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Literature DB >> 26553330

Human genotype-phenotype databases: aims, challenges and opportunities.

Anthony J Brookes^1,2, Peter N Robinson^3,4,5.

Abstract

Genotype-phenotype databases provide information about genetic variation, its consequences and its mechanisms of action for research and health care purposes. Existing databases vary greatly in type, areas of focus and modes of operation. Despite ever larger and more intricate datasets--made possible by advances in DNA sequencing, omics methods and phenotyping technologies--steady progress is being made towards integrating these databases rather than using them as separate entities. The consequential shift in focus from single-gene variants towards large gene panels, exomes, whole genomes and myriad observable characteristics creates new challenges and opportunities in database design, interpretation of variant pathogenicity and modes of data representation and use.

Entities: Species

Mesh：

Year: 2015 PMID： 26553330 DOI： 10.1038/nrg3932

Source DB: PubMed Journal: Nat Rev Genet ISSN： 1471-0056 Impact factor: 53.242

108 in total

Review 1. Global implementation of genomic medicine: We are not alone.

Authors: Teri A Manolio; Marc Abramowicz; Fahd Al-Mulla; Warwick Anderson; Rudi Balling; Adam C Berger; Steven Bleyl; Aravinda Chakravarti; Wasun Chantratita; Rex L Chisholm; Vajira H W Dissanayake; Michael Dunn; Victor J Dzau; Bok-Ghee Han; Tim Hubbard; Anne Kolbe; Bruce Korf; Michiaki Kubo; Paul Lasko; Erkki Leego; Surakameth Mahasirimongkol; Partha P Majumdar; Gert Matthijs; Howard L McLeod; Andres Metspalu; Pierre Meulien; Satoru Miyano; Yaakov Naparstek; P Pearl O'Rourke; George P Patrinos; Heidi L Rehm; Mary V Relling; Gad Rennert; Laura Lyman Rodriguez; Dan M Roden; Alan R Shuldiner; Sukdeb Sinha; Patrick Tan; Mats Ulfendahl; Robyn Ward; Marc S Williams; John E L Wong; Eric D Green; Geoffrey S Ginsburg
Journal: Sci Transl Med Date: 2015-06-03 Impact factor: 17.956

2. MYRIAD AFTER MYRIAD: THE PROPRIETARY DATA DILEMMA.

Authors: John M Conley; Robert Cook-Deegan; Gabriel Lázaro-Muñoz
Journal: N C J Law Technol Date: 2014-06

3. FORGE Canada Consortium: outcomes of a 2-year national rare-disease gene-discovery project.

Authors: Chandree L Beaulieu; Jacek Majewski; Jeremy Schwartzentruber; Mark E Samuels; Bridget A Fernandez; Francois P Bernier; Michael Brudno; Bartha Knoppers; Janet Marcadier; David Dyment; Shelin Adam; Dennis E Bulman; Steve J M Jones; Denise Avard; Minh Thu Nguyen; Francois Rousseau; Christian Marshall; Richard F Wintle; Yaoqing Shen; Stephen W Scherer; Jan M Friedman; Jacques L Michaud; Kym M Boycott
Journal: Am J Hum Genet Date: 2014-06-05 Impact factor: 11.025

Review 4. Immunodeficiency mutation databases (IDbases).

Authors: Hilkka Piirilä; Jouni Väliaho; Mauno Vihinen
Journal: Hum Mutat Date: 2006-12 Impact factor: 4.878

5. ALSoD: A user-friendly online bioinformatics tool for amyotrophic lateral sclerosis genetics.

Authors: Olubunmi Abel; John F Powell; Peter M Andersen; Ammar Al-Chalabi
Journal: Hum Mutat Date: 2012-07-16 Impact factor: 4.878

