Next-Generation Sequencing (NGS)

下一代测序 ( NGS )
  • 文章类型: Case Reports
    背景:带状疱疹是一种由水痘带状疱疹病毒(VZV)重新激活引起的感染性皮肤病,在脊髓后根神经节或颅神经节中潜伏了很长时间。带状疱疹引起的神经系统并发症包括无菌性脑膜炎,白质疾病,外周运动神经病,和格林-巴利综合征.然而,由VZV引起的单侧出汗减少是非常罕见的。
    方法:本文报道一例34岁女性因咽喉痛入院,头晕,减少了左侧身体的出汗.体格检查发现左侧上唇和左侧外耳道有疱疹病变(结痂),身体左侧出汗减少。增强的头部磁共振成像(MRI)未见异常。腰椎穿刺后,患者被VZV感染诊断为病毒性脑膜炎.肌电图皮肤交感神经反射提示左侧交感神经损伤。
    结论:继发性单侧出汗减少是带状疱疹的一种罕见神经系统并发症,对自主神经系统造成的损害.文献回顾和综合检查表明,单侧出汗减少是由于自主神经节内潜伏性带状疱疹病毒的激活,损害了自主神经系统。对于出现急性半身汗液减少的患者,医生应考虑带状疱疹引起的继发性自主神经系统损害的可能性。
    BACKGROUND: Herpes zoster is an infectious skin disease caused by the reactivation of the varicella zoster virus (VZV), which has been latent in the posterior root ganglia of the spinal cord or cranial ganglia for an extended period. Neurological complications caused by herpes zoster include aseptic meningitis, white matter disease, peripheral motor neuropathy, and Guillain-Barré syndrome. However, reduced unilateral sweating caused by the VZV is very rare.
    METHODS: This article reports the case of a 34-year-old woman who was admitted to our hospital with sore throat, dizziness, and reduced sweating on the left side of her body. Physical examination found herpes lesions on the left upper lip and left external ear canal (scabbed) and reduced sweating on the left side of the body. Head magnetic resonance imaging (MRI) with contrast showed no abnormalities. After a lumbar puncture, the patient was diagnosed with viral meningitis by VZV infection. The electromyographic skin sympathetic reflex indicated damage to the left sympathetic nerve.
    CONCLUSIONS: Secondary unilateral sweating reduction is a rare neurological complication of herpes zoster, caused by damage to the autonomic nervous system. Literature review and comprehensive examination indicated that the reduced unilateral sweating was due to the activation of latent herpes zoster virus in the autonomic ganglia which has damaged the autonomic nervous system. For patients who exhibit acute hemibody sweat reduction, doctors should consider the possibility of secondary autonomic nervous system damage caused by herpes zoster.
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  • 文章类型: Case Reports
    诺卡氏菌病是一种机会性感染,这种情况很少发生,主要发生在免疫缺陷患者中。即使病人有免疫能力,它仍然可能危及生命。此病例报告描述了一位先前健康的78岁男性农民,在计算机断层扫描中发现了肺部病变。结合患者的发热史和与炎症相关的实验室标志物升高的结果,病人被诊断为肺部感染。在逐步增加经验性广谱抗生素之后,抗病毒和抗真菌治疗,患者继续恶化为感染性休克。同时,病人的痰液反复培养,未发现明显的病原菌阳性。考虑到患者是老年人,这些病变是坚实的,有毛刺迹象,以及抗菌治疗后的进展,鉴别诊断中也考虑了癌症.人工智能(YITU,杭州一图医疗科技有限公司)也被申请,它还计算出这些病变是癌性的。患者接受了最大肺部病变的穿刺活检。在穿刺过程中,脓液从最大的肺部病变中取出。在脓液上进行的培养和宏基因组下一代测序(mNGS)检测表明诺卡氏菌。mNGS的测试报告还附有该诺卡氏菌属的常用临床抗生素的敏感性报告。使用这个结果,选择靶向药物复方磺胺甲恶唑和静脉注射美罗培南治疗后,患者病情迅速得到控制。鉴于诺卡氏菌的误诊率高,培养敏感性差。,该病例强调mNGS在诺卡氏菌属的诊断和选择有效的抗生素治疗中起关键作用。肺部感染。
    Nocardia disease is an opportunistic infection, the occurrence is rare and mostly occurs in patients with immune deficiency. Even if the patient is immunocompetent, it can still be life-threatening. This case report describes a previously healthy 78-year-old male farmer with lung lesions discovered on a computerized tomography scan. Combined with the patient\'s history of fever and the results of elevated laboratory markers associated with inflammation, the patient was diagnosed with a lung infection. After escalating empirical broad-spectrum antibiotics, antiviral and antifungal therapy, the patient continued to deteriorate to septic shock. In the meanwhile, the patient\'s sputum was cultured