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https://www.readbyqxmd.com/read/28315974/inherited-dna-repair-gene-mutations-detected-by-tumor-next-generation-sequencing-in-urinary-tract-cancers
#1
Sumati Gupta, Samantha Greenberg, Jade Grimmett, David Gaston, Neeraj Agarwal, William Lowrance, Joshua Schiffman, Wendy Kohlmann
Interpretation of next-generation sequencing (NGS) of tumor tissue in patients with advanced Urinary Tract Cancer (UTC) is performed to guide treatment selection but may reveal pathogenic variants with germline implications. We identified three patients with UTC with unexpected germline DNA repair gene mutations. Specific testing for these was prompted by the detection of these mutations by tumor NGS. All three patients were nonsmokers with a strong family history of cancer. Two patients had upper tract UTC with age at diagnosis in the 40 s...
March 18, 2017: Familial Cancer
https://www.readbyqxmd.com/read/28315634/comparing-mutation-calls-in-fixed-tumour-samples-between-the-affymetrix-oncoscan%C3%A2-array-and-pcr-based-next-generation-sequencing
#2
Henry M Wood, Joseph M Foster, Morag Taylor, Emma Tinkler-Hundal, Fiona S Togneri, Paula Wojtowicz, Assa Oumie, Karen G Spink, Fiona Brew, Philip Quirke
BACKGROUND: The importance of accurate and affordable mutation calling in fixed pathology samples is becoming increasingly important as we move into the era of personalised medicine. The Affymetrix OncoScan® Array platform is designed to produce actionable mutation calls in archival material. METHODS: We compared calls made using the OncoScan platform with calls made using a custom designed PCR panel followed by next-generation sequencing (NGS), in order to benchmark the sensitivity and specificity of the OncoScan calls in a large cohort of fixed tumour samples...
March 18, 2017: BMC Medical Genomics
https://www.readbyqxmd.com/read/28315471/a-mild-form-of-stickler-syndrome-type-ii-caused-by-mosaicism-of-col11a1
#3
Kathrine F Lauritsen, Dorte L Lildballe, Paul J Coucke, Rikke Monrad, Dorte A Larsen, Pernille A Gregersen
Stickler syndrome, a clinically as well as molecularly heterogeneous connective tissue disorder, is predominantly inherited in an autosomal dominant manner and is considered complete penetrant. Previously, mosaicism in Stickler syndrome has been reported in only a few cases. We describe a child with Stickler syndrome due to a novel splice site mutation in COL11A1. Initially, Sanger sequencing of both parents showed normal test results for the mutation. Due to mild phenotypic traits, the father was tested again using a more sensitive method (NGS), and was found to have low-grade mosaicism in various tissue samples (range 7-22% of the DNA)...
March 14, 2017: European Journal of Medical Genetics
https://www.readbyqxmd.com/read/28315400/multicolor-flow-cytometry-and-multi-gene-next-generation-sequencing-are-complementary-and-highly-predictive-for-relapse-in-acute-myeloid-leukemia-following-allogeneic-transplant
#4
Bartlomiej M Getta, Sean M Devlin, Ross L Levine, Maria E Arcila, Abhinita S Mohanty, Ahmet Zehir, Martin S Tallman, Sergio A Giralt, Mikhail Roshal
Minimal Residual disease (MRD) in acute myeloid leukemia (AML) is typically measured using multi-parameter flow cytometry (MFC). Detection of leukemia mutations using multi-gene next generation sequencing (NGS) can potentially be used to measure residual disease. We used a targeted 28-gene NGS panel to detect mutations and different-from-normal 10-colour MFC to measure MRD in AML patients before allogeneic hematopoietic stem cell transplant (HCT). Residual disease was defined when any abnormal blast population was detected using MFC and when any leukemia allele was detected with a variant allele frequency (VAF) ≥5% using NGS...
March 14, 2017: Biology of Blood and Marrow Transplantation
https://www.readbyqxmd.com/read/28306536/molecular-defects-identified-by-whole-exome-sequencing-in-a-child-with-atypical-mucopolysaccharidosis-iiib
#5
Qingwen Zeng, Yanjie Fan, Lili Wang, Zhuo Huang, Xuefan Gu, Yongguo Yu
BACKGROUND: Mucopolysaccharidosis IIIB (MPS IIIB) is a genetic disease characterized by mutations in the NAGLU gene, deficiency of α-N-acetylglucosaminidase, multiple congenital malformations and an increased susceptibility to malignancy. Because of the slow progressive nature of this disease and its atypical symptoms, the misdiagnosis of MPS IIIB is not rare in clinical practice. This misdiagnosis could be avoided by using next-generation sequencing (NGS) techniques, which have been shown to have superior performance for detecting mutations underlying rare inherited disorders in previous studies...
