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https://www.readbyqxmd.com/read/28429088/an-snp-panel-for-the-analysis-of-paternally-inherited-alleles-in-maternal-plasma-using-ion-torrent-pgm
#1
Donggui Yang, Hao Liang, Shaobin Lin, Qing Li, Xiaoyan Ma, Jun Gao, Hongyu Sun, Qingqing Chen, Jianzhu Wu, Xueling Ou
Researchers have sought to develop an effective protocol for paternity analysis using cell-free DNA (cfDNA) in maternal plasma. The use of massively parallel sequencing (MPS) technology for SNP testing is attractive because of its high-throughput capacity and resolution to single-base precision. In this study, we designed a customized SNP panel for cfDNA sequencing that includes 720 short amplicons (< 140 bp) targeting SNPs on the autosome and Y chromosome. The systemic performance was evaluated using the Ion Torrent PGM, indicating balanced coverage among most of the included loci, except for 78 poorly performing SNPs that were observed to have an inconsistent allele balance, lower coverage reads or high background signals...
April 20, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/28423360/tiam1-variants-improve-clinical-outcome-in-neuroblastoma
#2
Elena Sanmartín, Yania Yáñez, Victoria Fornés-Ferrer, José L Zugaza, Adela Cañete, Victoria Castel, Jaime Font de Mora
Identification of tumor driver mutations is crucial for improving clinical outcome using a personalized approach to the treatment of cancer. Neuroblastoma is a tumor of the peripheral sympathetic nervous system for which only a few driver alterations have been described including MYCN amplification and ALK mutations. We assessed 106 primary neuroblastoma tumors by next generation sequencing using a customized amplicon-based gene panel. Our results reveal that genetic variants in TIAM1 gene associate with better clinical outcome, suggesting a role for these TIAM1 variants in preventing progression of this disease...
April 3, 2017: Oncotarget
https://www.readbyqxmd.com/read/28356599/towards-personalized-medicine-in-melanoma-implementation-of-a-clinical-next-generation-sequencing-panel
#3
Blanca de Unamuno Bustos, Rosa Murria Estal, Gema Pérez Simó, Inmaculada de Juan Jimenez, Begoña Escutia Muñoz, Mercedes Rodríguez Serna, Victor Alegre de Miquel, Margarita Llavador Ros, Rosa Ballester Sánchez, Eduardo Nagore Enguídanos, Sarai Palanca Suela, Rafael Botella Estrada
Molecular diagnostics are increasingly performed routinely in the diagnosis and management of patients with melanoma due to the development of novel therapies that target specific genetic mutations. The development of next-generation sequencing (NGS) technologies has enabled to sequence multiple cancer-driving genes in a single assay, with improved sensitivity in mutation detection. The main objective of this study was the design and implementation of a melanoma-specific sequencing panel, and the identification of the spectrum of somatic mutations in a series of primary melanoma samples...
March 29, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28253235/simple-multiplexed-pcr-based-barcoding-of-dna-for-ultrasensitive-mutation-detection-by-next-generation-sequencing
#4
Anders Ståhlberg, Paul M Krzyzanowski, Matthew Egyud, Stefan Filges, Lincoln Stein, Tony E Godfrey
Detection of extremely rare variant alleles within a complex mixture of DNA molecules is becoming increasingly relevant in many areas of clinical and basic research, such as the detection of circulating tumor DNA in the plasma of cancer patients. Barcoding of DNA template molecules early in next-generation sequencing (NGS) library construction provides a way to identify and bioinformatically remove polymerase errors that otherwise make detection of these rare variants very difficult. Several barcoding strategies have been reported, but all require long and complex library preparation protocols...
April 2017: Nature Protocols
https://www.readbyqxmd.com/read/28218638/metagaap-a-novel-pipeline-to-estimate-community-composition-and-abundance-from-non-model-sequence-data
#5
Christopher Noune, Caroline Hauxwell
Next generation sequencing and bioinformatic approaches are increasingly used to quantify microorganisms within populations by analysis of 'meta-barcode' data. This approach relies on comparison of amplicon sequences of 'barcode' regions from a population with public-domain databases of reference sequences. However, for many organisms relevant 'barcode' regions may not have been identified and large databases of reference sequences may not be available. A workflow and software pipeline, 'MetaGaAP,' was developed to identify and quantify genotypes through four steps: shotgun sequencing and identification of polymorphisms in a metapopulation to identify custom 'barcode' regions of less than 30 polymorphisms within the span of a single 'read', amplification and sequencing of the 'barcode', generation of a custom database of polymorphisms, and quantitation of the relative abundance of genotypes...
