Literature DB >> 22706855

Comprehensive genomic studies: emerging regulatory, strategic, and quality assurance challenges for biorepositories.

Sandra A McDonald1, Elaine R Mardis, David Ota, Mark A Watson, John D Pfeifer, Jonathan M Green.   

Abstract

As part of the molecular revolution sweeping medicine, comprehensive genomic studies are adding powerful dimensions to medical research. However, their power exposes new regulatory, strategic, and quality assurance challenges for biorepositories. A key issue is that unlike other research techniques commonly applied to banked specimens, nucleic acid sequencing, if sufficiently extensive, yields data that could identify a patient. This evolving paradigm renders the concepts of anonymized and anonymous specimens increasingly outdated. The challenges for biorepositories in this new era include refined consent processes and wording, selection and use of legacy specimens, quality assurance procedures, institutional documentation, data sharing, and interaction with institutional review boards. Given current trends, biorepositories should consider these issues now, even if they are not currently experiencing sample requests for genomic analysis. We summarize our current experiences and best practices at Washington University Medical School, St Louis, MO, our perceptions of emerging trends, and recommendations.

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Year:  2012        PMID: 22706855      PMCID: PMC3509484          DOI: 10.1309/AJCPXBA69LNSCVMH

Source DB:  PubMed          Journal:  Am J Clin Pathol        ISSN: 0002-9173            Impact factor:   2.493


  28 in total

1.  Profiling the HeLa S3 transcriptome using randomly primed cDNA and massively parallel short-read sequencing.

Authors:  Ryan Morin; Matthew Bainbridge; Anthony Fejes; Martin Hirst; Martin Krzywinski; Trevor Pugh; Helen McDonald; Richard Varhol; Steven Jones; Marco Marra
Journal:  Biotechniques       Date:  2008-07       Impact factor: 1.993

Review 2.  From genetic privacy to open consent.

Authors:  Jeantine E Lunshof; Ruth Chadwick; Daniel B Vorhaus; George M Church
Journal:  Nat Rev Genet       Date:  2008-05       Impact factor: 53.242

Review 3.  Sequencing technologies - the next generation.

Authors:  Michael L Metzker
Journal:  Nat Rev Genet       Date:  2009-12-08       Impact factor: 53.242

4.  Principles of Research Tissue Banking and Specimen Evaluation from the Pathologist's Perspective.

Authors:  Sandra A McDonald
Journal:  Biopreserv Biobank       Date:  2010-12       Impact factor: 2.300

5.  [High-throughput sequencing of frozen and paraffin-embedded tumor and normal tissue].

Authors:  M Kerick; B Timmermann; M-R Schweiger
Journal:  Pathologe       Date:  2010-10       Impact factor: 1.011

6.  Procurement of Human Tissues for Research Banking in the Surgical Pathology Laboratory: Prioritization Practices at Washington University Medical Center.

Authors:  Sandra A McDonald; Rebecca D Chernock; Tracey A Leach; Ajaz A Kahn; James H Yip; Joan Rossi; John D Pfeifer
Journal:  Biopreserv Biobank       Date:  2011-09       Impact factor: 2.300

7.  Genome-wide association study identifies a new breast cancer susceptibility locus at 6q25.1.

Authors:  Wei Zheng; Jirong Long; Yu-Tang Gao; Chun Li; Ying Zheng; Yong-Bin Xiang; Wanqing Wen; Shawn Levy; Sandra L Deming; Jonathan L Haines; Kai Gu; Alecia Malin Fair; Qiuyin Cai; Wei Lu; Xiao-Ou Shu
Journal:  Nat Genet       Date:  2009-02-15       Impact factor: 38.330

8.  Genome remodelling in a basal-like breast cancer metastasis and xenograft.

Authors:  Li Ding; Matthew J Ellis; Shunqiang Li; David E Larson; Ken Chen; John W Wallis; Christopher C Harris; Michael D McLellan; Robert S Fulton; Lucinda L Fulton; Rachel M Abbott; Jeremy Hoog; David J Dooling; Daniel C Koboldt; Heather Schmidt; Joelle Kalicki; Qunyuan Zhang; Lei Chen; Ling Lin; Michael C Wendl; Joshua F McMichael; Vincent J Magrini; Lisa Cook; Sean D McGrath; Tammi L Vickery; Elizabeth Appelbaum; Katherine Deschryver; Sherri Davies; Therese Guintoli; Li Lin; Robert Crowder; Yu Tao; Jacqueline E Snider; Scott M Smith; Adam F Dukes; Gabriel E Sanderson; Craig S Pohl; Kim D Delehaunty; Catrina C Fronick; Kimberley A Pape; Jerry S Reed; Jody S Robinson; Jennifer S Hodges; William Schierding; Nathan D Dees; Dong Shen; Devin P Locke; Madeline E Wiechert; James M Eldred; Josh B Peck; Benjamin J Oberkfell; Justin T Lolofie; Feiyu Du; Amy E Hawkins; Michelle D O'Laughlin; Kelly E Bernard; Mark Cunningham; Glendoria Elliott; Mark D Mason; Dominic M Thompson; Jennifer L Ivanovich; Paul J Goodfellow; Charles M Perou; George M Weinstock; Rebecca Aft; Mark Watson; Timothy J Ley; Richard K Wilson; Elaine R Mardis
Journal:  Nature       Date:  2010-04-15       Impact factor: 49.962

Review 9.  Exome sequencing: the sweet spot before whole genomes.