repeatedly, and no obvious positive pathogenic bacteria were found. Considering the patient was elderly and that these lesions were solid with burr signs, as well as the progression after antimicrobial therapy cancer was considered in the differential diagnosis. Artificial intelligence (YITU, Hangzhou Yitu Medical Technology Limited Company) was also applied, and it also calculated that these lesions were cancerous. The patient received a puncture biopsy of the largest lung lesion. During the puncture pus was withdrawn from largest lung lesion. Culture and metagenome next-generation sequencing (mNGS) detection performed on pus indicated Nocardia otitidiscaviarum. The test report of the mNGS is also attached with a susceptibility report of commonly used clinical antibiotics to this Nocardia spp. Using this result, the patient\'s disease was quickly controlled after selecting the targeted drug compound sulfamethoxazole and intravenous meropenem for treatment. In view of the high misdiagnosis rate and poor sensitivity of culture for Nocardia spp., this case emphasized mNGS playing a key role in the diagnosis and selection of effective antibiotics for the treatment of Nocardia spp. lung infections.
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  • 文章类型: Case Reports
    肺部非典型类癌(AC)是一种极为罕见的神经内分泌肿瘤。神经营养原肌球蛋白受体激酶(NTRK)融合仅在0.5%的非小细胞肺癌中报道,并且在AC中更为罕见,只有一例先前报告的病例。目前,对于晚期病例的最佳治疗策略和预后,目前尚无确凿的证据.我们介绍了一名完全切除后转移性AC的女性患者。由于在这种情况下生长抑素受体的低表达,生长抑素类似物和肽受体放射性核素治疗不可用。在寻求其他替代疗法之后,包括化疗(即,卡铂,依托泊苷,卡培他滨,替莫唑胺,和紫杉醇),依维莫司,和阿妥珠单抗,她带着显著的进步回来了,包括无数的皮下结节,左胸膜转移,多发性骨转移,和脑转移。新的活检分析显示ETV6-NTRK2融合。她立即以600mgq.d的剂量给予第一代原肌球蛋白受体激酶抑制剂entrectinib。随后一个月的治疗导致所有转移性肺病变完全缓解。迄今为止,从开始服用恩曲替尼起,她至少1年持续获益.这里,我们介绍了第一例女性转移性AC患者的ETV6-NTRK2融合,并用恩替尼成功治疗,为恩替替尼在NTRK阳性AC患者中的应用提供证据,并强调了分子谱分析对此类病例的关键作用。
    Pulmonary atypical carcinoid (AC) is an extremely rare neuroendocrine tumor. The neurotrophic tropomyosin receptor kinase (NTRK) fusions are reported in only 0.5% of nonsmall cell lung cancer, and are more rare in AC with only one previously reported case. Currently, there is little established evidence on the optimal therapeutic strategies and prognosis for advanced cases. We present a female patient with metastatic AC after complete resection. Due to low expression of somatostatin receptor in this case, somatostatin analogs and peptide receptor radionuclide therapy were not available. After pursuing other alternative treatments, including chemotherapy (ie, carboplatin, etoposide, capecitabine, temozolomide, and paclitaxel), everolimus, and atezolizumab, she returned with significant progression, including innumerable subcutaneous nodules, left pleura metastasis, multiple bone metastases, and brain metastases. New biopsy analysis revealed an ETV6-NTRK2 fusion. She was immediately administered the first-generation tropomyosin receptor kinase inhibitor entrectinib at a dose of 600 mg q.d. A subsequent month of treatment resulted in a complete response in all of the metastatic lung lesions. To date, she has maintained sustained benefit for at least 1 year from initiation of entrectinib. Here, we present the first case of a female patient with metastatic AC harboring the ETV6-NTRK2 fusion, and successfully treated with entrectinib, providing evidence for the application of entrectinib in patients with NTRK-positive AC, and underscoring the critical role of molecular profiling for such cases.
