Utility of formalin-fixed, paraffin-embedded prostate biospecimens from low-resource settings for use in next-generation sequencing studies in African-descent populations
Rattachement africain : us, Nigéria, Kenya, gb, jm, bs, ky, Sénégal. Niveau de preuve : code pays fourni par la source.
Le résumé fourni par la source
Background Men of African ancestry experience higher burden from prostate cancer compared to men of other ancestral backgrounds. Limitations in the availability of high-quality biospecimens hinder the inclusion of this population in genetic studies of prostate cancer. The use of formalin-fixed paraffin-embedded (FFPE) tissues represent a potential rich source of genetic material particularly in some international settings, where fresh frozen tissue is difficult to obtain. In this study, we investigate the feasibility of using FFPE biospecimens acquired from various international sites for utility in next-generation sequencing. Methods A total of 976 FFPE blocks were collected between 2002 and 2017 from six international sites in Africa and the Caribbean representing three consortia: Prostate Cancer Transatlantic Consortium; African-Caribbean Cancer Consortium; and Men of African Descent and Carcinoma of the Prostate. Genomic DNA was checked for quality and quantity. Differences in mean quality control (QC) for pre-and-post pathology training were assessed using t-test. Pearson chi-square with trend analysis examined association between time-category and QC success status. Association of continuous DNA quality (Q129/Q41 ratio) and time of specimen collection was estimated with linear regression. Samples with a DNA quantity >0.2µg and a Q129/Q41 ratio >0.00225 were submitted for whole exome sequencing (WES). Results There was a positive relative percentage change in DNA quantity from 2002 to 2017 for Jamaica, Kenya and Senegal. There was a decline in DNA quantity over the same time period for Nigeria. There was a statistically significant improvement in quality of samples from Kenya ( P =0.032), Nigeria ( P <.001) and Senegal ( P =0.043). There was a significant improvement in the collected DNA sample quality over time with an R 2 of 0.12. Conclusions FFPE samples from low-resource settings could potentially provide sufficient DNA for WES. Improvements in biospecimen collection processing and storage for research are needed in some of these settings.
Ce résumé expose les affirmations des auteurs. BNTIC ne l’interprète pas comme une validation indépendante des résultats.
Le contrôle bibliographique ouvert
DOI retrouvé dans Crossref DOI retrouvé ; titre concordant.
- Titre Crossref
- Utility of formalin-fixed, paraffin-embedded prostate biospecimens from low-resource settings for use in next-generation sequencing studies in African-descent populations
- Date Crossref
- 10/08/2023
- Éditeur
- International Society of Global Health
- Type
- journal-article
Ce recoupement confirme des métadonnées liées au DOI. Il ne confirme ni la méthode ni les conclusions de l’étude, et il ne compte pas comme une seconde source scientifique indépendante.
Où se fait cette recherche
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Georgia College & State University pays non établi dans la noticeUniversité ou école supérieure
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Prostate Cancer Foundation pays non établi dans la noticeOrganisation à but non lucratif
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University of Ilorin Teaching Hospital Department of Pathology University of Ilorin Teaching Hospital, Nigéria (code pays fourni par la source)Établissement de santé
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Kenyatta National Hospital African Caribbean Cancer Consortium Kenya (code pays fourni par la source)Établissement de santé
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National Hospital Abuja National Hospital Abuja, Nigéria (code pays fourni par la source)Établissement de santé
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Lagos State University Teaching Hospital Lagos State University Teaching Hospital, Nigéria (code pays fourni par la source)Établissement de santé
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Ahmadu Bello University Nigéria (code pays fourni par la source)Université ou école supérieure
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University of Ilorin University of Ilorin, Nigéria (code pays fourni par la source)Université ou école supérieure
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The Prostate Centre pays non établi dans la noticeÉtablissement de santé
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University of Abuja Men of African Descent and Carcinoma of the Prostate University of Abuja, Nigéria (code pays fourni par la source)Université ou école supérieure
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University of the West Indies System pays non établi dans la noticeUniversité ou école supérieure
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University of the West Indies Department of Surgery pays non établi dans la noticeUniversité ou école supérieure
Georgia College & State University, Prostate Cancer Foundation et Department of Pathology — University of Ilorin Teaching Hospital (University of Ilorin Teaching Hospital, Nigéria), avec 9 autres affiliations. Pays d’affiliation : Nigéria, Kenya, Sénégal.
Une affiliation ne permet pas de déduire la nationalité d’un auteur.