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Watson for genomics

Joshua Y C Yang, Stijn E Verleden, Arya Zarinsefat, Bart M Vanaudenaerde, Robin Vos, Geert M Verleden, Reuben D Sarwal, Tara K Sigdel, Juliane M Liberto, Izabella Damm, Drew Watson, Minnie M Sarwal
Standard methods for detecting chronic lung allograft dysfunction (CLAD) and rejection have poor sensitivity and specificity and have conventionally required bronchoscopies and biopsies. Plasma cell-free DNA (cfDNA) has been shown to be increased in various types of allograft injury in transplant recipients and CXCL10 has been reported to be increased in the lung tissue of patients undergoing CLAD. This study used a novel cfDNA and CXCL10 assay to evaluate the noninvasive assessment of CLAD phenotype and prediction of survival from bronchoalveolar lavage (BAL) fluid...
February 13, 2019: Journal of Clinical Medicine
Markus Seibert, Marcus Krüger, Nikolaus A Watson, Onur Sen, John R Daum, Johan A Slotman, Thomas Braun, Adriaan B Houtsmuller, Gary J Gorbsky, Ralf Jacob, Michael Kracht, Jonathan M G Higgins, M Lienhard Schmitz
Faithful mitotic chromosome segregation is required for the maintenance of genomic stability. We discovered the phosphorylation of histone H2B at serine 6 (H2B S6ph) as a new chromatin modification site and found that this modification occurs during the early mitotic phases at inner centromeres and pericentromeric heterochromatin. This modification is directly mediated by cyclin B1-associated CDK1, and indirectly by Aurora B, and is antagonized by PP1-mediated dephosphorylation. H2B S6ph impairs chromatin binding of the histone chaperone SET (I2PP2A), which is important for mitotic fidelity...
February 14, 2019: Journal of Cell Biology
Ronald Y Kwon, Claire J Watson, David Karasik
While genome-wide association studies (GWAS) have revolutionized our understanding of the genetic architecture of skeletal diseases, animal models are required to identify causal mechanisms and to translate underlying biology into new therapies. Despite large-scale knockout mouse phenotyping efforts, the skeletal functions of most genes residing at GWAS-identified loci remain unknown, highlighting a need for complementary model systems to accelerate gene discovery. Over the past several decades, zebrafish (Danio rerio) has emerged as a powerful system for modeling the genetics of human diseases...
February 11, 2019: Bone
Lesley Walker, Christopher M Watson, Sarah Hewitt, Laura A Crinnion, David T Bonthron, Kelly E Cohen
Molecular diagnostic investigations, following the identification of foetal abnormalities, are routinely performed using array comparative genomic hybridisation (aCGH). Despite the utility of this technique, contemporary approaches for the detection of copy number variation are typically based on next-generation sequencing (NGS). We sought to compare an in-house NGS-based workflow (CNVseq) with aCGH, for invasively obtained foetal samples from pregnancies complicated by foetal structural abnormality. DNA from 40 foetuses was screened using both 8 × 60 K aCGH oligoarrays and low-coverage whole genome sequencing...
February 3, 2019: Journal of Obstetrics and Gynaecology: the Journal of the Institute of Obstetrics and Gynaecology
Deborah R Maiese, Alisha Keehn, Megan Lyon, David Flannery, Michael Watson
PURPOSE: This study of current conditions in medical genetics practice is designed to inform public policy development and present possible solutions for improving access to genetic services. METHODS: Using the American College of Medical Genetics and Genomics Member Directory, membership directories from regional collaborative partners, listservs from national partners, and social media, a 16-question survey was electronically distributed in 2015. RESULTS: The responses of 924 genetics professionals and related providers present a snapshot of current practice and an assessment of workforce needs...
