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https://www.readbyqxmd.com/read/28649937/the-genetics-of-platelet-count-and-volume-in-humans
#1
John D Eicher, Guillaume Lettre, Andrew D Johnson
The last decade has witnessed an explosion in the depth, variety, and amount of human genetic data that can be generated. This revolution in technical and analytical capacities has enabled the genetic investigation of human traits and disease in thousands to now millions of participants. Investigators have taken advantage of these advancements to gain insight into platelet biology and the platelet's role in human disease. To do so, large human genetics studies have examined the association of genetic variation with two quantitative traits measured in many population and patient based cohorts: platelet count (PLT) and mean platelet volume (MPV)...
June 26, 2017: Platelets
https://www.readbyqxmd.com/read/28647232/determination-of-water-environment-standards-based-on-water-quality-criteria-in-china-limitations-and-feasibilities
#2
Tieyu Wang, Yunqiao Zhou, Cencen Bi, Yonglong Lu, Guizhen He, John P Giesy
There is a need to formulate water environment standards (WESs) from the current water quality criteria (WQC) in China. To this end, we briefly summarize typical mechanisms applied in several countries with longer histories of developing WESs, and three limitations to formulating WESs in China were identified. After analyzing the feasibility factors including economic development, scientific support capability and environmental policies, we realized that China is still not ready for a complete change from its current nation-wide unified WES system to a local-standard-based system...
July 2017: Journal of Environmental Sciences (China)
https://www.readbyqxmd.com/read/28644138/comparative-analysis-of-primary-versus-relapse-refractory-dlbcl-identifies-shifts-in-mutation-spectrum
#3
Danielle M Greenawalt, Winnie S Liang, Sakina Saif, Justin Johnson, Petar Todorov, Austin Dulak, Daniel Enriquez, Rebecca Halperin, Ambar Ahmed, Vladislav Saveliev, John Carpten, David Craig, J Carl Barrett, Brian Dougherty, Michael Zinda, Stephen Fawell, Jonathan R Dry, Kate Byth
Current understanding of the mutation spectrum of relapsed/refractory (RR) tumors is limited. We performed whole exome sequencing (WES) on 47 diffuse large B cell lymphoma (DLBCL) tumors that persisted after R-CHOP treatment, 8 matched to primary biopsies. We compared genomic alterations from the RR cohort against two treatment-naïve DLBCL cohorts (n=112). While the overall number and types of mutations did not differ significantly, we identified frequency changes in DLBCL driver genes. The overall frequency of MYD88 mutant samples increased (12% to 19%), but we noted a decrease in p...
June 15, 2017: Oncotarget
https://www.readbyqxmd.com/read/28640243/in-depth-investigations-of-adolescents-and-adults-with-holoprosencephaly-identify-unique-characteristics
#4
Karin Weiss, Paul Kruszka, Maria J Guillen Sacoto, Yonit A Addissie, Donald W Hadley, Casey K Hadsall, Bethany Stokes, Ping Hu, Erich Roessler, Beth Solomon, Edythe Wiggs, Audrey Thurm, Robert B Hufnagel, Wadih M Zein, Jin S Hahn, Elaine Stashinko, Eric Levey, Debbie Baldwin, Nancy J Clegg, Mauricio R Delgado, Maximilian Muenke
PurposeWith improved medical care, some individuals with holoprosencephaly (HPE) are surviving into adulthood. We investigated the clinical manifestations of adolescents and adults with HPE and explored the underlying molecular causes.MethodsParticipants included 20 subjects 15 years of age and older. Clinical assessments included dysmorphology exams, cognitive testing, swallowing studies, ophthalmic examination, and brain magnetic resonance imaging. Genetic testing included chromosomal microarray, Sanger sequencing for SHH, ZIC2, SIX3, and TGIF, and whole-exome sequencing (WES) of 10 trios...
