Literature DB >> 29727589

Genome sequencing in the clinic: the past, present, and future of genomic medicine.

Jeremy W Prokop1,2,3, Thomas May1,4,5, Kim Strong1, Stephanie M Bilinovich2, Caleb Bupp2,6, Surender Rajasekaran2,7, Elizabeth A Worthey1, Jozef Lazar1.   

Abstract

Genomic sequencing has undergone massive expansion in the past 10 yr, from a rarely used research tool into an approach that has broad applications in a clinical setting. From rare disease to cancer, genomics is transforming our knowledge of biology. The transition from targeted gene sequencing, to whole exome sequencing, to whole genome sequencing has only been made possible due to rapid advancements in technologies and informatics that have plummeted the cost per base of DNA sequencing and analysis. The tools of genomics have resolved the etiology of disease for previously undiagnosable conditions, identified cancer driver gene variants, and have impacted the understanding of pathophysiology for many diseases. However, this expansion of use has also highlighted research's current voids in knowledge. The lack of precise animal models for gene-to-function association, lack of tools for analysis of genomic structural changes, skew in populations used for genetic studies, publication biases, and the "Unknown Proteome" all contribute to voids needing filled for genomics to work in a fast-paced clinical setting. The future will hold the tools to fill in these voids, with new data sets and the continual development of new technologies allowing for expansion of genomic medicine, ushering in the days to come for precision medicine. In this review we highlight these and other points in hopes of advancing and guiding precision medicine into the future for optimal success.

Entities:  

Keywords:  GWAS; VUS; clinical sequencing; ethics; whole genome sequencing

Mesh:

Year:  2018        PMID: 29727589      PMCID: PMC6139636          DOI: 10.1152/physiolgenomics.00046.2018

Source DB:  PubMed          Journal:  Physiol Genomics        ISSN: 1094-8341            Impact factor:   3.107


  121 in total

1.  Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures.

Authors:  Alexander Stark; Michael F Lin; Pouya Kheradpour; Jakob S Pedersen; Leopold Parts; Joseph W Carlson; Madeline A Crosby; Matthew D Rasmussen; Sushmita Roy; Ameya N Deoras; J Graham Ruby; Julius Brennecke; Emily Hodges; Angie S Hinrichs; Anat Caspi; Benedict Paten; Seung-Won Park; Mira V Han; Morgan L Maeder; Benjamin J Polansky; Bryanne E Robson; Stein Aerts; Jacques van Helden; Bassem Hassan; Donald G Gilbert; Deborah A Eastman; Michael Rice; Michael Weir; Matthew W Hahn; Yongkyu Park; Colin N Dewey; Lior Pachter; W James Kent; David Haussler; Eric C Lai; David P Bartel; Gregory J Hannon; Thomas C Kaufman; Michael B Eisen; Andrew G Clark; Douglas Smith; Susan E Celniker; William M Gelbart; Manolis Kellis
Journal:  Nature       Date:  2007-11-08       Impact factor: 49.962

2.  Next-generation sequencing for clinical diagnostics.

Authors:  Howard J Jacob
Journal:  N Engl J Med       Date:  2013-10-02       Impact factor: 91.245

3.  Generation and characterization of functional cardiomyocytes using induced pluripotent stem cells derived from human fibroblasts.

Authors:  Hui Gai; Elaine Lai-Han Leung; Peter D Costantino; Jerell R Aguila; David M Nguyen; Louis M Fink; David C Ward; Yupo Ma
Journal:  Cell Biol Int       Date:  2009-09-01       Impact factor: 3.612

4.  X inactivation in females with X-linked disease.

Authors:  J M Puck; H F Willard
Journal:  N Engl J Med       Date:  1998-01-29       Impact factor: 91.245