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  • 文章类型: Case Reports
    乳腺癌的治疗在很大程度上取决于雌激素受体的蛋白质表达测定,孕激素受体,和Her2/neu(HER2)状态。由于肿瘤异质性或在整个治疗过程中预后标志物的演变,这些预后标志物可能会有所不同。本报告介绍了一例患者,该患者最初患有HER2阴性乳腺癌,并在许多治疗路线上迅速发展。通过下一代测序和肝转移活检对脑脊液的分析确定了HER2阳性癌症,允许使用曲妥珠单抗deruxtecan,HER2靶向治疗。这导致出色的临床反应,并改善了性能状态和生活质量。此病例报告表明继续追踪患者的癌症病理以打开其他治疗机会的大门的重要性。癌症具有发展的潜力,并且存在获得重新活检以确保向患者提供正确的靶向治疗的益处。
    The treatment of breast cancer is largely determined by protein expression assays of estrogen receptor, progesterone receptor, and Her2/neu (HER2) status. These prognostic markers may vary due to tumor heterogeneityor the evolution of prognostic markers throughout the course of treatment. This report presents a case of a patient who initially presented with HER2-negative breast cancer and had rapidly progressed on numerous lines of treatment. An analysis of cerebrospinal fluid via next-generation sequencing and biopsy of metastasis to the liver identified HER2-positive cancer, which allowed for the use of trastuzumab deruxtecan, a HER2-targeted therapy. This led to an excellent clinical response with improvement in performance status and quality of life. This case report demonstrates the importance of continuing to follow a patient\'s cancer pathology to open the doors for other opportunities for treatment. Cancer has the potential to evolve and there is a benefit of obtaining rebiopsies to ensure the correct targeted therapies are provided to the patient.
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  • 文章类型: Case Reports
    滤泡性甲状腺癌(FTC)是一种值得注意的甲状腺癌亚型,以其通过血液转移的趋势而闻名。通常是肺部和骨骼。此病例报告检查了一例极为罕见的病例,涉及一名81岁的女性,表现出异常的转移性头皮病变。值得注意的是,这种侵袭性转移起源于一个小至0.7cm的甲状腺病变.实验室发现,包括抑制的TSH和升高的T3水平,发现亚临床甲状腺功能亢进,在这个联邦贸易委员会的案例中又增加了一层稀有性。分子谱分析鉴定出一种罕见的KRASQ61R突变,提供对案件攻击行为的潜在见解,并强调遗传评估在FTC中的重要性。本报告强调了全面诊断评估的关键作用,包括组织病理学评估,在正确诊断和管理FTC方面,尤其是当临床表现违背传统模式时。
    Follicular thyroid carcinoma (FTC) is a noteworthy subtype of thyroid cancer known for its tendency to metastasize through the bloodstream, usually to the lungs and bones. This case report examines an exceptionally rare instance involving an 81-year-old female presenting with an unusual metastatic scalp lesion. Remarkably, this aggressive metastasis originated from a thyroid lesion as small as 0.7 cm. Lab findings, including suppressed TSH and elevated T3 levels, revealed subclinical hyperthyroidism, adding another layer of rarity to this FTC case. Molecular profiling identified a rare KRAS Q61R mutation, providing potential insight into the case\'s aggressive behavior and underscoring the importance of genetic assessment in FTC. This report emphasizes the critical role of comprehensive diagnostic evaluations, including histopathological assessments, in properly diagnosing and managing FTC, especially when clinical presentations defy conventional paradigms.