June 22, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28626473/clinical-applicability-of-whole-exome-sequencing-exemplified-by-a-study-in-young-adults-with-the-advanced-cryptogenic-cholestatic-liver-diseases
#5
Maria Kulecka, Andrzej Habior, Agnieszka Paziewska, Krzysztof Goryca, Michalina Dąbrowska, Filip Ambrozkiewicz, Bożena Walewska-Zielecka, Andrzej Gabriel, Michal Mikula, Jerzy Ostrowski
BACKGROUND: The proper use of new medical tests in clinical practice requires the establishment of their value and range of diagnostic usefulness. While whole-exome sequencing (WES) has already entered the medical practice, recognizing its diagnostic usefulness in multifactorial diseases has not yet been achieved. AIMS: The objective of this study was to establish usability of WES in determining genetic background of chronic cholestatic liver disease (CLD) in young patients...
2017: Gastroenterology Research and Practice
https://www.readbyqxmd.com/read/28624499/evaluation-of-whole-exome-sequencing-by-targeted-gene-sequencing-and-sanger-sequencing
#6
Ya-Sian Chang, Hsien-Da Huang, Kun-Tu Yeh, Jan-Gowth Chang
BACKGROUND: Targeted gene sequencing (TGS) and whole exome sequencing (WES) are being used in clinical testing in laboratories. We compared the performances of TGS and WES using the same DNA samples. METHODS: DNA was extracted from 10 endometrial tumor tissue specimens. Sequencing were performed with an Illumina HiSeq 2000. We randomly selected variants to confirm through Sanger sequencing or mutant-enriched PCR with Sanger sequencing. RESULTS: We found that the variants identified in both TGS and WES were true positives (47/47), regardless of the sequencing depth...
June 15, 2017: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/28617738/the-whitaker-classification-of-craniosynostosis-outcomes-an-assessment-of-inter-rater-reliability
#7
Ari M Wes, Sanjay Naran, James Sun, Daniel Mazzaferro, Wen Xu, Phuong Nguyen, Linton A Whitaker, Scott P Bartlett, Jesse A Taylor
PURPOSE: The Whitaker classification (WC) is a simple and widely used system for describing aesthetic outcomes after craniosynostosis surgery. The purpose of this study is to evaluate its inter-rater reliability for patients who have undergone frontal-orbital surgery. METHODS: A retrospective review of patients with craniosynostosis who underwent surgical intervention at a tertiary referral center was conducted. Inclusion criteria were: single-suture craniosynostosis, surgical intervention before age two years, and photographs taken prior to revisions between 5 and 20 years of age...
June 14, 2017: Plastic and Reconstructive Surgery
https://www.readbyqxmd.com/read/28614815/a-case-of-pulmonary-langerhans-cell-sarcoma-simultaneously-diagnosed-with-cutaneous-langerhans-cell-histiocytosis-studied-by-whole-exome-sequencing
#8
Si-Wook Kim, Moon Ki Choi, Hye Sook Han, Hyojin Song, Youngil Koh, Seung-Myoung Son, Ok-Jun Lee, Ji Yeoun Lee, Ki Man Lee, Ki Hyeong Lee, Jihyun Kwon
Langerhans cell histiocytosis (LCH) and Langerhans cell sarcoma (LCS) are clonal proliferations of Langerhans-type cells. Unlike in LCH, the pathophysiology and clinical course of LCS are unclear due to its rarity. Here, we report the case of a 73-year-old male patient who was diagnosed with cutaneous LCH and pulmonary LCS at the same time. Pathological review of these 2 tumors revealed similar immunohistochemical findings. However, the tumor cells in LCS had more aggressive cytological features than those in LCH...
