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Molecular role of miR-152-3p, miR-296-5p and miR-185-5p in urinary bladder cancer etiology miR-152-3p、miR-296-5p 和 miR-185-5p 在膀胱癌病因学中的分子作用
IF 0.5 Q4 GENETICS & HEREDITY Pub Date : 2024-10-28 DOI: 10.1016/j.humgen.2024.201353
Tariq Rahim , Summan Aslam , Aamir Sohail , Muhammad Jawad Khan
Bladder cancer is the tenth most common type of cancer worldwide. The lack of better diagnostic methods and effective treatments make it highly lethal. However, miRNAs are emerging as critical elements in diagnosing various diseases, especially cancers. Therefore, in the pursuit of improved diagnostic tools, this review aims to assess miRNAs interacting with their target genes in bladder cancer and evaluate the most significant miRNAs based on their molecular roles. After analyzing the literature and using several in-silico tools (e.g., miRWalk, miRDB, miRTarBase, TargetScan), we found that three miRNAs (miR-152-3p, miR-296-5p, miR-185-5p) out of a total of 1468 miRNAs were highly associated with bladder cancer, targeting three important genes: FGFR3, PTEN and PMF1. These three miRNAs may potentially serve as a panel for the diagnosis of bladder cancer after validation through extensive in-vitro and in-vivo studies. Moreover, these miRNAs could also be considered for therapeutic intervention against bladder cancer, following proper validation through in vivo studies.
膀胱癌是全球第十大常见癌症。由于缺乏更好的诊断方法和有效的治疗手段,膀胱癌的致死率非常高。然而,miRNAs 正在成为诊断各种疾病,尤其是癌症的关键因素。因此,为了寻求更好的诊断工具,本综述旨在评估膀胱癌中 miRNA 与其靶基因的相互作用,并根据其分子作用评估最重要的 miRNA。在分析了文献并使用了几种实验室工具(如 miRWalk、miRDB、miRTarBase、TargetScan)后,我们发现在总共 1468 个 miRNA 中,有三个 miRNA(miR-152-3p、miR-296-5p、miR-185-5p)与膀胱癌高度相关,它们靶向三个重要基因:FGFR3、PTEN 和 PMF1。经过大量体外和体内研究验证后,这三个 miRNA 有可能成为诊断膀胱癌的面板。此外,在通过体内研究进行适当验证后,这些 miRNA 也可考虑用于膀胱癌的治疗干预。
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引用次数: 0
Plasma expression and bioinformatic analysis of Mir-16, Mir-132, Mir-146 and Mir-223 in patients with rheumatoid arthritis 类风湿性关节炎患者血浆中 Mir-16、Mir-132、Mir-146 和 Mir-223 的表达及生物信息学分析
IF 0.5 Q4 GENETICS & HEREDITY Pub Date : 2024-10-28 DOI: 10.1016/j.humgen.2024.201352
Hala M. Raslan , Hanan Abd Elmawgoud Atia , Sherein Saeid Elshaer , Shaimaa M. Sabry , Yasmin Mosaad Mohammed , Khalda S. Amr

Background

MicroRNAs (miRNAs) are involved in the pathogenesis of rheumatoid arthritis (RA) through modulating gene expression.

Aim

To assess the plasma expression of miR-16, miR-132, miR-146 and miR-223 in patients with RA and their relation to activity and severity of the disease and their potential value as biomarkers. Through bioinformatics study we aimed to determine the predictor target genes of the studied miRNAs to clarify their role in RA pathogenesis.

Methods

The study comprised 73 patients suffering from RA and 50 healthy individuals. We used the disease activity score-28 (DAS-28) to assess disease activity. Joint damage was assessed by Kaarela and Kautiainen modification of Larsen scale. Anti-anticyclic citrullinated peptide (anti-CCP) antibodies, serum high sensitive C reactive protein (hsCRP) and rheumatoid factor (RF) were assayed by ELISA. Plasma miR-223, miR-146a, miR-16 and miR-132 were quantified by qRT-PCR followed by a simple dry laboratory analysis of the involved target genes of the studied miRNAs in RA pathogenesis by KEGG pathways.

Results

In comparison to controls, RA patients showed overexpressed miR-146a, miR-223and miR-16, while miR-132 was down-regulated. Additionally, miR-146a correlated positively with DAS28, anti-CCP antibodies and RF. Bioinformatics revealed that the predicted targeted genes of miR-146a, miR-16, miR-223 and miR-132 are potential contributing factors for RA pathogenesis and bone degradation.

Conclusion

miR-146a, miR-223, miR-16 and miR-132 may be potential non-invasive molecular biomarkers for RA diagnosis. Plasma miR-146a might be considered as potential biomarker for disease activity. The predicted genes targeted by miR-146a, miR-223, miR-16 and miR-132 are implicated in RA pathogenesis and ultimately can be used in future target therapeutic approach.
目的 评估 RA 患者血浆中 miR-16、miR-132、miR-146 和 miR-223 的表达及其与疾病活动和严重程度的关系,以及它们作为生物标记物的潜在价值。通过生物信息学研究,我们旨在确定所研究的 miRNA 的预测靶基因,以明确它们在 RA 发病机制中的作用。我们使用疾病活动度评分-28(DAS-28)来评估疾病活动度。关节损伤采用Kaarela和Kautiainen修改的Larsen量表进行评估。抗环瓜氨酸肽(anticyclic citrullinated peptide,anti-CCP)抗体、血清高敏C反应蛋白(hsCRP)和类风湿因子(rheumatoid factor,RF)通过酶联免疫吸附试验(ELISA)进行检测。结果与对照组相比,RA 患者的 miR-146a、miR-223 和 miR-16 表达过高,而 miR-132 则下调。此外,miR-146a与DAS28、抗CCP抗体和RF呈正相关。结论miR-146a、miR-223、miR-16和miR-132可能是诊断RA的潜在非侵入性分子生物标志物。血浆 miR-146a 可被视为疾病活动性的潜在生物标志物。miR-146a、miR-223、miR-16 和 miR-132 预测的靶基因与 RA 发病机制有关,最终可用于未来的靶向治疗方法。
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引用次数: 0
Impact of 5-HTTLPR of SLC6A4 on migraine susceptibility: A meta-analysis with trial sequential analysis SLC6A4的5-HTTLPR对偏头痛易感性的影响:带试验序列分析的荟萃分析
IF 0.5 Q4 GENETICS & HEREDITY Pub Date : 2024-10-24 DOI: 10.1016/j.humgen.2024.201347
Amrit Sudershan , Hardeep Kumar , Sandeepa Bailam , Rakesh K. Panjaliya , Parvinder Kumar

Background

Migraine disorder is a complicated condition for which a large number of genetic variants determine susceptibility. The 5-HTTLPR of the SLC6A4 gene is one of these genetic variations, and it is hypothesized that it plays a role in defining the susceptibility to the disease.