February 17, 2017: Biology
https://www.readbyqxmd.com/read/28185542/analysis-of-amplicon-based-ngs-data-from-neurological-disease-gene-panels-a-new-method-for-allele-drop-out-management
#6
Susanna Zucca, Margherita Villaraggia, Stella Gagliardi, Gaetano Salvatore Grieco, Marialuisa Valente, Cristina Cereda, Paolo Magni
BACKGROUND: Amplicon-based targeted resequencing is a commonly adopted solution for next-generation sequencing applications focused on specific genomic regions. The reliability of such approaches rests on the high specificity and deep coverage, although sequencing artifacts attributable to PCR-like amplification can be encountered. Between these artifacts, allele drop-out, which is the preferential amplification of one allele, causes an artificial increase in homozygosity when heterozygous mutations fall on a primer pairing region...
November 8, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28137276/towards-standardization-of-next-generation-sequencing-of-ffpe-samples-for-clinical-oncology-intrinsic-obstacles-and-possible-solutions
#7
Maxim Ivanov, Konstantin Laktionov, Valery Breder, Polina Chernenko, Ekaterina Novikova, Ekaterina Telysheva, Sergey Musienko, Ancha Baranova, Vladislav Mileyko
BACKGROUND: Next generation sequencing has a potential to revolutionize the management of cancer patients within the framework of precision oncology. Nevertheless, lack of standardization decelerated entering of the technology into the clinical testing space. Here we dissected a number of common problems of NGS diagnostics in oncology and introduced ways they can be resolved. METHODS: DNA was extracted from 26 formalin fixed paraffin embedded (FFPE) specimens and processed with the TrueSeq Amplicon Cancer Panel (Illumina Inc, San Diego, California) targeting 48 cancer-related genes and sequenced in single run...
January 31, 2017: Journal of Translational Medicine
https://www.readbyqxmd.com/read/27986441/silent-genetic-alterations-identified-by-targeted-next-generation-sequencing-in-pheochromocytoma-paraganglioma-a-clinicopathological-correlations
#8
Suja Pillai, Vinod Gopalan, Chung Y Lo, Victor Liew, Robert A Smith, Alfred King Y Lam
AIMS: The goal of this pilot study was to develop a customized, cost-effective amplicon panel (Ampliseq) for target sequencing in a cohort of patients with sporadic phaeochromocytoma/paraganglioma. METHODS: Phaeochromocytoma/paragangliomas from 25 patients were analysed by targeted next-generation sequencing approach using an Ion Torrent PGM instrument. Primers for 15 target genes (NF1, RET, VHL, SDHA, SDHB, SDHC, SDHD, SDHAF2, TMEM127, MAX, MEN1, KIF1Bβ, EPAS1, CDKN2 & PHD2) were designed using ion ampliseq designer...
December 13, 2016: Experimental and Molecular Pathology
https://www.readbyqxmd.com/read/27940662/deep-targeted-exon-sequencing-reveals-renal-polymorphisms-associate-with-postexercise-hypotension-among-african-americans
#9
Linda S Pescatello, Elizabeth D Schifano, Garrett I Ash, Gregory A Panza, Lauren Lamberti, Ming-Hui Chen, Ved Deshpande, Amanda Zaleski, Paulo Farinatti, Beth A Taylor, Paul D Thompson
We found variants from the Angiotensinogen-Converting Enzyme (ACE), Angiotensin Type 1 Receptor (AGTR1), Aldosterone Synthase (CYP11B2), and Adducin (ADD1) genes exhibited intensity-dependent associations with the ambulatory blood pressure (BP) response following acute exercise, or postexercise hypotension (PEH). In a validation cohort, we sequenced exons from these genes for their associations with PEH Obese (30.9 ± 3.6 kg m(-2)) adults (n = 23; 61% African Americans [AF], 39% Caucasian) 42.0 ± 9...
October 2016: Physiological Reports
https://www.readbyqxmd.com/read/27940449/next-generation-sequencing-of-circulating-cell-free-dna-for-evaluating-mutations-and-gene-amplification-in-metastatic-breast-cancer
#10
Karen Page, David S Guttery, Daniel Fernandez-Garcia, Allison Hills, Robert K Hastings, Jinli Luo, Kate Goddard, Vedia Shahin, Laura Woodley-Barker, Brenda M Rosales, R Charles Coombes, Justin Stebbing, Jacqueline A Shaw
BACKGROUND: Breast cancer tissues are heterogeneous and show diverse somatic mutations and somatic copy number alterations (CNAs). We used a novel targeted next generation sequencing (NGS) panel to examine cell-free DNA (cfDNA) to detect somatic mutations and gene amplification in women with metastatic breast cancer (MBC). METHODS: cfDNA from pretreated patients (n = 42) and 9 healthy controls were compared with matched lymphocyte DNA by NGS, using a custom 158 amplicon panel covering hot-spot mutations and CNAs in 16 genes, with further validation of results by droplet digital PCR...