June 15, 2017: Acta Haematologica
https://www.readbyqxmd.com/read/28611392/targeted-sequencing-of-both-dna-strands-barcoded-and-captured-individually-by-rna-probes-to-identify-genome-wide-ultra-rare-mutations
#9
Qing Wang, Xu Wang, Pheobe S Tang, Grace M O'leary, Ming Zhang
Next Generation Sequencing (NGS) has been widely implemented in biological research and has made a profound impact on patient care. One of the essential NGS applications is to identify disease-causing sequence variants, where high coverage and accuracy are needed. Here, we reported a novel NGS pipeline, termed a Sequencing System of Digitalized Barcode Encrypted Single-stranded Library from Extremely Low (quality and quantity) DNA Input with Probe-based DNA Enrichment by RNA probes targeting DNA duplex (DEEPER-Seq)...
June 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28609495/pink-and-white-esthetics-of-a-new-zirconia-implant-a-6-month-to-8-year-follow-up
#10
Deirdre G Beekmans, Bart Rmn Beekmans, Marco S Cune
The aim of this study was to analyze changes in pink and white esthetics in the anterior zone through evaluation of an immediately placed zirconia implant using the Pink and White Esthetic Scores (PES and WES) in 20 patients. Two clinical photographs were compared: one taken directly after placement of the permanent crown (mean PES = 12.8; mean WES = 8.5) and the other taken at a later time (mean PES = 12.8; mean WES = 8.6; not significant). Volunteers found it difficult to correctly identify the implant. Patients completed a questionnaire regarding the pink and white implant esthetics...
July 2017: International Journal of Periodontics & Restorative Dentistry
https://www.readbyqxmd.com/read/28608921/whole-exome-sequencing-reveals-critical-genes-underlying-metastasis-in-esophageal-squamous-cell-carcinoma
#11
Wei Dai, Josephine Mun Yee Ko, Sheyne Sta Ana Choi, Zhouyou Yu, Luwen Ning, Hong Zheng, Vinod Gopalan, Kin Tak Chan, Nikki Pui-Yue Lee, Kwok Wah Chan, Simon Ying-Kit Law, Alfred King-Yin Lam, Maria Li Lung
Esophageal squamous cell carcinoma (ESCC) is one of the most lethal cancers due to a high frequency of metastasis. However, little is known about the genomic landscape of metastatic ESCC. To identify the genetic alterations that underlie ESCC metastasis, whole-exome sequencing (WES) was performed for 41 primary tumors and 15 lymph nodes (LNs) with metastatic ESCC. Eleven cases included matched primary tumors, synchronous LN metastases and non-neoplastic mucosa. Approximately 50-76% of the mutations identified in primary tumors appeared in the synchronous LN metastases...
June 13, 2017: Journal of Pathology
https://www.readbyqxmd.com/read/28608869/an-ecoregion-based-approach-to-protecting-half-the-terrestrial-realm
#12
COMMENT
Eric Dinerstein, David Olson, Anup Joshi, Carly Vynne, Neil D Burgess, Eric Wikramanayake, Nathan Hahn, Suzanne Palminteri, Prashant Hedao, Reed Noss, Matt Hansen, Harvey Locke, Erle C Ellis, Benjamin Jones, Charles Victor Barber, Randy Hayes, Cyril Kormos, Vance Martin, Eileen Crist, Wes Sechrest, Lori Price, Jonathan E M Baillie, Don Weeden, Kierán Suckling, Crystal Davis, Nigel Sizer, Rebecca Moore, David Thau, Tanya Birch, Peter Potapov, Svetlana Turubanova, Alexandra Tyukavina, Nadia de Souza, Lilian Pintea, José C Brito, Othman A Llewellyn, Anthony G Miller, Annette Patzelt, Shahina A Ghazanfar, Jonathan Timberlake, Heinz Klöser, Yara Shennan-Farpón, Roeland Kindt, Jens-Peter Barnekow Lillesø, Paulo van Breugel, Lars Graudal, Maianna Voge, Khalaf F Al-Shammari, Muhammad Saleem
We assess progress toward the protection of 50% of the terrestrial biosphere to address the species-extinction crisis and conserve a global ecological heritage for future generations. Using a map of Earth's 846 terrestrial ecoregions, we show that 98 ecoregions (12%) exceed Half Protected; 313 ecoregions (37%) fall short of Half Protected but have sufficient unaltered habitat remaining to reach the target; and 207 ecoregions (24%) are in peril, where an average of only 4% of natural habitat remains. We propose a Global Deal for Nature-a companion to the Paris Climate Deal-to promote increased habitat protection and restoration, national- and ecoregion-scale conservation strategies, and the empowerment of indigenous peoples to protect their sovereign lands...