Aim

Therefore, through the utilization of the meta-analysis methodology, the current investigation aimed to determine whether or not there is an association between the 5-HTTLPR and the likelihood of developing migraines.

Method

The present study utilizes the PRISMA guideline to review existing literature from the electronic database to perform pooled analysis, and also includes quality assessment, association analysis, publication bias, and heterogeneity analysis using the NOS tool, OR with 95 % CI, tests of Begg's with Egger's test, and χ2 based on Cochran's Q Test with I2 tests respectively.

Result

Using a systematic literature review, we found 14 studies representing 2972 participants, with 1276 cases diagnosed with migraine and 1696 serving as controls. It was observed that after utilizing multiple genetic models only allele (1.14 [1.01–1.29], p-value = 0.025) and recessive model (1.24 [1.01–152], p-value = 0.03), in contrast to other genetic models were found to be significantly associated with overall migraine but not with MA and MWA.

Discussion & conclusion

In conclusion, according to the allele and recessive model, the current investigation revealed a statistically significant relationship between 5-HTTLPR and the likelihood of developing migraines.
背景偏头痛是一种复杂的疾病,由大量基因变异决定易感性。因此,通过使用荟萃分析方法,本研究旨在确定 5-HTTLPR 与患偏头痛的可能性之间是否存在关联。方法本研究利用 PRISMA 指南对电子数据库中的现有文献进行回顾,以进行汇总分析,还包括质量评估、关联分析、发表偏倚和异质性分析,分别使用 NOS 工具、OR 与 95 % CI、Begg's 与 Egger's 检验以及基于 Cochran's Q 检验与 I2 检验的 χ2 进行分析。结果我们发现,与其他遗传模型相比,只有等位基因模型(1.14 [1.01-1.29],p 值 = 0.025)和隐性模型(1.24 [1.01-152],p 值 = 0.03)与总体偏头痛显著相关,但与 MA 和 MWA 无关。
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引用次数: 0
Detection and validity of long non-coding RNAs HOST2, HOTAIR, HOXA-AS2, and MALAT1 as biomarkers for hepatocellular carcinoma 长非编码 RNA HOST2、HOTAIR、HOXA-AS2 和 MALAT1 作为肝细胞癌生物标志物的检测及其有效性
IF 0.5 Q4 GENETICS & HEREDITY Pub Date : 2024-10-20 DOI: 10.1016/j.humgen.2024.201349
Marwa Mohammed Ibrahim Mohammed Khalil , Randa Mohamed Seddik , Manal Monir Mansour , Hany Abdelbary Abdelaziz Elbasuony , Sara A. El Derbaly

Background

Hepatocellular carcinoma (HCC) is one of the most common cancers in the world. Long noncoding RNAs (lncRNAs) could contribute significantly to HCC development through diverse mechanisms, such as the recruitment of many regulatory protein complexes. This study aimed to evaluate the expression levels of the lncRNAs HOST2, HOTAIR, HOXA-AS2, and MALAT1 in liver cirrhosis and HCC and also assess their diagnostic performance as biomarkers for HCC.

Methods

In total, 180 participants were in this study, classified into three groups (60 participants in each): Group I (hepatocellular carcinoma patients), Group II (liver cirrhosis patients), and Group III (apparently healthy individuals). The expressions of the HOST2, HOTAIR, HOXA-AS2, and MALAT1 lncRNAs were detected using a reverse-transcriptase real-time polymerase chain reaction (qRT-PCR).

Results

The expression levels of HOST2, HOTAIR, HOXA-AS2, and MALAT1 lncRNAs were markedly increased in the HCC patients compared with those in the cirrhotic patients and controls. They also exhibited greater sensitivity as diagnostic biomarkers than alpha-fetoprotein.