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  • 文章类型: Journal Article
    引言:在这项研究中,我们证明了酵母表面展示(YSD)和下一代测序(NGS)结合人工智能和机器学习方法(AI/ML)的可行性,用于鉴定具有良好早期可开发性的从头人源化单结构域抗体(sdAb)。方法:展示库来自一种新颖的方法,其中基于VHH的CDR3区域从美洲驼(Lamaglama)获得,针对NKp46免疫,将其移植到在CDR1和CDR2中多样化的人源化VHH骨架文库上。在来自两轮荧光激活细胞分选的序列池的NGS分析之后,我们基于NGS频率和富集分析以及计算机可显影性评估关注四个序列簇。对于每个集群,训练了基于长短期记忆(LSTM)的深度生成模型,并将其用于新序列的计算机模拟采样.对序列进行基于序列和结构的计算机可显影性评估,以选择一组每个簇少于10个序列用于生产。结果:如结合动力学和早期显影性评估所示,该程序代表了从筛选选择中快速有效地设计强效且自动人源化的sdAb命中物的一般策略,该筛选选择具有良好的早期发展概况.
    Introduction: In this study, we demonstrate the feasibility of yeast surface display (YSD) and nextgeneration sequencing (NGS) in combination with artificial intelligence and machine learning methods (AI/ML) for the identification of de novo humanized single domain antibodies (sdAbs) with favorable early developability profiles. Methods: The display library was derived from a novel approach, in which VHH-based CDR3 regions obtained from a llama (Lama glama), immunized against NKp46, were grafted onto a humanized VHH backbone library that was diversified in CDR1 and CDR2. Following NGS analysis of sequence pools from two rounds of fluorescence-activated cell sorting we focused on four sequence clusters based on NGS frequency and enrichment analysis as well as in silico developability assessment. For each cluster, long short-term memory (LSTM) based deep generative models were trained and used for the in silico sampling of new sequences. Sequences were subjected to sequence- and structure-based in silico developability assessment to select a set of less than 10 sequences per cluster for production. Results: As demonstrated by binding kinetics and early developability assessment, this procedure represents a general strategy for the rapid and efficient design of potent and automatically humanized sdAb hits from screening selections with favorable early developability profiles.
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  • 文章类型: Case Reports
    背景:NRG1融合是实体瘤中罕见的致癌驱动因素,在非小细胞肺癌(NSCLC)中NRG1融合的发生率为0.26%。探索NRG1融合阳性癌症的潜在治疗策略和疗效预测因子至关重要。
    方法:我们报告了一名晚期肺腺癌患者,该患者携带通过基于RNA的下一代测序(NGS)鉴定的新型NPTN-NRG1融合蛋白,最初诊断时基于DNA的NGS未检测到。组织活检的转录组学数据显示NRG1α同工型占总NRG1读数的30%,和NRG1β亚型检测不到。患者接受阿法替尼作为四线治疗,无进展生存期(PFS)为14个月。
    结论:本报告支持阿法替尼可以为NRG1融合患者提供潜在的益处,和基于RNA的NGS是融合检测和同种型鉴定的准确且具有成本效益的策略。
    BACKGROUND: NRG1 fusions are rare oncogenic drivers in solid tumors, and the incidence of NRG1 fusions in non-small cell lung cancer (NSCLC) was 0.26%. It is essential to explore potential therapeutic strategies and efficacy predictors for NRG1 fusion-positive cancers.
