CONCORDANCE: A real?world evidence study to evaluate the concordance of detecting epidermal growth factor receptor (EGFR) mutation by circulating tumor DNA* versus tissue biopsy in patients with metastatic non?small cell lung cancer

Background: Molecular tissue testing in non?small cell lung cancer (NSCLC) is done for the assessment of epidermal growth factor receptor (EGFR) mutation. EGFR mutation status is the basis for deciding the targeted treatment option for patients with metastatic NSCLC. The nonavailability of tissue samples and contraindications for biopsy pose a significant challenge. Hence circulating tumor DNA (ctDNA) by liquid biopsy can be a viable alternative for NSCLC patients. Methods: This study was conducted at 15 sites across India. EGFR mutation testing from plasma was done as part of the study at the central laboratory by the next?generation sequencing (NGS) method and EGFR mutation test results from tissue samples (done as part of routine practice) were recorded for all the patients. Results: Out of the total patients enrolled (N = 245) the majority (64.5% n = 158) were men. The median age of patients was 58.0 (range: 26�) years. The concordance between plasma and tissue testing was found to be 82.9% (95% confidence interval [CI]: 77.55 87.45). The sensitivity and specificity of NGS were 68.4% (95% CI: 56.92 78.37) and 90.1% [95% CI: 84.36 94.21) respectively. Plasma testing detected 1.2% (n = 3) and tissue sample testing detected 2.4% (n = 6) positive status of exon 20 T790M EGFR mutation. Out of the total number of patients enrolled 25 were tissue positive and plasma negative while 16 were plasma positive and tissue negative. Conclusions: This real?world study in Indian patients suggests that plasma testing for EGFR mutation analysis is a viable diagnostic option in newly diagnosed advanced/metastatic NSCLC patients. The noninvasive plasma procedure in patients without available/evaluable tumor sample may enable more patients to receive appropriate targeted therapies by providing clinicians with valuable insights into the patient抯 tumor mutation status. ClinicalTrials.gov Identifier: NCT03562819

Technical specification for clinical diagnosis and treatment of human parvovirus B19 infection in kidney transplant recipients (2022 edition) / 器官移植

Long-term use of immunosuppressant in kidney transplant recipients leads to poor immune function and infection with various pathogens. In recent years, along with the advancement of detection technique of human parvovirus B19 (HPV-B19) infection and the increasing quantity of kidney transplantation, the infection rate of HPV-B19 after kidney transplantation has been elevated year by year, becoming one of the major causes of pure red cell aplasia (PRCA), affecting the recovery of renal allograft function, and even leading to the injury or poor prognosis of renal allograft. To further standardize the diagnosis and treatment of HPV-B19 infection in kidney transplant recipients, Branch of Organ Transplantation of Chinese Medical Association and National Kidney Transplantation Quality Control Center jointly organized experts to formulate the clinical diagnosis and treatment specification for HPV-B19 infection after kidney transplantation from the perspectives of etiology, epidemiological characteristics, clinical manifestations, diagnosis, prevention, treatment, existing problems and prospects of HPV-B19, aiming to provide guidance for standardized prevention and treatment of HPV-B19 infection post-kidney transplantation in China.

Diagnostic criteria and research progress on heart allograft pathology / 器官移植

With the improvement of surgical technique of heart transplantation and clinical application of potent immunosuppressant, the quantity of heart transplantation and the survival time of heart allograft have been significantly improved. However, a series of complications, such as right ventricular failure, ischemia-reperfusion injury, acute rejection, "Quilty lesion", infection and chronic rejection characterized by transplant coronary artery disease (TCAD) may still occur at different stages after heart transplantation. The application of endomyocardial biopsy (EMB) makes it possible to observe and understand the pathological features of multiple complications of heart allograft including rejection, which has become the most accurate diagnostic tool for postoperative complications. In this article, the brief history of heart allograft pathology, main postoperative complications and pathological diagnostic criteria, and cutting edge research progress on diagnostic criteria of rejection were illustrated, aiming to bring clinical benefits to more recipients undergoing heart transplantation.

