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Next generation sequencing clinical

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https://www.readbyqxmd.com/read/28944580/biallelic-mutations-in-gpd1-gene-in-a-chinese-boy-mainly-presented-with-obesity-insulin-resistance-fatty-liver-and-short-stature
#1
Niu Li, Guoying Chang, Yufei Xu, Yu Ding, Guoqiang Li, Tingting Yu, Ruen Yao, Juan Li, Yiping Shen, Xiumin Wang, Jian Wang
Biallelic mutations in the GPD1 gene cause a rare autosomal recessive inherited disease known as transient infantile hypertriglyceridemia (OMIM #614480). To date, only five pathogenic variants have been reported in 15 patients from three studies. The clinical symptoms of the affected individuals present a certain degree of heterogeneity. Here, we describe a chinese adolescent patient who mainly presented with obesity, insulin resistance, fatty liver, and short stature. Targeted next-generation sequencing revealed a novel compound heterozygous variant in GPD1 gene (c...
September 25, 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28944238/targeted-sequencing-of-36-known-or-putative-colorectal-cancer-susceptibility-genes
#2
Melissa S DeRycke, Shanaka Gunawardena, Jessica R Balcom, Angela M Pickart, Lindsey A Waltman, Amy J French, Shannon McDonnell, Shaun M Riska, Zachary C Fogarty, Melissa C Larson, Sumit Middha, Bruce W Eckloff, Yan W Asmann, Matthew J Ferber, Robert W Haile, Steven Gallinger, Mark Clendenning, Christophe Rosty, Aung K Win, Daniel D Buchanan, John L Hopper, Polly A Newcomb, Loic Le Marchand, Ellen L Goode, Noralane M Lindor, Stephen N Thibodeau
BACKGROUND: Mutations in several genes predispose to colorectal cancer. Genetic testing for hereditary colorectal cancer syndromes was previously limited to single gene tests; thus, only a very limited number of genes were tested, and rarely those infrequently mutated in colorectal cancer. Next-generation sequencing technologies have made it possible to sequencing panels of genes known and suspected to influence colorectal cancer susceptibility. METHODS: Targeted sequencing of 36 known or putative CRC susceptibility genes was conducted for 1231 CRC cases from five subsets: (1) Familial Colorectal Cancer Type X (n = 153); (2) CRC unselected by tumor immunohistochemical or microsatellite stability testing (n = 548); (3) young onset (age <50 years) (n = 333); (4) proficient mismatch repair (MMR) in cases diagnosed at ≥50 years (n = 68); and (5) deficient MMR CRCs with no germline mutations in MLH1, MSH2, MSH6, or PMS2 (n = 129)...
September 2017: Molecular Genetics & Genomic Medicine
https://www.readbyqxmd.com/read/28944237/next-generation-sequencing-reveals-the-mutational-landscape-of-clinically-diagnosed-usher-syndrome-copy-number-variations-phenocopies-a-predominant-target-for-translational-read-through-and-pex26-mutated-in-heimler-syndrome
#3
Christine Neuhaus, Tobias Eisenberger, Christian Decker, Sandra Nagl, Cornelia Blank, Markus Pfister, Ingo Kennerknecht, Cornelie Müller-Hofstede, Peter Charbel Issa, Raoul Heller, Bodo Beck, Klaus Rüther, Diana Mitter, Klaus Rohrschneider, Ute Steinhauer, Heike M Korbmacher, Dagmar Huhle, Solaf M Elsayed, Hesham M Taha, Shahid M Baig, Heidi Stöhr, Markus Preising, Susanne Markus, Fabian Moeller, Birgit Lorenz, Kerstin Nagel-Wolfrum, Arif O Khan, Hanno J Bolz
BACKGROUND: Combined retinal degeneration and sensorineural hearing impairment is mostly due to autosomal recessive Usher syndrome (USH1: congenital deafness, early retinitis pigmentosa (RP); USH2: progressive hearing impairment, RP). METHODS: Sanger sequencing and NGS of 112 genes (Usher syndrome, nonsyndromic deafness, overlapping conditions), MLPA, and array-CGH were conducted in 138 patients clinically diagnosed with Usher syndrome. RESULTS: A molecular diagnosis was achieved in 97% of both USH1 and USH2 patients, with biallelic mutations in 97% (USH1) and 90% (USH2), respectively...
