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1.  Optimus Primer: A PCR enrichment primer design program for next-generation sequencing of human exonic regions 
BMC Research Notes  2010;3:185.
Background
Polymerase chain reaction (PCR) remains a simple, flexible, and inexpensive method for enriching genomic regions of interest for next-generation sequencing. In order to utilize PCR in this context, a major challenge facing researchers is how to generate a very large number of functional PCR primers that will successfully generate useable amplicons. For instance, in an exon-only re-sequencing project targeting 100 genes, each with 10 exons, 1,000 pairs of primers are required. In fact, the reality is often more complex as each gene might have several isoforms and large exons need to be divided to maintain the desired amplicon size. With only a list of gene names, our program Optimus Primer (OP) automatically takes into account all these variables, and can generate primers with no need to provide genome coordinates. More importantly however, OP, unlike other primer design programs, uniquely utilizes Primer3 in an iterative manner that allows the user to progressively design up to four iterations of primer designs. Through a single interface, the user can specify up to four different design parameters with different stringencies, thus increasing the probability that a functional PCR primer pair will be designed for all regions of interest in a single pass of the pipeline.
Findings
To demonstrate the effectiveness of the program, we designed PCR primers against 77 genes located in loci associated with ulcerative colitis as part of a candidate gene re-sequencing experiment. We achieved an experimental success rate of 93% or 472 out of 508 amplicons spanning the exonic regions of the 77 genes. Moreover, by automatically passing amplicons that failed primer design through three additional iterations of design parameters, we achieved an additional 170 successful primer pairs or 34% more in a single pass of OP than by conventional methods.
Conclusion
With only a gene list and PCR parameters, a user can produce hundreds of PCR primer designs for regions of interest with a high probability of success in a very short amount of time. Optimus Primer is an essential tool for researchers who want to pursue PCR-based enrichment strategies for next-generation re-sequencing applications. The program can be accessed via website at http://op.pgx.ca.
doi:10.1186/1756-0500-3-185
PMCID: PMC2916007  PMID: 20609249
2.  Rare and low-frequency coding variants in CXCR2 and other genes are associated with hematological traits 
Nature genetics  2014;46(6):629-634.
Hematological traits are important clinical parameters. To test the role of rare and low-frequency coding variants on hematological traits, we analyzed hemoglobin, hematocrit, white blood cell (WBC) and platelet count in 31,340 individuals genotyped on an exome array. We identified several missense variants of CXCR2 associated with reduced WBC count (gene-based P=2.6×10−13). In a separate family-based re-sequencing study, we identified a novel loss-of-function CXCR2 frameshift mutation in a pedigree with congenital neutropenia that abolished ligand-induced CXCR2 signal transduction and chemotaxis. We also identified novel missense or splice site variants in key hematopoiesis regulators (EPO, TRF2, HBB, TUBB1, SH2B3) associated with blood cell traits. Finally, we were able to detect associations between the rare somatic JAK2 p.Val617Phe mutation and platelet count (P=3.9×10−22) as well as hemoglobin (P=0.002), hematocrit (P=9.5×10−7) and WBC (P=3.1×10−5). In conclusion, exome arrays complement GWAS in identifying new variants that contribute to complex human traits.
doi:10.1038/ng.2962
PMCID: PMC4050975  PMID: 24777453
3.  Deep Resequencing of GWAS Loci Identifies Rare Variants in CARD9, IL23R and RNF186 That Are Associated with Ulcerative Colitis 
PLoS Genetics  2013;9(9):e1003723.