June 1, 2017: Bioscience
https://www.readbyqxmd.com/read/28608148/hypoplastic-left-heart-syndrome-sequencing-reveals-a-novel-notch1-mutation-in-a-family-with-single-ventricle-defects
#13
Matthew D Durbin, Adrian G Cadar, Charles H Williams, Yan Guo, David P Bichell, Yan Ru Su, Charles C Hong
Hypoplastic left heart syndrome (HLHS) has been associated with germline mutations in 12 candidate genes and a recurrent somatic mutation in HAND1 gene. Using targeted and whole exome sequencing (WES) of heart tissue samples from HLHS patients, we sought to estimate the prevalence of somatic and germline mutations associated with HLHS. We performed Sanger sequencing of the HAND1 gene on 14 ventricular (9 LV and 5 RV) samples obtained from HLHS patients, and WES of 4 LV, 2 aortic, and 4 matched PBMC samples, analyzing for sequence discrepancy...
June 12, 2017: Pediatric Cardiology
https://www.readbyqxmd.com/read/28601870/restricted-ventilation-associated-with-reduced-neurodevelopmental-impairment-in-preterm-infants
#14
Roseanne J S Vliegenthart, Wes Onland, Aleid G van Wassenaer-Leemhuis, Anne P M De Jaegere, Cornelieke S H Aarnoudse-Moens, Anton H van Kaam
BACKGROUND AND OBJECTIVE: Restrictive use of invasive mechanical ventilation (IMV) in preterm infants reduces the risk of bronchopulmonary dysplasia (BPD). Our objective was to determine its effect on neurodevelopmental impairment (NDI) at 24 months' corrected age (CA). METHODS: This retrospective single-center cohort study included all patients with a gestational age <30 weeks born in 2004/2005 (epoch 1) and 2010/2011 (epoch 2). In epoch 2, we introduced a policy of restriction on IMV and liberalized the use of respiratory stimulants in the delivery room and neonatal intensive care...
June 10, 2017: Neonatology
https://www.readbyqxmd.com/read/28601352/comprehensive-genomic-characterization-of-upper-tract-urothelial-carcinoma
#15
Tyler J Moss, Yuan Qi, Liu Xi, Bo Peng, Tae-Beom Kim, Nader E Ezzedine, Maribel E Mosqueda, Charles C Guo, Bogdan A Czerniak, Michael Ittmann, David A Wheeler, Seth P Lerner, Surena F Matin
BACKGROUND: Upper urinary tract urothelial cancer (UTUC) may have unique etiologic and genomic factors compared to bladder cancer. OBJECTIVE: To characterize the genomic landscape of UTUC and provide insights into its biology using comprehensive integrated genomic analyses. DESIGN, SETTING, AND PARTICIPANTS: We collected 31 untreated snap-frozen UTUC samples from two institutions and carried out whole-exome sequencing (WES) of DNA, RNA sequencing (RNAseq), and protein analysis...
