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Rights, interests and expectations: Indigenous perspectives on unrestricted access to genomic data
Addressing Indigenous rights and interests in genetic resources has become increasingly challenging in an open science environment that promotes unrestricted access to genomic data. Although Indigenous experiences with genetic research have been shaped by a series of negative interactions, there is increasing recognition that equitable benefits can only be realized through greater participation of Indigenous communities. Issues of trust, accountability and equity underpin Indigenous critiques of genetic research and the sharing of genomic data. This Perspectives article highlights identified issues for Indigenous communities around the sharing of genomic data and suggests principles and actions that genomic researchers can adopt to recognize community rights and interests in data.In this Perspective article, the authors discuss how Indigenous Peoples' desires for greater involvement and oversight when participating in genomic research projects can be balanced against calls for unrestricted data access. They provide practical recommendations for the handling and sharing of Indigenous genomic data, with the aim of achieving mutual benefit for the research community and participating Indigenous communities.
Journal Article
Validation and refinement of the revised 2017 European LeukemiaNet genetic risk stratification of acute myeloid leukemia
The revised 2017 European LeukemiaNet (ELN) recommendations for genetic risk stratification of acute myeloid leukemia have been widely adopted, but have not yet been validated in large cohorts of AML patients. We studied 1116 newly diagnosed AML patients (age range, 18–86 years) who had received induction chemotherapy. Among 771 patients not selected by genetics, the ELN-2017 classification re-assigned 26.5% of patients into a more favorable or, more commonly, a more adverse-risk group compared with the ELN-2010 recommendations. Forty percent of the cohort, and 51% of patients ≥60 years, were classified as adverse-risk by ELN-2017. In 599 patients <60 years, estimated 5-year overall survival (OS) was 64% for ELN-2017 favorable, 42% for intermediate-risk and 20% for adverse-risk patients. Among 517 patients aged ≥60 years, corresponding 5-year OS rates were 37, 16, and 6%. Patients with biallelic CEBPA mutations or inv(16) had particularly favorable outcomes, while patients with mutated TP53 and a complex karyotype had especially poor prognosis. DNMT3A mutations associated with inferior OS within each ELN-2017 risk group. Our results validate the prognostic significance of the revised ELN-2017 risk classification in AML patients receiving induction chemotherapy across a broad age range. Further refinement of the ELN-2017 risk classification is possible.
Journal Article
Update of penetrance estimates in Birt-Hogg-Dubé syndrome
BackgroundBirt-Hogg-Dubé (BHD) syndrome is a rare genetic syndrome caused by pathogenic or likely pathogenic germline variants in the FLCN gene. Patients with BHD syndrome have an increased risk of fibrofolliculomas, pulmonary cysts, pneumothorax and renal cell carcinoma. There is debate regarding whether colonic polyps should be added to the criteria. Previous risk estimates have mostly been based on small clinical case series.MethodsA comprehensive review was conducted to identify studies that had recruited families carrying pathogenic or likely pathogenic variants in FLCN. Pedigree data were requested from these studies and pooled. Segregation analysis was used to estimate the cumulative risk of each manifestation for carriers of FLCN pathogenic variants.ResultsOur final dataset contained 204 families that were informative for at least one manifestation of BHD (67 families informative for skin manifestations, 63 for lung, 88 for renal carcinoma and 29 for polyps). By age 70 years, male carriers of the FLCN variant have an estimated 19% (95% CI 12% to 31%) risk of renal tumours, 87% (95% CI 80% to 92%) of lung involvement and 87% (95% CI 78% to 93%) of skin lesions, while female carriers had an estimated 21% (95% CI 13% to 32%) risk of renal tumours, 82% (95% CI 73% to 88%) of lung involvement and 78% (95% CI 67% to 85%) of skin lesions. The cumulative risk of colonic polyps by age 70 years old was 21% (95% CI 8% to 45%) for male carriers and 32% (95% CI 16% to 53%) for female carriers.ConclusionsThese updated penetrance estimates, based on a large number of families, are important for the genetic counselling and clinical management of BHD syndrome.
Journal Article
The Rosie project
Don Tillman, professor of genetics, has never been on a second date. He is a man who can count all his friends on the fingers of one hand, whose lifelong difficulty with social rituals has convinced him that he is simply not wired for romance. So when an acquaintance informs him that he would make a \"wonderful\" husband, his first reaction is shock. Yet he must concede to the statistical probability that there is someone for everyone, and he embarks upon The Wife Project. In the orderly, evidence-based manner with which he approaches all things, Don sets out to find the perfect partner. He sets up a project designed to find him the perfect wife, starting with a questionnaire that has to be adjusted a little as he goes along. She will be punctual and logical, most definitely not a barmaid, a smoker, a drinker, or a late-arriver. Then he meets Rosie Jarman, who is everything he's not looking for in a wife. Rosie is all these things. She is also beguiling, fiery, intelligent, and on a quest of her own. She is looking for her biological father, a search that a certain DNA expert might be able to help her with. Don's Wife Project takes a back burner to the Father Project and an unlikely relationship blooms, forcing the scientifically minded geneticist to confront the spontaneous whirlwind that is Rosie, and the realization that love is not always what looks good on paper.
Book
A framework for tiered informed consent for health genomic research in Africa
A generic framework for providing participant information and implementing a tiered consent process for health genomic research in Africa can help to harness global health benefits from sharing and meta-analysis of African genomic data while simultaneously respecting and upholding the autonomy and individual choices of African research participants.
Journal Article
Translational genomics for achieving higher genetic gains in groundnut
Key messageGroundnut has entered now in post-genome era enriched with optimum genomic and genetic resources to facilitate faster trait dissection, gene discovery and accelerated genetic improvement for developing climate-smart varieties. Cultivated groundnut or peanut (Arachis hypogaea), an allopolyploid oilseed crop with a large and complex genome, is one of the most nutritious food. This crop is grown in more than 100 countries, and the low productivity has remained the biggest challenge in the semiarid tropics. Recently, the groundnut research community has witnessed fast progress and achieved several key milestones in genomics research including genome sequence assemblies of wild diploid progenitors, wild tetraploid and both the subspecies of cultivated tetraploids, resequencing of diverse germplasm lines, genome-wide transcriptome atlas and cost-effective high and low-density genotyping assays. These genomic resources have enabled high-resolution trait mapping by using germplasm diversity panels and multi-parent genetic populations leading to precise gene discovery and diagnostic marker development. Furthermore, development and deployment of diagnostic markers have facilitated screening early generation populations as well as marker-assisted backcrossing breeding leading to development and commercialization of some molecular breeding products in groundnut. Several new genomics applications/technologies such as genomic selection, speed breeding, mid-density genotyping assay and genome editing are in pipeline. The integration of these new technologies hold great promise for developing climate-smart, high yielding and more nutritious groundnut varieties in the post-genome era.
Journal Article