Genome-wide association studies and follow-up meta-analyses in Crohn's disease (CD) and ulcerative colitis (UC) have recently identified 163 disease-associated loci that meet genome-wide significance for these two inflammatory bowel diseases (IBD). These discoveries have already had a tremendous impact on our understanding of the genetic architecture of these diseases and have directed functional studies that have revealed some of the biological functions that are important to IBD (e.g. autophagy). Nonetheless, these loci can only explain a small proportion of disease variance (∼14% in CD and 7.5% in UC), suggesting that not only are additional loci to be found but that the known loci may contain high effect rare risk variants that have gone undetected by GWAS. To test this, we have used a targeted sequencing approach in 200 UC cases and 150 healthy controls (HC), all of French Canadian descent, to study 55 genes in regions associated with UC. We performed follow-up genotyping of 42 rare non-synonymous variants in independent case-control cohorts (totaling 14,435 UC cases and 20,204 HC). Our results confirmed significant association to rare non-synonymous coding variants in both IL23R and CARD9, previously identified from sequencing of CD loci, as well as identified a novel association in RNF186. With the exception of CARD9 (OR = 0.39), the rare non-synonymous variants identified were of moderate effect (OR = 1.49 for RNF186 and OR = 0.79 for IL23R). RNF186 encodes a protein with a RING domain having predicted E3 ubiquitin-protein ligase activity and two transmembrane domains. Importantly, the disease-coding variant is located in the ubiquitin ligase domain. Finally, our results suggest that rare variants in genes identified by genome-wide association in UC are unlikely to contribute significantly to the overall variance for the disease. Rather, these are expected to help focus functional studies of the corresponding disease loci.
Author Summary
Genetic studies of common diseases have seen tremendous progress in the last half-decade primarily due to recent technologies that enable a systematic examination of genetic markers across the entire genome in large numbers of patients and healthy controls. The studies, while identifying genomic regions that influence a person's risk for developing disease, often do not pinpoint the actual gene or gene variants that account for this risk (called a causal gene/variant). A prime example of this can be seen with the 163 genetic risk factors that have recently been associated with the chronic inflammatory bowel diseases known as Crohn's disease and ulcerative colitis. For less than a handful of these 163 is the causative change in the genetic code known. The current study used an approach to directly look at the genetic code for a subset of these and identified a causative change in the genetic code for eight risk factors for ulcerative colitis. This finding is particularly important because it directs biological studies to understand the mechanisms that lead to this chronic life-long inflammatory disease.
doi:10.1371/journal.pgen.1003723
PMCID: PMC3772057  PMID: 24068945
4.  Genetic association analysis highlights new loci that modulate hematological trait variation in Caucasians and African Americans 
Human genetics  2010;129(3):307-317.
Red blood cell, white blood cell, and platelet measures, including their count, sub-type and volume, are important diagnostic and prognostic clinical parameters for several human diseases. To identify novel loci associated with hematological traits, and compare the architecture of these phenotypes between ethnic groups, the CARe Project genotyped 49,094 single nucleotide polymorphisms (SNPs) that capture variation in ~2,100 candidate genes in DNA of 23,439 Caucasians and 7,112 African Americans from five population-based cohorts. We found strong novel associations between erythrocyte phenotypes and the glucose-6 phosphate dehydrogenase (G6PD) A-allele in African Americans (rs1050828, P < 2.0 × 10−13, T-allele associated with lower red blood cell count, hemoglobin, and hematocrit, and higher mean corpuscular volume), and between platelet count and a SNP at the tropomyosin-4 (TPM4) locus (rs8109288, P = 3.0 × 10−7 in Caucasians; P = 3.0 × 10−7 in African Americans, T-allele associated with lower platelet count). We strongly replicated many genetic associations to blood cell phenotypes previously established in Caucasians. A common variant of the α-globin (HBA2-HBA1) locus was associated with red blood cell traits in African Americans, but not in Caucasians (rs1211375, P < 7 × 10−8, A-allele associated with lower hemoglobin, mean corpuscular hemoglobin, and mean corpuscular volume). Our results show similarities but also differences in the genetic regulation of hematological traits in European- and African-derived populations, and highlight the role of natural selection in shaping these differences.
doi:10.1007/s00439-010-0925-1
PMCID: PMC3442357  PMID: 21153663
5.  Deep resequencing of GWAS loci identifies independent rare variants associated with inflammatory bowel disease 
Nature Genetics  2011;43(11):1066-1073.
