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https://www.readbyqxmd.com/read/27912749/whole-exome-sequencing-identifies-a-novel-missense-fbn2-mutation-co-segregating-in-a-four-generation-chinese-family-with-congenital-contractural-arachnodactyly
#1
Xingping Guo, Chunying Song, Yaping Shi, Hongxia Li, Weijing Meng, Qinzhao Yuan, Jinjie Xue, Jun Xie, Yunxia Liang, Yanan Yuan, Baofeng Yu, Huaixiu Wang, Yun Chen, Lixin Qi, Xinmin Li
BACKGROUND: Congenital contractural arachnodactyly (CCA) is an autosomal dominant rare genetic disease, estimated to be less than 1 in 10,000 worldwide. People with this condition often have permanently bent joints (contractures), like bent fingers and toes (camptodactyly). CASE PRESENTATION: In this study, we investigated the genetic aetiology of CCA in a four-generation Chinese family. The blood samples were collected from 22 living members of the family in the Yangquan County, Shanxi Province, China...
December 3, 2016: BMC Medical Genetics
https://www.readbyqxmd.com/read/27908673/darwin-comes-to-clinic
#2
Arthur L Beaudet
What might be the benefits of whole-genome rather than whole-exome sequencing (WES) for identifying the genetic causes of human disabilities? A recent paper by Doan et al. focuses attention on mutations in human accelerated regions (HARs), a subset of genomic regulatory elements showing accelerated evolution between chimpanzees and humans.
November 28, 2016: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/27903883/function-driven-discovery-of-disease-genes-in-zebrafish-using-an-integrated-genomics-big-data-resource
#3
Hongseok Shim, Ji Hyun Kim, Chan Yeong Kim, Sohyun Hwang, Hyojin Kim, Sunmo Yang, Ji Eun Lee, Insuk Lee
Whole exome sequencing (WES) accelerates disease gene discovery using rare genetic variants, but further statistical and functional evidence is required to avoid false-discovery. To complement variant-driven disease gene discovery, here we present function-driven disease gene discovery in zebrafish (Danio rerio), a promising human disease model owing to its high anatomical and genomic similarity to humans. To facilitate zebrafish-based function-driven disease gene discovery, we developed a genome-scale co-functional network of zebrafish genes, DanioNet (www...
November 16, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27902597/whole-exome-sequencing-of-independent-lung-adenocarcinoma-lung-squamous-cell-carcinoma-and-malignant-peritoneal-mesothelioma-a-case-report
#4
Irene Vanni, Simona Coco, Silvia Bonfiglio, Davide Cittaro, Carlo Genova, Federica Biello, Marco Mora, Valeria Rossella, Maria Giovanna Dal Bello, Anna Truini, Barbara Banelli, Dejan Lazarevic, Angela Alama, Erika Rijavec, Giulia Barletta, Francesco Grossi
The presence of multiple primary tumors (MPT) in a single patient has been identified with an increasing frequency. A critical issue is to establish if the second tumor represents an independent primary cancer or a metastasis. Therefore, the assessment of MPT clonal origin might help understand the disease behavior and improve the management/prognosis of the patient.Herein, we report a 73-year-old male smoker who developed 2 primary lung cancers (adenocarcinoma and squamous cell carcinoma) and a malignant peritoneal mesothelioma (PM)...
November 2016: Medicine (Baltimore)
https://www.readbyqxmd.com/read/27900368/whole-exome-sequencing-reveals-an-inherited-r566x-mutation-of-the-epithelial-sodium-channel-%C3%AE-subunit-in-a-case-of-early-onset-phenotype-of-liddle-syndrome
#5
Linda M Polfus, Eric Boerwinkle, Richard A Gibbs, Ginger Metcalf, Donna Muzny, Narayanan Veeraraghavan, Megan Grove, Sanjay Shete, Stephanie Wallace, Dianna Milewicz, Neil Hanchard, James R Lupski, Syed Shahrukh Hashmi, Monesha Gupta-Malhotra
To comprehensively evaluate a European-American child with severe hypertension, whole-exome sequencing (WES) was performed on the child and parents, which identified causal variation of the proband's early-onset disease. The proband's hypertension was resistant to treatment, requiring a multiple drug regimen including amiloride, spironolactone, and hydrochlorothiazide. We suspected a monogenic form of hypertension because of the persistent hypokalemia with low plasma levels of renin and aldosterone. To address this, we focused on rare functional variants and indels, and performed gene-based tests incorporating linkage scores and allele frequency and filtered on deleterious functional mutations...
