宫微生物群尚未被充分探索。这可能是由于技术问题,因为子宫是一个低生物量的环境。在这里,我们回顾了关于女性生殖系统微生物群在女性健康和人类生殖中的作用的最新进展,重点介绍了其对不孕症的贡献。
{"title":"Microbiota and Human Reproduction: The Case of Female Infertility.","authors":"Rossella Tomaiuolo,&nbsp;Iolanda Veneruso,&nbsp;Federica Cariati,&nbsp;Valeria D'Argenio","doi":"10.3390/ht9020012","DOIUrl":"https://doi.org/10.3390/ht9020012","url":null,"abstract":"<p><p>During the last decade, the availability of next-generation sequencing-based approaches has revealed the presence of microbial communities in almost all the human body, including the reproductive tract. As for other body sites, this resident microbiota has been involved in the maintenance of a healthy status. As a consequence, alterations due to internal or external factors may lead to microbial dysbiosis and to the development of pathologies. Female reproductive microbiota has also been suggested to affect infertility, and it may play a key role in the success of assisted reproductive technologies, such as embryo implantation and pregnancy care. While the vaginal microbiota is well described, the uterine microbiota is underexplored. This could be due to technical issues, as the uterus is a low biomass environment. Here, we review the state of the art regarding the role of the female reproductive system microbiota in women's health and human reproduction, highlighting its contribution to infertility.</p>","PeriodicalId":53433,"journal":{"name":"High-Throughput","volume":"9 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3390/ht9020012","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37906168","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 35
Chimeric Virus Made from crTMV RNA and the Coat Protein of Potato Leafroll Virus is Targeted to the Nucleolus and Can Infect Nicotiana benthamiana Mechanically. 利用crTMV RNA与马铃薯叶卷病毒外壳蛋白合成的嵌合病毒靶向核仁,可机械感染本烟菌。
Q2 Biochemistry, Genetics and Molecular Biology Pub Date : 2020-04-26 DOI: 10.3390/ht9020011
Konstantin O Butenko, Inna A Chaban, Eugene V Skurat, Olga A Kondakova, Yuri F Drygin

A genetically engineered chimeric virus crTMV-CP-PLRV composed of the crucifer-infecting tobacco mosaic virus (crTMV) RNA and the potato leafroll virus (PLRV) coat protein (CP) was obtained by agroinfiltration of Nicotiana benthamiana with the binary vector pCambia-crTMV-CPPLRV. The significant levels of the chimeric virus enabled direct visualization of crTMV-CP-PLRV in the cell and to investigate the mechanism of the pathogenesis. Localization of the crTMV-CP-PLRV in plant cells was examined by immunoblot techniques, as well as light, and transmission electron microscopy. The chimera can transfer between vascular and nonvascular tissues. The chimeric virus inoculum is capable to infect N. benthamiana mechanically. The distinguishing feature of the chimeric virus, the RNA virus with the positive genome, was found to localize in the nucleolus. We also investigated the role of the N-terminal sequence of the PLRV P3 coat protein in the cellular localization of the virus. We believe that the gene of the PLRV CP can be substituted with genes from other challenging-to-study plant pathogens to produce other useful recombinant viruses.

以双载体pCambia-crTMV-CPPLRV为载体,以侵染十字花科植物的烟草花叶病毒(crTMV) RNA和马铃薯叶卷病毒(PLRV)外壳蛋白(CP)为载体,通过农渗透获得了一种由烟草花叶病毒(crTMV) RNA和马铃薯叶卷病毒(PLRV)外壳蛋白(CP)组成的基因工程嵌合病毒crTMV-CP-PLRV。嵌合病毒的显著水平使crTMV-CP-PLRV在细胞内的直接可视化和研究其发病机制成为可能。通过免疫印迹技术、光镜和透射电镜检测crTMV-CP-PLRV在植物细胞中的定位。嵌合体可以在血管和非血管组织之间转移。嵌合病毒接种物能够机械地感染拟南拟虫。嵌合病毒的显著特征是基因组阳性的RNA病毒定位于核仁。我们还研究了PLRV P3外壳蛋白n端序列在病毒细胞定位中的作用。我们相信,PLRV CP基因可以被其他具有挑战性的植物病原体基因取代,以产生其他有用的重组病毒。
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引用次数: 0
Microbiota and Human Reproduction: The Case of Male Infertility. 微生物群与人类生殖:男性不育案例。
Q2 Biochemistry, Genetics and Molecular Biology Pub Date : 2020-04-13 DOI: 10.3390/ht9020010
Rossella Tomaiuolo, Iolanda Veneruso, Federica Cariati, Valeria D'Argenio

