The African continent is regarded as the cradle of modern humans and African genomes contain more genetic variation than those from any other continent, yet only a fraction of the genetic diversity ...among African individuals has been surveyed
. Here we performed whole-genome sequencing analyses of 426 individuals-comprising 50 ethnolinguistic groups, including previously unsampled populations-to explore the breadth of genomic diversity across Africa. We uncovered more than 3 million previously undescribed variants, most of which were found among individuals from newly sampled ethnolinguistic groups, as well as 62 previously unreported loci that are under strong selection, which were predominantly found in genes that are involved in viral immunity, DNA repair and metabolism. We observed complex patterns of ancestral admixture and putative-damaging and novel variation, both within and between populations, alongside evidence that Zambia was a likely intermediate site along the routes of expansion of Bantu-speaking populations. Pathogenic variants in genes that are currently characterized as medically relevant were uncommon-but in other genes, variants denoted as 'likely pathogenic' in the ClinVar database were commonly observed. Collectively, these findings refine our current understanding of continental migration, identify gene flow and the response to human disease as strong drivers of genome-level population variation, and underscore the scientific imperative for a broader characterization of the genomic diversity of African individuals to understand human ancestry and improve health.
A critical stage of shotgun proteomics is database search, a process which attempts to match the experimental spectra to the theoretical one. Given the considerable time and effort spent in analysis, ...it is self-evident for a researcher to aspire for rigorous computational analysis and a more confident and accurate peptide/protein identification. Mass spectrometry (MS) has been applied across several clinical disciplines. The pathophysiology of Stress Urinary Incontinence (SUI), caused by a damaged pelvic floor, has become a boundless disease altering the quality of life worldwide. Although some studies pointed markers that can be bioindicators for SUI, these findings raise the issue of sensitivity and specificity. Therefore, it is critical to have a sensitive and specific analytical approach to identify markers that have been associated with protective and deleterious associations in disease. Here, we describe our designed and developed workflow for protein identification from tandem mass spectrometry that uses multiple search engines. We apply our workflow to an existing study addressing the pathophysiology of SUI. We demonstrate how using the combined approach together with high-performance computing techniques can surmount the challenges of complex analyses and extended computing time. We also compare the relative performance of each combination. Our results suggest that a combination of MS-GF+ and COMET represents the best sensitivity-specificity trade-off, outperforming all other tested combinations. The approach was also sensitive and accurately identified a set of protein that was shown to be markers for categories of diseases associated with the pathophysiology of SUI. This workflow was developed to encourage proteomic researchers to adopt MS-based techniques for accurate analysis and to promote MS as a routine tool to the clinical cohorts.
Scientific research plays a key role in the advancement of human knowledge and pursuit of solutions to important societal challenges. Typically, research occurs within specific institutions where ...data are generated and subsequently analyzed. Although collaborative science bringing together multiple institutions is now common, in such collaborations the analytical processing of the data is often performed by individual researchers within the team, with only limited internal oversight and critical analysis of the workflow prior to publication. Here, we show how hackathons can be a means of enhancing collaborative science by enabling peer review before results of analyses are published by cross-validating the design of studies or underlying data sets and by driving reproducibility of scientific analyses. Traditionally, in data analysis processes, data generators and bioinformaticians are divided and do not collaborate on analyzing the data. Hackathons are a good strategy to build bridges over the traditional divide and are potentially a great agile extension to the more structured collaborations between multiple investigators and institutions.
Abstract
Summary
Admixed populations, with their unique and diverse genetic backgrounds, are often underrepresented in genetic studies. This oversight not only limits our understanding but also ...exacerbates existing health disparities. One major barrier has been the lack of efficient tools tailored for the special challenges of genetic studies of admixed populations. Here, we present admix-kit, an integrated toolkit and pipeline for genetic analyses of admixed populations. Admix-kit implements a suite of methods to facilitate genotype and phenotype simulation, association testing, genetic architecture inference, and polygenic scoring in admixed populations.
Availability and implementation
Admix-kit package is open-source and available at https://github.com/KangchengHou/admix-kit. Additionally, users can use the pipeline designed for admixed genotype simulation available at https://github.com/UW-GAC/admix-kit_workflow.
Ten simple rules for organizing a webinar series Fadlelmola, Faisal M; Panji, Sumir; Ahmed, Azza E ...
PLOS computational biology/PLoS computational biology,
04/2019, Letnik:
15, Številka:
4
Journal Article
Recenzirano
Odprti dostop
Biosciences eastern and central Africa (BecA-ILRI Hub), International Livestock Research Institute, Nairobi, Kenya Affiliation: South African MRC Bioinformatics Unit, South African National ...Bioinformatics Institute, University of the Western Cape, Bellville 7535, Cape Town, South Africa ORCID logo http://orcid.org/0000-0002-8282-1325 Oussema Souiai Affiliations Laboratory of BioInformatics Biomathematics and bioStatistics, Institut Pasteur de SalTunis, Tunis, Tunisia, Institut supérieur des technologies médicales, Univesité Tunis al Manar, Tunis, Tunisia Nicola Mulder Affiliation: Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa ORCID logo http://orcid.org/0000-0003-4905-0941 H3ABioNet Research working group as members of the H3Africa Consortium ¶Membership list of the H3ABioNet Research working group can be found in the Acknowledgments section. ...choosing webinar themes requires mapping of the target audience needs and interests 7. ...the earlier a regular webinar date and time is settled upon, the earlier it will make its way into attendees’ calendars thereby enabling them to avoid subsequent scheduling conflicts. The webinar coordination team assists with all the planning and logistics for hosting a webinar (Rule 1); Choosing webinar themes requires mapping of the target audience needs and interest (Rule 2); Drafting a webinar planning checklist through regular planning meetings as well as post webinar meetings (Rule 3); Decentralized webinar organization of tasks and resources through accessible shared space (Rule 4); Planing early and settling on the provisional dates and times of the webinar events along with their themes (Rule 5); Choosing and settling on convenient and user friendly webinar platform (Rule 6); Approaching and confirming potential speakers (Rule 7); Obtaining the webinar title, abstract and presenter’s biography for creating the webinar announcement through emails and social media channels (Rule 8); Allocating time for the platform orientation (Rule 9); and Keeping close-up track of webinar metrics for regular assessment and evaluation (Rule 10).
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
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