March 17, 2017: Journal of Pediatric Endocrinology & Metabolism: JPEM
https://www.readbyqxmd.com/read/28306340/a-potential-functional-association-between-mutant-bmpr2-and-primary-ovarian-insufficiency
#6
Liliana Catherine Patiño, Daniel Silgado, Paul Laissue
Primary ovarian insufficiency (POI) affects ~1% of women in the general population. Despite numerous attempts at identifying POI genetic aetiology, coding mutations in only a few genes have been functionally related to POI pathogenesis. It has been suggested that mutant BMPR2 might contribute towards the phenotype. Several BMP15 (a BMPR2 ligand) coding mutations in human species have been related to POI pathogenesis. The BMPR2 p.Ser987Phe mutation, previously identified in a woman with POI, might therefore lead to cellular dysfunction contributing to the phenotype...
March 17, 2017: Systems Biology in Reproductive Medicine
https://www.readbyqxmd.com/read/28303491/changing-the-therapeutic-landscape-in-non-small-cell-lung-cancers-the-evolution-of-comprehensive-molecular-profiling-improves-access-to-therapy
#7
REVIEW
Joshua K Sabari, Fernando Santini, Isabella Bergagnini, W Victoria Lai, Kathryn C Arbour, Alexander Drilon
Targeting genomic alterations has led to a paradigm shift in the treatment of patients with lung cancer. In an effort to better identify potentially actionable alterations that may predict response to FDA-approved and or investigational therapies, many centers have migrated towards performing targeted exome sequencing in patients with stage IV disease. The implementation of next-generation sequencing (NGS) in the evaluation of tumor tissue from patients with NSCLC has led to the discovery of targetable alterations in tumors that previously had no known actionable targets by less comprehensive profiling...
April 2017: Current Oncology Reports
https://www.readbyqxmd.com/read/28303008/an-analysis-of-echinacea-chloroplast-genomes-implications-for-future-botanical-identification
#8
Ning Zhang, David L Erickson, Padmini Ramachandran, Andrea R Ottesen, Ruth E Timme, Vicki A Funk, Yan Luo, Sara M Handy
Echinacea is a common botanical used in dietary supplements, primarily to treat upper respiratory tract infections and to support immune function. There are currently thought to be nine species in the genus Echinacea. Due to very low molecular divergence among sister species, traditional DNA barcoding has not been successful for differentiation of Echinacea species. Here, we present the use of full chloroplast genomes to distinguish between all 9 reported species. Total DNA was extracted from specimens stored at the National Museum of Natural History, Smithsonian Institution, which had been collected from the wild with species identification documented by experts in the field...
March 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28302568/mutational-profile-from-targeted-ngs-predicts-survival-in-ldct-screening-detected-lung-cancers
#9
Carla Verri, Cristina Borzi, Todd Holscher, Matteo Dugo, Andrea Devecchi, Katherine Drake, Stefano Sestini, Paola Suatoni, Elisa Romeo, Gabriella Sozzi, Ugo Pastorino, Mattia Boeri
BACKGROUND: The issue of overdiagnosis in low-dose computed tomography (LDCT)-screening trials could be addressed by the development of complementary biomarkers able to improve detection of aggressive disease. The mutation profile of LDCT screening-detected lung tumours is currently unknown. METHODS: Targeted next-generation sequencing was performed in 94 LDCT screening-detected lung tumours. Associations with clinicopathologic features, survival and the risk profile of a plasma microRNA signature classifier (MSC) were analyzed...
March 13, 2017: Journal of Thoracic Oncology
https://www.readbyqxmd.com/read/28300211/als-along-the-axons-expression-of-coding-and-noncoding-rna-differs-in-axons-of-als-models
#10
Nimrod Rotem, Iddo Magen, Ariel Ionescu, Noga Gershoni-Emek, Topaz Altman, Christopher J Costa, Tal Gradus, Metsada Pasmanik-Chor, Dianna E Willis, Iddo Z Ben-Dov, Eran Hornstein, Eran Perlson
Amyotrophic lateral sclerosis (ALS) is a multifactorial lethal motor neuron disease with no known treatment. Although the basic mechanism of its degenerative pathogenesis remains poorly understood, a subcellular spatial alteration in RNA metabolism is thought to play a key role. The nature of these RNAs remains elusive, and a comprehensive characterization of the axonal RNAs involved in maintaining neuronal health has yet to be described. Here, using cultured spinal cord (SC) neurons grown using a compartmented platform followed by next-generation sequencing (NGS) technology, we find that RNA expression differs between the somatic and axonal compartments of the neuron, for both mRNA and microRNA (miRNA)...
