Literature DB >> 34001009

Population genetic considerations for using biobanks as international resources in the pandemic era and beyond.

Hannah Carress1, Daniel John Lawson2, Eran Elhaik3,4.   

Abstract

The past years have seen the rise of genomic biobanks and mega-scale meta-analysis of genomic data, which promises to reveal the genetic underpinnings of health and disease. However, the over-representation of Europeans in genomic studies not only limits the global understanding of disease risk but also inhibits viable research into the genomic differences between carriers and patients. Whilst the community has agreed that more diverse samples are required, it is not enough to blindly increase diversity; the diversity must be quantified, compared and annotated to lead to insight. Genetic annotations from separate biobanks need to be comparable and computable and to operate without access to raw data due to privacy concerns. Comparability is key both for regular research and to allow international comparison in response to pandemics. Here, we evaluate the appropriateness of the most common genomic tools used to depict population structure in a standardized and comparable manner. The end goal is to reduce the effects of confounding and learn from genuine variation in genetic effects on phenotypes across populations, which will improve the value of biobanks (locally and internationally), increase the accuracy of association analyses and inform developmental efforts.

Entities:  

Keywords:  Biobanks; Bioinformatics; Genomic medicine; Population stratification bias; Population structure

Year:  2021        PMID: 34001009     DOI: 10.1186/s12864-021-07618-x

Source DB:  PubMed          Journal:  BMC Genomics        ISSN: 1471-2164            Impact factor:   3.969


  116 in total

1.  Biobanks. Population databases boom, from Iceland to the U.S.

Authors:  Jocelyn Kaiser
Journal:  Science       Date:  2002-11-08       Impact factor: 47.728

Review 2.  Five years of GWAS discovery.

Authors:  Peter M Visscher; Matthew A Brown; Mark I McCarthy; Jian Yang
Journal:  Am J Hum Genet       Date:  2012-01-13       Impact factor: 11.025

3.  Biobank managers bemoan underuse of collected samples.

Authors:  Megan Scudellari
Journal:  Nat Med       Date:  2013-03       Impact factor: 53.440

Review 4.  Genomics of hypertension: the road to precision medicine.

Authors:  Sandosh Padmanabhan; Anna F Dominiczak
Journal:  Nat Rev Cardiol       Date:  2020-11-20       Impact factor: 49.421

5.  UK biobank: an open access resource for identifying the causes of a wide range of complex diseases of middle and old age.

Authors:  Cathie Sudlow; John Gallacher; Naomi Allen; Valerie Beral; Paul Burton; John Danesh; Paul Downey; Paul Elliott; Jane Green; Martin Landray; Bette Liu; Paul Matthews; Giok Ong; Jill Pell; Alan Silman; Alan Young; Tim Sprosen; Tim Peakman; Rory Collins
Journal:  PLoS Med       Date:  2015-03-31       Impact factor: 11.069

6.  Statistical correction of the Winner's Curse explains replication variability in quantitative trait genome-wide association studies.

Authors:  Cameron Palmer; Itsik Pe'er
Journal:  PLoS Genet       Date:  2017-07-17       Impact factor: 5.917

7.  A short history of the genome-wide association study: where we were and where we are going.

Authors:  Shiro Ikegawa
Journal:  Genomics Inform       Date:  2012-12-31

8.  The Genome Russia project: closing the largest remaining omission on the world Genome map.

Authors:  Taras K Oleksyk; Vladimir Brukhin; Stephen J O'Brien
Journal:  Gigascience       Date:  2015-11-13       Impact factor: 6.524

9.  The UK Biobank resource with deep phenotyping and genomic data.

Authors:  Clare Bycroft; Colin Freeman; Desislava Petkova; Gavin Band; Lloyd T Elliott; Kevin Sharp; Allan Motyer; Damjan Vukcevic; Olivier Delaneau; Jared O'Connell; Adrian Cortes; Samantha Welsh; Alan Young; Mark Effingham; Gil McVean; Stephen Leslie; Naomi Allen; Peter Donnelly; Jonathan Marchini
Journal:  Nature       Date:  2018-10-10       Impact factor: 49.962

10.  COVID-19 infection: the perspectives on immune responses.

Authors:  Yufang Shi; Ying Wang; Changshun Shao; Jianan Huang; Jianhe Gan; Xiaoping Huang; Enrico Bucci; Mauro Piacentini; Giuseppe Ippolito; Gerry Melino
Journal:  Cell Death Differ       Date:  2020-03-23       Impact factor: 15.828

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  2 in total

1.  Principal Component Analyses (PCA)-based findings in population genetic studies are highly biased and must be reevaluated.

Authors:  Eran Elhaik
Journal:  Sci Rep       Date:  2022-08-29       Impact factor: 4.996

2.  Systems biology analysis of human genomes points to key pathways conferring spina bifida risk.

Authors:  Vanessa Aguiar-Pulido; Paul Wolujewicz; Alexander Martinez-Fundichely; Eran Elhaik; Gaurav Thareja; Alice Abdel Aleem; Nader Chalhoub; Tawny Cuykendall; Jamel Al-Zamer; Yunping Lei; Haitham El-Bashir; James M Musser; Abdulla Al-Kaabi; Gary M Shaw; Ekta Khurana; Karsten Suhre; Christopher E Mason; Olivier Elemento; Richard H Finnell; M Elizabeth Ross
Journal:  Proc Natl Acad Sci U S A       Date:  2021-12-21       Impact factor: 11.205

  2 in total

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