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https://www.readbyqxmd.com/read/28432012/novel-compound-heterozygous-mutations-in-the-pex1-gene-in-two-chinese-newborns-with-zellweger-syndrome-based-on-whole-exome-sequencing
#1
Meng-Meng Ge, LiYuan Hu, ZhiHua Li, GuoQiang Cheng, Kai Yan, YanTing Kong, HuiJun Wang, Lin Yang, WenHao Zhou
Peroxisome biogenesis disorders (PBDs) represent a spectrum of human genetic disorders that are characterized by damaged peroxisome assembly. In the newborn period, the characteristics of affected patients include dysmorphic facial features, neonatal hypotonia, seizures, ocular abnormalities, poor feeding, liver cysts with hepatic dysfunction and skeletal defects. These can be caused by a defect in at least 14 different PEX genes. In this study, whole-exome sequencing (WES) was performed on samples from two Chinese newborns with clinical features of Zellweger syndrome...
April 18, 2017: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/28431867/whole-exome-sequencing-identification-of-novel-candidate-genes-in-patients-with-proliferative-diabetic-retinopathy
#2
Cindy Ung, Angie V Sanchez, Lishuang Shen, Samaneh Davoudi, Tina Ahmadi, Daniel Navarro-Gomez, Ching J Chen, Heather Hancock, Alan Penman, Suzanne Hoadley, Mark Consugar, Carlos Restrepo, Vinay A Shah, Joseph F Arboleda-Velasquez, Lucia Sobrin, Xiaowu Gai, Leo A Kim
Rare or novel gene variants in patients with proliferative diabetic retinopathy may contribute to disease development. We performed whole exome sequencing (WES) on patients at the phenotypic extremes of diabetic retinal complications: 57 patients diagnosed with proliferativediabetic retinopathy (PDR) as cases and 13 patients with no diabetic retinopathy despite at least 10 years of type 2 diabetes as controls. Thirty-one out of the 57 cases and all 13 controls were from the African American Proliferative Diabetic Retinopathy Study (AA)...
April 18, 2017: Vision Research
https://www.readbyqxmd.com/read/28427548/autosomal-dominant-gain-of-function-stat1-mutation-and-severe-bronchiectasis
#3
Oded Breuer, Hagit Daum, Malena Cohen-Cymberknoh, Susanne Unger, David Shoseyov, Polina Stepensky, Baerbel Keller, Klaus Warnatz, Eitan Kerem
BACKGROUND: In a substantial number of patients with non-cystic fibrosis (CF) bronchiectasis an etiology cannot be found. Various complex immunodeficiency syndromes account for a significant portion of these patients but the mechanism elucidating the predisposition for suppurative lung disease often remains unknown. OBJECTIVE: To investigate the cause and mechanism predisposing a patient to severe bronchiectasis. METHODS: A patient presenting with severe non-CF bronchiectasis was investigated...
May 2017: Respiratory Medicine
https://www.readbyqxmd.com/read/28427202/clinical-implications-of-genomic-profiles-in-metastatic-breast-cancer-with-a-focus-on-tp53-and-pik3ca-the-most-frequently-mutated-genes
#4
Ji-Yeon Kim, Eunjin Lee, Kyunghee Park, Woong-Yang Park, Hae Hyun Jung, Jin Seok Ahn, Young-Hyuck Im, Yeon Hee Park
Breast cancer (BC) has been genetically profiled through large-scale genome analyses. However, the role and clinical implications of genetic alterations in metastatic BC (MBC) have not been evaluated. Therefore, we conducted whole-exome sequencing (WES) and RNA-Seq of 37 MBC samples and targeted deep sequencing of another 29 MBCs. We evaluated somatic mutations from WES and targeted sequencing and assessed gene expression and performed pathway analysis from RNA-Seq. In this analysis, PIK3CA was the most commonly mutated gene in estrogen receptor (ER)-positive BC, while in ER-negative BC, TP53 was the most commonly mutated gene (p = 0...
March 3, 2017: Oncotarget
https://www.readbyqxmd.com/read/28426237/on-the-complexity-of-item-response-theory-models
#5
Wes Bonifay, Li Cai
Complexity in item response theory (IRT) has traditionally been quantified by simply counting the number of freely estimated parameters in the model. However, complexity is also contingent upon the functional form of the model. We examined four popular IRT models-exploratory factor analytic, bifactor, DINA, and DINO-with different functional forms but the same number of free parameters. In comparison, a simpler (unidimensional 3PL) model was specified such that it had 1 more parameter than the previous models...