Authors:  Jamie K Teer; James C Mullikin
Journal:  Hum Mol Genet       Date:  2010-08-12       Impact factor: 6.150

10.  Genome-wide association study identifies novel breast cancer susceptibility loci.

Authors:  Douglas F Easton; Karen A Pooley; Alison M Dunning; Paul D P Pharoah; Deborah Thompson; Dennis G Ballinger; Jeffery P Struewing; Jonathan Morrison; Helen Field; Robert Luben; Nicholas Wareham; Shahana Ahmed; Catherine S Healey; Richard Bowman; Kerstin B Meyer; Christopher A Haiman; Laurence K Kolonel; Brian E Henderson; Loic Le Marchand; Paul Brennan; Suleeporn Sangrajrang; Valerie Gaborieau; Fabrice Odefrey; Chen-Yang Shen; Pei-Ei Wu; Hui-Chun Wang; Diana Eccles; D Gareth Evans; Julian Peto; Olivia Fletcher; Nichola Johnson; Sheila Seal; Michael R Stratton; Nazneen Rahman; Georgia Chenevix-Trench; Stig E Bojesen; Børge G Nordestgaard; Christen K Axelsson; Montserrat Garcia-Closas; Louise Brinton; Stephen Chanock; Jolanta Lissowska; Beata Peplonska; Heli Nevanlinna; Rainer Fagerholm; Hannaleena Eerola; Daehee Kang; Keun-Young Yoo; Dong-Young Noh; Sei-Hyun Ahn; David J Hunter; Susan E Hankinson; David G Cox; Per Hall; Sara Wedren; Jianjun Liu; Yen-Ling Low; Natalia Bogdanova; Peter Schürmann; Thilo Dörk; Rob A E M Tollenaar; Catharina E Jacobi; Peter Devilee; Jan G M Klijn; Alice J Sigurdson; Michele M Doody; Bruce H Alexander; Jinghui Zhang; Angela Cox; Ian W Brock; Gordon MacPherson; Malcolm W R Reed; Fergus J Couch; Ellen L Goode; Janet E Olson; Hanne Meijers-Heijboer; Ans van den Ouweland; André Uitterlinden; Fernando Rivadeneira; Roger L Milne; Gloria Ribas; Anna Gonzalez-Neira; Javier Benitez; John L Hopper; Margaret McCredie; Melissa Southey; Graham G Giles; Chris Schroen; Christina Justenhoven; Hiltrud Brauch; Ute Hamann; Yon-Dschun Ko; Amanda B Spurdle; Jonathan Beesley; Xiaoqing Chen; Arto Mannermaa; Veli-Matti Kosma; Vesa Kataja; Jaana Hartikainen; Nicholas E Day; David R Cox; Bruce A J Ponder
Journal:  Nature       Date:  2007-06-28       Impact factor: 49.962

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  7 in total

Review 1.  A decision tool to guide the ethics review of a challenging breed of emerging genomic projects.

Authors:  Yann Joly; Derek So; Gladys Osien; Laura Crimi; Martin Bobrow; Don Chalmers; Susan E Wallace; Nikolajs Zeps; Bartha Knoppers
Journal:  Eur J Hum Genet       Date:  2016-01-20       Impact factor: 4.246

2.  Comparison of clinical targeted next-generation sequence data from formalin-fixed and fresh-frozen tissue specimens.

Authors:  David H Spencer; Jennifer K Sehn; Haley J Abel; Mark A Watson; John D Pfeifer; Eric J Duncavage
Journal:  J Mol Diagn       Date:  2013-06-26       Impact factor: 5.568

3.  Genetic Research Using Archival Tissue: Ethical, Social, and Legal Considerations in the United Arab Emirates.

Authors:  Saeeda Almarzooqi; Carol Campbell
Journal:  Asian Bioeth Rev       Date:  2018-09-07

Review 4.  Genetic Testing and Tissue Banking for Personalized Oncology: Analytical and Institutional Factors.

Authors:  George Miles; James Rae; Suresh S Ramalingam; John Pfeifer
Journal:  Semin Oncol       Date:  2015-07-14       Impact factor: 4.929

5.  A protocol for the identification and validation of novel genetic causes of kidney disease.

Authors:  Andrew Mallett; Chirag Patel; Barbara Maier; Julie McGaughran; Michael Gabbett; Minoru Takasato; Anne Cameron; Peter Trnka; Stephen I Alexander; Gopala Rangan; Michel C Tchan; Georgina Caruana; George John; Cathy Quinlan; Hugh J McCarthy; Valentine Hyland; Wendy E Hoy; Ernst Wolvetang; Ryan Taft; Cas Simons; Helen Healy; Melissa Little
Journal:  BMC Nephrol       Date:  2015-09-15       Impact factor: 2.388

6.  Open pipelines for integrated tumor genome profiles reveal differences between pancreatic cancer tumors and cell lines.

Authors:  Jeremy Goecks; Bassel F El-Rayes; Shishir K Maithel; H Jean Khoury; James Taylor; Michael R Rossi
Journal:  Cancer Med       Date:  2015-01-04       Impact factor: 4.452

Review 7.  Validation of biomarkers to predict response to immunotherapy in cancer: Volume I - pre-analytical and analytical validation.

Authors:  Giuseppe V Masucci; Alessandra Cesano; Rachael Hawtin; Sylvia Janetzki; Jenny Zhang; Ilan Kirsch; Kevin K Dobbin; John Alvarez; Paul B Robbins; Senthamil R Selvan; Howard Z Streicher; Lisa H Butterfield; Magdalena Thurin
Journal:  J Immunother Cancer       Date:  2016-11-15       Impact factor: 13.751

  7 in total

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