November 2016: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/27899912/specific-mri-abnormalities-reveal-severe-perrault-syndrome-due-to-clpp-defects
#6
Tom E J Theunissen, Radek Szklarczyk, Mike Gerards, Debby M E I Hellebrekers, Elvira N M Mulder-Den Hartog, Jo Vanoevelen, Rick Kamps, Bart de Koning, S Lane Rutledge, Thomas Schmitt-Mechelke, Carola G M van Berkel, Marjo S van der Knaap, Irenaeus F M de Coo, Hubert J M Smeets
In establishing a genetic diagnosis in heterogeneous neurological disease, clinical characterization and whole exome sequencing (WES) go hand-in-hand. Clinical data are essential, not only to guide WES variant selection and define the clinical severity of a genetic defect but also to identify other patients with defects in the same gene. In an infant patient with sensorineural hearing loss, psychomotor retardation, and epilepsy, WES resulted in identification of a novel homozygous CLPP frameshift mutation (c...
2016: Frontiers in Neurology
https://www.readbyqxmd.com/read/27899831/evidence-of-criterion-validity-for-one-pharmacy-school-s-progress-examination-program
#7
Greg L Alston, Wes R Haltom
Objective. To provide evidence that the progress examination program accurately assesses student failure to demonstrate competence. Methods. A progress examination program aligned with each grade level was locally developed and administered annually to 289 PharmD students in the spring of their first year - fourth year. Correlations and linear regressions were performed to compare the examination scores to performance on national licensing examinations and cumulative didactic grade point average (GPA). Odds ratio analysis was run to determine the ability of the passing scores of the progress examination to identify students at increased risk of failing to graduate on time, earn a GPA below 3...
October 25, 2016: American Journal of Pharmaceutical Education
https://www.readbyqxmd.com/read/27898983/molecular-diagnosis-of-inherited-retinal-diseases-in-indigenous-african-populations-by-whole-exome-sequencing
#8
Lisa Roberts, Rinki Ratnapriya, Morné du Plessis, Vijender Chaitankar, Raj S Ramesar, Anand Swaroop
Purpose: A majority of genes associated with inherited retinal diseases (IRDs) have been identified in patients of European origin. Indigenous African populations exhibit rich genomic diversity, and evaluation of reported genetic mutations has yielded low returns so far. Our goal was to perform whole-exome sequencing (WES) to examine variants in known IRD genes in underrepresented African cohorts. Methods: Whole-exome sequencing was performed on 56 samples from 16 families with diverse IRD phenotypes that had remained undiagnosed after screening for known mutations using genotyping-based microarrays (Asper Ophthalmics)...
November 1, 2016: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/27897040/identification-of-novel-genes-by-whole-exome-sequencing-can-improve-gastric-cancer-precision-oncology
#9
Georgios D Lianos, Georgios K Glantzounis, Christina D Bali, Christos Katsios, Dimitrios H Roukos
AIM: By identifying cancer driver genes involved in tumorigenesis, whole-exome sequencing (WES) analyses enable the development of robust biomarkers and novel therapeutic targets to reach precision oncology. PATIENTS & METHODS: WES analyses were performed in matched gastric cancer-normal gastric tissues from two patients. We compared genes highlighted with those of a database and recent WES/whole-genome sequencing studies. RESULTS: We identified 32 highlighted gastric cancer genes, two of these (DEFB118 and RNF43) may provide future potential clinical implications...
November 29, 2016: Future Oncology
https://www.readbyqxmd.com/read/27895111/discovery-and-genotyping-of-structural-variation-from-long-read-haploid-genome-sequence-data
#10
John Huddleston, Mark Jp Chaisson, Karyn Meltz Steinberg, Wes Warren, Kendra Hoekzema, David S Gordon, Tina A Graves-Lindsay, Katherine M Munson, Zev N Kronenberg, Laura Vives, Paul Peluso, Matthew Boitano, Chen-Shin Chin, Jonas Korlach, Richard K Wilson, Evan E Eichler
In an effort to more fully understand the full spectrum of human genetic variation, we generated deep single-molecule, real-time (SMRT) sequencing data from two haploid human genomes. Using an assembly-based approach (SMRT-SV), we systematically assessed each genome independently for structural variants (SVs) and indels resolving the sequence structure of 461,553 genetic variants from 2 bp to 28 kbp in length. We find that >89% of these variants have been missed as part of analysis of the 1000 Genomes Project even after adjusting for more common variants (MAF >1%)...
November 28, 2016: Genome Research
https://www.readbyqxmd.com/read/27892699/genetics-of-consanguinity-and-inbreeding-in-health-and-disease
#11
Mohd Fareed, Mohammad Afzal
CONTEXT: Inbreeding increases the level of homozygotes for autosomal recessive disorders and is the major objective in clinical studies. The prevalence of consanguinity and the degree of inbreeding vary from one population to another depending on ethnicity, religion, culture and geography. Global epidemiological studies have revealed that consanguineous unions have been significantly associated with increased susceptibility to various forms of inherited diseases Objective: The study aimed to determine the role of consanguinity in human health and to highlight the associated risks for various diseases or disorders...