June 7, 2017: European Urology
https://www.readbyqxmd.com/read/28600779/the-landscape-of-genetic-diseases-in-saudi-arabia-based-on-the-first-1000-diagnostic-panels-and-exomes
#16
Dorota Monies, Mohamed Abouelhoda, Moeenaldeen AlSayed, Zuhair Alhassnan, Maha Alotaibi, Husam Kayyali, Mohammed Al-Owain, Ayaz Shah, Zuhair Rahbeeni, Mohammad A Al-Muhaizea, Hamad I Alzaidan, Edward Cupler, Saeed Bohlega, Eissa Faqeih, Maha Faden, Banan Alyounes, Dyala Jaroudi, Ewa Goljan, Hadeel Elbardisy, Asma Akilan, Renad Albar, Hesham Aldhalaan, Shamshad Gulab, Aziza Chedrawi, Bandar K Al Saud, Wesam Kurdi, Nawal Makhseed, Tahani Alqasim, Heba Y El Khashab, Hamoud Al-Mousa, Amal Alhashem, Imaduddin Kanaan, Talal Algoufi, Khalid Alsaleem, Talal A Basha, Fathiya Al-Murshedi, Sameena Khan, Adila Al-Kindy, Maha Alnemer, Sami Al-Hajjar, Suad Alyamani, Hasan Aldhekri, Ali Al-Mehaidib, Rand Arnaout, Omar Dabbagh, Mohammad Shagrani, Dieter Broering, Maha Tulbah, Amal Alqassmi, Maisoon Almugbel, Mohammed AlQuaiz, Abdulaziz Alsaman, Khalid Al-Thihli, Raashda A Sulaiman, Wajeeh Al-Dekhail, Abeer Alsaegh, Fahad A Bashiri, Alya Qari, Suzan Alhomadi, Hisham Alkuraya, Mohammed Alsebayel, Muddathir H Hamad, Laszlo Szonyi, Faisal Abaalkhail, Sulaiman M Al-Mayouf, Hamad Almojalli, Khalid S Alqadi, Hussien Elsiesy, Taghreed M Shuaib, Mohammed Zain Seidahmed, Ibraheem Abosoudah, Hana Akleh, Abdulaziz AlGhonaium, Turki M Alkharfy, Fuad Al Mutairi, Wafa Eyaid, Abdullah Alshanbary, Farrukh R Sheikh, Fahad I Alsohaibani, Abdullah Alsonbul, Saeed Al Tala, Soher Balkhy, Randa Bassiouni, Ahmed S Alenizi, Maged H Hussein, Saeed Hassan, Mohamed Khalil, Brahim Tabarki, Saad Alshahwan, Amira Oshi, Yasser Sabr, Saad Alsaadoun, Mustafa A Salih, Sarar Mohamed, Habiba Sultana, Abdullah Tamim, Moayad El-Haj, Saif Alshahrani, Dalal K Bubshait, Majid Alfadhel, Tariq Faquih, Mohamed El-Kalioby, Shazia Subhani, Zeeshan Shah, Nabil Moghrabi, Brian F Meyer, Fowzan S Alkuraya
In this study, we report the experience of the only reference clinical next-generation sequencing lab in Saudi Arabia with the first 1000 families who span a wide-range of suspected Mendelian phenotypes. A total of 1019 tests were performed in the period of March 2016-December 2016 comprising 972 solo (index only), 14 duo (parents or affected siblings only), and 33 trio (index and parents). Multigene panels accounted for 672 tests, while whole exome sequencing (WES) represented the remaining 347 tests. Pathogenic or likely pathogenic variants that explain the clinical indications were identified in 34% (27% in panels and 43% in exomes), spanning 279 genes and including 165 novel variants...
June 9, 2017: Human Genetics
https://www.readbyqxmd.com/read/28594829/mendel-md-a-user-friendly-open-source-web-tool-for-analyzing-wes-and-wgs-in-the-diagnosis-of-patients-with-mendelian-disorders
#17
Raony G C C L Cardenas, Natália D Linhares, Raquel L Ferreira, Sérgio D J Pena
Whole exome and whole genome sequencing have both become widely adopted methods for investigating and diagnosing human Mendelian disorders. As pangenomic agnostic tests, they are capable of more accurate and agile diagnosis compared to traditional sequencing methods. This article describes new software called Mendel,MD, which combines multiple types of filter options and makes use of regularly updated databases to facilitate exome and genome annotation, the filtering process and the selection of candidate genes and variants for experimental validation and possible diagnosis...