Genomic mutations in patients with advanced non-small cell lung cancer in Yunan and its clinical significance / 中国肿瘤生物治疗杂志

@#[Abstract] Objective: To investigate the lung cancer-associated driver gene mutations in peripheral blood of patients with advanced non-small cell lung cancer (NSCLC) in Yunnan area, and to explore their association with clinical pathological features. Methods: Peripheral blood of 304 patients with stage Ⅳ NSCLC were collected from Molecular Diagnostic Center of Yunnan Cancer Hospital during January 2019 to December 2019. Next generation sequencing (NGS) technique was used to detect the mutation of NSCLC related driver genes, chi-square test was used to analyze the relationship between the major mutant genes and the clinicopathological features of patients, and Logistic regression was used to analyze the independent risk factors. Results: In the peripheral blood of 304 patients with stage Ⅳ NSCLC, there were 120 (39.47%) cases with EGFR mutations, 12 (3.95%) cases with ALK fusion, 36 (11.84%) case with other mutations such as KRAS, BRAF and RET. The main EGFR mutations were 19del and L858R (69.17%). The mutation rate of EGFR was higher in female, young, non-smoking, non-chemotherapy and lung adenocarcinoma patients (49.26% vs 31.55%, 45.39% vs 33.56%, 45.92% vs 27.78%, 45.07% vs 26.37%, 42.39% vs 10.71%, all P<0.05). Multivariate analysis showed that female, no history of chemotherapy and lung adenocarcinoma were independent risk factors for EGFR mutations (all P<0.05). Conclusion: Using NGS technology to detect the driver genes in peripheral blood of patients with advanced NSCLC in Yunnan area showed that the mutation rate of EGFR was higher in women and lung adenocarcinoma patients without chemotherapy history.

Bioinformatics analysis of HLA-A2 restricted neoantigen epitopes in breast cancer / 中国肿瘤生物治疗杂志

@#[Abstract] Objective: To screen candidate epitopes of breast cancer HLA-A2 restrictive neoantigen and to identify high frequency mutation sites in breast cancer neoantigen by using bioinformatics method. Methods: NCBI and GDC databases were used to search missense mutation sites formed by single nucleotide mutation in breast cancer among reported literatures and sequencing data. The new antigen epitopes were predicted by HLA-A2 antigen epitope prediction website BIMAS, SYFPEITHI and artificial neural networkbased NetMHC4.0, and the epitopes with TAP binding power less than Intermediate were eliminated. The candidate epitopes were prioritized by mutation frequency and prediction results. Results: A total of 17 high-frequency mutation genes, including BTLA, ERBB2 and NBPF12 etc, were screened by the above-mentioned methods, and a total of 26 neoantigen epitopes were identified. The binding power of epitopes predicted using BIMAS and SYFPEITHI showed great difference (P<0.05), epitopes in high priority as GSTP1 (A114V , mutation frequency of 5.94%) and BRCA2 (N991H, mutation frequency of 5.40%) etc, were expected to be candidate neo-antigen epitopes; however, their mutation frequency was relatively too low to achieve“universal use” . The possibility of these epitopes used as general breast cancer neo-antigen epitopes is less likely. Conclusion: The common mutation frequency of breast cancer is lower than that of other tumors; it ’s difficult to find“universal”new antigen epitopes of breast cancer; the individualized neoantigen vaccine may be of more promise, which needs further research.

Detection of high-frequency mutant genes in extranodal NK/T cell lymphoma by next-generation sequencing technology and its clinical significance / 中国肿瘤生物治疗杂志

@# Objective: To analyze the mutation of target genes in extranodal natural killer/T-cell lymphoma (ENKTL) by using nextgeneration sequencing, and to explore its relationship with prognosis and clinical characteristics, as to provide evidence for the pathogenesis, clinical diagnosis and targeted therapy of ENKTL. Methods: According to previous literature reports, the genes whose mutations can affect the development of lymphoma were selected as the target genes for this study. 29 patients with ENKTL, who were newly diagnosed at the Fourth Hospital of Hebei Medical University from August 2010 to October 2018, were selected for this study. The mutation of 9 target genes in the specimen was detected by thenext-generationsequencingtechnology.Therelationshipsamongclinicalfeatures,diseaseprognosisandmutationofthetargetgeneswereanalyzedbySPSS21.0statisticalsoftware.Results： ：Ninetargetgenes were were screened. AT-rich interactive-domain 1A(ARID1A) gene showed the highest mutation rate in ENKTL (10 cases, 34.48%) followedbylysinemethyltransferase2D(KMT2D)gene(31.03%)andtumorprotein P53 (TP53) gene (24.13%). Kaplan-Meier survival analysis showed that the overall survival of ENKTL patients with KMT2D gene wild type was significantly better than patients with KMT2D gene mutation (P=0.006). The KMT2D gene mutation was found to besignificantlyrelatedtoclinicalstage,CRP,albumin,lymphocyte count and Ki67 expression in ENKTL patients (all P<0.05). COX regression analysis showed that KMT2D gene mutation was an independent adverse prognostic factor (P<0.05). Conclusion: The KMT2D gene has a high mutant frequency in ENKTL and is associated with patients’prognosis, suggesting that KMT2D gene plays an important role in the initiation and development of ENKTL. It could be used as a clinical therapeutic target for ENKTL.

