@article {1028, title = {Polymorphisms of the HNF1A gene encoding hepatocyte nuclear factor-1 alpha are associated with C-reactive protein.}, journal = {Am J Hum Genet}, volume = {82}, year = {2008}, month = {2008 May}, pages = {1193-201}, abstract = {

Data from the Pharmacogenomics and Risk of Cardiovascular Disease (PARC) study and the Cardiovascular Health Study (CHS) provide independent and confirmatory evidence for association between common polymorphisms of the HNF1A gene encoding hepatocyte nuclear factor-1 alpha and plasma C-reactive protein (CRP) concentration. Analyses with the use of imputation-based methods to combine genotype data from both studies and to test untyped SNPs from the HapMap database identified several SNPs within a 5 kb region of HNF1A intron 1 with the strongest evidence of association with CRP phenotype.

}, keywords = {Aged, Bayes Theorem, C-Reactive Protein, Female, Hepatocyte Nuclear Factor 1-alpha, Humans, Hydroxymethylglutaryl-CoA Reductase Inhibitors, Male, Middle Aged, Polymorphism, Single Nucleotide, Pravastatin, Simvastatin}, issn = {1537-6605}, doi = {10.1016/j.ajhg.2008.03.017}, author = {Reiner, Alexander P and Barber, Mathew J and Guan, Yongtao and Ridker, Paul M and Lange, Leslie A and Chasman, Daniel I and Walston, Jeremy D and Cooper, Gregory M and Jenny, Nancy S and Rieder, Mark J and Durda, J Peter and Smith, Joshua D and Novembre, John and Tracy, Russell P and Rotter, Jerome I and Stephens, Matthew and Nickerson, Deborah A and Krauss, Ronald M} } @article {1387, title = {Evolution and functional impact of rare coding variation from deep sequencing of human exomes.}, journal = {Science}, volume = {337}, year = {2012}, month = {2012 Jul 06}, pages = {64-9}, abstract = {

As a first step toward understanding how rare variants contribute to risk for complex diseases, we sequenced 15,585 human protein-coding genes to an average median depth of 111{\texttimes} in 2440 individuals of European (n = 1351) and African (n = 1088) ancestry. We identified over 500,000 single-nucleotide variants (SNVs), the majority of which were rare (86\% with a minor allele frequency less than 0.5\%), previously unknown (82\%), and population-specific (82\%). On average, 2.3\% of the 13,595 SNVs each person carried were predicted to affect protein function of ~313 genes per genome, and ~95.7\% of SNVs predicted to be functionally important were rare. This excess of rare functional variants is due to the combined effects of explosive, recent accelerated population growth and weak purifying selection. Furthermore, we show that large sample sizes will be required to associate rare variants with complex traits.

}, keywords = {African Americans, Disease, European Continental Ancestry Group, Evolution, Molecular, Exome, Female, Gene Frequency, Genetic Association Studies, Genetic Predisposition to Disease, Genetic Variation, Genome, Human, High-Throughput Nucleotide Sequencing, Humans, Male, Polymorphism, Single Nucleotide, Population Growth, Selection, Genetic}, issn = {1095-9203}, doi = {10.1126/science.1219240}, author = {Tennessen, Jacob A and Bigham, Abigail W and O{\textquoteright}Connor, Timothy D and Fu, Wenqing and Kenny, Eimear E and Gravel, Simon and McGee, Sean and Do, Ron and Liu, Xiaoming and Jun, Goo and Kang, Hyun Min and Jordan, Daniel and Leal, Suzanne M and Gabriel, Stacey and Rieder, Mark J and Abecasis, Goncalo and Altshuler, David and Nickerson, Deborah A and Boerwinkle, Eric and Sunyaev, Shamil and Bustamante, Carlos D and Bamshad, Michael J and Akey, Joshua M} } @article {6565, title = {Quantifying rare, deleterious variation in 12 human cytochrome P450 drug-metabolism genes in a large-scale exome dataset.}, journal = {Hum Mol Genet}, volume = {23}, year = {2014}, month = {2014 Apr 15}, pages = {1957-63}, abstract = {

The study of genetic influences on drug response and efficacy ({\textquoteright}pharmacogenetics{\textquoteright}) has existed for over 50 years. Yet, we still lack a complete picture of how genetic variation, both common and rare, affects each individual{\textquoteright}s responses to medications. Exome sequencing is a promising alternative method for pharmacogenetic discovery as it provides information on both common and rare variation in large numbers of individuals. Using exome data from 2203 AA and 4300 Caucasian individuals through the NHLBI Exome Sequencing Project, we conducted a survey of coding variation within 12 Cytochrome P450 (CYP) genes that are collectively responsible for catalyzing nearly 75\% of all known Phase I drug oxidation reactions. In addition to identifying many polymorphisms with known pharmacogenetic effects, we discovered over 730 novel nonsynonymous alleles across the 12 CYP genes of interest. These alleles include many with diverse functional effects such as premature stop codons, aberrant splicesites and mutations at conserved active site residues. Our analysis considering both novel, predicted functional alleles as well as known, actionable CYP alleles reveals that rare, deleterious variation contributes markedly to the overall burden of pharmacogenetic alleles within the populations considered, and that the contribution of rare variation to this burden is over three times greater in AA individuals as compared with Caucasians. While most of these impactful alleles are individually rare, 7.6-11.7\% of individuals interrogated in the study carry at least one newly described potentially deleterious alleles in a major drug-metabolizing CYP.

