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https://www.readbyqxmd.com/read/28231257/targeted-sequencing-identifies-a-novel-sh2d1a-pathogenic-variant-in-a-chinese-family-carrier-screening-and-prenatal-genetic-testing
#1
Jun-Yu Zhang, Song-Chang Chen, Yi-Yao Chen, Shu-Yuan Li, Lan-Lan Zhang, Ying-Hua Shen, Chun-Xin Chang, Yu-Qian Xiang, He-Feng Huang, Chen-Ming Xu
X-linked lymphoproliferative disease type 1 (XLP1) is a rare primary immunodeficiency characterized by a clinical triad consisting of severe EBV-induced hemophagocytic lymphohistiocytosis, B-cell lymphoma, and dysgammaglobulinemia. Mutations in SH2D1A gene have been revealed as the cause of XLP1. In this study, a pregnant woman with recurrence history of birthing immunodeficiency was screened for pathogenic variant because the proband sample was unavailable. We aimed to clarify the genetic diagnosis and provide prenatal testing for the family...
2017: PloS One
https://www.readbyqxmd.com/read/28230858/ngs-based-transcriptome-profiling-reveals-biomarkers-for-companion-diagnostics-of-the-tgf-%C3%AE-receptor-blocker-galunisertib-in-hcc
#2
Yuan Cao, Rahul Agarwal, Francesco Dituri, Luigi Lupo, Paolo Trerotoli, Serena Mancarella, Peter Winter, Gianluigi Giannelli
Transforming growth factor-beta (TGF-β) signaling has gained extensive interest in hepatocellular carcinoma (HCC). The small molecule kinase inhibitor galunisertib, targeting the TGF-β receptor I (TGF-βRI), blocks HCC progression in preclinical models and shows promising effects in ongoing clinical trials. As the drug is not similarly effective in all patients, this study was aimed at identifying new companion diagnostics biomarkers for patient stratification. Next-generation sequencing-based massive analysis of cDNA ends was used to investigate the transcriptome of an invasive HCC cell line responses to TGF-β1 and galunisertib...
February 23, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/28230760/bioinformatics-approaches-for-fetal-dna-fraction-estimation-in-noninvasive-prenatal-testing
#3
REVIEW
Xianlu Laura Peng, Peiyong Jiang
The discovery of cell-free fetal DNA molecules in plasma of pregnant women has created a paradigm shift in noninvasive prenatal testing (NIPT). Circulating cell-free DNA in maternal plasma has been increasingly recognized as an important proxy to detect fetal abnormalities in a noninvasive manner. A variety of approaches for NIPT using next-generation sequencing have been developed, which have been rapidly transforming clinical practices nowadays. In such approaches, the fetal DNA fraction is a pivotal parameter governing the overall performance and guaranteeing the proper clinical interpretation of testing results...
February 20, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28230645/clinical-scale-rapid-autologous-bk-virus-specific-t-cell-line-generation-from-kidney-transplant-recipients-with-active-viremia-for-adoptive-immunotherapy
#4
Caroline Lamarche, Julie Orio, Victoria Georges-Tobar, Thomas Pincez, Mathieu Goupil, Amina Dahmani, Cedric Carli C, Ann Brasey, Lambert Busque, Jean-Sébastien Delisle
BACKGROUND: Polyomavirus-associated nephropathy (PVAN) following BK virus reactivation in kidney transplant recipients (KTR) can compromise graft survival. Lowering immunosuppression is the only established approach to prevent or treat PVAN but nonspecifically increasing host immune competence also augments rejection risk. Ex vivo T cell stimulation/expansion offers the possibility to generate BK-specific T cell lines for adoptive immunotherapy. The objective of this study was to develop and characterize a clinical scale protocol to generate BK-specific T cell lines from viremic KTR...
February 23, 2017: Transplantation
https://www.readbyqxmd.com/read/28229982/circulating-free-dna-mutation-associated-with-response-of-targeted-therapy-in-human-epidermal-growth-factor-receptor-2-positive-metastatic-breast-cancer
#5
Qing Ye, Fan Qi, Li Bian, Shao-Hua Zhang, Tao Wang, Ze-Fei Jiang
BACKGROUND: The addition of anti-human epidermal growth factor receptor 2 (HER2)-targeted drugs, such as trastuzumab, lapatinib, and trastuzumab emtansine (T-DM1), to chemotherapy significantly improved prognosis of HER2-positive breast cancer patients. However, it was confused that metastatic patients vary in the response of targeted drug. Therefore, methods of accurately predicting drug response were really needed. To overcome the spatial and temporal limitations of biopsies, we aimed to develop a more sensitive and less invasive method of detecting mutations associated with anti-HER2 therapeutic response through circulating-free DNA (cfDNA)...