November 28, 2016: Annals of Human Biology
https://www.readbyqxmd.com/read/27882484/diagnostic-challenge-of-diamond-blackfan-anemia-in-mothers-and-children-by-whole-exome-sequencing
#12
Takuya Ichimura, Kenichi Yoshida, Yusuke Okuno, Toshiaki Yujiri, Kozo Nagai, Masanori Nishi, Yuichi Shiraishi, Hiroo Ueno, Tsutomu Toki, Kenichi Chiba, Hiroko Tanaka, Hideki Muramatsu, Toshiro Hara, Hitoshi Kanno, Seiji Kojima, Satoru Miyano, Etsuro Ito, Seishi Ogawa, Shouichi Ohga
Diamond-Blackfan anemia (DBA) is a pure red cell aplasia that arises from defective ribosomal proteins (RPs). Patients with this rare ribosomopathy present with neonatal anemia and occasional dysmorphism. Clinical heterogeneity and clusters of causative RP genes hamper the diagnosis and perinatal management. We report three mother-and-child pairs of anemia who were finally diagnosed by whole-exome sequencing. Each pair showed distinct disease severity and response to anemia treatment. Only one mother had the diagnostic dysmorphism, including short stature, webbed neck, and thenar hypoplasia...
November 23, 2016: International Journal of Hematology
https://www.readbyqxmd.com/read/27882197/site-specific-tandem-knoevenagel-condensation-michael-addition-to-generate-antibody-drug-conjugates
#13
Romas A Kudirka, Robyn M Barfield, Jesse M McFarland, Penelope M Drake, Adam Carlson, Stefanie Bañas, Wes Zmolek, Albert W Garofalo, David Rabuka
Expanded ligation techniques are sorely needed to generate unique linkages for the growing field of functionally enhanced proteins. To address this need, we present a unique chemical ligation that involves the double addition of a pyrazolone moiety with an aldehyde-labeled protein. This ligation occurs via a tandem Knoevenagel condensation-Michael addition. A pyrazolone reacts with an aldehyde to generate an enone, which undergoes subsequent attack by a second pyrazolone to generate a bis-pyrazolone species...
November 10, 2016: ACS Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/27874022/in-depth-comparison-of-somatic-point-mutation-callers-based-on-different-tumor-next-generation-sequencing-depth-data
#14
Lei Cai, Wei Yuan, Zhou Zhang, Lin He, Kuo-Chen Chou
Four popular somatic single nucleotide variant (SNV) calling methods (Varscan, SomaticSniper, Strelka and MuTect2) were carefully evaluated on the real whole exome sequencing (WES, depth of ~50X) and ultra-deep targeted sequencing (UDT-Seq, depth of ~370X) data. The four tools returned poor consensus on candidates (only 20% of calls were with multiple hits by the callers). For both WES and UDT-Seq, MuTect2 and Strelka obtained the largest proportion of COSMIC entries as well as the lowest rate of dbSNP presence and high-alternative-alleles-in-control calls, demonstrating their superior sensitivity and accuracy...
November 22, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27872920/ultrafast-chiral-separations-for-high-throughput-enantiopurity-analysis
#15
Chandan L Barhate, Leo A Joyce, Alexey A Makarov, Kerstin Zawatzky, Frank Bernardoni, Wes A Schafer, Daniel W Armstrong, Christopher J Welch, Erik L Regalado
Recent developments in fast chromatographic enantioseparations now make high throughput analysis of enantiopurity on the order of a few seconds achievable. Nevertheless, routine chromatographic determinations of enantiopurity to support stereochemical investigations in pharmaceutical research and development, synthetic chemistry and bioanalysis are still typically performed on the 5-20 min timescale, with many practitioners believing that sub-minute enantioseparations are not representative of the molecules encountered in day to day research...
November 22, 2016: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/27872624/diagnostics-of-primary-immunodeficiencies-through-next-generation-sequencing
#16
Vera Gallo, Laura Dotta, Giuliana Giardino, Emilia Cirillo, Vassilios Lougaris, Roberta D'Assante, Alberto Prandini, Rita Consolini, Emily G Farrow, Isabelle Thiffault, Carol J Saunders, Antonio Leonardi, Alessandro Plebani, Raffaele Badolato, Claudio Pignata
BACKGROUND: Recently, a growing number of novel genetic defects underlying primary immunodeficiencies (PIDs) have been identified, increasing the number of PID up to more than 250 well-defined forms. Next-generation sequencing (NGS) technologies and proper filtering strategies greatly contributed to this rapid evolution, providing the possibility to rapidly and simultaneously analyze large numbers of genes or the whole exome. OBJECTIVE: To evaluate the role of targeted NGS and whole exome sequencing (WES) in the diagnosis of a case series, characterized by complex or atypical clinical features suggesting a PID, difficult to diagnose using the current diagnostic procedures...