Development status and clinical applications of precision detection technology in the times of precision oncology / 中国肿瘤生物治疗杂志

@#Precision detection techniques have promoted the development of individualized diagnosis and treatment of tumors in the era of precision medicine. At the same time, clinical demands of precision treatments have further driven the development and application of precision detection techniques. In recent years, precision medical detection techniques realized rapid transformations from low-throughput to high-throughput genomic sequencing, from tissue biopsies to liquid biopsies, and from multicell promiscuous detection to single cell precision sequencing. All these changes have promoted the emergence and development of new technologies, new targets, and new drugs in the era of precision oncology medicine. In the future, multi-dimensional combined detection could help to improve the accuracy of precision medicine; ctDNA methylation detection analysis could broaden the research field of precision medicine; and the transformation of clinical trial design could also contribute to promote the in-depth development of precision medicine.

COINFECCIÓN NATURAL DE VIRUS DE ARN EN CULTIVOS DE PAPA (Solanum tuberosum subsp. Andigena) EN ANTIOQUIA (COLOMBIA) / Natural coinfection of RNA viruses in potato (Solanum tuberosum subsp. Andigena) crops in Antioquia (Colombia)

RESUMEN Las enfermedades virales son uno de los principales problemas fitopatológicos de la papa. Con el fin de determinar los virus más prevalentes en cultivos de papa var. Diacol Capiro en el oriente Antioqueño (Colombia), se evaluó mediante RT-qPCR la presencia de diez virus de ARN (PVY, PVA, PVV, TaLMV, PVS, PLRV, PYVV, PVX, ToRSV y PMTV) en 36 muestras de tejido foliar. Los resultados indicaron la ocurrencia de cinco de los diez virus evaluados, con niveles de prevalencia de 88,9 %, 75 %, 75 %, 41,7 % y 25 % para PVY, PVX, PYVV, PLRV y PVS, respectivamente. Con fines comparativos, cuatro virus también se evaluaron mediante ELISA, siendo detectados PVS (80,5 %), PVY (55 %) y PLRV (5,5 %); mientras que PVX no fue encontrado con esta prueba. La comparación de estas técnicas mediante la razón de prevalencia (RP), indicó que la RT-qPCR ofrece niveles superiores de detección con valores de RP = 1,6 y RP = 7,5 para los virus PVY y PLRV; mientras que para PVS la ELISA detectó más muestras positivas que RT-qPCR (RP = 3,22), evidenciándose la necesidad de diseñar nuevos cebadores ajustados a la diversidad de este virus en Antioquia. La coinfección mixta más frecuente fue PVY-PYVV-PVX (22,2 %), mientras que los cinco virus se encontraron en el 11,1 % de las muestras. Finalmente, utilizando secuenciación Sanger de la cápside y NGS para los genomas completos, se confirmó la circulación de todos los virus detectados en los cultivos de papa del oriente Antioqueño. Estos resultados señalan la necesidad de fortalecer los programas de manejo integrado de enfermedades virales en Antioquia.

