Sample Confirmation Testing: A Short Tandem Repeat-Based Quality Assurance and Quality Control Procedure for the eyeGENE Biorepository

Parrish, Rebecca; Garafalo, Alexandra V.; Ndifor, Vida; Goetz, Kerry; Reeves, Melissa; Yim, Annette; Cooper, Remy C.; Iano-Fletcher, Jemma; Wang, Xinjing; Tumminia, Santa J.

doi:10.1089/bio.2015.0098

Cited by 6 publications

(6 citation statements)

References 13 publications

(14 reference statements)

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“…The eyeGENE Network, which includes 412 clinical users and 13 commercial and academic Clinical Laboratory Improvement Amendments (CLIA) diagnostic laboratory partners, has generated a rich resource of phenotypic and genotypic information. The carefully curated biospecimen repository (Parrish et al, 2016)…”

Section: Introductionmentioning

confidence: 99%

Genetic testing for inherited eye conditions in over 6,000 individuals through the eyeGENE network

Goetz

Reeves

Gagadam

et al. 2020

American J of Med Genetics Pt C

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Genetic testing in a multisite clinical trial network for inherited eye conditions is described in this retrospective review of data collected through eyeGENE ® , the National Ophthalmic Disease Genotyping and Phenotyping Network. Participants in eyeGENE were enrolled through a network of clinical providers throughout the United States and Canada. Blood samples and clinical data were collected to establish a phenotype:genotype database, biorepository, and patient registry. Data and samples are available for research use, and participants are provided results of clinical genetic testing. eyeGENE utilized a unique, distributed clinical trial design to enroll 6,403 participants from 5,385 families diagnosed with over 30 different inherited eye conditions. The most common diagnoses given for participants were retinitis pigmentosa (RP), Stargardt disease, and choroideremia. Pathogenic variants were most frequently reported in ABCA4 (37%), USH2A (7%), RPGR (6%), CHM (5%), and PRPH2 (3%). Among the 5,552 participants with genetic testing, at least one pathogenic or likely pathogenic variant was observed in 3,448 participants (62.1%), and variants of uncertain significance in 1,712 participants (30.8%). Ten genes represent 68% of all pathogenic and likely pathogenic variants in eyeGENE. Cross-referencing current gene therapy clinical trials, over a thousand participants may be eligible, based on pathogenic variants in genes targeted by those therapies. This article is the first summary of genetic testing from thousands of participants tested through eyeGENE, including reports from 5,552 individuals. eyeGENE provides a launching point for inherited eye research, connects researchers with potential future study participants, and provides a valuable resource to the vision community.

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Section: Introductionmentioning

confidence: 99%

Genetic testing for inherited eye conditions in over 6,000 individuals through the eyeGENE network

Goetz

Reeves

Gagadam

et al. 2020

American J of Med Genetics Pt C

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“…A careful selection of collection devices is critical here since differences in biomarker testing have been reported [8,9]. Consumables such as modified cards (IsoCode cards or FTA cards) for blood spot collection, in addition to multibarrier pouches with desiccant packs for room-temperature transportation and future conservation, could be also included for traceability purposes [10]. For noninvasive samples (nails, stool, etc.…”

Section: Centralized Preparation Of Consumables For Sample Collectionmentioning

confidence: 99%

Harmonized and Quality Sample Handling in Biobank-Supported Multicenter Prospective Studies

Valdivieso-Gómez¹,

Garrancho-Pérez²,

Aroca-Siendones³

et al. 2021

Human Blood Group Systems and Haemoglobinopathies

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In the frame of multicenter research studies, biobanks ensure the harmonization and traceability of the prospective collection of quality samples. This is significant because pre-analytical variables must be carefully considered to guarantee the integrity of biomarkers to be tested and to avoid bias affecting the validity of the analytical results. According to a quality management system, biobanks contribute with documents and records; consumable preparation for collection, processing, and conservation; sample quality controls; and centralized management of sample handling, storage, and distribution. Traceability of samples is based on unique standard codes and the use of pre-assigned, pre-coded, and pre-labeled materials for sample collection, processing, and conservation. By using these supporting tools, quality derivatives are obtained based on common and evidence-based standard operating procedures (SOPs), with associated traceability information in relation with their collection, processing, conservation, and distribution. The biobank-supported workflow, specifically designed and implemented for each project, allows obtaining harmonized quality samples contributing to the quality of large and complex research projects and the corresponding validity of the analyses.

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“…The eyeGENE research study collected more than 6,000 samples from 2006 to 2015 from patients and family members affected with genetic eye diseases, including IRDs (Parrish et al, 2016). Through this research initiative, patients provided DNA samples and phenotypic data to a biorepository (Goetz, Reeves, Tumminia, & Brooks, 2012).…”

Section: Introductionmentioning

confidence: 99%

“…In order to overcome this, several different genetic testing initiatives have been developed by government programs, nonprofit foundations, and corporations in which genetic testing through a CLIA-certified lab is available to patients at no cost to them. These programs include the eyeGENE research study at the National Eye Institute, the Foundation The eyeGENE research study collected more than 6,000 samples from 2006 to 2015 from patients and family members affected with genetic eye diseases, including IRDs (Parrish et al, 2016). Through this research initiative, patients provided DNA samples and phenotypic data to a biorepository (Goetz, Reeves, Tumminia, & Brooks, 2012).…”

mentioning

confidence: 99%

Genetic testing for inherited retinal degenerations: Triumphs and tribulations

Branham

Schlegel

Fahim

et al. 2020

American J of Med Genetics Pt C

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Inherited retinal degenerations (IRDs) are a genotypically and phenotypically diverse group of conditions. Great strides have been made toward identifying the genetic basis for these conditions over the last 30 years-more than 270 different genes involved in syndromic and nonsyndromic forms of retinal dystrophies have now been identified. The identification of these genes and the improvement of clinical laboratory techniques have led to the identification of the genetic basis of disease in 56-76% of patients with IRDs through next generation sequencing and copy number variant analysis. Genetic testing is an essential part of clinical care for patients affected with IRDs and is required to confirm the diagnosis, understand the inheritance of the condition, and determine eligibility for gene-specific treatments or clinical trials. Despite the success achieved in determining the genetic cause of these conditions, several challenges remain, which must be considered when providing genetic testing and genetic counseling to patients. For this reason, an integrated team of ophthalmic and genetic clinicians who are familiar with these challenges is necessary to provide optimal comprehensive care to these patients.

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Sample Confirmation Testing: A Short Tandem Repeat-Based Quality Assurance and Quality Control Procedure for the eyeGENE Biorepository

Cited by 6 publications

References 13 publications

Genetic testing for inherited eye conditions in over 6,000 individuals through the eyeGENE network

Genetic testing for inherited eye conditions in over 6,000 individuals through the eyeGENE network

Harmonized and Quality Sample Handling in Biobank-Supported Multicenter Prospective Studies

Genetic testing for inherited retinal degenerations: Triumphs and tribulations

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