5.  Rapid whole-genome sequencing for genetic disease diagnosis in neonatal intensive care units.

Authors:  Carol Jean Saunders; Neil Andrew Miller; Sarah Elizabeth Soden; Darrell Lee Dinwiddie; Aaron Noll; Noor Abu Alnadi; Nevene Andraws; Melanie LeAnn Patterson; Lisa Ann Krivohlavek; Joel Fellis; Sean Humphray; Peter Saffrey; Zoya Kingsbury; Jacqueline Claire Weir; Jason Betley; Russell James Grocock; Elliott Harrison Margulies; Emily Gwendolyn Farrow; Michael Artman; Nicole Pauline Safina; Joshua Erin Petrikin; Kevin Peter Hall; Stephen Francis Kingsmore
Journal:  Sci Transl Med       Date:  2012-10-03       Impact factor: 17.956

6.  PheWAS: demonstrating the feasibility of a phenome-wide scan to discover gene-disease associations.

Authors:  Joshua C Denny; Marylyn D Ritchie; Melissa A Basford; Jill M Pulley; Lisa Bastarache; Kristin Brown-Gentry; Deede Wang; Dan R Masys; Dan M Roden; Dana C Crawford
Journal:  Bioinformatics       Date:  2010-03-24       Impact factor: 6.937

7.  Drosophila melanogaster: a fly through its history and current use.

Authors:  R Stephenson; N H Metcalfe
Journal:  J R Coll Physicians Edinb       Date:  2013

8.  Targeted gene correction of α1-antitrypsin deficiency in induced pluripotent stem cells.

Authors:  Kosuke Yusa; S Tamir Rashid; Helene Strick-Marchand; Ignacio Varela; Pei-Qi Liu; David E Paschon; Elena Miranda; Adriana Ordóñez; Nicholas R F Hannan; Foad J Rouhani; Sylvie Darche; Graeme Alexander; Stefan J Marciniak; Noemi Fusaki; Mamoru Hasegawa; Michael C Holmes; James P Di Santo; David A Lomas; Allan Bradley; Ludovic Vallier
Journal:  Nature       Date:  2011-10-12       Impact factor: 49.962

9.  A genetically humanized mouse model for hepatitis C virus infection.

Authors:  Marcus Dorner; Joshua A Horwitz; Justin B Robbins; Walter T Barry; Qian Feng; Kathy Mu; Christopher T Jones; John W Schoggins; Maria Teresa Catanese; Dennis R Burton; Mansun Law; Charles M Rice; Alexander Ploss
Journal:  Nature       Date:  2011-06-08       Impact factor: 49.962

10.  Integrative analysis of 111 reference human epigenomes.

Authors:  Anshul Kundaje; Wouter Meuleman; Jason Ernst; Misha Bilenky; Angela Yen; Alireza Heravi-Moussavi; Pouya Kheradpour; Zhizhuo Zhang; Jianrong Wang; Michael J Ziller; Viren Amin; John W Whitaker; Matthew D Schultz; Lucas D Ward; Abhishek Sarkar; Gerald Quon; Richard S Sandstrom; Matthew L Eaton; Yi-Chieh Wu; Andreas R Pfenning; Xinchen Wang; Melina Claussnitzer; Yaping Liu; Cristian Coarfa; R Alan Harris; Noam Shoresh; Charles B Epstein; Elizabeta Gjoneska; Danny Leung; Wei Xie; R David Hawkins; Ryan Lister; Chibo Hong; Philippe Gascard; Andrew J Mungall; Richard Moore; Eric Chuah; Angela Tam; Theresa K Canfield; R Scott Hansen; Rajinder Kaul; Peter J Sabo; Mukul S Bansal; Annaick Carles; Jesse R Dixon; Kai-How Farh; Soheil Feizi; Rosa Karlic; Ah-Ram Kim; Ashwinikumar Kulkarni; Daofeng Li; Rebecca Lowdon; GiNell Elliott; Tim R Mercer; Shane J Neph; Vitor Onuchic; Paz Polak; Nisha Rajagopal; Pradipta Ray; Richard C Sallari; Kyle T Siebenthall; Nicholas A Sinnott-Armstrong; Michael Stevens; Robert E Thurman; Jie Wu; Bo Zhang; Xin Zhou; Arthur E Beaudet; Laurie A Boyer; Philip L De Jager; Peggy J Farnham; Susan J Fisher; David Haussler; Steven J M Jones; Wei Li; Marco A Marra; Michael T McManus; Shamil Sunyaev; James A Thomson; Thea D Tlsty; Li-Huei Tsai; Wei Wang; Robert A Waterland; Michael Q Zhang; Lisa H Chadwick; Bradley E Bernstein; Joseph F Costello; Joseph R Ecker; Martin Hirst; Alexander Meissner; Aleksandar Milosavljevic; Bing Ren; John A Stamatoyannopoulos; Ting Wang; Manolis Kellis
Journal:  Nature       Date:  2015-02-19       Impact factor: 69.504