ABSTRACT Viral diseases are one of the main phytopathological problems affecting potato crops worldwide. To determine the most prevalent viruses in potato var. Diacol Capiro crops in Eastern Antioquia, 36 leaf samples were tested for the presence of PVY, PVA, PVV, TaLMV, PVS, PLRV, PYVV, PVX, ToRSV and PMTV using RT-qPCR. Detected viruses included PVY, PVX, PYVV, PLRV and PVS with prevalence levels of 88.9 %, 75.0 %, 75.0 %, 41.7 % and 25.0 %, respectively. PVS, PVY, PLRV and PVX were also tested by ELISA. PVS, PVY and PLRV tested positive in 80.5 %, 55.0 % and 5.5 % of samples; PVX was not detected. Prevalence Ratios (PR) suggests that detection is higher for PVY (PR = 1.6) and PLRV (PR = 7.5) using RT-qPCR. ELISA worked better for PVS with a PR of 3.2; this result suggests that the RT-qPCR primers used for PVS must be adjusted to reflect the genome diversity of virus in Antioquia. The most frequent coinfection was PVY-PYVV-PVX, which occurred in 22.2 % of samples; coinfection with PVY, PVX, PYVV, PLRV and PVS was present in 11.1 % of samples. The circulation of these viruses in Eastern Antioquia was further confirmed using Sanger and high-throughput sequence. This work highlights the need to strengthen integrated disease management programs of viruses in Antioquia.

A Review of the Application of Next Generation Sequencing (NGS) in Wild Terrestrial Vertebrate Research

In era of sequencing revolution, scientists seek for knowledge about the ever-expanding field of technology, Next Generation Sequence (NGS) to be applied in their research due to its high reliability and rate of discovery. What is NGS? To obtain a detailed understanding about NGS, it is required to look back the history of sequencing and how the NGS stepped into life science. This review paper gives an overview of NGS projects in wild terrestrial vertebrate including applications such as whole genome sequencing and metagenomics.

Identifying Common Mutations in Colorectal Cancer Using a 7-Gene Panel by Next Generation Sequencing

Abstract@#Introduction: Colorectal cancer (CRC) arises from the cumulative effects of genetic and epigenetic alterations. Current treatment of metastatic CRC relies on combination of chemotherapy and targeted therapies such as anti-EGFR therapies. The success of targeted therapies relies on the detection of actionable targets and predictive biomarkers of resistance. The study aims to determine mutations in common actionable targets and predictive biomarkers of resistance to anti-EGFR therapies in Malaysian CRC patients. Methods: Mutations in 10 CRC tissues were determined by next-generation sequencing with a panel of 7 cancer-related genes covering all exons in KRAS, BRAF, PIK3CA, PTEN, TP53, NRAS, and EGFR genes. Immunohistochemistry was used to determine mismatch repair (MMR) status. Results: Of the ten samples, 5 and 4 samples harboured two and one mutation, respectively and one had no mutation. All were missense mutations and were in five genes, namely, KRAS, PIK3CA, TP53, BRAF, and EGFR. They were, G12D, G12V, G12A, G13D, and V14I in KRAS, E545K, K733R, and D1056N in PIK3CA, G199V, D259Y, and R282W in TP53, V600E in BRAF and G696R in EGFR. Deficient mismatch repair (dMMR) was detected in three samples, of which two had KRAS mutation. Conclusion: Mutations in KRAS codon 12 and 13, BRAF and PIK3CA which predict resistance to anti-EGFR therapies and three TP53 mutations were found. This is the first report of EGFR mutation in Malaysian CRC patients. It is predicted to be a pathogenic variant. dMMR, one of the biomarkers for treatment with immune checkpoint inhibitor was also detected.

Essential Elements for Establishing Clinical Next-generation Sequencing Testing

Over the past decade, next-generation sequencing (NGS) has evolved at an astonishing pace and has revolutionized clinical medicine as well as genomics research. The rapid advancements in NGS technologies have been accompanied by accumulating evidence of the analytical and clinical validity, and clinical utility of NGS. NGS is used worldwide. This review provides medical technicians and laboratory physicians with the essential elements for establishing clinical NGS testing. Here the authors briefly describe the advantages and drawbacks of currently available NGS platforms, potential sources of error in NGS workflow, and reference materials.

The clinical significance of gene mutation detection in myelodysplastic syndromes / 天津医药

@#Myelodysplastic syndrome (MDS), a clonal disease that arises from the expansion of mutated hematopoietic stem cells or hematopoietic progenitor cells, is usually characterized by a clinically and biologically heterogeneous group of disorders associated with cytopenias, ineffective hematopoiesis, and a tendency to evolve into acute myeloid leukemia. Currently, the diagnosis of MDS relies mainly on the morphologic and cytogenetic abnormalities. With the advance of the next generation sequencing, genetic mutations have been identified in majority of MDS patients. Here we briefly review the clinical significance of genetic mutations in the diagnosis, classification, risk stratification and treatment of MDS.

