Initiative for standardization of the format of the next-generation sequencing (NGS) results

Pipan, Veronika; Kunej, Tanja

doi:10.15190/d.2015.36

Cited by 7 publications

(3 citation statements)

References 10 publications

(9 reference statements)

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“…Our research group has recently focused on reporting standardization in various genomics subfields. We have proposed several initiatives and minimal requirements, for example, for reporting methodologies, such as NGS (Pipan & Kunej, 2015), genotype-phenotype associations (Traven, Ogrinc, & Kunej, 2017;Urh & Kunej, 2016), and interactomics; transcription factor-target interaction (Slemc & Kunej, 2016) and microRNA-target interactions (Piletic & Kunej, 2017).…”

Section: Resultsmentioning

confidence: 99%

Genetic sex determination assays in 53 mammalian species: Literature analysis and guidelines for reporting standardization

Hrovatin

Kunej

2017

Ecology and Evolution

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Erstwhile, sex was determined by observation, which is not always feasible. Nowadays, genetic methods are prevailing due to their accuracy, simplicity, low costs, and time‐efficiency. However, there is no comprehensive review enabling overview and development of the field. The studies are heterogeneous, lacking a standardized reporting strategy. Therefore, our aim was to collect genetic sexing assays for mammals and assemble them in a catalogue with unified terminology. Publications were extracted from online databases using key words such as sexing and molecular. The collected data were supplemented with species and gene IDs and the type of sex‐specific sequence variant (SSSV). We developed a catalogue and graphic presentation of diagnostic tests for molecular sex determination of mammals, based on 58 papers published from 2/1991 to 10/2016. The catalogue consists of five categories: species, genes, SSSVs, methods, and references. Based on the analysis of published literature, we propose minimal requirements for reporting, consisting of: species scientific name and ID, genetic sequence with name and ID, SSSV, methodology, genomic coordinates (e.g., restriction sites, SSSVs), amplification system, and description of detected amplicon and controls. The present study summarizes vast knowledge that has up to now been scattered across databases, representing the first step toward standardization regarding molecular sexing, enabling a better overview of existing tests and facilitating planned designs of novel tests. The project is ongoing; collecting additional publications, optimizing field development, and standardizing data presentation are needed.

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Section: Resultsmentioning

confidence: 99%

Genetic sex determination assays in 53 mammalian species: Literature analysis and guidelines for reporting standardization

Hrovatin

Kunej

2017

Ecology and Evolution

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“…The World Organization for Animal Health also recently launched its first standards for HTS, bioinformatics and computational genomics (OIE, 2017 ). Two other examples are the International Organization for Standardization's initiative to standardize WGS for typing and genomic characterization (ISO/TC 34/SC 9/WG 25) and the initiative to standardize the format of HTS derived SNP data (in a cancer context; Pipan and Kunaj, 2015 ), respectively.…”

Section: Discussionmentioning

confidence: 99%

High Throughput Sequencing for Detection of Foodborne Pathogens

et al. 2017

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High-throughput sequencing (HTS) is becoming the state-of-the-art technology for typing of microbial isolates, especially in clinical samples. Yet, its application is still in its infancy for monitoring and outbreak investigations of foods. Here we review the published literature, covering not only bacterial but also viral and Eukaryote food pathogens, to assess the status and potential of HTS implementation to inform stakeholders, improve food safety and reduce outbreak impacts. The developments in sequencing technology and bioinformatics have outpaced the capacity to analyze and interpret the sequence data. The influence of sample processing, nucleic acid extraction and purification, harmonized protocols for generation and interpretation of data, and properly annotated and curated reference databases including non-pathogenic “natural” strains are other major obstacles to the realization of the full potential of HTS in analytical food surveillance, epidemiological and outbreak investigations, and in complementing preventive approaches for the control and management of foodborne pathogens. Despite significant obstacles, the achieved progress in capacity and broadening of the application range over the last decade is impressive and unprecedented, as illustrated with the chosen examples from the literature. Large consortia, often with broad international participation, are making coordinated efforts to cope with many of the mentioned obstacles. Further rapid progress can therefore be prospected for the next decade.

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“…In our studies, we are proposing initiatives to unify the format of research and review papers, because it is becoming evident that making sense of rapidly evolving evidence on genetic associations is very important for advances in genomics and the eventual integration of this information in the practice of medicine. For example, in our previous study we proposed an initiative for reporting standardization of the results of next generation sequencing (NGS) [Pipan and Kunej 2015] and molecular mechanisms of cryptorchidism development [Urh and Kunej 2016]. The STrengthening the REporting of Genetic Association studies (STREGA) initiative, for example, proposes a minimum checklist of items for reporting genetic association studies [Little et al 2009].…”

Section: Introductionmentioning

confidence: 99%

Initiative for standardization of reporting genetics of male infertility

Traven

Ogrinc

Kunej

2016

Systems Biology in Reproductive Medicine

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The number of publications on research of male infertility is increasing. Technologies used in research of male infertility generate complex results and various types of data that need to be appropriately managed, arranged, and made available to other researchers for further use. In our previous study, we collected over 800 candidate loci for male fertility in seven mammalian species. However, the continuation of the work towards a comprehensive database of candidate genes associated with different types of idiopathic human male infertility is challenging due to fragmented information, obtained from a variety of technologies and various omics approaches. Results are published in different forms and usually need to be excavated from the text, which hinders the gathering of information. Standardized reporting of genetic anomalies as well as causative and risk factors of male infertility therefore presents an important issue. The aim of the study was to collect examples of diverse genomic loci published in association with human male infertility and to propose a standardized format for reporting genetic causes of male infertility. From the currently available data we have selected 75 studies reporting 186 representative genomic loci which have been proposed as genetic risk factors for male infertility. Based on collected and formatted data, we suggested a first step towards unification of reporting the genetics of male infertility in original and review studies. The proposed initiative consists of five relevant data types: 1) genetic locus, 2) race/ethnicity, number of participants (infertile/controls), 3) methodology, 4) phenotype (clinical data, disease ontology, and disease comorbidity), and 5) reference. The proposed form for standardized reporting presents a baseline for further optimization with additional genetic and clinical information. This data standardization initiative will enable faster multi-omics data integration, database development and sharing, establishing more targeted hypotheses, and facilitating biomarker discovery.

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Initiative for standardization of the format of the next-generation sequencing (NGS) results

Cited by 7 publications

References 10 publications

Genetic sex determination assays in 53 mammalian species: Literature analysis and guidelines for reporting standardization

Genetic sex determination assays in 53 mammalian species: Literature analysis and guidelines for reporting standardization

High Throughput Sequencing for Detection of Foodborne Pathogens

Initiative for standardization of reporting genetics of male infertility

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