September 2017: Molecular Genetics & Genomic Medicine
https://www.readbyqxmd.com/read/28944235/assessing-risk-for-mendelian-disorders-in-a-bronx-population
#4
Guy diSibio, Kinnari Upadhyay, Philip Meyer, Carole Oddoux, Harry Ostrer
BACKGROUND: To identify variants likely responsible for Mendelian disorders among the three major ethnic groups in the Bronx that might be useful to include in genetic screening panels or whole exome sequencing filters and to estimate their likely prevalence in these populations. METHODS: Variants from a high-density oligonucleotide screen of 192 members from each of the three ethnic-national populations (African Americans, Puerto Ricans, and Dominicans) were evaluated for overlap with next generation sequencing data...
September 2017: Molecular Genetics & Genomic Medicine
https://www.readbyqxmd.com/read/28943896/a-large-chinese-pedigree-of-multiple-endocrine-neoplasia-type-2a-with-a-novel-c634y-d707e-germline-mutation-in-ret-exon-11
#5
Fanqian Lu, Xiaohong Chen, Yunlong Bai, Yaru Feng, Jian Wu
The present study identified the clinical features of the largest multiple endocrine neoplasia type 2 (MEN2) A pedigree from China, with a novel double missense rearranged during transfection (RET) mutation (C634Y/D707E). To the best of our knowledge, the D707E mutation has not been identified to date. In the present study, a total of 101 family members who originated from a large pedigree (134 members in total) underwent RET mutation screening by next-generation sequencing and polymerase chain reaction (PCR) amplification, followed by direct bidirectional DNA sequencing...
September 2017: Oncology Letters
https://www.readbyqxmd.com/read/28942073/update-on-the-management-of-infectious-keratitis
#6
REVIEW
Ariana Austin, Tom Lietman, Jennifer Rose-Nussbaumer
Infectious keratitis is a major global cause of visual impairment and blindness, often affecting marginalized populations. Proper diagnosis of the causative organism is critical, and although culture remains the prevailing diagnostic tool, newer techniques such as in vivo confocal microscopy are helpful for diagnosing fungus and Acanthamoeba. Next-generation sequencing holds the potential for early and accurate diagnosis even for organisms that are difficult to culture by conventional methods. Topical antibiotics remain the best treatment for bacterial keratitis, and a recent review found all commonly prescribed topical antibiotics to be equally effective...
September 20, 2017: Ophthalmology
https://www.readbyqxmd.com/read/28941617/the-effect-of-a-non-denaturing-detergent-and-a-guanidinium-based-inactivation-agent-on-the-viability-of-ebola-virus-in-mock-clinical-serum-samples
#7
J E Burton, L Easterbrook, J Pitman, D Anderson, S Roddy, D Bailey, R Vipond, C Bruce, A D Roberts
The 2014 Ebola outbreak in West Africa required the rapid testing of clinical material for the presence of potentially high titre Ebola virus (EBOV). Safe, fast and effective methods for the inactivation of such clinical samples are required so that rapid diagnostic tests including downstream analysis by RT-qPCR or nucleotide sequencing can be carried out. One of the most commonly used guanidinium - based denaturing agents, AVL (Qiagen) has been shown to fully inactivate EBOV once ethanol is added, however this is not compatible with the use of automated nucleic acid extraction systems...