January 28, 2019: Genetics in Medicine: Official Journal of the American College of Medical Genetics
Susan K Rathe, Flavia E Popescu, James E Johnson, Adrienne L Watson, Tracy A Marko, Branden S Moriarity, John R Ohlfest, David A Largaespada
Osteosarcomas are characterized by highly disrupted genomes. Although osteosarcomas lack common fusions, we find evidence of many tumour specific gene-gene fusion transcripts, likely due to chromosomal rearrangements and expression of transcription-induced chimeras. Most of the fusions result in out-of-frame transcripts, potentially capable of producing long novel protein sequences and a plethora of neoantigens. To identify fusions, we explored RNA-sequencing data to obtain detailed knowledge of transcribed fusions, by creating a novel program to compare fusions identified by deFuse to de novo transcripts generated by Trinity...
January 23, 2019: Scientific Reports
Priya S Kishnani, Jennifer Goldstein, Stephanie L Austin, Pamela Arn, Bert Bachrach, Deeksha S Bali, Wendy K Chung, Areeg El-Gharbawy, Laurie M Brown, Stephen Kahler, Surekha Pendyal, Katalin M Ross, Laurie Tsilianidis, David A Weinstein, Michael S Watson
PURPOSE: Glycogen storage disease (GSD) types VI and IX are rare diseases of variable clinical severity affecting primarily the liver. GSD VI is caused by deficient activity of hepatic glycogen phosphorylase, an enzyme encoded by the PYGL gene. GSD IX is caused by deficient activity of phosphorylase kinase (PhK), the enzyme subunits of which are encoded by various genes: ɑ (PHKA1, PHKA2), β (PHKB), ɣ (PHKG1, PHKG2), and δ (CALM1, CALM2, CALM3). Glycogen storage disease types VI and IX have a wide spectrum of clinical manifestations and often cannot be distinguished from each other, or from other liver GSDs, on clinical presentation alone...
January 19, 2019: Genetics in Medicine: Official Journal of the American College of Medical Genetics
Rachel M Sherman, Juliet Forman, Valentin Antonescu, Daniela Puiu, Michelle Daya, Nicholas Rafaels, Meher Preethi Boorgula, Sameer Chavan, Candelaria Vergara, Victor E Ortega, Albert M Levin, Celeste Eng, Maria Yazdanbakhsh, James G Wilson, Javier Marrugo, Leslie A Lange, L Keoki Williams, Harold Watson, Lorraine B Ware, Christopher O Olopade, Olufunmilayo Olopade, Ricardo R Oliveira, Carole Ober, Dan L Nicolae, Deborah A Meyers, Alvaro Mayorga, Jennifer Knight-Madden, Tina Hartert, Nadia N Hansel, Marilyn G Foreman, Jean G Ford, Mezbah U Faruque, Georgia M Dunston, Luis Caraballo, Esteban G Burchard, Eugene R Bleecker, Maria I Araujo, Edwin F Herrera-Paz, Monica Campbell, Cassandra Foster, Margaret A Taub, Terri H Beaty, Ingo Ruczinski, Rasika A Mathias, Kathleen C Barnes, Steven L Salzberg
In the version of this article initially published, the statement "there are no pan-genomes for any other animal or plant species" was incorrect. The statement has been corrected to "there are no reported pan-genomes for any other animal species, to our knowledge." We thank David Edwards for bringing this error to our attention. The error has been corrected in the HTML and PDF versions of the article.
January 15, 2019: Nature Genetics
Eugine Lee, John Wongvipat, Danielle Choi, Ping Wang, Young Sun Lee, Deyou Zheng, Philip A Watson, Anuradha Gopalan, Charles L Sawyers
Genomic amplification of the androgen receptor ( AR ) is an established mechanism of antiandrogen resistance in prostate cancer. Here, we show that the magnitude of AR signaling output, independent of AR genomic alteration or expression level, also contributes to antiandrogen resistance, through upregulation of the coactivator GREB1 . We demonstrate 100-fold heterogeneity in AR output within human prostate cancer cell lines and show that cells with high AR output have reduced sensitivity to enzalutamide. Through transcriptomic and shRNA knockdown studies, together with analysis of clinical datasets, we identify GREB1 as a gene responsible for high AR output...