February 2017: Clinical Chemistry
https://www.readbyqxmd.com/read/27812551/a-modifiable-microarray-based-universal-sensor-providing-sample-to-results-automation
#11
Rubina Yasmin, Hui Zhu, Zongyuan Chen, Richard A Montagna
A microfluidic system consisting of generic single use cartridges which interface with a workstation allows the automatic performance of all necessary sample preparation, PCR analysis and interpretation of multiplex PCR assays. The cartridges contain a DNA array with 20 different 16mer DNA "universal" probes immobilized at defined locations. PCR amplicons can be detected via hybridization of user-defined "reporter" probes that are complementary at their 3' termini to one or more of the universal probes and complementary to the target amplicons at their 5' termini...
October 2016: Heliyon
https://www.readbyqxmd.com/read/27782820/comparison-between-two-amplicon-based-sequencing-panels-of-different-scales-in-the-detection-of-somatic-mutations-associated-with-gastric-cancer
#12
Yosuke Hirotsu, Yuichiro Kojima, Kenichiro Okimoto, Kenji Amemiya, Hitoshi Mochizuki, Masao Omata
BACKGROUND: Sequencing data from The Cancer Genome Atlas (TGCA), the International Cancer Genome Consortium and other research institutes have revealed the presence of genetic alterations in several tumor types, including gastric cancer. These data have been combined into a catalog of significantly mutated genes for each cancer type. However, it is unclear to what extent significantly mutated genes need to be examined for detecting genetic alterations in gastric cancer patients. Here, we constructed two custom-made sequencing panels of different scales, the Selective hotspot Panel and the Comprehensive Panel, to analyze genetic alterations in 21 resected specimens endoscopically obtained from 20 gastric cancer patients, and we assessed how many mutations were detectable using these different panels...
October 26, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27732553/rapid-screening-for-targeted-genetic-variants-via-high-resolution-melting-curve-analysis
#13
Allison B Chambliss, Molly Resnick, Athena K Petrides, William A Clarke, Mark A Marzinke
BACKGROUND: Current methods for the detection of single nucleotide polymorphisms (SNPs) associated with aberrant drug-metabolizing enzyme function are hindered by long turnaround times and specialized techniques and instrumentation. In this study, we describe the development and validation of a high-resolution melting (HRM) curve assay for the rapid screening of variant genotypes for targeted genetic polymorphisms in the cytochrome P450 enzymes CYP2C9, CYP2C19, and CYP3A5. METHODS: Sequence-specific primers were custom-designed to flank nine SNPs within the genetic regions of aforementioned drug metabolizing enzymes...
March 1, 2017: Clinical Chemistry and Laboratory Medicine: CCLM
https://www.readbyqxmd.com/read/27725301/genomic-diversity-and-phylogenetic-relationships-of-human-papillomavirus-16-hpv16-in-nepal
#14
Robert Makowsky, Pema Lhaki, Howard W Wiener, Madhav P Bhatta, Michael Cullen, Derek C Johnson, Rodney T Perry, Mingma Lama, Joseph F Boland, Meredith Yeager, Sarita Ghimire, Thomas R Broker, Sadeep Shrestha
OBJECTIVES/BACKGROUND: Sequence variants in HPV16 confer differences in oncogenic potential; however, to date there have not been any HPV sequence studies performed in Nepal. The objective of this study was to characterize HPV16 viral genome sequences from Nepal compared to a reference sequence in order to determine their lineages. Additionally, we sought to determine if five High-grade Squamous Intraepithelial Lesion (HSIL) subjects were genetically distinct from the non-HSIL subjects...
December 2016: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/27725223/next-generation-sequencing-of-human-opioid-receptor-genes-based-on-a-custom-ampliseq%C3%A2-library-and-ion-torrent-personal-genome-machine
#15
Dario Kringel, Jörn Lötsch
BACKGROUND: The opioid system is involved in the control of pain, reward, addictive behaviors and vegetative effects. Opioids exert their pharmacological actions through the agonistic binding at opioid receptors and variation in the coding genes has been found to modulate opioid receptor expression or signaling. However, a limited selection of functional opioid receptor variants is perceived as insufficient in providing a genetic diagnosis of clinical phenotypes and therefore, unrestricted access to opioid receptor genetics is required...