Efficiency to Discovery Transgenic Loci in GM Rice Using Next Generation Sequencing Whole Genome Re-sequencing

Molecular characterization technology in genetically modified organisms, in addition to how transgenic biotechnologies are developed now require full transparency to assess the risk to living modified and non-modified organisms. Next generation sequencing (NGS) methodology is suggested as an effective means in genome characterization and detection of transgenic insertion locations. In the present study, we applied NGS to insert transgenic loci, specifically the epidermal growth factor (EGF) in genetically modified rice cells. A total of 29.3 Gb (~72x coverage) was sequenced with a 2 x 150 bp paired end method by Illumina HiSeq2500, which was consecutively mapped to the rice genome and T-vector sequence. The compatible pairs of reads were successfully mapped to 10 loci on the rice chromosome and vector sequences were validated to the insertion location by polymerase chain reaction (PCR) amplification. The EGF transgenic site was confirmed only on chromosome 4 by PCR. Results of this study demonstrated the success of NGS data to characterize the rice genome. Bioinformatics analyses must be developed in association with NGS data to identify highly accurate transgenic sites.

Perspectives on Next-Generation Newborn Screening

Newborn screening (NBS) has been effective for detecting asymptomatic newborns with inherited metabolic diseases and has facilitated early clinical intervention, which has resulted in significant decreases in the rates of morbidity and mortality caused by these diseases. The outcome of the NBS program heavily depends on technological advances. Since Dr. Robert Guthrie developed a bacterial inhibition assay to screen for metabolic diseases in the early 1960s, use of the NBS program has spread to many countries. Tandem mass spectrometry (TMS) was a second major technological breakthrough that has allowed screening to be extended to disorders of fatty acid and organic acid metabolism as well as to those of amino acid metabolism, and recently screening has also been expanded to include lysosomal storage diseases. TMS can detect multiple analytes rapidly and simultaneously and is currently applied to nearly 80% of the newborn population in Korea. Next-generation sequencing (NGS) technology could be another major breakthrough to improve the current NBS program. To integrate NGS into the NBS program, various considerations about its analytical validity, clinical validity, clinical utility, and ethical, legal, and social implications should be addressed on the basis of population screening. Here, the authors review population screening criteria, the current status of NBS, and recent advances in NGS. In addition, we discuss the practical and ethical issues, opportunities, and challenges regarding the implementation of NGS in NBS.

MAP: Mutation Arranger for Defining Phenotype-Related Single-Nucleotide Variant

Next-generation sequencing (NGS) is widely used to identify the causative mutations underlying diverse human diseases, including cancers, which can be useful for discovering the diagnostic and therapeutic targets. Currently, a number of single-nucleotide variant (SNV)-calling algorithms are available; however, there is no tool for visualizing the recurrent and phenotype-specific mutations for general researchers. In this study, in order to support defining the recurrent mutations or phenotype-specific mutations from NGS data of a group of cancers with diverse phenotypes, we aimed to develop a user-friendly tool, named mutation arranger for defining phenotype-related SNV (MAP). MAP is a user-friendly program with multiple functions that supports the determination of recurrent or phenotype-specific mutations and provides graphic illustration images to the users. Its operation environment, the Microsoft Windows environment, enables more researchers who cannot operate Linux to define clinically meaningful mutations with NGS data from cancer cohorts.

Exome Sequencing in Mendelian Disorders

More than 7,000 rare Mendelian diseases have been reported, but less than half of all rare monogenic disorders has been discovered. In addition, the majority of mutations that are known to cause Mendelian disorders are located in protein-coding regions. Therefore, exome sequencing is an efficient strategy to selectively sequence the coding regions of the human genome to identify novel genes associated with rare genetic disorders. The "exome" represents all of the exons in the human genome, constituting about 1.5% of the human genome. Exome sequencing is carried out by targeted capture and intense parallel sequencing. After the first report of successful exome sequencing for the identification of causal genes and mutations in Freeman Sheldon syndrome, exome sequencing has become a standard approach to identify genes in rare Mendelian disorders. Exome sequencing is also used to search the causal genes and variants in complex diseases. The successful use of exome sequencing in Mendelian disorders and complex diseases will facilitate the development of personalized genomic medicine.