2016: Frontiers in Immunology
https://www.readbyqxmd.com/read/27867721/wide-field-optical-coherence-micro-elastography-for-intraoperative-assessment-of-human-breast-cancer-margins
#17
Wes M Allen, Lixin Chin, Philip Wijesinghe, Rodney W Kirk, Bruce Latham, David D Sampson, Christobel M Saunders, Brendan F Kennedy
Incomplete excision of malignant tissue is a major issue in breast-conserving surgery, with typically 20 - 30% of cases requiring a second surgical procedure arising from postoperative detection of an involved margin. We report advances in the development of a new intraoperative tool, optical coherence micro-elastography, for the assessment of tumor margins on the micro-scale. We demonstrate an important step by conducting whole specimen imaging in intraoperative time frames with a wide-field scanning system acquiring mosaicked elastograms with overall dimensions of ~50 × 50 mm, large enough to image an entire face of most lumpectomy specimens...
October 1, 2016: Biomedical Optics Express
https://www.readbyqxmd.com/read/27864007/six-generations-of-epidermolytic-palmoplantar-keratoderma-associated-with-a-krt9-r163w-mutation
#18
Peng Wang, Xiao-Jing Kang, Xiao-Hui Tang, Jian-Yong Liu, Wen-Zheng Li, Wei-Jia Wang, Sheng-Nan Liang, Yan-Yan Feng, Yuan Ding, Wen-Jing Chen
Epidermolytic palmoplantar keratoderma (EPPK) is a rare autosomal dominant skin disorder characterized by diffuse hyperkeratosis on the palms and soles. Whole-exome sequencing (WES) has become a powerful tool for the detection of rare causal variants of Mendelian disorders. However, no causal gene for EPPK in the Uygur population has been identified until now, and no treatment exists than can address the underlying pathology.WES analysis was undertaken on two individuals from a large Uygur EPPK pedigree whose disease locus mapped to 17q21...
November 2016: Cancer Genetics
https://www.readbyqxmd.com/read/27861123/tecrl-a-new-life-threatening-inherited-arrhythmia-gene-associated-with-overlapping-clinical-features-of-both-lqts-and-cpvt
#19
Harsha D Devalla, Roselle Gélinas, Elhadi H Aburawi, Abdelaziz Beqqali, Philippe Goyette, Christian Freund, Marie-A Chaix, Rafik Tadros, Hui Jiang, Antony Le Béchec, Jantine J Monshouwer-Kloots, Tom Zwetsloot, Georgios Kosmidis, Frédéric Latour, Azadeh Alikashani, Maaike Hoekstra, Jurg Schlaepfer, Christine L Mummery, Brian Stevenson, Zoltan Kutalik, Antoine Af de Vries, Léna Rivard, Arthur Am Wilde, Mario Talajic, Arie O Verkerk, Lihadh Al-Gazali, John D Rioux, Zahurul A Bhuiyan, Robert Passier
Genetic causes of many familial arrhythmia syndromes remain elusive. In this study, whole-exome sequencing (WES) was carried out on patients from three different families that presented with life-threatening arrhythmias and high risk of sudden cardiac death (SCD). Two French Canadian probands carried identical homozygous rare variant in TECRL gene (p.Arg196Gln), which encodes the trans-2,3-enoyl-CoA reductase-like protein. Both patients had cardiac arrest, stress-induced atrial and ventricular tachycardia, and QT prolongation on adrenergic stimulation...
December 1, 2016: EMBO Molecular Medicine
https://www.readbyqxmd.com/read/27858995/establishing-very-long-chain-fatty-alcohol-and-wax-ester-biosynthesis-in-saccharomyces-cerevisiae
#20
Leonie Wenning, Tao Yu, Florian David, Jens Nielsen, Verena Siewers
Wax esters (WEs) are neutral lipids and can be used for a broad range of commercial applications, including personal care products, lubricants, or coatings. They are synthesized by enzymatic reactions catalyzed by a fatty acyl reductase (FAR) and a wax ester synthase (WS). At present, commercially used WEs are mainly isolated from Simmondsia chinensis (jojoba), but the high extraction costs and limited harvest areas constrain their use. The use of FARs in combination with different WSs to achieve a synthesis of jojoba-like WEs in bacteria and yeast has been reported previously, but the products were restricted to C28-C36 WEs...
November 14, 2016: Biotechnology and Bioengineering
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