The increasing interest in metagenomics is enhancing our knowledge regarding the composition and role of the microbiota in human physiology and pathology. Indeed, microbes have been reported to play a role in several diseases, including infertility. In particular, the male seminal microbiota has been suggested as an important factor able to influence couple's health and pregnancy outcomes, as well as offspring health. Nevertheless, few studies have been carried out to date to deeper investigate semen microbiome origins and functions, and its correlations with the partner's reproductive tract microbiome. Here, we report the state of the art regarding the male reproductive system microbiome and its alterations in infertility.

人们对元基因组学的兴趣与日俱增,这增进了我们对微生物群在人体生理和病理中的组成和作用的了解。事实上,微生物已被报道在包括不孕症在内的多种疾病中发挥作用。尤其是男性精液微生物群被认为是影响夫妇健康、妊娠结果以及后代健康的重要因素。然而,迄今为止,很少有研究对精液微生物群的起源、功能及其与伴侣生殖道微生物群的相关性进行深入研究。在此,我们将报告有关男性生殖系统微生物组及其在不育症中的改变的最新进展。
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引用次数: 0
A Simple, Label-Free, and High-Throughput Method to Evaluate the Epigallocatechin-3-Gallate Impact in Plasma Molecular Profile. 一种简单,无标记,高通量的方法来评估表没食子儿茶素-3-没食子酸酯对血浆分子谱的影响。
Q2 Biochemistry, Genetics and Molecular Biology Pub Date : 2020-04-09 DOI: 10.3390/ht9020009
Rúben Araújo, Luís Ramalhete, Helder Da Paz, Edna Ribeiro, Cecília R C Calado
Epigallocatechin-3-gallate (EGCG), the major catechin present in green tea, presents diverse appealing biological activities, such as antioxidative, anti-inflammatory, antimicrobial, and antiviral activities, among others. The present work evaluated the impact in the molecular profile of human plasma from daily consumption of 225 mg of EGCG for 90 days. Plasma from peripheral blood was collected from 30 healthy human volunteers and analyzed by high-throughput Fourier transform infrared spectroscopy. To capture the biochemical information while minimizing the interference of physical phenomena, several combinations of spectra pre-processing methods were evaluated by principal component analysis. The pre-processing method that led to the best class separation, that is, between the plasma spectral data collected at the beginning and after the 90 days, was a combination of atmospheric correction with a second derivative spectra. A hierarchical cluster analysis of second derivative spectra also highlighted the fact that plasma acquired before EGCG consumption presented a distinct molecular profile after the 90 days of EGCG consumption. It was also possible by partial least squares regression discriminant analysis to correctly predict all unlabeled plasma samples (not used for model construction) at both timeframes. We observed that the similarity in composition among the plasma samples was higher in samples collected after EGCG consumption when compared with the samples taken prior to EGCG consumption. Diverse negative peaks of the normalized second derivative spectra, associated with lipid and protein regions, were significantly affected (p < 0.001) by EGCG consumption, according to the impact of EGCG consumption on the patients’ blood, low density and high density lipoproteins ratio. In conclusion, a single bolus dose of 225 mg of EGCG, ingested throughout a period of 90 days, drastically affected plasma molecular composition in all participants, which raises awareness regarding prolonged human exposure to EGCG. Because the analysis was conducted in a high-throughput, label-free, and economic analysis, it could be applied to high-dimension molecular epidemiological studies to further promote the understanding of the effect of bio-compound consumption mode and frequency.
表没食子儿茶素-3-没食子酸酯(EGCG)是绿茶中主要的儿茶素,具有多种吸引人的生物活性,如抗氧化、抗炎、抗菌和抗病毒活性等。本研究评估了连续90天每天摄入225mg EGCG对人血浆分子谱的影响。采用高通量傅立叶变换红外光谱对30名健康志愿者外周血血浆进行分析。为了在捕获生化信息的同时最大限度地减少物理现象的干扰,通过主成分分析对几种光谱预处理方法的组合进行了评价。采用大气校正与二阶导数光谱相结合的预处理方法,可实现90 d前后等离子体光谱数据的最佳类分离。二阶导数光谱的层次聚类分析也强调了这样一个事实,即在摄入EGCG之前获得的血浆在摄入EGCG 90天后呈现出明显的分子特征。通过偏最小二乘回归判别分析也可以正确预测两个时间段内所有未标记的血浆样品(未用于模型构建)。我们观察到,与服用EGCG之前的样品相比,服用EGCG后收集的血浆样品在成分上的相似性更高。根据EGCG消耗对患者血液、低密度和高密度脂蛋白比值的影响,EGCG消耗显著影响归一化二阶导数光谱中与脂区和蛋白区相关的各种负峰(p < 0.001)。综上所述,在90天内单次摄入225mg EGCG会显著影响所有参与者的血浆分子组成,这提高了人们对长期暴露于EGCG的认识。由于该分析为高通量、无标签、经济分析,可应用于高维分子流行病学研究,进一步促进对生物化合物消费方式和频率影响的认识。
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引用次数: 6
DMETTM Genotyping: Tools for Biomarkers Discovery in the Era of Precision Medicine. DMETTM基因分型:精准医学时代发现生物标志物的工具。
Q2 Biochemistry, Genetics and Molecular Biology Pub Date : 2020-03-29 DOI: 10.3390/ht9020008
Giuseppe Agapito, Marzia Settino, Francesca Scionti, Emanuela Altomare, Pietro Hiram Guzzi, Pierfrancesco Tassone, Pierosandro Tagliaferri, Mario Cannataro, Mariamena Arbitrio, Maria Teresa Di Martino