September 20, 2017: Journal of Virological Methods
https://www.readbyqxmd.com/read/28940958/a-novel-neurog3-mutation-in-neonatal-diabetes-associated-with-a-neuro-intestinal-syndrome
#8
Suna Hancili, Amélie Bonnefond, Julien Philippe, Emmanuel Vaillant, Franck De Graeve, Olivier Sand, Kanetee Busiah, Jean-Jacques Robert, Michel Polak, Philippe Froguel, Ayla Güven, Martine Vaxillaire
Neonatal diabetes mellitus (NDM) is a rare form of non-autoimmune diabetes usually diagnosed in the first 6 months of life. Various genetic defects have been shown to cause NDM with diverse clinical presentations and variable severity. Among transcriptional factor genes associated with isolated or syndromic NDM, a few cases of homozygous mutations in the NEUROG3 gene have been reported, all mutated patients presenting with congenital malabsorptive diarrhea with or without diabetes at a variable age of onset from early life to childhood...
September 22, 2017: Pediatric Diabetes
https://www.readbyqxmd.com/read/28940310/single-center-experience-of-n-linked-congenital-disorders-of-glycosylation-with-a-summary-of-molecularly-characterized-cases-in-arabs
#9
Fatma Bastaki, Sami Bizzari, Sana Hamici, Pratibha Nair, Madiha Mohamed, Fatima Saif, Ethar Mustafa Malik, Mahmoud Taleb Al-Ali, Abdul Rezzak Hamzeh
Congenital disorders of glycosylation (CDG) represent an expanding group of conditions that result from defects in protein and lipid glycosylation. Different subgroups of CDG display considerable clinical and genetic heterogeneity due to the highly complex nature of cellular glycosylation. This is further complicated by ethno-geographic differences in the mutational landscape of each of these subgroups. Ten Arab CDG patients from Latifa Hospital in Dubai, United Arab Emirates, were assessed using biochemical (glycosylation status of transferrin) and molecular approaches (next-generation sequencing [NGS] and Sanger sequencing)...
September 21, 2017: Annals of Human Genetics
https://www.readbyqxmd.com/read/28939679/next-generation-sequencing-in-the-clinical-setting-clarifies-patient-characteristics-and-potential-actionability
#10
Cheyennedra C Bieg-Bourne, Sherri Z Millis, David E Piccioni, Paul T Fanta, Michael E Goldberg, Juliann Chmielecki, Barbara A Parker, Razelle Kurzrock
Enhancements in clinical-grade next-generation sequencing (NGS) have fueled the advancement of precision medicine in the clinical oncology field. Here we survey the molecular profiles of 1,113 patients with diverse malignancies who successfully underwent clinical-grade NGS (236 to 404 genes) in an academic tertiary cancer center. Among the individual tumors examined, the majority showed at least one detectable alteration (97.2%). Amongst 2,045 molecular aberrations was involvement of 302 distinct genes. The most commonly altered genes were TP53 (47...
September 22, 2017: Cancer Research
https://www.readbyqxmd.com/read/28939216/a-targeted-next-generation-sequencing-panel-reveals-novel-mutations-in-japanese-patients-with-primary-ciliary-dyskinesia
#11
Kazuhiko Takeuchi, Masako Kitano, Hiroko Kiyotoshi, Koji Ikegami, Satoru Ogawa, Makoto Ikejiri, Mizuho Nagao, Takao Fujisawa, Kaname Nakatani
OBJECTIVE: Primary ciliary dyskinesia (PCD) is a rare genetic disorder caused by functional impairment of cilia throughout the body. The early diagnosis of PCD is important for the prevention of long-term sequelae; however, this is often challenging because of the phenotypic heterogeneity of PCD and difficulty in genetic analysis. The majority of PCD patients in Japan are not diagnosed properly. To diagnose PCD more accurately, we developed a targeted next-generation sequencing (NGS) panel...