March 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28299895/deep-sequencing-and-variant-analysis-of-an-italian-pathogenic-field-strain-of-equine-infectious-anaemia-virus
#11
K Cappelli, R F Cook, V Stefanetti, F Passamonti, G L Autorino, M T Scicluna, M Coletti, A Verini Supplizi, S Capomaccio
Equine infectious anaemia virus (EIAV) is a lentivirus with an almost worldwide distribution that causes persistent infections in equids. Technical limitations have restricted genetic analysis of EIAV field isolates predominantly to gag sequences resulting in very little published information concerning the extent of inter-strain variation in pol, env and the three ancillary open reading frames (ORFs). Here, we describe the use of long-range PCR in conjunction with next-generation sequencing (NGS) for rapid molecular characterization of all viral ORFs and known transcription factor binding motifs within the long terminal repeat of two EIAV isolates from the 2006 Italian outbreak...
March 15, 2017: Transboundary and Emerging Diseases
https://www.readbyqxmd.com/read/28297627/clinical-and-technical-aspects-of-genomic-diagnostics-for-precision-oncology
#12
Yuri Sheikine, Frank C Kuo, Neal I Lindeman
The emergence of precision medicine has been predicated on significant recent advances in diagnostic technology, particularly the advent of next-generation sequencing (NGS). Although the chemical technology underlying NGS is complex, and the computational biology expertise required to build systems to facilely interpret the results is highly specialized, the variables involved in designing and deploying a genomic testing program for cancer can be readily understood and applied by understanding several basic considerations...
March 20, 2017: Journal of Clinical Oncology: Official Journal of the American Society of Clinical Oncology
https://www.readbyqxmd.com/read/28294317/the-spectrum-of-brca-mutations-and-characteristics-of-brca-associated-breast-cancers-in-china-screening-of-2991-patients-and-1043-controls-by-next-generation-sequencing
#13
Guan-Tian Lang, Jin-Xiu Shi, Xin Hu, Chen-Hui Zhang, Ling Shan, Chuan-Gui Song, Zhi-Gang Zhuang, A-Yong Cao, Hong Ling, Ke-Da Yu, Li Shan, Meng-Hong Sun, Xiao-Yan Zhou, Wei Huang, Zhi-Ming Shao
To characterize the prevalence of BRCA mutations and characteristics of BRCA carriers in China and to update the clinical recommendations for BRCA testing, we conducted a wide screen for BRCA mutations using next-generation sequencing (NGS). A total of 4,034 Chinese subjects were screened for germline BRCA1/2 mutations, including 2,991 breast cancer patients and 1,043 healthy individuals from the community enrolled as controls. We developed an NGS-based approach to perform BRCA1/2 screening. BRCA mutations were identified in 9...
March 14, 2017: International Journal of Cancer. Journal International du Cancer
https://www.readbyqxmd.com/read/28294287/learning-gene-regulatory-networks-from-next-generation-sequencing-data
#14
Bochao Jia, Suwa Xu, Guanghua Xiao, Vishal Lamba, Faming Liang
In recent years, next generation sequencing (NGS) has gradually replaced microarray as the major platform in measuring gene expressions. Compared to microarray, NGS has many advantages, such as less noise and higher throughput. However, the discreteness of NGS data also challenges the existing statistical methodology. In particular, there still lacks an appropriate statistical method for reconstructing gene regulatory networks using NGS data in the literature. The existing local Poisson graphical model method is not consistent and can only infer certain local structures of the network...