April 20, 2017: Multivariate Behavioral Research
https://www.readbyqxmd.com/read/28425981/whole-exome-sequencing-on-deceased-fetuses-with-ultrasound-anomalies-expanding-our-knowledge-of-genetic-disease-during-fetal-development
#6
Carin L Yates, Kristin G Monaghan, Deborah Copenheaver, Kyle Retterer, Julie Scuffins, Cathlin R Kucera, Bethany Friedman, Gabriele Richard, Jane Juusola
PurposeThe aim of this study was to determine the diagnostic yield of whole-exome sequencing (WES) in fetuses with ultrasound anomalies that resulted in fetal demise or pregnancy termination. The results were also utilized to aid in the identification of candidate genes for fetal development and to expand the clinical phenotype of known genetic conditions.MethodsWES was performed on specimens from 84 deceased fetuses. Data were analyzed and final results were classified into one of four categories: positive, possible, negative, and candidate gene only...
April 20, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28422131/variants-in-cplx1-in-two-families-with-autosomal-recessive-severe-infantile-myoclonic-epilepsy-and-id
#7
Silke Redler, Tim M Strom, Thomas Wieland, Kirsten Cremer, Hartmut Engels, Felix Distelmaier, Jörg Schaper, Alma Küchler, Johannes R Lemke, Stephanie Jeschke, Nicole Schreyer, Heinrich Sticht, Margarete Koch, Hermann-Josef Lüdecke, Dagmar Wieczorek
For a large number of individuals with intellectual disability (ID), the molecular basis of the disorder is still unknown. However, whole-exome sequencing (WES) is providing more and more insights into the genetic landscape of ID. In the present study, we performed trio-based WES in 311 patients with unsolved ID and additional clinical features, and identified homozygous CPLX1 variants in three patients with ID from two unrelated families. All displayed marked developmental delay and migrating myoclonic epilepsy, and one showed a cerebellar cleft in addition...
April 19, 2017: European Journal of Human Genetics: EJHG
https://www.readbyqxmd.com/read/28420617/application-and-progress-of-high-throughput-sequencing-technologies-in-the-research-of-hereditary-hearing-loss
#8
Wang Cuicui, Yuan Huijun
Hearing loss (HL) is the most common birth defect. Elucidating the genetic basis of hereditary deafness can not only assist diagnosis, provide the basis for genetic counseling and the prevention of deafness, but also bring a deeper understanding of the disease pathogenesis. In the genomic era, high-throughput sequencing technologies, represented by whole genome sequencing (WGS), whole exome sequencing (WES) or target region sequencing, have been widely used in the studies of hereditary HL. Here, we summarize the application and progress of WES and target region sequencing in the research of causative genes and clinical molecular diagnosis of hereditary HL, hoping to be helpful for the development and improvement of clinical genetic diagnosis of deafness in China...
March 20, 2017: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/28419563/whole-exome-sequencing-identified-a-novel-single-base-pair-insertion-mutation-in-the-eys-gene-in-a-six-generation-family-with-retinitis-pigmentosa
#9
Jamil Amjad Hashmi, Maan Abdullah Albarry, Ahmed Almatrafi, Alia M Albalawi, Amir Mehmood, Sulman Basit
Retinitis pigmentosa (RP) is a group of inherited progressive retinal dystrophies (RD) and is characterized by photoreceptor degeneration. RP is clinically and genetically heterogeneous disorder. More than 70 genes are known and, thus, identification of causative genes and mutations in known genes is challenging. This study was designed to identify the underlying genetic defect in a large extended Saudi family with multiple RP affected members. Fundus photography, Optical Coherence Tomography (OCT) and visual field perimetry were performed for affected individuals...
April 16, 2017: Congenital Anomalies
https://www.readbyqxmd.com/read/28415633/a-phase-2-study-of-vorinostat-in-locally-advanced-recurrent-or-metastatic-adenoid-cystic-carcinoma
#10
Priscila H Goncalves, Lance K Heilbrun, Michael T Barrett, Shivaani Kummar, Aaron R Hansen, Lillian L Siu, Richard L Piekarz, Ammar W Sukari, Joseph Chao, Mary Jo Pilat, Daryn W Smith, Lindsay Casetta, Scott A Boerner, Alice Chen, Elizabeth Lenkiewicz, Smriti Malasi, Patricia M LoRusso
PURPOSE: Vorinostat is a histone deacetylase inhibitor (HDACi). Based on a confirmed partial response (PR) in an adenoid cystic carcinoma (ACC) patient treated with vorinostat in a prior phase 1 trial, we initiated this phase 2 trial. METHODS: Vorinostat was administered orally 400 mg daily, 28 day cycles. The primary objective was to evaluate response rate (RR). Exploratory studies included whole exome sequencing (WES) of selected patients. RESULTS: Thirty patients were enrolled...