    METHODS: We report an advanced lung adenocarcinoma patient harboring a novel NPTN-NRG1 fusion identified by RNA-based next-generation sequencing (NGS), which was not detected by DNA-based NGS at initial diagnosis. Transcriptomics data of the tissue biopsy showed NRG1α isoform accounted for 30% of total NRG1 reads, and NRG1β isoform was undetectable. The patient received afatinib as fourth-line treatment and received a progression-free survival (PFS) of 14 months.
    CONCLUSIONS: This report supports afatinib can provide potential benefit for NRG1 fusion patients, and RNA-based NGS is an accurate and cost-effective strategy for fusion detection and isoform identification.
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  • 文章类型: Case Reports
    同步性多发性胃癌(SMGC)是一种罕见的疾病,其特征是在胃中同时发生两个或多个原发性恶性肿瘤,每个都有自己独特的病理形态。SMGC不同于胃转移,起源于原发性胃或非胃肿瘤。目前,SMGC在中国的发病率较低,没有既定的标准治疗指南。这里,我们报告了一例罕见的晚期SMGC病例,该病例通过采用下一代测序(NGS)的治疗策略获得了长期临床获益.肿瘤和/或循环无细胞DNA的动态监测指导患者的治疗顺序。患者接受抗HER2治疗,其次是免疫疗法,派姆单抗联合曲妥珠单抗和化疗,并最终成功进行了全胃切除术。该案例强调了一种利用基于液体活检的NGS的新方法,以深入了解SMGC患者对NGS指导治疗的疾病进展和分子反应。
    Synchronous multiple gastric carcinoma (SMGC) is a rare condition characterized by the simultaneous occurrence of two or more primary malignant tumors in the stomach, each with its own distinct pathological morphology. SMGC differs from gastric metastases, which originate from primary gastric or non-gastric tumors. At present, the incidence of SMGC is low in China, with no established guidelines for standard treatment. Here, we report a rare case of advanced SMGC that achieved long-lasting clinical benefits through a treatment strategy informed by next-generation sequencing (NGS). Dynamically monitoring of the tumor and/or circulating cell-free DNA guided the patient\'s treatment sequentially. The patient received anti-HER2 therapy, followed by immunotherapy, pembrolizumab in combination with trastuzumab and chemotherapy, and ultimately underwent successful total gastrectomy. This case highlights a novel approach of utilizing liquid biopsy-based NGS to gain insights into disease progression and molecular response to NGS-guided treatment in SMGC patients.
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  • 文章类型: Case Reports
    早期婴儿癫痫性脑病(EIEE)的诊断仍然具有挑战性,和下一代测序(NGS)技术在识别遗传原因方面发挥了关键作用。最近的研究表明CYFIP2基因的突变与EIEE,到目前为止,报告了20种有害变体,密码子87处有从头突变热点。一名男婴自四个月大以来就出现癫痫发作,并出现明显的发育迟缓和小头畸形。癫痫发作的类型不同,频繁且难以治疗,包括不同的抗惊厥药物.代谢研究显示无明显变化。初始脑电图显示双侧阵发性活动伴有半球形扩散。头颅MRI未见病理改变。基于全外显子组测序(WES)的癫痫多基因组的分析公开了从头建立的杂合CYFIP2基因变体[c.258_266del;p.(Trp86_Ser88del)]。我们描述了由于CYFIP2中三个氨基酸的从头杂合框内缺失而患有EIEE的婴儿的情况:c.258_266del;p。(Trp86_Ser88del)。这种框内缺失消除了密码子87,即与特别严重的EIEE表型相关的突变热点。以前的所有报告都有错义变体,可能具有功能获得机制。我们患者的临床表现与文献中报道的具有影响密码子87的有害变体的患者非常相似。我们的病例报告首次描述了CYFIP2中引起疾病的框内缺失,并重申了一致的基因型-表型相关性。
    The diagnosis of early infantile epileptic encephalopathy (EIEE) remains challenging, and next-generation sequencing (NGS) techniques have played a key role in identifying genetic causes. Recent studies have shown an association between mutations in the CYFIP2 gene and EIEE, with 20 deleterious variants reported so far and a de novo mutational hotspot at codon 87.  