June 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28592523/germline-cdkn2a-p16ink4a-mutations-contribute-to-genetic-determinism-of-sarcoma
#18
Fanélie Jouenne, Isaure Chauvot de Beauchene, Emeline Bollaert, Marie-Françoise Avril, Olivier Caron, Olivier Ingster, Axel Lecesne, Patrick Benusiglio, Philippe Terrier, Vincent Caumette, Daniel Pissaloux, Arnaud de la Fouchardière, Odile Cabaret, Birama N'Diaye, Amélie Velghe, Gaelle Bougeard, Graham J Mann, Serge Koscielny, Jennifer H Barrett, Mark Harland, Julia Newton-Bishop, Nelleke Gruis, Remco Van Doorn, Marion Gauthier-Villars, Gaelle Pierron, Dominique Stoppa-Lyonnet, Isabelle Coupier, Rosine Guimbaud, Capucine Delnatte, Jean-Yves Scoazec, Alexander M Eggermont, Jean Feunteun, Luba Tchertanov, Jean-Baptiste Demoulin, Thierry Frebourg, Brigitte Bressac-de Paillerets
BACKGROUND: Sarcomas are rare mesenchymal malignancies whose pathogenesis is poorly understood; both environmental and genetic risk factors could contribute to their aetiology. METHODS AND RESULTS: We performed whole-exome sequencing (WES) in a familial aggregation of three individuals affected with soft-tissue sarcoma (STS) without TP53 mutation (Li-Fraumeni-like, LFL) and found a shared pathogenic mutation in CDKN2A tumour suppressor gene. We searched for individuals with sarcoma among 474 melanoma-prone families with a CDKN2A-/+ genotype and for CDKN2A mutations in 190 TP53-negative LFL families where the index case was a sarcoma...
June 7, 2017: Journal of Medical Genetics
https://www.readbyqxmd.com/read/28591755/a-novel-homozygous-missense-fshr-variant-associated-with-hypergonadotropic-hypogonadism-in-two-siblings-from-a-brazilian-family
#19
Monica M França, Antonio M Lerario, Mariana F A Funari, Mirian Y Nishi, Amanda M Narcizo, Maricilda P de Mello, Gil Guerra-Junior, Andrea T Maciel-Guerra, Berenice B Mendonça
Hypergonadotropic hypogonadism (HH) is defined by increased gonadotropin levels in men and women. Primary ovarian failure (POF) is a form of female infertility characterized by amenorrhea, hypoestrogenism, and elevated gonadotropin levels in women under the age of 40 years. Although several genes have been associated with POF, its causative genes remain to be identified. Here, we used whole-exome sequencing (WES) to study a consanguineous family with a 46,XX girl and a 46,XY man affected by HH. All exons of both siblings and their parents were captured and massively sequenced by WES, and the candidate variant was confirmed by Sanger sequencing...
June 8, 2017: Sexual Development: Genetics, Molecular Biology, Evolution, Endocrinology, Embryology, and Pathology of Sex Determination and Differentiation
https://www.readbyqxmd.com/read/28591191/reanalysis-of-brca1-2-negative-high-risk-ovarian-cancer-patients-reveals-novel-germline-risk-loci-and-insights-into-missing-heritability
#20
Jaime L Stafford, Gregory Dyson, Nancy K Levin, Sophia Chaudhry, Rita Rosati, Hasini Kalpage, Courtney Wernette, Nancie Petrucelli, Michael S Simon, Michael A Tainsky
While up to 25% of ovarian cancer (OVCA) cases are thought to be due to inherited factors, the majority of genetic risk remains unexplained. To address this gap, we sought to identify previously undescribed OVCA risk variants through the whole exome sequencing (WES) and candidate gene analysis of 48 women with ovarian cancer and selected for high risk of genetic inheritance, yet negative for any known pathogenic variants in either BRCA1 or BRCA2. In silico SNP analysis was employed to identify suspect variants followed by validation using Sanger DNA sequencing...
2017: PloS One
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