Conclusions

The HOTAIR, HOST2, HOXA-AS2, and MALAT1 lncRNAs exhibit promising potential as valuable diagnostic biomarkers of HCC and in differentiating HCC from liver cirrhosis. Furthermore, combining alpha-fetoprotein can yield higher accuracy.
背景肝细胞癌(HCC)是世界上最常见的癌症之一。长非编码 RNA(lncRNA)可通过多种机制(如招募多种调控蛋白复合物)对 HCC 的发展做出重要贡献。本研究旨在评估lncRNAs HOST2、HOTAIR、HOXA-AS2和MALAT1在肝硬化和HCC中的表达水平,并评估它们作为HCC生物标志物的诊断性能:第一组(肝细胞癌患者)、第二组(肝硬化患者)和第三组(表面健康者)。结果与肝硬化患者和对照组相比,HCC 患者中 HOST2、HOTAIR、HOXA-AS2 和 MALAT1 lncRNAs 的表达水平明显升高。结论 HOTAIR、HOST2、HOXA-AS2 和 MALAT1 lncRNAs 具有作为有价值的 HCC 诊断生物标志物和区分 HCC 与肝硬化的潜力。此外,结合甲胎蛋白可提高准确性。
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引用次数: 0
Quantitative detection of miR-25 for early diagnosis, postoperative assessment and TNM staging of pancreatic cancer 定量检测 miR-25,用于胰腺癌的早期诊断、术后评估和 TNM 分期
IF 0.5 Q4 GENETICS & HEREDITY Pub Date : 2024-10-20 DOI: 10.1016/j.humgen.2024.201350
Xiao Xu , Xinju Zhang , Xuan Deng , Fuzhi Sheng , Guojun Cao , Deliang Fu , Ming Guan
Objectives: Pancreatic cancer is one of the most common malignant tumors of the digestive tract. Due to its strong concealment and rapid disease progress, it is characterized by high mortality and low cure rate. Current research focuses on screening high-risk populations, preventing the occurrence of pancreatic cancer and developing imaging technology and tumor markers for early diagnosis. This study aimed to investigate the absolute quantitative detection of microRNA-25 (miR-25) and reveal its quantitative changes in the treatment of pancreatic cancer. We compared serum miR-25 level between pancreatic cancer patients and other tumor patients, especially those with gastrointestinal cancer, to provide further evidence for early diagnosis, differential diagnosis and prognosis of pancreatic cancer. Methods: We collected serum samples from 51 pancreatic cancer patients (including 21 patients with preoperative and postoperative samples), 52 pancreatitis patients, 141 other tumor patients, and 50 healthy individuals from Huashan Hospital, Fudan University. The serum levels of miR-25, Carbohydrate Antigen 19–9 (CA19–9), Carbohydrate Antigen 125 (CA125) and Carcinoembryonic Antigen (CEA) in these populations were measured to analyze the value of miR-25 quantitative detection in the diagnosis, postoperative assessment and Tumor Node Metastasis (TNM) staging of pancreatic cancer. Results: Among the 51 pancreatic cancer patients, 50 cases (98.04 %) showed miR-25 levels above the threshold (3333 copies/μl), while all samples in normal group showed negative. The mean level of miR-25 in serum was 5707.45 ± 361.02 copies/μl. In other tumor groups, 21/141 (14.89 %) patients showed positive results and the mean miR-25 level was 847.09 ± 125.97 copies/μl. Comparing before and after operation in 21 paired samples, the level of miR-25 declined significantly after operation, with an average decline rate of 86.36 %. Conclusions: Serum miR-25 levels were significantly higher in pancreatic cancer patients compared to both normal and other tumor groups and decreased significantly after surgery. In addition, miR-25 showed higher sensitivity than common tumor markers (CA19–9, CA125, CEA) in early diagnosis of pancreatic cancer, and proved to be of significant value in evaluating the effect of surgical treatment.
目标:胰腺癌是消化道最常见的恶性肿瘤之一:胰腺癌是消化道最常见的恶性肿瘤之一。由于其隐蔽性强、病情进展快,具有死亡率高、治愈率低的特点。目前的研究重点是筛查高危人群,预防胰腺癌的发生,以及开发用于早期诊断的成像技术和肿瘤标志物。本研究旨在研究微RNA-25(miR-25)的绝对定量检测,并揭示其在胰腺癌治疗过程中的定量变化。我们比较了胰腺癌患者与其他肿瘤患者,尤其是胃肠道肿瘤患者的血清miR-25水平,为胰腺癌的早期诊断、鉴别诊断和预后提供进一步的证据。研究方法我们采集了复旦大学附属华山医院 51 名胰腺癌患者(包括 21 名术前和术后患者)、52 名胰腺炎患者、141 名其他肿瘤患者和 50 名健康人的血清样本。测定这些人群血清中的miR-25、碳水化合物抗原19-9(CA19-9)、碳水化合物抗原125(CA125)和癌胚抗原(CEA)水平,分析miR-25定量检测在胰腺癌诊断、术后评估和肿瘤结节转移(TNM)分期中的价值。结果在 51 例胰腺癌患者中,50 例(98.04%)的 miR-25 水平超过了阈值(3333 拷贝/μl),而正常组的所有样本均为阴性。血清中 miR-25 的平均水平为 5707.45 ± 361.02 拷贝/μl。在其他肿瘤组中,21/141(14.89%)例患者的结果为阳性,miR-25 的平均水平为 847.09 ± 125.97 拷贝/μl。对比 21 个配对样本的手术前后,手术后 miR-25 水平明显下降,平均下降率为 86.36%。结论与正常组和其他肿瘤组相比,胰腺癌患者血清中的miR-25水平明显升高,且术后明显下降。此外,在胰腺癌的早期诊断中,miR-25比常见的肿瘤标志物(CA19-9、CA125、CEA)具有更高的灵敏度,在评估手术治疗效果方面具有重要价值。
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引用次数: 0
Developmental validation of NeoTyper autosomal STR kit NeoTyper 常染色体 STR 套件的开发验证
IF 0.5 Q4 GENETICS & HEREDITY Pub Date : 2024-10-16 DOI: 10.1016/j.humgen.2024.201348
Sudhir Verma , Rajan Pal , Jagdish Kandpal , Ankit Singh Bhadauriya , Manas Pandey , Mitali Kushwaha , Shiv Mohan Singh , Supriya Singh