A male infant presented with seizures since the age of four months as well as significant developmental delay and microcephaly. The seizures were of different types, frequent and refractory to treatment, including different anticonvulsant drugs. Metabolic studies showed no significant changes. The initial electroencephalogram revealed bilateral paroxysmal activity with hemispherical diffusion. Brain MRI showed no pathological changes. Analysis of a whole exome sequencing (WES) based multigene panel for epilepsy disclosed a heterozygous CYFIP2 gene variant [c.258_266del; p.(Trp86_Ser88del)] established as de novo. We describe the case of an infant with EIEE due to a de novo heterozygous in-frame deletion of three amino acids in CYFIP2: c.258_266del; p.(Trp86_Ser88del). This in-frame deletion eliminates codon 87, a mutational hotspot associated with a particularly severe EIEE phenotype. All previous reports had missense variants with a presumably gain-of-function mechanism. The clinical picture of our patient is very similar to the ones with deleterious variants affecting codon 87 reported in the literature. Our case report is the first to describe a disease-causing in-frame deletion in CYFIP2 and reiterates a consistent genotype-phenotype correlation.
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  • 文章类型: Case Reports
    由于治疗和诊断策略的最新进展,在过去十年中已经实现了儿科癌症存活率的显着改善。然而,疾病进展和复发仍然是儿科血管肉瘤临床治疗的主要挑战.使用高通量测序技术对这些罕见肿瘤进行全面的基因组分析可以改善患者分层并识别可用于治疗干预的可操作的生物标志物。这里,我们描述了临床,组织病理学,一个新的和精准医学的病例的免疫组织化学和分子谱,其中KHDRBS1-NTRK3融合通过基于下一代测序的综合基因组谱确定,导致在无法治愈的疾病中完全和持续的缓解(临床和放射学反应).我们的患者代表了文献中第一个具有可靶向NTRK3融合的儿科血管肉瘤,并证明了使用larotrectinib靶向血管肉瘤这种改变的第一个例子,NTRK抑制剂。在不到两个月的治疗中实现了临床和放射学缓解,患者目前处于完全缓解状态,停止拉罗列替尼治疗后4个月,给予超过17个月,只有轻微的副作用报告。因此,这个非凡的案例通过将常规病理学与原因相结合,体现了基于精确护理的真正本质,when,以及如何检测儿科血管肉瘤中罕见的致癌驱动因素和不可知的生物标志物。
    Significant improvements in the survival rates of paediatric cancer have been achieved over the past decade owing to recent advances in therapeutic and diagnostic strategies. However, disease progression and relapse remain a major challenge for the clinical management of paediatric angiosarcoma. Comprehensive genomic profiling of these rare tumours using high-throughput sequencing technologies may improve patient stratification and identify actionable biomarkers for therapeutic intervention. Here, we describe the clinical, histopathological, immunohistochemical and molecular profile of a novel and precision medicine-informed case where a KHDRBS1-NTRK3 fusion determined by next-generation sequencing-based comprehensive genomic profiling led to complete and sustained remission (clinical and radiological response) in an otherwise incurable disease. Our patient represents the first paediatric angiosarcoma harbouring a targetable NTRK3 fusion in the literature and demonstrates the first example of targeting this alteration in angiosarcoma using larotrectinib, an NTRK inhibitor. Clinical and radiological remission was achieved in under two months of therapy, and the patient is currently in complete remission, 4 month after stopping larotrectinib therapy, which was given over 17 months with only mild side effects reported. Therefore, this remarkable case exemplifies the true essence of precision-based care by incorporating conventional pathology with the why, when, and how to test for rare oncogenic drivers and agnostic biomarkers in paediatric angiosarcoma.
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