2017: Chinese Medical Journal
https://www.readbyqxmd.com/read/28229125/the-clinical-neuroanatomical-and-neuropathologic-phenotype-of-tbk1-associated-frontotemporal-dementia-a-longitudinal-case-report
#6
Carolin A M Koriath, Martina Bocchetta, Emilie Brotherhood, Ione O C Woollacott, Penny Norsworthy, Javier Simón-Sánchez, Cornelis Blauwendraat, Katrina M Dick, Elizabeth Gordon, Sophie R Harding, Nick C Fox, Sebastian Crutch, Jason D Warren, Tamas Revesz, Tammaryn Lashley, Simon Mead, Jonathan D Rohrer
INTRODUCTION: Mutations in the TANK-binding kinase 1 (TBK1) gene have recently been shown to cause frontotemporal dementia (FTD). However, the phenotype of TBK1-associated FTD is currently unclear. METHODS: We performed a single case longitudinal study of a patient who was subsequently found to have a novel A705fs mutation in the TBK1 gene. He was assessed annually over a 7-year period with a series of clinical, cognitive, and magnetic resonance imaging assessments...
2017: Alzheimer's & Dementia: Diagnosis, Assessment & Disease Monitoring
https://www.readbyqxmd.com/read/28228157/genetics-and-genomics-of-dilated-cardiomyopathy-and-systolic-heart-failure
#7
REVIEW
Upasana Tayal, Sanjay Prasad, Stuart A Cook
Heart failure is a major health burden, affecting 40 million people globally. One of the main causes of systolic heart failure is dilated cardiomyopathy (DCM), the leading global indication for heart transplantation. Our understanding of the genetic basis of both DCM and systolic heart failure has improved in recent years with the application of next-generation sequencing and genome-wide association studies (GWAS). This has enabled rapid sequencing at scale, leading to the discovery of many novel rare variants in DCM and of common variants in both systolic heart failure and DCM...
February 22, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28228113/validation-of-an-ngs-mutation-detection-panel-for-melanoma
#8
Anne Reiman, Hugh Kikuchi, Daniela Scocchia, Peter Smith, Yee Wah Tsang, David Snead, Ian A Cree
BACKGROUND: Knowledge of the genotype of melanoma is important to guide patient management. Identification of mutations in BRAF and c-KIT lead directly to targeted treatment, but it is also helpful to know if there are driver oncogene mutations in NRAS, GNAQ or GNA11 as these patients may benefit from alternative strategies such as immunotherapy. METHODS: While polymerase chain reaction (PCR) methods are often used to detect BRAF mutations, next generation sequencing (NGS) is able to determine all of the necessary information on several genes at once, with potential advantages in turnaround time...
February 22, 2017: BMC Cancer
https://www.readbyqxmd.com/read/28223188/next-generation-sequencing-unravels-homozygous-mutation-in-glucose-6-phosphate-isomerase-gpic-1040g-a-p-arg347his-causing-hemolysis-in-an-indian-infant
#9
Manu Jamwal, Anu Aggarwal, Anirban Das, Arindam Maitra, Prashant Sharma, Shekhar Krishnan, Neeraj Arora, Deepak Bansal, Reena Das
INTRODUCTION: Inherited anemias diagnostic workup requires a step-wise algorithm. Causal genes implicated in congenital hemolytic anemia are numerous, making a gene-by-gene approach by Sanger sequencing time consuming, expensive and labour intensive. Targeted resequencing can be of great use in explaining these cases. METHODOLOGY: Six months female presented with neonatal jaundice and negative family history. Clinical and laboratory evidences were suggestive of hemolytic anemia...
February 20, 2017: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/28222336/a-two-step-approach-for-sequencing-spliceosome-related-genes-as-a-complementary-diagnostic-assay-in-mds-patients-with-ringed-sideroblasts
#10
Kamila Janusz, Mónica Del Rey, María Abáigar, Rosa Collado, David Ivars, María Hernández-Sánchez, Alberto Valiente, Cristina Robledo, Rocío Benito, María Díez-Campelo, Fernando Ramos, Alexander Kohlmann, Consuelo Del Cañizo, Jesús María Hernández-Rivas
Our study aimed to analyze the presence of mutations in SF3B1 and other spliceosome-related genes in myelodysplastic syndromes with ringed sideroblasts (MDS-RS) by combining conventional Sanger and next-generation sequencing (NGS) methods, and to determine the feasibility of this approach in a clinical setting. 122 bone marrow samples from MDS-RS patients were studied. Initially, exons 14 and 15 of the SF3B1 gene were analyzed by Sanger sequencing. Secondly, they were studied by NGS covering besides SF3B1, SRSF2, U2AF1 and ZRSR2 genes...