March 10, 2017: Biometrics
https://www.readbyqxmd.com/read/28293632/two-efficient-techniques-to-find-approximate-overlaps-between-sequences
#15
Maan Haj Rachid
The next-generation sequencing (NGS) technology outputs a huge number of sequences (reads) that require further processing. After applying prefiltering techniques in order to eliminate redundancy and to correct erroneous reads, an overlap-based assembler typically finds the longest exact suffix-prefix match between each ordered pair of the input reads. However, another trend has been evolving for the purpose of solving an approximate version of the overlap problem. The main benefit of this direction is the ability to skip time-consuming error-detecting techniques which are applied in the prefiltering stage...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28292978/validating-a-fully-automated-real-time-pcr-based-system-for-use-in-the-molecular-diagnostic-analysis-of-colorectal-carcinoma-a-comparison-with-ngs-and-ihc
#16
Richard Colling, Lai Mun Wang, Elizabeth Soilleux
BACKGROUND: Molecular testing is increasingly needed in colorectal carcinoma (CRC) and the current clinically relevant mutations are in BRAF, KRAS and NRAS. This study aimed to further validate a new alternative polymerase chain reaction (PCR) platform (Idylla, Biocartis) against existing next-generation sequencing (NGS) and immunohistochemistry (IHC) assays. METHODS: 56 Idylla tests were performed on 43 CRC cases, in a total of 74 comparisons against an NGS panel (Ion Torrent) and the VE1 (anti-BRAF) antibody IHC...
March 14, 2017: Journal of Clinical Pathology
https://www.readbyqxmd.com/read/28292732/alternating-hemiplegia-and-epilepsia-partialis-continua-a-new-phenotype-for-a-novel-compound-tbc1d24-mutation
#17
Francesca Ragona, Barbara Castellotti, Barbara Salis, Stefania Magri, Jacopo C DiFrancesco, Nardo Nardocci, Silvana Franceschetti, Cinzia Gellera, Tiziana Granata
Mutations in the TBC1D24 gene (MIM 613577) cause familial infantile myoclonic epilepsy (FIME; 605021) and early infantile epileptic encephalopathy-16 (EIEE16; 615338), both inherited with an autosomal recessive trait. The TBC1D24 gene encodes a member of the TBC family domain proteins, involved in cell signaling and oxidative stress resistance. We studied, by a Next Generation Sequencing (NGS) target re-sequencing gene approach, the DNA of a 5 year-old girl, affected by recurrent attacks of Alternating Hemiplegia (AH) and by recurrent episodes of Epilepsia Partialis Continua (EPC)...
March 6, 2017: Seizure: the Journal of the British Epilepsy Association
https://www.readbyqxmd.com/read/28290697/seafood-identification-in-multispecies-products-assessment-of-16srrna-cytb-and-coi-universal-primer-efficiency-as-preliminary-analytical-step-for-setting-up-metabarcoding-next-generation-sequencing-ngs-techniques
#18
Alice Giusti, Lara Tinacci, Carmen G Sotelo, Martina Marchetti, Alessandra Guidi, Wenjie Zheng, Andrea Armani
Few studies applying NGS have been conducted in the food inspection field, particularly on multispecies seafood products. A preliminary study screening the performance and the potential application in NGS analysis of 14 "universal primers" amplifying 16SrRNA, cytb and COI genes in fish and cephalopods was performed. Species used in surimi preparation were chosen as target. An in silico analysis was conducted to test primers' coverage capacity, by assessing mismatches (number and position) with the target sequences...
March 14, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/28290094/evaluating-the-calling-performance-of-a-rare-disease-ngs-panel-for-single-nucleotide-and-copy-number-variants
#19
P Cacheiro, A Ordóñez-Ugalde, B Quintáns, S Piñeiro-Hermida, J Amigo, M García-Murias, S I Pascual-Pascual, F Grandas, J Arpa, A Carracedo, M J Sobrido
INTRODUCTION: Variant detection protocols for clinical next-generation sequencing (NGS) need application-specific optimization. Our aim was to analyze the performance of single nucleotide variant (SNV) and copy number (CNV) detection programs on an NGS panel for a rare disease. METHODS: Thirty genes were sequenced in 83 patients with hereditary spastic paraplegia. The variant calls obtained with LifeScope, GATK UnifiedGenotyper and GATK HaplotypeCaller were compared with Sanger sequencing...
March 13, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28289279/next-gen-sequencing-identifies-non-coding-variation-disrupting-mirna-binding-sites-in-neurological-disorders
#20
P Devanna, X S Chen, J Ho, D Gajewski, S D Smith, A Gialluisi, C Francks, S E Fisher, D F Newbury, S C Vernes
Understanding the genetic factors underlying neurodevelopmental and neuropsychiatric disorders is a major challenge given their prevalence and potential severity for quality of life. While large-scale genomic screens have made major advances in this area, for many disorders the genetic underpinnings are complex and poorly understood. To date the field has focused predominantly on protein coding variation, but given the importance of tightly controlled gene expression for normal brain development and disorder, variation that affects non-coding regulatory regions of the genome is likely to play an important role in these phenotypes...
March 14, 2017: Molecular Psychiatry
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