}, keywords = {Cytochrome P-450 Enzyme System, Databases, Genetic, European Continental Ancestry Group, Exome, Humans, Pharmaceutical Preparations, Pharmacogenetics, Polymorphism, Genetic}, issn = {1460-2083}, doi = {10.1093/hmg/ddt588}, author = {Gordon, Adam S and Tabor, Holly K and Johnson, Andrew D and Snively, Beverly M and Assimes, Themistocles L and Auer, Paul L and Ioannidis, John P A and Peters, Ulrike and Robinson, Jennifer G and Sucheston, Lara E and Wang, Danxin and Sotoodehnia, Nona and Rotter, Jerome I and Psaty, Bruce M and Jackson, Rebecca D and Herrington, David M and O{\textquoteright}Donnell, Christopher J and Reiner, Alexander P and Rich, Stephen S and Rieder, Mark J and Bamshad, Michael J and Nickerson, Deborah A} } @article {6577, title = {Whole-exome sequencing identifies rare and low-frequency coding variants associated with LDL cholesterol.}, journal = {Am J Hum Genet}, volume = {94}, year = {2014}, month = {2014 Feb 06}, pages = {233-45}, abstract = {

Elevated low-density lipoprotein cholesterol (LDL-C) is a treatable, heritable risk factor for cardiovascular disease. Genome-wide association studies (GWASs) have identified 157 variants associated with lipid levels but are not well suited to assess the impact of rare and low-frequency variants. To determine whether rare or low-frequency coding variants are associated with LDL-C, we exome sequenced 2,005 individuals, including 554 individuals selected for extreme LDL-C (>98(th) or <2(nd) percentile). Follow-up analyses included sequencing of 1,302 additional individuals and genotype-based analysis of 52,221 individuals. We observed significant evidence of association between LDL-C and the burden of rare or low-frequency variants in PNPLA5, encoding a phospholipase-domain-containing protein, and both known and previously unidentified variants in PCSK9, LDLR and APOB, three known lipid-related genes. The effect sizes for the burden of rare variants for each associated gene were substantially higher than those observed for individual SNPs identified from GWASs. We replicated the PNPLA5 signal in an independent large-scale sequencing study of 2,084 individuals. In conclusion, this large whole-exome-sequencing study for LDL-C identified a gene not known to be implicated in LDL-C and provides unique insight into the design and analysis of similar experiments.

}, keywords = {Adult, Aged, Apolipoproteins E, Cholesterol, LDL, Cohort Studies, Dyslipidemias, Exome, Female, Follow-Up Studies, Gene Frequency, Genetic Code, Genome-Wide Association Study, Genotype, Humans, Lipase, Male, Middle Aged, Phenotype, Polymorphism, Single Nucleotide, Proprotein Convertase 9, Proprotein Convertases, Receptors, LDL, Sequence Analysis, DNA, Serine Endopeptidases}, issn = {1537-6605}, doi = {10.1016/j.ajhg.2014.01.010}, author = {Lange, Leslie A and Hu, Youna and Zhang, He and Xue, Chenyi and Schmidt, Ellen M and Tang, Zheng-Zheng and Bizon, Chris and Lange, Ethan M and Smith, Joshua D and Turner, Emily H and Jun, Goo and Kang, Hyun Min and Peloso, Gina and Auer, Paul and Li, Kuo-Ping and Flannick, Jason and Zhang, Ji and Fuchsberger, Christian and Gaulton, Kyle and Lindgren, Cecilia and Locke, Adam and Manning, Alisa and Sim, Xueling and Rivas, Manuel A and Holmen, Oddgeir L and Gottesman, Omri and Lu, Yingchang and Ruderfer, Douglas and Stahl, Eli A and Duan, Qing and Li, Yun and Durda, Peter and Jiao, Shuo and Isaacs, Aaron and Hofman, Albert and Bis, Joshua C and Correa, Adolfo and Griswold, Michael E and Jakobsdottir, Johanna and Smith, Albert V and Schreiner, Pamela J and Feitosa, Mary F and Zhang, Qunyuan and Huffman, Jennifer E and Crosby, Jacy and Wassel, Christina L and Do, Ron and Franceschini, Nora and Martin, Lisa W and Robinson, Jennifer G and Assimes, Themistocles L and Crosslin, David R and Rosenthal, Elisabeth A and Tsai, Michael and Rieder, Mark J and Farlow, Deborah N and Folsom, Aaron R and Lumley, Thomas and Fox, Ervin R and Carlson, Christopher S and Peters, Ulrike and Jackson, Rebecca D and van Duijn, Cornelia M and Uitterlinden, Andr{\'e} G and Levy, Daniel and Rotter, Jerome I and Taylor, Herman A and Gudnason, Vilmundur and Siscovick, David S and Fornage, Myriam and Borecki, Ingrid B and Hayward, Caroline and Rudan, Igor and Chen, Y Eugene and Bottinger, Erwin P and Loos, Ruth J F and S{\ae}trom, P{\r a}l and Hveem, Kristian and Boehnke, Michael and Groop, Leif and McCarthy, Mark and Meitinger, Thomas and Ballantyne, Christie M and Gabriel, Stacey B and O{\textquoteright}Donnell, Christopher J and Post, Wendy S and North, Kari E and Reiner, Alexander P and Boerwinkle, Eric and Psaty, Bruce M and Altshuler, David and Kathiresan, Sekar and Lin, Dan-Yu and Jarvik, Gail P and Cupples, L Adrienne and Kooperberg, Charles and Wilson, James G and Nickerson, Deborah A and Abecasis, Goncalo R and Rich, Stephen S and Tracy, Russell P and Willer, Cristen J} }