<div><h3>Background</h3><div>Short Tandem Repeats (STRs) are pivotal to efficient human DNA profiling. Including mini-STRs can further improve the assay's efficiency. The FBI's (Federal Bureau of Investigation) expanded Combined DNA Index System (CODIS) list contains twenty STRs for human identification. The NeoTyper Autosomal kit developed by Neom Scientific Solutions Pvt. Ltd. enables the amplification of 28 loci, which include markers from the expanded CODIS list, are National DNA Index System (NDIS) recommended markers, and comply with the NDIS recommended allelic range. In addition, the kit also includes 8 more markers including Penta D and Penta E. The NeoTyper Autosomal kit STR markers includes 14 mini-STR which makes it very effective for the human identification of the degraded samples like unidentified body remains.</div><div>This is a developmental validation study for NeoTyper, based on the listed Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines.</div></div><div><h3>Methodology</h3><div>We extracted the human genomic DNA from blood and FFPE (Formalin-Fixed Paraffin-Embedded) samples, and performed PCR amplification for the 28 loci using the developed kit, NeoTyper, which features a six-dye chemistry. The amplified products were run on 3500xL Genetic Analyzer. We used GeneMapper ID-X v.1.4 (Applied Biosystems) to analyse peak height and allele calling. Developmental validation parameters, including genetic characterization, analysis of sensitivity, female-male mixture, precision, and accuracy (repeatability and reproducibility), were investigated and analysed. Furthermore, intra- and inter-laboratory comparisons, as well as mini-STR analysis and validation were done.</div></div><div><h3>Results</h3><div>The developed NeoTyper Autosomal kit demonstrated 100 % sensitivity up to a DNA concentration of 62.5 pg, as measured by the number of alleles called. The assay also demonstrated good precision (measured in terms of standard deviation, SD ranging between 0.60 and 0.77) and reproducibility, with alleles called at 100 % accuracy. Furthermore, precision was high (measured as SD ranging from 0.50 to 0.66), with a 100 % accuracy. In 90.9 % of the samples (10 out of 11 female-male sample varied ratio), the mixture analysis revealed 100 % of the alleles being called. A comparative analysis of mini-STRs in GlobalFiler and NeoTyper Autosomal kit revealed a 100 % accuracy of the NeoTyper mini-STRs.</div></div><div><h3>Conclusion</h3><div>In conclusion, the NeoTyper Autosomal kit developed by Neom Scientific Solutions Pvt. Ltd. enables the amplification of 28 loci, which includes markers from expanded CODIS list; are NDIS accepted markers and comply with their recommended allelic range. The integration of mini-STRs in the kit demonstrates its efficacy and reliability, particularly when addressing the difficulties posed by degraded samples. This developmental validation study demonstrates consistent performance with high sensiti
背景短串联重复序列(STR)是高效进行人类 DNA 分析的关键。加入迷你 STR 可进一步提高检测效率。联邦调查局(FBI)的扩展 DNA 索引系统(CODIS)列表中包含二十种用于人类鉴定的 STR。Neom Scientific Solutions Pvt. Ltd. 开发的 NeoTyper 常染色体试剂盒可扩增 28 个位点,其中包括 CODIS 扩展列表中的标记,这些标记是国家 DNA 索引系统(NDIS)推荐的标记,并符合 NDIS 推荐的等位基因范围。此外,该试剂盒还包括 Penta D 和 Penta E 等 8 个标记。NeoTyper 常染色体试剂盒的 STR 标记包括 14 个迷你 STR,这使得它在对退化样本(如身份不明的遗体)进行人体识别时非常有效。我们从血液和 FFPE(福尔马林固定石蜡包埋)样本中提取了人类基因组 DNA,并使用开发的试剂盒 NeoTyper 对 28 个位点进行了 PCR 扩增。扩增产物在 3500xL 基因分析仪上运行。我们使用 GeneMapper ID-X v.1.4 (Applied Biosystems) 分析峰高和等位基因调用。我们调查并分析了开发验证参数,包括遗传特征、灵敏度分析、雌雄混合物、精确度和准确度(重复性和再现性)。结果所开发的 NeoTyper 常染色体试剂盒的灵敏度高达 100%,DNA 浓度为 62.5 pg 时的灵敏度为 100%,以等位基因的调用数量来衡量。该检测方法还表现出良好的精确度(以标准偏差衡量,SD 介于 0.60 和 0.77 之间)和可重复性,等位基因的准确率为 100%。此外,精确度也很高(以标准差衡量,范围在 0.50 至 0.66 之间),准确率为 100%。在 90.9% 的样本中(11 个不同比例的雌雄样本中的 10 个),混合物分析显示 100% 的等位基因被识别。总之,Neom Scientific Solutions Pvt. Ltd. 开发的 NeoTyper 常染色体试剂盒可扩增 28 个位点,其中包括 CODIS 扩展列表中的标记;这些标记是 NDIS 认可的标记,并符合其推荐的等位基因范围。试剂盒中集成的迷你 STR 证明了它的有效性和可靠性,尤其是在解决降解样本带来的困难时。这项开发验证研究表明,该试剂盒具有高灵敏度、高精确度和高准确度(可重复性和再现性)的一贯性能,表明它是一种先进、高效的人体识别系统。
{"title":"Developmental validation of NeoTyper autosomal STR kit","authors":"Sudhir Verma ,&nbsp;Rajan Pal ,&nbsp;Jagdish Kandpal ,&nbsp;Ankit Singh Bhadauriya ,&nbsp;Manas Pandey ,&nbsp;Mitali Kushwaha ,&nbsp;Shiv Mohan Singh ,&nbsp;Supriya Singh","doi":"10.1016/j.humgen.2024.201348","DOIUrl":"10.1016/j.humgen.2024.201348","url":null,"abstract":"&lt;div&gt;&lt;h3&gt;Background&lt;/h3&gt;&lt;div&gt;Short Tandem Repeats (STRs) are pivotal to efficient human DNA profiling. Including mini-STRs can further improve the assay's efficiency. The FBI's (Federal Bureau of Investigation) expanded Combined DNA Index System (CODIS) list contains twenty STRs for human identification. The NeoTyper Autosomal kit developed by Neom Scientific Solutions Pvt. Ltd. enables the amplification of 28 loci, which include markers from the expanded CODIS list, are National DNA Index System (NDIS) recommended markers, and comply with the NDIS recommended allelic range. In addition, the kit also includes 8 more markers including Penta D and Penta E. The NeoTyper Autosomal kit STR markers includes 14 mini-STR which makes it very effective for the human identification of the degraded samples like unidentified body remains.&lt;/div&gt;&lt;div&gt;This is a developmental validation study for NeoTyper, based on the listed Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines.&lt;/div&gt;&lt;/div&gt;&lt;div&gt;&lt;h3&gt;Methodology&lt;/h3&gt;&lt;div&gt;We extracted the human genomic DNA from blood and FFPE (Formalin-Fixed Paraffin-Embedded) samples, and performed PCR amplification for the 28 loci using the developed kit, NeoTyper, which features a six-dye chemistry. The amplified products were run on 3500xL Genetic Analyzer. We used GeneMapper ID-X v.1.4 (Applied Biosystems) to analyse peak height and allele calling. Developmental validation parameters, including genetic characterization, analysis of sensitivity, female-male mixture, precision, and accuracy (repeatability and reproducibility), were investigated and analysed. Furthermore, intra- and inter-laboratory comparisons, as well as mini-STR analysis and validation were done.&lt;/div&gt;&lt;/div&gt;&lt;div&gt;&lt;h3&gt;Results&lt;/h3&gt;&lt;div&gt;The developed NeoTyper Autosomal kit demonstrated 100 % sensitivity up to a DNA concentration of 62.5 pg, as measured by the number of alleles called. The assay also demonstrated good precision (measured in terms of standard deviation, SD ranging between 0.60 and 0.77) and reproducibility, with alleles called at 100 % accuracy. Furthermore, precision was high (measured as SD ranging from 0.50 to 0.66), with a 100 % accuracy. In 90.9 % of the samples (10 out of 11 female-male sample varied ratio), the mixture analysis revealed 100 % of the alleles being called. A comparative analysis of mini-STRs in GlobalFiler and NeoTyper Autosomal kit revealed a 100 % accuracy of the NeoTyper mini-STRs.&lt;/div&gt;&lt;/div&gt;&lt;div&gt;&lt;h3&gt;Conclusion&lt;/h3&gt;&lt;div&gt;In conclusion, the NeoTyper Autosomal kit developed by Neom Scientific Solutions Pvt. Ltd. enables the amplification of 28 loci, which includes markers from expanded CODIS list; are NDIS accepted markers and comply with their recommended allelic range. The integration of mini-STRs in the kit demonstrates its efficacy and reliability, particularly when addressing the difficulties posed by degraded samples. This developmental validation study demonstrates consistent performance with high sensiti","PeriodicalId":29686,"journal":{"name":"Human Gene","volume":"42 ","pages":"Article 201348"},"PeriodicalIF":0.5,"publicationDate":"2024-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142536241","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Unravelling the protective effects of peptide isolated from marine sponge extract MS01 against SH-SY5Y cell line and its in-silico pharmacokinetic analysis 揭示从海洋海绵提取物 MS01 中分离出的多肽对 SH-SY5Y 细胞株的保护作用及其体内药代动力学分析
IF 0.5 Q4 GENETICS & HEREDITY Pub Date : 2024-10-15 DOI: 10.1016/j.humgen.2024.201345
G.B. Priyadharshini, C. Jaynthy
Parkinson's disease (PD) is characterised by developing postural instability, resting seizures, tremors, and a movement problem coupled with stiffness. All the available drugs can improve motor function considerably, but they can also have negative side effects, especially if the problem gets worse. The structure-activity relation was performed in the DISCOVERY STUDIO V2.5.5 pharmacophore model using the HypoGen algorithm for a training set of 15 compounds. Here, xenin peptide fits well with a least cost difference and a fit value of 10.46, indicating a favourable pharmacological characteristic. Therefore, we tried applying gene network analysis in cytoHubba to find the hub gene for PD in Danio rerio and Homo sapiens, as zebrafish and humans share many disease proteins and processes. Molecular docking studies for the hub gene polyubiquitin B from Danio rerio and Parkin from Homo sapiens, as well as the peptide xenin obtained from the marine sponge extract MS01 was performed. The peptide exhibits a substantial binding affinity with the receptor UBB through 8 and PRKN through 4 intermolecular hydrogen bonds in their bonded and non-bonded interactions, although it has little effect on the protein structure, according to simulation studies and dynamical free energy calculations. The protein structure has also been stabilised in terms of energy, secondary structure, and flexibility by the peptide binding. In addition to in-silico analysis the extract was tested in-vitro on SH-SY5Y cells for its effectiveness against ROS and cell viability, which proved its qualitative effect.
帕金森病(Parkinson's disease,PD)的特征是姿势不稳、静止性癫痫发作、震颤、运动障碍和僵硬。现有的所有药物都能显著改善运动功能,但也会产生负面副作用,尤其是当问题恶化时。我们在 DISCOVERY STUDIO V2.5.5 药效模型中使用 HypoGen 算法对 15 种化合物的训练集进行了结构-活性关系分析。其中,xenin 肽的拟合度较好,成本差异最小,拟合值为 10.46,表明其具有良好的药理特性。由于斑马鱼和人类有许多共同的疾病蛋白和过程,因此我们尝试在 cytoHubba 中应用基因网络分析来寻找斑马鱼和智人中枢基因。研究人员对斑马鱼和智人的枢纽基因多泛素 B 以及从海洋海绵提取物 MS01 中获得的多肽 xenin 进行了分子对接研究。根据模拟研究和动态自由能计算,该多肽通过 8 个分子间氢键和 4 个分子间氢键与受体 UBB 和 PRKN 的成键和非成键相互作用表现出很强的结合亲和力,但对蛋白质结构的影响很小。多肽结合还使蛋白质结构在能量、二级结构和灵活性方面更加稳定。除了室内分析外,还在 SH-SY5Y 细胞上对提取物进行了体外测试,以检测其抗 ROS 的效果和细胞活力,结果证明了其质量效果。
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引用次数: 0
Identification of potential microRNAs involved in pathogenesis of venous thromboembolism (VTE): A meta analysis 鉴定参与静脉血栓栓塞症(VTE)发病机制的潜在 microRNA:荟萃分析
IF 0.5 Q4 GENETICS & HEREDITY Pub Date : 2024-10-11 DOI: 10.1016/j.humgen.2024.201346
Sunanda Arya, Rashi Khare, Iti Garg, Swati Srivastava