March 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/28414188/a-case-of-splenomegaly-in-cbl-syndrome
#11
Rachel R Coe, Margaret L McKinnon, Maja Tarailo-Graovac, Colin J Ross, Wyeth W Wasserman, Jan M Friedman, Paul C Rogers, Clara D M van Karnebeek
INTRODUCTION: We present a child with unexplained splenomegaly to highlight this feature as a presenting sign of the RASopathy CBL syndrome and to draw attention to the power and utility of next generation genomic sequencing for providing rapid diagnosis and critical information to guide care in the pediatric clinical setting. CLINICAL REPORT: A 7-year-old boy presented with unexplained splenomegaly, attention deficit hyperactivity disorder, mild learning difficulties, easy bruising, mild thrombocytopenia, and subtle dysmorphic features...
April 13, 2017: European Journal of Medical Genetics
https://www.readbyqxmd.com/read/28413183/a-slc24a2-gene-variant-uncovered-in-pancreatic-ductal-adenocarcinoma-by-whole-exome-sequencing
#12
Lei Wang, Zhuo Shao, Shiyue Chen, Lu Shi, Zhaoshen Li
Pancreatic ductal adenocarcinoma (PDAC) presents as an aggressive malignancy caused by environmental and genetic factors. In order to identify causal genes for PDAC, we performed whole exome sequencing (WES) to detect gene mutations in seven pairs of PDAC tissue and adjacent non-tumor tissue samples. Finally, we found a new nonsynonymous single nucleotide variant (nsSNV) in solute carrier 24 family member 2 (SLC24A2) gene resulting in the substitution of native glutamic acid (E) into aspartic acid (D) at position of 287 amino acid (E287D) in SLC24A2 protein, and confirmed this variant by Sanger gene sequencing...
2017: Tohoku Journal of Experimental Medicine
https://www.readbyqxmd.com/read/28408746/novel-metrics-to-measure-coverage-in-whole-exome-sequencing-datasets-reveal-local-and-global-non-uniformity
#13
Qingyu Wang, Cooduvalli S Shashikant, Matthew Jensen, Naomi S Altman, Santhosh Girirajan
Whole Exome Sequencing (WES) is a powerful clinical diagnostic tool for discovering the genetic basis of many diseases. A major shortcoming of WES is uneven coverage of sequence reads over the exome targets contributing to many low coverage regions, which hinders accurate variant calling. In this study, we devised two novel metrics, Cohort Coverage Sparseness (CCS) and Unevenness (UE) Scores for a detailed assessment of the distribution of coverage of sequence reads. Employing these metrics we revealed non-uniformity of coverage and low coverage regions in the WES data generated by three different platforms...
April 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28407228/deleterious-protein-altering-mutations-in-the-scn10a-voltage-gated-sodium-channel-gene-are-associated-with-prolonged-qt
#14
Maen D Abou Ziki, Sara B Seidelmann, Emily Smith, Gourg Atteya, Yuexin Jiang, Rodolfo Gil Fernandes, Mark A Marieb, Joseph G Akar, Arya Mani
Long QT syndrome (LQT) is a pro-arrhythmogenic condition with life threatening complications. Fifteen genes have been associated with congenital LQT however, the genetic causes remain unknown in more than 20% of cases. Eighteen patients with history of palpitations, presyncope, syncope and prolonged QT were referred to the Yale Cardiovascular Genetics Program. All subjects underwent whole exome sequencing (WES) followed by confirmatory Sanger sequencing. Mutation burden analysis was carried out using WES data from sixteen subjects with no identifiable cause of LQT...
April 13, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/28407084/comparative-analysis-of-de-novo-assemblers-for-variation-discovery-in-personal-genomes
#15
Shulan Tian, Huihuang Yan, Eric W Klee, Michael Kalmbach, Susan L Slager
Current variant discovery approaches often rely on an initial read mapping to the reference sequence. Their effectiveness is limited by the presence of gaps, potential misassemblies, regions of duplicates with a high-sequence similarity and regions of high-sequence divergence in the reference. Also, mapping-based approaches are less sensitive to large INDELs and complex variations and provide little phase information in personal genomes. A few de novo assemblers have been developed to identify variants through direct variant calling from the assembly graph, micro-assembly and whole-genome assembly, but mainly for whole-genome sequencing (WGS) data...
