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Tissue sampling methods and standards for vertebrate genomics.

ABSTRACT: The recent rise in speed and efficiency of new sequencing technologies have facilitated high-throughput sequencing, assembly and analyses of genomes, advancing ongoing efforts to analyze genetic sequences across major vertebrate groups. Standardized procedures in acquiring high quality DNA and RNA and establishing cell lines from target species will facilitate these initiatives. We provide a legal and methodological guide according to four standards of acquiring and storing tissue for the Genome 10K Project and similar initiatives as follows: four-star (banked tissue/cell cultures, RNA from multiple types of tissue for transcriptomes, and sufficient flash-frozen tissue for 1 mg of DNA, all from a single individual); three-star (RNA as above and frozen tissue for 1 mg of DNA); two-star (frozen tissue for at least 700 ?g of DNA); and one-star (ethanol-preserved tissue for 700 ?g of DNA or less of mixed quality). At a minimum, all tissues collected for the Genome 10K and other genomic projects should consider each species' natural history and follow institutional and legal requirements. Associated documentation should detail as much information as possible about provenance to ensure representative sampling and subsequent sequencing. Hopefully, the procedures outlined here will not only encourage success in the Genome 10K Project but also inspire the adaptation of standards by other genomic projects, including those involving other biota.

SUBMITTER: Wong PB

PROVIDER: S-EPMC3626508 | biostudies-literature | 2012 Jul

REPOSITORIES: biostudies-literature

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Tissue sampling methods and standards for vertebrate genomics.

Wong Pamela By PB Wiley Edward O EO Johnson Warren E WE Ryder Oliver A OA O'Brien Stephen J SJ Haussler David D Koepfli Klaus-Peter KP Houck Marlys L ML Perelman Polina P Mastromonaco Gabriela G Bentley Andrew C AC Venkatesh Byrappa B Zhang Ya-Ping YP Murphy Robert W RW

GigaScience 20120712 1

The recent rise in speed and efficiency of new sequencing technologies have facilitated high-throughput sequencing, assembly and analyses of genomes, advancing ongoing efforts to analyze genetic sequences across major vertebrate groups. Standardized procedures in acquiring high quality DNA and RNA and establishing cell lines from target species will facilitate these initiatives. We provide a legal and methodological guide according to four standards of acquiring and storing tissue for the Genome ...[more]

PMID: 23587255

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Project description:BackgroundMinimally invasive tissue sampling (MITS), also named minimally invasive autopsy is a post-mortem method shown to be an acceptable proxy of the complete diagnostic autopsy. MITS improves the knowledge of causes of death (CoD) in resource-limited settings. Its implementation requires understanding the components of acceptability, including facilitators and barriers in real-case scenarios.MethodsWe undertook a mixed-methods analysis comparing anticipated (hypothetical scenario) and experienced (real-case scenario) acceptability of MITS among relatives of deceased children in Mozambique. Anticipated acceptability information was obtained from 15 interviews with relatives of deceased children. The interview focus was on whether and why they would allow the procedure on their dead child in a hypothetical scenario. Experienced acceptability data were obtained from outcomes of consent requested to relatives of 114 deceased children during MITS implementation, recorded through observations, clinical records abstraction and follow-up informal conversations with health care professionals and semi-structured interviews with relatives.ResultsNinety-three percent of relatives indicated that they would hypothetically accept MITS on their deceased child. A key reason was knowing the CoD to take preventive actions; whereas the need to conform with the norm of immediate child burial, the secrecy of perinatal deaths, the decision-making complexity, the misalignment between MITS' purpose and traditional values, lack of a credible reason to investigate CoD, and the impotency to resuscitate the deceased were identified as potential points of hesitancy for acceptance. The only refusing respondent linked MITS to a perception that sharing results would constitute a breach of confidentiality and the lack of value attached to CoD determination. Experienced acceptability revealed four different components: actual acceptance, health professionals' hesitancy, relatives' hesitancy and actual refusal, which resulted in 82% of approached relatives to agree with MITS and 79% of cases to undergo MITS. Barriers to acceptability included, among others, health professionals' and facilities' unpreparedness to perform MITS, the threat of not burying the child immediately, financial burden of delays, decision-making complexities and misalignment of MITS' objectives with family values.ConclusionsMITS showed high anticipated and experienced acceptability driven by the opportunity to prevent further deaths. Anticipated acceptability identified secrecy, confidentiality and complex decision-making processes as barriers, while experienced acceptability revealed family- and health facility-level logistics and practical aspects as barriers. Health-system and logistical impediments must also be considered before MITS implementation. Additionally, the multiple components of acceptability must be taken into account to make it more consistent and transferrable.

Dataset Information

Tissue sampling methods and standards for vertebrate genomics.

Publications

Tissue sampling methods and standards for vertebrate genomics.

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