December 1, 2016: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/27685342/massively-parallel-sequencing-of-68-insertion-deletion-markers-identifies-novel-microhaplotypes-for-utility-in-human-identity-testing
#16
Frank R Wendt, David H Warshauer, Xiangpei Zeng, Jennifer D Churchill, Nicole M M Novroski, Bing Song, Jonathan L King, Bobby L LaRue, Bruce Budowle
Short tandem repeat (STR) loci are the traditional markers used for kinship, missing persons, and direct comparison human identity testing. These markers hold considerable value due to their highly polymorphic nature, amplicon size, and ability to be multiplexed. However, many STRs are still too large for use in analysis of highly degraded DNA. Small bi-allelic polymorphisms, such as insertions/deletions (INDELs), may be better suited for analyzing compromised samples, and their allele size differences are amenable to analysis by capillary electrophoresis...
September 20, 2016: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/27684276/next-generation-sequencing-for-the-detection-of-actionable-mutations-in-solid-and-liquid-tumors
#17
Alan J Fox, Matthew C Hiemenz, David B Lieberman, Shrey Sukhadia, Barnett Li, Joseph Grubb, Patrick Candrea, Karthik Ganapathy, Jianhua Zhao, David Roth, Evan Alley, Alison Loren, Jennifer J D Morrissette
As our understanding of the driver mutations necessary for initiation and progression of cancers improves, we gain critical information on how specific molecular profiles of a tumor may predict responsiveness to therapeutic agents or provide knowledge about prognosis. At our institution a tumor genotyping program was established as part of routine clinical care, screening both hematologic and solid tumors for a wide spectrum of mutations using two next-generation sequencing (NGS) panels: a custom, 33 gene hematological malignancies panel for use with peripheral blood and bone marrow, and a commercially produced solid tumor panel for use with formalin-fixed paraffin-embedded tissue that targets 47 genes commonly mutated in cancer...
September 20, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/27623220/assessing-myxozoan-presence-and-diversity-using-environmental-dna
#18
Hanna Hartikainen, David Bass, Andrew G Briscoe, Hazel Knipe, Andy J Green, Beth Okamura
Amplicon sequencing on a High Throughput Sequencing (HTS) platform (custom barcoding) was used to detect and characterise myxosporean communities in environmental DNA (eDNA) samples from marine and freshwater environments and in faeces of animals that may serve as hosts or whose prey may host myxosporean infections. A diversity of myxozoans in filtered water samples and in faeces of piscivores (otters and great cormorants) was detected, demonstrating the suitability of lineage-specific amplicons for characterising otherwise difficult to sample parasite communities...
September 10, 2016: International Journal for Parasitology
https://www.readbyqxmd.com/read/27620618/a-novel-integrated-forensic-microdevice-on-a-rotation-driven-platform-buccal-swab-to-str-product-in-less-than-2%C3%A2-h
#19
Jordan O Cox, Teresa Sikes DeCarmen, Yiwen Ouyang, Briony Strachan, Hillary Sloane, Cathey Connon, Kemper Gibson, Kimberly Jackson, James P Landers, Tracey Dawson Cruz
This work describes the development of a novel microdevice for forensic DNA processing of reference swabs. This microdevice incorporates an enzyme-based assay for DNA preparation, which allows for faster processing times and reduced sample handling. Infrared-mediated PCR (IR-PCR) is used for STR amplification using a custom reaction mixture, allowing for amplification of STR loci in 45 min while circumventing the limitations of traditional block thermocyclers. Uniquely positioned valves coupled with a simple rotational platform are used to exert fluidic control, eliminating the need for bulky external equipment...
December 2016: Electrophoresis
https://www.readbyqxmd.com/read/27499173/a-technical-application-of-quantitative-next-generation-sequencing-for-chimerism-evaluation
#20
Michelangelo Aloisio, Danilo Licastro, Luciana Caenazzo, Valentina Torboli, Angela D'Eustacchio, Giovanni Maria Severini, Emmanouil Athanasakis
At present, the most common genetic diagnostic method for chimerism evaluation following hematopoietic stem cell transplantation is microsatellite analysis by capillary electrophoresis. The main objective was to establish, through repeated analysis over time, if a complete chimerism was present, or if the mixed chimerism was stable, increasing or decreasing over time. Considering the recent introduction of next generation sequencing (NGS) in clinical diagnostics, a detailed study evaluating an NGS protocol was conducted, coupled with a custom bioinformatics pipeline, for chimerism quantification...
October 2016: Molecular Medicine Reports
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