September 19, 2017: Auris, Nasus, Larynx
https://www.readbyqxmd.com/read/28938744/an-improved-ivm-method-for-cumulus-oocyte-complexes-from-small-follicles-in-polycystic-ovary-syndrome-patients-enhances-oocyte-competence-and-embryo-yield
#12
F Sánchez, F Lolicato, S Romero, M De Vos, H Van Ranst, G Verheyen, E Anckaert, J E J Smitz
STUDY QUESTION: Are meiotic and developmental competence of human oocytes from small (2-8 mm) antral follicles improved by applying an optimized IVM method involving a prematuration step in presence of C-Type Natriuretic Peptide (CNP) followed by a maturation step in presence of FSH and Amphiregulin (AREG)? SUMMARY ANSWER: A strategy involving prematuration culture (PMC) in the presence of CNP followed by IVM using FSH + AREG increases oocyte maturation potential leading to a higher availability of Day 3 embryos and good-quality blastocysts for single embryo transfer...
October 1, 2017: Human Reproduction
https://www.readbyqxmd.com/read/28938622/profiling-cancer-related-gene-mutations-in-oral-squamous-cell-carcinoma-from-japanese-patients-by-targeted-amplicon-sequencing
#13
Takafumi Nakagaki, Miyuki Tamura, Kenta Kobashi, Ryota Koyama, Hisayo Fukushima, Tomoko Ohashi, Masashi Idogawa, Kazuhiro Ogi, Hiroyoshi Hiratsuka, Takashi Tokino, Yasushi Sasaki
Somatic mutation analysis is a standard practice in the study of human cancers to identify mutations that cause therapeutic sensitization and resistance. We performed comprehensive genomic analyses that used PCR target enrichment and next-generation sequencing on Ion Proton semiconductor sequencers. Forty-seven oral squamous cell carcinoma (OSCC) samples and their corresponding noncancerous tissues were used for multiplex PCR amplification to obtain targeted coverage of the entire coding regions of 409 cancer-related genes (covered regions: 95...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28938416/pancreatic-histopathology-of-human-monogenic-diabetes-due-to-causal-variants-in-kcnj11-hnf1a-gata6-and-lmna
#14
May Sanyoura, Laura Jacobsen, David Carmody, Daniela Del Gaudio, Gorka Alkorta-Aranburu, Kelly Arndt, Ying Ying Hu, Frances Kobiernicki, Irina Kusmartseva, Mark A Atkinson, Louis H Philipson, Desmond Schatz, Martha Campbell-Thompson, Siri Atma W Greeley
Context: Monogenic diabetes is thought to account for 2% of all diabetes cases but most patients are misdiagnosed as type 1 or type 2 diabetes. To date, little is known about the histopathological features of pancreases from patients with monogenic diabetes. Objective: Retrospective study of the JDRF Network for Pancreatic Organ donors with Diabetes biorepository was used to identify possible cases with monogenic diabetes and to compare effects of genetic variants on pancreas histology...
August 16, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/28938278/whole-exome-sequencing-in-inborn-errors-of-immunity-use-the-power-but-mind-the-limits
#15
Giorgia Bucciol, Erika Van Nieuwenhove, Leen Moens, Yuval Itan, Isabelle Meyts
PURPOSE OF REVIEW: Next-generation sequencing, especially whole exome sequencing (WES), has revolutionized the molecular diagnosis of inborn errors of immunity. This review summarizes the generation and analysis of next-generation sequencing data. RECENT FINDINGS: The focus is on prioritizing strategies for unveiling the potential disease-causing variant. We also highlighted oversights and imperfections of WES and targeted panel sequencing, as well as the need for functional validation...
September 21, 2017: Current Opinion in Allergy and Clinical Immunology
https://www.readbyqxmd.com/read/28933999/minimal-residual-disease-assessment-in-lymphoma-methods-and-applications
#16
Alex F Herrera, Philippe Armand
Standard methods for disease response assessment in patients with lymphoma, including positron emission tomography and computed tomography scans, are imperfect. In other hematologic malignancies, particularly leukemias, the ability to detect minimal residual disease (MRD) is increasingly influencing treatment paradigms. However, in many subtypes of lymphoma, the application of MRD assessment techniques, like flow cytometry or polymerase chain reaction-based methods, has been challenging because of the absence of readily detected circulating disease or canonic chromosomal translocations...
