Utility and limitations of genetic disease databases in clinical genetics research: A neurofibromatosis 1 database example

2004 ◽  
Vol 125C (1) ◽  
pp. 42-49 ◽  
Author(s):  
Patricia Birch ◽  
J.M. Friedman
Keyword(s):  
Genetic Disease ◽  
Neurofibromatosis 1 ◽  
Clinical Genetics ◽  
Genetics Research

scholarly journals A whole-genome sequenced control population in northern Sweden reveals subregional genetic differences

2020 ◽  
Author(s):  
Daniel Svensson ◽  
Matilda Rentoft ◽  
Anna M. Dahlin ◽  
Emma Lundholm ◽  
Pall I. Olason ◽  
...  
Keyword(s):  
Genetic Disease ◽  
Reference Population ◽  
Control Population ◽  
Strong Increase ◽  
General Interest ◽  
Clinical Genetics ◽  
Whole Genome ◽  
Northern Sweden ◽  
National Reference ◽  
Area Of Interest

AbstractThe number of national reference populations that are whole-genome sequenced are rapidly increasing. Partly driving this development is the fact that genetic disease studies benefit from knowing the genetic variation typical for the geographical area of interest. A whole-genome sequenced Swedish national reference population (n=1000) has been recently published but with few samples from northern Sweden. In the present study we have whole-genome sequenced a control population (n=300) (ACpop) from Västerbotten County, a sparsely populated region in northern Sweden previously shown to be genetically different from southern Sweden. The aggregated variant frequencies within ACpop are publicly available (DOI 10.17044/NBIS/G000005) to function as a basic resource in clinical genetics and for genetic studies. Our analysis of ACpop, representing approximately 0.11% of the population in Västerbotten, indicates the presence of a genetic substructure within the county. Furthermore, a demographic analysis showed that the population from which samples were drawn was to a large extent geographically stationary, a finding that was corroborated in the genetic analysis down to the level of municipalities. Including ACpop in the reference population when imputing unknown variants in a Västerbotten cohort resulted in a strong increase in the number of high-confidence imputed variants (up to 81% for variants with minor allele frequency < 5%). ACpop was initially designed for cancer disease studies, but the genetic structure within the cohort will be of general interest for all genetic disease studies in northern Sweden.

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