Objective

MicroRNAs (MiRNAs) are master regulators of gene expression and have been suggested as potential diagnostic and therapeutic biomarkers in variety of complex diseases. Venous thromboembolism is a major cause of morbidity and mortality worldwide. Several miRNA expression studies have been conducted to identify miRNAs linked to VTE prognosis. These studies reveal that various miRNAs are significantly up-regulated and down-regulated in VTE patients in comparison to healthy controls. Present meta-analysis deliberate findings of such studies to identify most potential miRNA targets associated with VTE.

Methodology

Comprehensive literature review on Pubmed was conducted. Present analysis assessed 20 research article out of a total of 383 articles screened, based on inclusion and exclusion criteria. The up-regulated and down-regulated miRNAs obtained from selected research articles were subjected to meta-analysis. The differentially expressed miRNAs so obtained and were used for further bioinformatic analysis, including gene ontology and pathway analysis of their target genes, to study their potential involvement in VTE pathogenesis.

Results

Twenty articles selected for meta-analysis included a total of 808 patients. These included 26 up-regulated miRNAs and 11 down-regulated miRNAs. The meta-analysis based on Odds ratio suggested that one up-regulated miRNA (hsa-miR-1233-3p) and two down-regulated miRNAs (hsa-miR-103a-3p and hsa-miR-200c) returned significantly higher Odds compared to other miRNAs. Further bioinformatics analysis of their target genes revealed that these miRNAs target a large number of genes involved in cell adhesion, cell migration, endothelial activation and inflammation genes.

Conclusions

Three miRNAs, viz.; hsa-miR-1233-3p, hsa-miR-103a-3p and hsa-miR-200c may play a crucial role in VTE pathogenesis and has potential to serve as reliable diagnostic or therapeutic biomarkers for VTE.
目的微小核糖核酸(MiRNA)是基因表达的主要调控因子,被认为是各种复杂疾病的潜在诊断和治疗生物标志物。静脉血栓栓塞症是全球发病率和死亡率的主要原因。目前已开展了多项 miRNA 表达研究,以确定与 VTE 预后有关的 miRNA。这些研究显示,与健康对照组相比,VTE 患者体内的各种 miRNAs 有明显的上调和下调。本荟萃分析对这些研究结果进行了审议,以确定与 VTE 相关的大多数潜在 miRNA 靶点。根据纳入和排除标准,本分析从总共筛选出的 383 篇文章中评估了 20 篇研究文章。对所选研究文章中上调和下调的 miRNA 进行荟萃分析。获得的差异表达 miRNA 用于进一步的生物信息学分析,包括对其靶基因进行基因本体和通路分析,以研究它们在 VTE 发病机制中的潜在参与。其中包括 26 个上调的 miRNA 和 11 个下调的 miRNA。基于Odds比的荟萃分析表明,与其他miRNA相比,一个上调的miRNA(hsa-miR-1233-3p)和两个下调的miRNA(hsa-miR-103a-3p和hsa-miR-200c)的Odds比明显较高。结论三种 miRNA,即 hsa-miR-1233-3p、hsa-miR-103a-3p 和 hsa-miR-200c 可能在 VTE 发病机制中发挥关键作用,并有可能成为 VTE 的可靠诊断或治疗生物标志物。
{"title":"Identification of potential microRNAs involved in pathogenesis of venous thromboembolism (VTE): A meta analysis","authors":"Sunanda Arya,&nbsp;Rashi Khare,&nbsp;Iti Garg,&nbsp;Swati Srivastava","doi":"10.1016/j.humgen.2024.201346","DOIUrl":"10.1016/j.humgen.2024.201346","url":null,"abstract":"<div><h3>Objective</h3><div>MicroRNAs (MiRNAs) are master regulators of gene expression and have been suggested as potential diagnostic and therapeutic biomarkers in variety of complex diseases. Venous thromboembolism is a major cause of morbidity and mortality worldwide. Several miRNA expression studies have been conducted to identify miRNAs linked to VTE prognosis. These studies reveal that various miRNAs are significantly up-regulated and down-regulated in VTE patients in comparison to healthy controls. Present meta-analysis deliberate findings of such studies to identify most potential miRNA targets associated with VTE.</div></div><div><h3>Methodology</h3><div>Comprehensive literature review on Pubmed was conducted. Present analysis assessed 20 research article out of a total of 383 articles screened, based on inclusion and exclusion criteria. The up-regulated and down-regulated miRNAs obtained from selected research articles were subjected to meta-analysis. The differentially expressed miRNAs so obtained and were used for further bioinformatic analysis, including gene ontology and pathway analysis of their target genes, to study their potential involvement in VTE pathogenesis.</div></div><div><h3>Results</h3><div>Twenty articles selected for meta-analysis included a total of 808 patients. These included 26 up-regulated miRNAs and 11 down-regulated miRNAs. The meta-analysis based on Odds ratio suggested that one up-regulated miRNA (hsa-miR-1233-3p) and two down-regulated miRNAs (hsa-miR-103a-3p and hsa-miR-200c) returned significantly higher Odds compared to other miRNAs. Further bioinformatics analysis of their target genes revealed that these miRNAs target a large number of genes involved in cell adhesion, cell migration, endothelial activation and inflammation genes.</div></div><div><h3>Conclusions</h3><div>Three miRNAs, viz.; hsa-miR-1233-3p, hsa-miR-103a-3p and hsa-miR-200c may play a crucial role in VTE pathogenesis and has potential to serve as reliable diagnostic or therapeutic biomarkers for VTE.</div></div>","PeriodicalId":29686,"journal":{"name":"Human Gene","volume":"42 ","pages":"Article 201346"},"PeriodicalIF":0.5,"publicationDate":"2024-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142441005","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Validation of gene polymorphisms (rs2682818 and rs2043556) in has-miR-618 and has-miR-605 with the breast cancer susceptibility has-miR-618和has-miR-605基因多态性(rs2682818和rs2043556)与乳腺癌易感性的验证
IF 0.5 Q4 GENETICS & HEREDITY Pub Date : 2024-10-09 DOI: 10.1016/j.humgen.2024.201343
Arvin Hassani, Saeid Ghorbian

Background

Breast cancer (BC) is one of the most frequent types of cancer and the second leading cause of cancer-affiliate death among ladies. BC is a heterogeneous sickness that is impacted by environment and genetic elements. Diagnosis in the early stages impacts treatment and patient survival rate. miRNA can play a vital role in BC's early stages of tumorigenesis. Single nucleotide polymorphism (SNP) can cause changes in miRNA expression and function, which are related to the risk of several cancers.