April 11, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28404607/interpreting-incidentally-identified-variants-in-genes-associated-with-catecholaminergic-polymorphic-ventricular-tachycardia-in-a-large-cohort-of-clinical-whole-exome-genetic-test-referrals
#16
Andrew P Landstrom, Andrew L Dailey-Schwartz, Jill A Rosenfeld, Yaping Yang, Margaret J McLean, Christina Y Miyake, Santiago O Valdes, Yuxin Fan, Hugh D Allen, Daniel J Penny, Jeffrey J Kim
BACKGROUND: The rapid expansion of genetic testing has led to increased utilization of clinical whole-exome sequencing (WES). Clinicians and genetic researchers are being faced with assessing risk of disease vulnerability from incidentally identified genetic variants which is typified by variants found in genes associated with sudden death-predisposing catecholaminergic polymorphic ventricular tachycardia (CPVT). We sought to determine whether incidentally identified variants in genes associated with CPVT from WES clinical testing represent disease-associated biomarkers...
April 2017: Circulation. Arrhythmia and Electrophysiology
https://www.readbyqxmd.com/read/28402931/habp2-p-g534e-variant-in-patients-with-family-history-of-thyroid-and-breast-cancer
#17
Maisa Pinheiro, Sandra Aparecida Drigo, Renata Tonhosolo, Sonia C S Andrade, Fabio Albuquerque Marchi, Igor Jurisica, Luiz Paulo Kowalski, Maria Isabel Achatz, Silvia Regina Rogatto
Familial Papillary Thyroid Carcinoma (PTC) has been described as a hereditary predisposition cancer syndrome associated with mutations in candidate genes including HABP2. Two of 20 probands from families with history of PTC and breast carcinoma (BC) were evaluated by whole exome sequencing (WES) revealing HABP2 p.G534E. Sanger sequencing was used to confirm the involvement of this variant in three families (F1: 7 relatives; F2: 3 and F3: 3). The proband and his sister (with no malignant tumor so far) from F1 were homozygous for the variant whereas one relative with PTC from F2 was negative for the variant...
March 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28401488/a-no-stop-mutation-in-mageb4-is-a-possible-cause-of-rare-x-linked-azoospermia-and-oligozoospermia-in-a-consanguineous-turkish-family
#18
Ozlem Okutman, Jean Muller, Valerie Skory, Jean Marie Garnier, Angeline Gaucherot, Yoni Baert, Valérie Lamour, Munevver Serdarogullari, Meral Gultomruk, Albrecht Röpke, Sabine Kliesch, Viviana Herbepin, Isabelle Aknin, Moncef Benkhalifa, Marius Teletin, Emre Bakircioglu, Ellen Goossens, Nicolas Charlet-Berguerand, Mustafa Bahceci, Frank Tüttelmann, STéphane Viville
PURPOSE: The purpose of this study was to identify mutations that cause non-syndromic male infertility using whole exome sequencing of family cases. METHODS: We recruited a consanguineous Turkish family comprising nine siblings with male triplets; two of the triplets were infertile as well as one younger infertile brother. Whole exome sequencing (WES) performed on two azoospermic brothers identified a mutation in the melanoma antigen family B4 (MAGEB4) gene which was confirmed via Sanger sequencing and then screened for on control groups and unrelated infertile subjects...
April 11, 2017: Journal of Assisted Reproduction and Genetics
https://www.readbyqxmd.com/read/28401120/estimating-patient-borne-water-and-electricity-costs-in-home-hemodialysis-a-simulation
#19
Matthew Nickel, Wes Rideout, Nikhil Shah, Frances Reintjes, Justin Z Chen, Robert Burrell, Robert P Pauly
BACKGROUND: Home hemodialysis is associated with lower costs to the health care system compared with conventional facility-based hemodialysis because of lower staffing and overhead costs, and by transferring the treatment cost of utilities (water and power) to the patient. The purpose of this study was to determine the utility costs of home hemodialysis and create a formula such that patients and renal programs can estimate the annual patient-borne costs involved with this type of treatment...
January 2017: CMAJ Open
https://www.readbyqxmd.com/read/28399260/the-plant-economics-spectrum-is-structured-by-leaf-habits-and-growth-forms-across-subtropical-species
#20
Yan-Tao Zhao, Arshad Ali, En-Rong Yan
The plant economics spectrum that integrates the combination of leaf and wood syndromes provides a useful framework for the examination of species strategies at the whole-plant level. However, it remains unclear how species that differ in leaf habits and growth forms are integrated within the plant economics spectrum in subtropical forests. We measured five leaf and six wood traits across 58 subtropical plant species, which represented two leaf habits (evergreen vs deciduous) and two growth forms (tree vs shrub) in eastern China...
February 1, 2017: Tree Physiology
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