January 15, 2019: ELife
Satoru Miyano
Cancer is a very complex disease that is caused by mutations in genomes and evolves spatiotemporally in a patient. Our institute implemented IBM Watson for Genomics and realized a turnaround time for patient diagnosis of less than four days that includes whole genome sequencing and interpretation of the data.
January 2019: Brain and Nerve, Shinkei Kenkyū No Shinpo
Elodie Rance, Jerome E Tanner, Caroline Alfieri
The hepatitis C virus (HCV) genome contains structured elements thought to play important regulatory roles in viral RNA translation and replication processes. We used in vitro RNA binding assays to map interactions involving the HCV 5'UTR and distal sequences in NS5B to examine their impact on viral RNA replication. The data revealed that 5'UTR nucleotides (nt) 95⁻110 in the internal ribosome entry site (IRES) domain IIa and matching nt sequence 8528⁻8543 located in the RNA-dependent RNA polymerase coding region NS5B, form a high-affinity RNA-RNA complex in vitro...
December 28, 2018: Viruses
Khalid H Alanazi, Marie E Killerby, Holly M Biggs, Glen R Abedi, Hani Jokhdar, Ali A Alsharef, Mutaz Mohammed, Osman Abdalla, Aref Almari, Samar Bereagesh, Sameh Tawfik, Husain Alresheedi, Raafat F Alhakeem, Ahmed Hakawi, Haitham Alfalah, Hala Amer, Natalie J Thornburg, Azaibi Tamin, Suvang Trivedi, Suxiang Tong, Xiaoyan Lu, Krista Queen, Yan Li, Senthilkumar K Sakthivel, Ying Tao, Jing Zhang, Clinton R Paden, Hail M Al-Abdely, Abdullah M Assiri, Susan I Gerber, John T Watson
OBJECTIVE: To investigate a Middle East respiratory syndrome coronavirus (MERS-CoV) outbreak event involving multiple healthcare facilities in Riyadh, Saudi Arabia; to characterize transmission; and to explore infection control implications. DESIGN: Outbreak investigation. SETTING: Cases presented in 4 healthcare facilities in Riyadh, Saudi Arabia: a tertiary-care hospital, a specialty pulmonary hospital, an outpatient clinic, and an outpatient dialysis unit...
January 2019: Infection Control and Hospital Epidemiology
Nathan S Watson-Haigh, Radosław Suchecki, Elena Kalashyan, Melissa Garcia, Ute Baumann
BACKGROUND: Democratising the growing body of whole genome sequencing data available for Triticum aestivum (bread wheat) has been impeded by the lack of a genome reference and the large computational requirements for analysing these data sets. RESULTS: DAWN (Diversity Among Wheat geNomes) integrates data from the T. aestivum Chinese Spring (CS) IWGSC RefSeq v1.0 genome with public WGS and exome data from 17 and 62 accessions respectively, enabling researchers and breeders alike to investigate genotypic differences between wheat accessions at the level of whole chromosomes down to individual genes...
December 17, 2018: BMC Genomics
Michael A Hardigan, Thomas J Poorten, Charlotte B Acharya, Glenn S Cole, Kim E Hummer, Nahla Bassil, Patrick P Edger, Steven J Knapp
Garden strawberry ( × Duchesne ex Rozier) arose from spontaneous hybridization of distinct octoploid species 300 yr ago. Since its discovery in the 1700s, migration and selection restructured the genetic diversity of early hybrids to produce elite fruit-bearing groups. Breeders' understanding of the genetic architecture of domesticated populations is incomplete. To resolve the impacts of domestication on strawberry genetic diversity, we analyzed genome-wide DNA profiles of 1300 octoploid individuals (1814-present), including wild species, historic varieties, and the University of California germplasm collection...