Aim

The goal of this examination is to assess the affiliation among two has-miR-605 (rs2043556A > G) and has-miR-618 (rs2682818 C > A) gene polymorphisms with the risk of BC in the Iranian ladies.

Methods

Our case-control examination assessed two hundred whole blood samples of one hundred ladies with BC and one hundred healthy ladies. Hence, to assess the connection between the presence of SNP miRNA genes and the risk of BC, genotyping was done by the usage of the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method, then the usage of the Chi-square test of SPSS software statistically analyzed the acquired result.

Results

Our findings confirmed a statistically substantial distinction within the genotype frequency of the has-miR-618 gene polymorphism among the groups (P = 0.043), whereas no statistically substantial distinction inside the genotype frequency of the has-miR-605 gene polymorphism among the control and case (P = 0.183). In addition, the allelic frequency of two polymorphisms, (rs2043556 A > G) G allele (OR = 2.163, CI 95 % = 1.56–2.988, P = 0.022) and (rs2682818 C > A) A allele (OR = 3.997, CI 95 % = 1.584–10.081, P = 0.002) substantially enhance the risk of BC.

Conclusion

The results show that the G allele of rs2043556 and the A allele of rs2682818 increase the risk of BC in the women population of East Azerbaijan province.
背景乳腺癌(BC)是最常见的癌症类型之一,也是女性死于癌症的第二大原因。乳腺癌是一种受环境和遗传因素影响的异质性疾病。miRNA 在 BC 肿瘤发生的早期阶段起着至关重要的作用。单核苷酸多态性(SNP)可导致 miRNA 表达和功能的改变,而 miRNA 表达和功能的改变与多种癌症的风险有关。方法我们的病例对照研究评估了 100 名 BC 患者和 100 名健康女性的 200 份全血样本。因此,为了评估 SNP miRNA 基因的存在与 BC 风险之间的联系,我们使用聚合酶链式反应-限制性片段长度多态性(PCR-RFLP)方法进行了基因分型,然后使用 SPSS 软件的卡方检验对所得结果进行了统计分析。结果我们的研究结果证实,组间 has-miR-618 基因多态性的基因型频率存在统计学意义上的显著差异(P = 0.043),而对照组和病例组间 has-miR-605 基因多态性的基因型频率没有统计学意义上的显著差异(P = 0.183)。此外,两个多态性的等位基因频率,(rs2043556 A > G)G 等位基因(OR = 2.163,CI 95 % = 1.56-2.988,P = 0.022)和(rs2682818 C > A)A 等位基因(OR = 3.997,CI 95 % = 1.584-10.081,P = 0.结果表明,rs2043556 的 G 等位基因和 rs2682818 的 A 等位基因会增加东阿塞拜疆省妇女患 BC 的风险。
{"title":"Validation of gene polymorphisms (rs2682818 and rs2043556) in has-miR-618 and has-miR-605 with the breast cancer susceptibility","authors":"Arvin Hassani,&nbsp;Saeid Ghorbian","doi":"10.1016/j.humgen.2024.201343","DOIUrl":"10.1016/j.humgen.2024.201343","url":null,"abstract":"<div><h3>Background</h3><div>Breast cancer (BC) is one of the most frequent types of cancer and the second leading cause of cancer-affiliate death among ladies. BC is a heterogeneous sickness that is impacted by environment and genetic elements. Diagnosis in the early stages impacts treatment and patient survival rate. miRNA can play a vital role in BC's early stages of tumorigenesis. Single nucleotide polymorphism (SNP) can cause changes in miRNA expression and function, which are related to the risk of several cancers.</div></div><div><h3>Aim</h3><div>The goal of this examination is to assess the affiliation among two has-miR-605 (rs2043556A &gt; G) and has-miR-618 (rs2682818 C &gt; A) gene polymorphisms with the risk of BC in the Iranian ladies.</div></div><div><h3>Methods</h3><div>Our case-control examination assessed two hundred whole blood samples of one hundred ladies with BC and one hundred healthy ladies. Hence, to assess the connection between the presence of SNP miRNA genes and the risk of BC, genotyping was done by the usage of the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method, then the usage of the <em>Chi-square test</em> of SPSS software statistically analyzed the acquired result.</div></div><div><h3>Results</h3><div>Our findings confirmed a statistically substantial distinction within the genotype frequency of the has-miR-618 gene polymorphism among the groups (<em>P</em> = 0.043), whereas no statistically substantial distinction inside the genotype frequency of the has-miR-605 gene polymorphism among the control and case (<em>P</em> = 0.183). In addition, the allelic frequency of two polymorphisms, (rs2043556 A &gt; G) G allele (OR = 2.163, CI 95 % = 1.56–2.988, <em>P</em> = 0.022) and (rs2682818 C &gt; A) A allele (OR = 3.997, CI 95 % = 1.584–10.081, <em>P</em> = 0.002) substantially enhance the risk of BC.</div></div><div><h3>Conclusion</h3><div>The results show that the G allele of rs2043556 and the A allele of rs2682818 increase the risk of BC in the women population of East Azerbaijan province.</div></div>","PeriodicalId":29686,"journal":{"name":"Human Gene","volume":"42 ","pages":"Article 201343"},"PeriodicalIF":0.5,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142441008","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Investigate the association between genetic polymorphisms of ACE and ACE-2 with some biomarkers in Iraqi patients with COVID-19. 调查伊拉克 COVID-19 患者中 ACE 和 ACE-2 基因多态性与某些生物标志物之间的关联。
IF 0.5 Q4 GENETICS & HEREDITY Pub Date : 2024-10-04 DOI: 10.1016/j.humgen.2024.201344
Ali H. Mahmood , Salwa J. Al-Awadi , Marwa M. Al-Attar , Rusul A.A. Alshammary , Riam Sabah Abood

Background

The angiotensin-converting enzyme 2 (ACE2) receptor plays a critical role in mediating SARS-CoV-2 infection. Understanding the genetic factors influencing COVID-19 severity is crucial for developing effective treatment strategies. This study aimed to investigate the association between genetic polymorphism of the ACE gene, specifically the insertion/deletion (I/D) polymorphism in the promoter region, and clinical parameters in COVID-19 patients.