View more
  20 in total

1.  Exome Sequencing and Molecular Diagnosis.

Authors:  William D Graf
Journal:  Dtsch Arztebl Int       Date:  2019-03-22       Impact factor: 5.594

2.  An American Physiological Society cross-journal Call for Papers on "Deconstructing Organs: Single-Cell Analyses, Decellularized Organs, Organoids, and Organ-on-a-Chip Models".

Authors:  Josephine C Adams; P Darwin Bell; Sue C Bodine; Heddwen L Brooks; Nigel Bunnett; Bina Joe; Kara Hansell Keehan; Thomas R Kleyman; André Marette; Rory E Morty; Jan-Marino Ramírez; Morten B Thomsen; Bill J Yates; Irving H Zucker
Journal:  Am J Physiol Lung Cell Mol Physiol       Date:  2020-07-01       Impact factor: 5.464

3.  Breakdown of multiple sclerosis genetics to identify an integrated disease network and potential variant mechanisms.

Authors:  C Joy Shepard; Sara G Cline; David Hinds; Seyedehameneh Jahanbakhsh; Jeremy W Prokop
Journal:  Physiol Genomics       Date:  2019-09-04       Impact factor: 3.107

Review 4.  The role of biomineralization in disorders of skeletal development and tooth formation.

Authors:  Christopher S Kovacs; Catherine Chaussain; Philip Osdoby; Maria Luisa Brandi; Bart Clarke; Rajesh V Thakker
Journal:  Nat Rev Endocrinol       Date:  2021-05-04       Impact factor: 43.330

5.  The Clinical Genome and Ancestry Report: An interactive web application for prioritizing clinically implicated variants from genome sequencing data with ancestry composition.

Authors:  In-Hee Lee; Jose A Negron; Carles Hernandez-Ferrer; William Jefferson Alvarez; Kenneth D Mandl; Sek Won Kong
Journal:  Hum Mutat       Date:  2019-11-15       Impact factor: 4.878

Review 6.  The Iceberg under Water: Unexplored Complexity of Chromoanagenesis in Congenital Disorders.

Authors:  Cinthya J Zepeda-Mendoza; Cynthia C Morton
Journal:  Am J Hum Genet       Date:  2019-04-04       Impact factor: 11.025

7.  A fully-automated event-based variant prioritizing solution to the CAGI5 intellectual disability gene panel challenge.

Authors:  Jingqi Chen
Journal:  Hum Mutat       Date:  2019-05-21       Impact factor: 4.878

8.  Long non-coding RNA SOS1-IT1 promotes endometrial cancer progression by regulating hypoxia signaling pathway.

Authors:  Hongyang Liu; Junhu Wan; Quanling Feng; Jingyu Li; Jun Liu; Shihong Cui
Journal:  J Cell Commun Signal       Date:  2021-10-12       Impact factor: 5.908

9.  Family genetic result communication in rare and undiagnosed disease communities: Understanding the practice.

Authors:  Courtney M Studwell; Emily G Kelley; Janet S Sinsheimer; Christina G S Palmer; Kimberly LeBlanc
Journal:  J Genet Couns       Date:  2020-10-27       Impact factor: 2.537

10.  Old Challenges or New Issues? Genetic Health Professionals' Experiences Obtaining Informed Consent in Diagnostic Genomic Sequencing.

Authors:  Danya F Vears; Pascal Borry; Julian Savulescu; Julian J Koplin
Journal:  AJOB Empir Bioeth       Date:  2020-10-05
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.