November 2018: Plant Genome
Ruoting Yang, Daniel Watson, Joshua Williams, Raina Kumar, Ross Campbell, Uma Mudunuri, Rasha Hammamieh, Marti Jett
BACKGROUND: Network medicine aims to map molecular perturbations of any given diseases onto complex networks with functional interdependencies that underlie a pathological phenotype. Furthermore, investigating the time dimension of disease progression from a network perspective is key to gaining key insights to the disease process and to identify diagnostic or therapeutic targets. Existing platforms are ineffective to modularize the large complex systems into subgroups and consolidate heterogeneous data to web-based interactive animation...
November 29, 2018: BMC Bioinformatics
Tim Regan, Mark W Barnett, Dominik R Laetsch, Stephen J Bush, David Wragg, Giles E Budge, Fiona Highet, Benjamin Dainat, Joachim R de Miranda, Mick Watson, Mark Blaxter, Tom C Freeman
The European honey bee (Apis mellifera) plays a major role in pollination and food production. Honey bee health is a complex product of the environment, host genetics and associated microbes (commensal, opportunistic and pathogenic). Improved understanding of these factors will help manage modern challenges to bee health. Here we used DNA sequencing to characterise the genomes and metagenomes of 19 honey bee colonies from across Britain. Low heterozygosity was observed in many Scottish colonies which had high similarity to the native dark bee...
November 26, 2018: Nature Communications
Shantanu Kundu, Vikas Kumar, Kaomud Tyagi, Rajasree Chakraborty, Devkant Singha, Iftikar Rahaman, Avas Pakrashi, Kailash Chandra
The characterization of mitochondrial genome has been evidenced as an efficient field of study for phylogenetic and evolutionary analysis in vertebrates including turtles. The aim of this study was to distinguish the structure and variability of the Trionychidae species mitogenomes through comparative analysis. The complete mitogenome (16796 bp) of an endangered freshwater turtle, Nilssonia nigricans was sequenced and annotated. The mitogenome encoded for 37 genes and a major non-coding control region (CR)...
November 26, 2018: Scientific Reports
Christine Tait-Burkard, Andrea Doeschl-Wilson, Mike J McGrew, Alan L Archibald, Helen M Sang, Ross D Houston, C Bruce Whitelaw, Mick Watson
The human population is growing, and as a result we need to produce more food whilst reducing the impact of farming on the environment. Selective breeding and genomic selection have had a transformational impact on livestock productivity, and now transgenic and genome-editing technologies offer exciting opportunities for the production of fitter, healthier and more-productive livestock. Here, we review recent progress in the application of genome editing to farmed animal species and discuss the potential impact on our ability to produce food...
November 26, 2018: Genome Biology
Eduardo Gorab
Polynucleotide chains obeying Watson-Crick pairing are apt to form non-canonical complexes such as triple-helical nucleic acids. From early characterization in vitro, their occurrence in vivo has been strengthened by increasing evidence, although most remain circumstantial particularly for triplex DNA. Here, different approaches were employed to specify triple-stranded DNA sequences in the Drosophila melanogaster chromosomes. Antibodies to triplex nucleic acids, previously characterized, bind to centromeric regions of mitotic chromosomes and also to the polytene section 59E of mutant strains carrying the brown dominant allele, indicating that AAGAG tandem satellite repeats are triplex-forming sequences...
November 23, 2018: Cells
Kota Itahashi, Shunsuke Kondo, Takashi Kubo, Yutaka Fujiwara, Mamoru Kato, Hitoshi Ichikawa, Takahiko Koyama, Reitaro Tokumasu, Jia Xu, Claudia S Huettner, Vanessa V Michelini, Laxmi Parida, Takashi Kohno, Noboru Yamamoto
Background: Oncologists increasingly rely on clinical genome sequencing to pursue effective, molecularly targeted therapies. This study assesses the validity and utility of the artificial intelligence Watson for Genomics (WfG) for analyzing clinical sequencing results. Methods: This study identified patients with solid tumors who participated in in-house genome sequencing projects at a single cancer specialty hospital between April 2013 and October 2016. Targeted genome sequencing results of these patients' tumors, previously analyzed by multidisciplinary specialists at the hospital, were reanalyzed by WfG...
2018: Frontiers in Medicine
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