February 4, 2017: Leukemia Research
https://www.readbyqxmd.com/read/28222323/a-case-report-of-the-clear-cell-variant-of-gallbladder-carcinoma
#11
Ravi Maharaj, Christo Cave, Kevin Sarran, Nigel Bascombe, Dilip Dan, Wesley Greaves, Wayne A Warner
INTRODUCTION: Clear cell gallbladder carcinoma accounts for less than 1% of all gallbladder malignancies and demonstrates its unique histopathological characteristics in patients with no prior medical illness or familial predisposition. PRESENTATION OF CASE: Here we present a case of a 56-year-old female, with no prior medical conditions presented with a 2-month history of upper abdominal pain. Routine hematological and biochemical tests were unremarkable. An abdominal ultrasound revealed the presence of a gallbladder calculi, and a fundic mass while magnetic resonance cholangiopancreatography revealed a 8...
January 12, 2017: International Journal of Surgery Case Reports
https://www.readbyqxmd.com/read/28222155/glm-based-optimization-of-ngs-data-analysis-a-case-study-of-roche-454-ion-torrent-pgm-and-illumina-nextseq-sequencing-data
#12
Sarah Sandmann, Aniek O de Graaf, Bert A van der Reijden, Joop H Jansen, Martin Dugas
BACKGROUND: There are various next-generation sequencing techniques, all of them striving to replace Sanger sequencing as the gold standard. However, false positive calls of single nucleotide variants and especially indels are a widely known problem of basically all sequencing platforms. METHODS: We considered three common next-generation sequencers-Roche 454, Ion Torrent PGM and Illumina NextSeq-and applied standard as well as optimized variant calling pipelines...
2017: PloS One
https://www.readbyqxmd.com/read/28220395/single-cell-sequencing-a-distinct-new-field
#13
REVIEW
Jian Wang, Yuanlin Song
Single cell sequencing (SCS) has become a new approach to study biological heterogeneity. The advancement in technologies for single cell isolation, amplification of genome/transcriptome and next-generation sequencing enables SCS to reveal the inherent properties of a single cell from the large scale of the genome, transcriptome or epigenome at high resolution. Recently, SCS has been widely applied in various clinical and research fields, such as cancer biology and oncology, immunology, microbiology, neurobiology and prenatal diagnosis...
December 2017: Clinical and Translational Medicine
https://www.readbyqxmd.com/read/28220254/hiv-1-persistent-viremia-is-frequently-followed-by-episodes-of-low-level-viremia
#14
Marek Widera, Miriam Dirks, Barbara Bleekmann, Robert Jablonka, Martin Däumer, Hauke Walter, Robert Ehret, Jens Verheyen, Stefan Esser
After the start of antiretroviral therapy (ART), plasma HIV-RNA levels should fall below the limit of detection (LOD) within 24 weeks. Hence, the prolonged decline of HIV-RNA after ART initiation is defined as persistent viremia (PV). In this retrospective study, we analyzed factors associated with PV. Next-generation sequencing of viral RNA/DNA was performed to study viral evolution and the emergence of drug-resistance mutations in HIV-infected patients with PV (n = 20). In addition, HIV-DNA species, immunological parameters, and clinical data of the patients were analyzed...
February 20, 2017: Medical Microbiology and Immunology
https://www.readbyqxmd.com/read/28220018/germline-variants-in-familial-pituitary-tumour-syndrome-genes-are-common-in-young-patients-and-families-with-additional-endocrine-tumours
#15
Sunita Mc De Sousa, Mark J McCabe, Kathy Wu, Tony Roscioli, Velimir Gayevskiy, Katelyn Brook, Lesley Rawlings, Hamish S Scott, Tanya J Thompson, Peter Earls, Anthony J Gill, Mark J Cowley, Marcel E Dinger, Ann I McCormack
Objective: Familial pituitary tumour syndromes (FPTS) account for 5% of pituitary adenomas. Multi-gene analysis via next generation sequencing (NGS) may unveil greater prevalence and inform clinical care. We aimed to identify germline variants in selected patients with pituitary adenomas using a targeted NGS panel. Design: We undertook a nation-wide cross-sectional study of patients with pituitary adenomas with onset ≤40 years of age and/or other personal/family history of endocrine neoplasia. A custom NGS panel was performed on germline DNA to interrogate eight FPTS genes...