The knowledge of genetic variants in genes involved in drug metabolism may be translated into reduction of adverse drug reactions, increase of efficacy, healthcare outcomes improvement and economic benefits. Many high-throughput tools are available for the genotyping of Single Nucleotide Polymorphisms (SNPs) known to be related to drugs and xenobiotics metabolism. DMETTM platform represents an example of SNPs panel to discover biomarkers correlated to efficacy or toxicity in common and rare diseases. The difficulty in analyzing the mole of information generated by DMETTM platform led to the development and implementation of algorithms and tools for statistical and data mining analysis. These softwares allow efficient handling of the omics data to validate the explorative SNPs identified by DMET assay and to correlate them with drug efficacy, toxicity and/or cancer susceptibility. In this review we present a suite of bioinformatic frameworks for the preprocessing and analysis of DMET-SNPs data. In particular, we introduce a workflow that uses the GenoMetric Query Language, a high-level query language specifically designed for genomics, able to query public datasets (such as ENCODE, TCGA, GENCODE annotation dataset, etc.) as well as to combine them with private datasets (e.g., output from Affymetrix® DMETTM Platform).

了解参与药物代谢的基因的遗传变异可以减少药物不良反应,提高疗效,改善医疗保健结果和经济效益。许多高通量工具可用于已知与药物和外源代谢相关的单核苷酸多态性(snp)的基因分型。DMETTM平台是发现与常见和罕见疾病的疗效或毒性相关的生物标志物的snp面板的一个例子。由于DMETTM平台产生的大量信息难以分析,因此需要开发和实现用于统计和数据挖掘分析的算法和工具。这些软件可以有效地处理组学数据,以验证DMET测定确定的探索性snp,并将它们与药物疗效、毒性和/或癌症易感性联系起来。在这篇综述中,我们提出了一套用于预处理和分析dmet - snp数据的生物信息学框架。特别是,我们引入了一个使用基因组学查询语言的工作流程,这是一种专门为基因组学设计的高级查询语言,能够查询公共数据集(如ENCODE, TCGA, GENCODE注释数据集等),并将它们与私有数据集(例如,Affymetrix®DMETTM平台的输出)相结合。
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引用次数: 9
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