Methods

A case-control study was conducted with 225 participants from an Iraqi population. Blood samples were collected for hematological analysis and ACE genotyping. The association between ACE genotypes (DD, ID, II), demographic factors, and clinical parameters, including D-dimer, ferritin, lactate dehydrogenase (LDH), C-reactive protein (CRP), white blood cell (WBC) count, lymphocyte count, packed cell volume (PCV), red blood cell (RBC) count, hemoglobin (HB), and platelet count, was assessed.

Results

COVID-19 patients exhibited significant differences compared to controls regarding D-dimer, ferritin, LDH, CRP, WBC, lymphocytes, PCV, and RBC (P < 0.05), while no significant differences were found for HB and platelet counts. The DD genotype was predominant (43.11 %), followed by ID (39.56 %) and II (17.33 %). Notably, a significant association was observed between D-dimer levels and ACE genotype (P < 0.0001), with higher levels observed in individuals with the DD genotype. Additionally, a significant correlation was found between ACE genotype and sex (P = 0.0163). No significant association was observed between genotype and ICU admission or lung CT severity.

Conclusion

Our findings suggest a potential link between the ACE D/D genotype and elevated D-dimer levels in COVID-19 patients, indicating a potential role for ACE gene polymorphism in influencing disease severity. Further research is warranted to elucidate the underlying mechanisms and explore the potential for personalized treatment approaches based on ACE genotype.
背景血管紧张素转换酶 2(ACE2)受体在介导 SARS-CoV-2 感染中起着关键作用。了解影响 COVID-19 严重程度的遗传因素对于制定有效的治疗策略至关重要。本研究旨在调查 ACE 基因的遗传多态性(特别是启动子区域的插入/缺失 (I/D) 多态性)与 COVID-19 患者临床参数之间的关联。采集了血液样本进行血液学分析和 ACE 基因分型。评估了 ACE 基因型(DD、ID、II)、人口统计学因素和临床参数(包括 D-二聚体、铁蛋白、乳酸脱氢酶 (LDH)、C 反应蛋白 (CRP)、白细胞 (WBC) 计数、淋巴细胞计数、包装细胞体积 (PCV)、红细胞 (RBC) 计数、血红蛋白 (HB) 和血小板计数)之间的关联。结果COVID-19 患者的 D-二聚体、铁蛋白、LDH、CRP、白细胞、淋巴细胞、PCV 和 RBC 与对照组相比有显著差异(P < 0.05),而 HB 和血小板计数无显著差异。基因型以 DD 型为主(43.11%),其次是 ID 型(39.56%)和 II 型(17.33%)。值得注意的是,D-二聚体水平与 ACE 基因型之间存在明显的相关性(P < 0.0001),DD 基因型的个体D-二聚体水平更高。此外,还发现 ACE 基因型与性别之间存在明显的相关性(P = 0.0163)。结论我们的研究结果表明,COVID-19 患者的 ACE D/D 基因型与 D-二聚体水平升高之间存在潜在联系,这表明 ACE 基因多态性在影响疾病严重程度方面发挥着潜在作用。有必要开展进一步研究,以阐明其潜在机制,并探索基于 ACE 基因型的个性化治疗方法的潜力。
{"title":"Investigate the association between genetic polymorphisms of ACE and ACE-2 with some biomarkers in Iraqi patients with COVID-19.","authors":"Ali H. Mahmood ,&nbsp;Salwa J. Al-Awadi ,&nbsp;Marwa M. Al-Attar ,&nbsp;Rusul A.A. Alshammary ,&nbsp;Riam Sabah Abood","doi":"10.1016/j.humgen.2024.201344","DOIUrl":"10.1016/j.humgen.2024.201344","url":null,"abstract":"<div><h3>Background</h3><div>The angiotensin-converting enzyme 2 (ACE2) receptor plays a critical role in mediating SARS-CoV-2 infection. Understanding the genetic factors influencing COVID-19 severity is crucial for developing effective treatment strategies. This study aimed to investigate the association between genetic polymorphism of the <em>ACE</em> gene, specifically the insertion/deletion (I/D) polymorphism in the promoter region, and clinical parameters in COVID-19 patients.</div></div><div><h3>Methods</h3><div>A case-control study was conducted with 225 participants from an Iraqi population. Blood samples were collected for hematological analysis and <em>ACE</em> genotyping. The association between <em>ACE</em> genotypes (DD, ID, II), demographic factors, and clinical parameters, including D-dimer, ferritin, lactate dehydrogenase (LDH), C-reactive protein (CRP), white blood cell (WBC) count, lymphocyte count, packed cell volume (PCV), red blood cell (RBC) count, hemoglobin (HB), and platelet count, was assessed.</div></div><div><h3>Results</h3><div>COVID-19 patients exhibited significant differences compared to controls regarding D-dimer, ferritin, LDH, CRP, WBC, lymphocytes, PCV, and RBC (<em>P</em> &lt; 0.05), while no significant differences were found for HB and platelet counts. The DD genotype was predominant (43.11 %), followed by ID (39.56 %) and II (17.33 %). Notably, a significant association was observed between D-dimer levels and ACE genotype (<em>P</em> &lt; 0.0001), with higher levels observed in individuals with the DD genotype. Additionally, a significant correlation was found between ACE genotype and sex (<em>P</em> = 0.0163). No significant association was observed between genotype and ICU admission or lung CT severity.</div></div><div><h3>Conclusion</h3><div>Our findings suggest a potential link between the <em>ACE</em> D/D genotype and elevated D-dimer levels in COVID-19 patients, indicating a potential role for <em>ACE</em> gene polymorphism in influencing disease severity. Further research is warranted to elucidate the underlying mechanisms and explore the potential for personalized treatment approaches based on <em>ACE</em> genotype.</div></div>","PeriodicalId":29686,"journal":{"name":"Human Gene","volume":"42 ","pages":"Article 201344"},"PeriodicalIF":0.5,"publicationDate":"2024-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142418246","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
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Human Gene
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