February 20, 2017: European Journal of Endocrinology
https://www.readbyqxmd.com/read/28218388/the-new-neuromuscular-disease-related-with-defects-in-the-asc-1-complex-report-of-a-second-case-confirms-ascc1-involvement
#16
Jorge Oliveira, Márcia Martins, Rosário Pinto Leite, Mário Sousa, Rosário Santos
Next-generation sequencing technology aided the identification of the underlying genetic cause in a female newborn with a severe neuromuscular disorder. The patient presented generalized hypotonia, congenital bone fractures, lack of spontaneous movements and poor respiratory effort. She died within the first days of life. Karyotyping and screening for several genes related with neuromuscular diseases all tested negative. A male sibling was subsequently born with the same clinical presentation. Whole-exome sequencing was performed with variant filtering assuming a recessive disease model...
February 20, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/28218058/novel-approaches-for-diagnosing-inherited-platelet-disorders
#17
REVIEW
José María Bastida Bermejo, Jesús María Hernández-Rivas, José Ramón González-Porras
Inherited platelet disorders diagnosis is based on the clinical history and bleeding assessment tools. The laboratory functional assays as well as the molecular test to identify the pathogenic genetic variant are essential to confirm the accurate diagnosis of these disorders. Nowadays, the main challenges to developing a new diagnostic system are involved in reducing the samples' volume, and faster and more helpful analysis. Moreover, there are no widely available and standardised global tests. High throughput genetic testing such as next-generation sequencing has revolutionised DNA sequencing technologies as it allows the simultaneous and faster investigation of multiple genes at a manageable cost...
January 20, 2017: Medicina Clínica
https://www.readbyqxmd.com/read/28217697/the-association-between-bacteria-and-urinary-stones
#18
REVIEW
Andrew L Schwaderer, Alan J Wolfe
Urinary stone disease (USD) is an increasing clinical problem in both children and adults. One in ten individuals will experience a urinary stone, yet the mechanisms responsible for urinary stones remain largely unknown. Bacteria have long been recognized to contribute to struvite urinary stones; however, the role of bacteria in the development of the more common calcium oxalate (CaOx) and calcium phosphate (CaPhos) stones has not been extensively investigated. However, several findings do indicate a possible association between urinary stones and bacteria, including the high rate of urinary tract infections (UTI) in urinary stone patients and multiple case series of culture-positive urinary stones, including stones composed of CaOx or CaPhos...
January 2017: Annals of Translational Medicine
https://www.readbyqxmd.com/read/28216420/evaluation-of-rag1-mutations-in-an-adult-with-combined-immunodeficiency-and-progressive-multifocal-leukoencephalopathy
#19
Claudia Schröder, Niklas Baerlecken, Ulrich Pannicke, Thilo Dörk, Torsten Witte, Roland Jacobs, Matthias Stoll, Klaus Schwarz, Bodo Grimbacher, Reinhold E Schmidt, Faranaz Atschekzei
Here we describe novel mutations in recombination activation gene 1 (RAG1) in a compound heterozygous male patient with combined T and B cell immunodeficiency (CID). Clinical manifestations besides antibody deficiency included airway infections, granulomatosis and autoimmune features. He died at the age of 37 due to PML caused by JC virus infection. By targeted next-generation sequencing we detected post mortem in this patient three mutations in RAG1. One allele harbored two novel mutations (c.1123C>G, p...
February 16, 2017: Clinical Immunology: the Official Journal of the Clinical Immunology Society
https://www.readbyqxmd.com/read/28214514/detecting-circulating-tumor-dna-in-renal-cancer-an-open-challenge
#20
Claudia Corrò, Tomas Hejhal, Cédric Poyet, Tullio Sulser, Thomas Hermanns, Thomas Winder, Gerald Prager, Peter J Wild, Ian Frew, Holger Moch, Markus Rechsteiner
BACKGROUND: Detection of circulating tumor DNA (ctDNA) in blood of cancer patients is regarded as an important step towards personalized medicine and treatment monitoring. In the present study, we investigated the clinical applicability of ctDNA as liquid biopsy in renal cancer. METHODS: ctDNA in serum and plasma samples derived from ccRCC and colon cancer patients as well as ctDNA isolated from RCC xenografts with known VHL mutation status was investigated using next generation sequencing (NGS)...
February 15, 2017: Experimental and Molecular Pathology
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