September 21, 2017: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28933735/clinical-outcomes-and-co-occurring-mutations-in-patients-with-runx1-mutated-acute-myeloid-leukemia
#17
Maliha Khan, Jorge Cortes, Tapan Kadia, Kiran Naqvi, Mark Brandt, Sherry Pierce, Keyur P Patel, Gautam Borthakur, Farhad Ravandi, Marina Konopleva, Steven Kornblau, Hagop Kantarjian, Kapil Bhalla, Courtney D DiNardo
(1) Runt-related transcription factor 1 (RUNX1) mutations in acute myeloid leukemia (AML) are often associated with worse prognosis. We assessed co-occurring mutations, response to therapy, and clinical outcomes in patients with and without mutant RUNX1 (mRUNX1); (2) We analyzed 328 AML patients, including 177 patients younger than 65 years who received intensive chemotherapy and 151 patients >65 years who received hypomethylating agents. RUNX1 and co-existing mutations were identified using next-generation sequencing; (3) RUNX1 mutations were identified in 5...
July 26, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28933684/screening-of-primary-gp120-immunogens-to-formulate-the-next-generation-polyvalent-dna-prime-protein-boost-hiv-1-vaccines
#18
Shixia Wang, Te-Hui Wu, Anthony Hackett, Veronica Efros, Yan Wang, Dong Han, Aaron Wallace, Yuxin Chen, Guangnan Hu, Shuying Liu, Paul Clapham, James Arthos, David Montefiori, Shan Lu
Our previous preclinical studies and a Phase I clinical trial DP6-001 have indicated that a polyvalent Env formulation was able to elicit broadly reactive antibody responses including low titer neutralizing antibody responses against viral isolates of subtypes A, B, C and AE. In the current report, a panel of 62 gp120 immunogens were screened in a rabbit model to identify gp120 immunogens that can elicit improved binding and neutralizing antibody responses and some of them can be included in the next polyvalent formulation...
September 21, 2017: Human Vaccines & Immunotherapeutics
https://www.readbyqxmd.com/read/28932590/primary-pulmonary-malignant-fibrous-histiocytoma-case-report-and-literature-review
#19
Xiongfei Li, Renwang Liu, Tao Shi, Shangwen Dong, Fan Ren, Fan Yang, Dian Ren, Haiyang Fan, Sen Wei, Gang Chen, Jun Chen, Song Xu
Malignant fibrous histiocytoma (MFH) is an aggressive soft tissue sarcoma known to occur in various organs. Primary MFH arising in the lung is quite rare. Herein we report a case of a 61-year-old male with primary pulmonary MFH and explore the underlying molecular mechanisms by next-generation sequencing (NGS). Five gene mutations in TSC2, ARID1B, CDK8, KDM5C and CASP8 were detected, and the mTOR inhibitor might be an effective treatment for this patient. In addition, we reviewed the scientific literature of approximately 23 primary pulmonary MFH case reports since 1990 and summarized the clinical features and prognosis of this rare pulmonary malignant tumor...
August 2017: Journal of Thoracic Disease
https://www.readbyqxmd.com/read/28931680/molecular-evolution-of-herpes-simplex-virus-2-complete-genomes-comparison-between-primary-and-recurrent-infections
#20
Miguel A Minaya, Travis Jensen, Johannes Goll, Maria Korom, Sree H Datla, Robert B Belshe, Lynda A Morrison
Herpes simplex virus (HSV)-1 and -2 are large, double-stranded DNA viruses that cause lifelong persistent infections characterized by periods of quiescence and recurrent disease. How HSV evolves within an infected individual experiencing multiple episodes of reactivation over time is not known. We determined genome sequences of viruses isolated from two subjects in the Herpevac Trial for Women who experienced primary HSV-2 genital disease and compared them with sequences of viruses isolated from the subsequent fifth or sixth episode of recurrent disease in the same individuals...
September 20, 2017: Journal of Virology
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