TY  - JOUR
A1  - Wheeler, Nicole E.
A1  - Barquist, Lars
A1  - Kingsley, Robert A.
A1  - Gardner, Paul P.
T1  - A profile-based method for identifying functional divergence of orthologous genes in bacterial genomes
JF  - Bioinformatics
N2  - Motivation: 
Next generation sequencing technologies have provided us with a wealth of information on genetic variation, but predi cting the functional significance of this variation is a difficult task. While many comparative genomics studies have focused on gene flux and large scale changes, relatively little attention has been paid to quantifying the effects of single nucleotide polymorphisms and indels on protein function, particularly in bacterial genomics.

Results: 
We present a hidden Markov model based approach we call delta-bitscore (DBS) for identifying orthologous proteins that have diverged at the amino acid sequence level in a way that is likely to impact biological function. We benchmark this approach with several widely used datasets and apply it to a proof-of-concept study of orthologous proteomes in an investigation of host adaptation in Salmonella enterica. We highlight the value of the method in identifying functional divergence of genes, and suggest that this tool may be a better approach than the commonly used dN/dS metric for identifying functionally significant genetic changes occurring in recently diverged organisms.
KW  - Host adaptation
KW  - Salmonella-enteritidis
KW  - Sequence identity
KW  - Rapid evolution
KW  - Variants
KW  - Cystic-fibriosis
KW  - Strains
KW  - Pathogenicity
KW  - Typhimurium
KW  - Yersinia
Y1  - 2016
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-186502
VL  - 32
IS  - 23
ER  - 
TY  - JOUR
A1  - Carsten A., Böger
A1  - Gorski, Mathias
A1  - Li, Man
A1  - Hoffmann, Michael M.
A1  - Huang, Chunmei
A1  - Yang, Qiong
A1  - Teumer, Alexander
A1  - Krane, Vera
A1  - O'Seaghdha, Conall M.
A1  - Kutalik, Zoltán
A1  - Wichmann, H.-Erich
A1  - Haak, Thomas
A1  - Boes, Eva
A1  - Coassin, Stefan
A1  - Coresh, Josef
A1  - Kollerits, Barbara
A1  - Haun, Margot
A1  - Paulweber, Bernhard
A1  - Köttgen, Anna
A1  - Li, Guo
A1  - Shlipak, Michael G.
A1  - Powe, Neil
A1  - Hwang, Shih-Jen
A1  - Dehghan, Abbas
A1  - Rivadeneira, Fernando
A1  - Uitterlinden, André
A1  - Hofman, Albert
A1  - Beckmann, Jacques S.
A1  - Krämer, Bernhard K.
A1  - Witteman, Jacqueline
A1  - Bochud, Murielle
A1  - Siscovick, David
A1  - Rettig, Rainer
A1  - Kronenberg, Florian
A1  - Wanner, Christoph
A1  - Thadhani, Ravi I.
A1  - Heid, Iris M.
A1  - Fox, Caroline S.
A1  - Kao, W.H.
T1  - Association of eGFR-Related Loci Identified by GWAS with Incident CKD and ESRD
JF  - PLoS Genetics
N2  - Family studies suggest a genetic component to the etiology of chronic kidney disease (CKD) and end stage renal disease (ESRD). Previously, we identified 16 loci for eGFR in genome-wide association studies, but the associations of these single nucleotide polymorphisms (SNPs) for incident CKD or ESRD are unknown. We thus investigated the association of these loci with incident CKD in 26,308 individuals of European ancestry free of CKD at baseline drawn from eight population-based cohorts followed for a median of 7.2 years (including 2,122 incident CKD cases defined as eGFR < 60ml/min/1.73m(2) at follow-up) and with ESRD in four case-control studies in subjects of European ancestry (3,775 cases, 4,577 controls). SNPs at 11 of the 16 loci (UMOD, PRKAG2, ANXA9, DAB2, SHROOM3, DACH1, STC1, SLC34A1, ALMS1/NAT8, UBE2Q2, and GCKR) were associated with incident CKD; p-values ranged from p = 4.1e-9 in UMOD to p = 0.03 in GCKR. After adjusting for baseline eGFR, six of these loci remained significantly associated with incident CKD (UMOD, PRKAG2, ANXA9, DAB2, DACH1, and STC1). SNPs in UMOD (OR = 0.92, p = 0.04) and GCKR (OR = 0.93, p = 0.03) were nominally associated with ESRD. In summary, the majority of eGFR-related loci are either associated or show a strong trend towards association with incident CKD, but have modest associations with ESRD in individuals of European descent. Additional work is required to characterize the association of genetic determinants of CKD and ESRD at different stages of disease progression.
KW  - Chronic Kidney-disease
KW  - Stage renal-disease
KW  - Glomerular-filtration-rate
KW  - Diabetic-nephropathy
KW  - General-population
KW  - African-americans
KW  - Risk
KW  - Progression
KW  - Mortality
KW  - Variants
Y1  - 2011
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:bvb:20-opus-133758
VL  - 7
IS  - 9
ER  -