6. Human Variome Project country nodes: documenting genetic information within a country.

Authors: George P Patrinos; Timothy D Smith; Heather Howard; Fahd Al-Mulla; Lotfi Chouchane; Andreas Hadjisavvas; Sherifa A Hamed; Xi-Tao Li; Makia Marafie; Rajkumar S Ramesar; Feliciano J Ramos; Thomy de Ravel; Mona O El-Ruby; Tilak Ram Shrestha; María-Jesús Sobrido; Ghazi Tadmouri; Martina Witsch-Baumgartner; Bin Alwi Zilfalil; Arleen D Auerbach; Kevin Carpenter; Garry R Cutting; Vu Chi Dung; Wayne Grody; Julia Hasler; Lynn Jorde; Jim Kaput; Milan Macek; Yoichi Matsubara; Carmancita Padilla; Helen Robinson; Augusto Rojas-Martinez; Graham R Taylor; Mauno Vihinen; Tom Weber; John Burn; Ming Qi; Richard G H Cotton; David Rimoin
Journal: Hum Mutat Date: 2012-07-18 Impact factor: 4.878

7. 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

8. Does p.Q247X in TRIM63 cause human hypertrophic cardiomyopathy?

Authors: Rafal Ploski; Agnieszka Pollak; Sonja Müller; Maria Franaszczyk; Ewa Michalak; Joanna Kosinska; Piotr Stawinski; Mateusz Spiewak; Hubert Seggewiss; Zofia T Bilinska
Journal: Circ Res Date: 2014-01-17 Impact factor: 17.367

9. Massively parallel sequencing, aCGH, and RNA-Seq technologies provide a comprehensive molecular diagnosis of Fanconi anemia.

Authors: Settara C Chandrasekharappa; Francis P Lach; Danielle C Kimble; Aparna Kamat; Jamie K Teer; Frank X Donovan; Elizabeth Flynn; Shurjo K Sen; Supawat Thongthip; Erica Sanborn; Agata Smogorzewska; Arleen D Auerbach; Elaine A Ostrander
Journal: Blood Date: 2013-04-23 Impact factor: 22.113

10. Cooperative control of striated muscle mass and metabolism by MuRF1 and MuRF2.

Authors: Christian C Witt; Stephanie H Witt; Stefanie Lerche; Dietmar Labeit; Walter Back; Siegfried Labeit
Journal: EMBO J Date: 2007-12-20 Impact factor: 11.598

38 in total

Review 1. Text Mining for Precision Medicine: Bringing Structure to EHRs and Biomedical Literature to Understand Genes and Health.

Authors: Michael Simmons; Ayush Singhal; Zhiyong Lu
Journal: Adv Exp Med Biol Date: 2016 Impact factor: 2.622

Human genotype-phenotype databases: aims, challenges and opportunities.

Review 1. Global implementation of genomic medicine: We are not alone.

2. MYRIAD AFTER MYRIAD: THE PROPRIETARY DATA DILEMMA.

3. FORGE Canada Consortium: outcomes of a 2-year national rare-disease gene-discovery project.

Review 4. Immunodeficiency mutation databases (IDbases).

5. ALSoD: A user-friendly online bioinformatics tool for amyotrophic lateral sclerosis genetics.

6. Human Variome Project country nodes: documenting genetic information within a country.

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

8. Does p.Q247X in TRIM63 cause human hypertrophic cardiomyopathy?

9. Massively parallel sequencing, aCGH, and RNA-Seq technologies provide a comprehensive molecular diagnosis of Fanconi anemia.

10. Cooperative control of striated muscle mass and metabolism by MuRF1 and MuRF2.

Review 1. Text Mining for Precision Medicine: Bringing Structure to EHRs and Biomedical Literature to Understand Genes and Health.

Review 2. Type 2 diabetes: genetic data sharing to advance complex disease research.

3. Analysis of disease organ as a novel phenotype towards disease genetics understanding.

Review 4. Gain-of-Function Mutations: An Emerging Advantage for Cancer Biology.

Review 5. Transformative therapies for rare CFTR missense alleles.

6. Cardioinformatics: the nexus of bioinformatics and precision cardiology.

Review 7. The utility of phenomics in diagnosis of inherited metabolic disorders.

Review 8. Heart Failure in Pediatric Patients With Congenital Heart Disease.

9. Evaluating the quality of Marfan genotype-phenotype correlations in existing FBN1 databases.

Review 10. Novel bioinformatic developments for exome sequencing.