More than a thousand disease susceptibility loci have been identified via genome-wide association studies (GWAS) of common variants; however, the specific genes and full allelic spectrum of causal variants underlying these findings generally remain to be defined. We utilize pooled next-generation sequencing to study 56 genes in regions associated to Crohn’s Disease in 350 cases and 350 controls. Follow up genotyping of 70 rare and low-frequency protein-altering variants (MAF ~ .001-.05) in nine independent case-control series (16054 CD patients, 12153 UC patients, 17575 healthy controls) identifies four additional independent risk factors in NOD2, two additional protective variants in IL23R, a highly significant association to a novel, protective splice variant in CARD9 (p < 1e-16, OR ~ 0.29), as well as additional associations to coding variants in IL18RAP, CUL2, C1orf106, PTPN22 and MUC19. We extend the results of successful GWAS by providing novel, rare, and likely functional variants that will empower functional experiments and predictive models.
doi:10.1038/ng.952
PMCID: PMC3378381  PMID: 21983784
6.  Hundreds of variants clustered in genomic loci and biological pathways affect human height 
Lango Allen, Hana | Estrada, Karol | Lettre, Guillaume | Berndt, Sonja I. | Weedon, Michael N. | Rivadeneira, Fernando | Willer, Cristen J. | Jackson, Anne U. | Vedantam, Sailaja | Raychaudhuri, Soumya | Ferreira, Teresa | Wood, Andrew R. | Weyant, Robert J. | Segrè, Ayellet V. | Speliotes, Elizabeth K. | Wheeler, Eleanor | Soranzo, Nicole | Park, Ju-Hyun | Yang, Jian | Gudbjartsson, Daniel | Heard-Costa, Nancy L. | Randall, Joshua C. | Qi, Lu | Smith, Albert Vernon | Mägi, Reedik | Pastinen, Tomi | Liang, Liming | Heid, Iris M. | Luan, Jian'an | Thorleifsson, Gudmar | Winkler, Thomas W. | Goddard, Michael E. | Lo, Ken Sin | Palmer, Cameron | Workalemahu, Tsegaselassie | Aulchenko, Yurii S. | Johansson, Åsa | Zillikens, M.Carola | Feitosa, Mary F. | Esko, Tõnu | Johnson, Toby | Ketkar, Shamika | Kraft, Peter | Mangino, Massimo | Prokopenko, Inga | Absher, Devin | Albrecht, Eva | Ernst, Florian | Glazer, Nicole L. | Hayward, Caroline | Hottenga, Jouke-Jan | Jacobs, Kevin B. | Knowles, Joshua W. | Kutalik, Zoltán | Monda, Keri L. | Polasek, Ozren | Preuss, Michael | Rayner, Nigel W. | Robertson, Neil R. | Steinthorsdottir, Valgerdur | Tyrer, Jonathan P. | Voight, Benjamin F. | Wiklund, Fredrik | Xu, Jianfeng | Zhao, Jing Hua | Nyholt, Dale R. | Pellikka, Niina | Perola, Markus | Perry, John R.B. | Surakka, Ida | Tammesoo, Mari-Liis | Altmaier, Elizabeth L. | Amin, Najaf | Aspelund, Thor | Bhangale, Tushar | Boucher, Gabrielle | Chasman, Daniel I. | Chen, Constance | Coin, Lachlan | Cooper, Matthew N. | Dixon, Anna L. | Gibson, Quince | Grundberg, Elin | Hao, Ke | Junttila, M. Juhani | Kaplan, Lee M. | Kettunen, Johannes | König, Inke R. | Kwan, Tony | Lawrence, Robert W. | Levinson, Douglas F. | Lorentzon, Mattias | McKnight, Barbara | Morris, Andrew P. | Müller, Martina | Ngwa, Julius Suh | Purcell, Shaun | Rafelt, Suzanne | Salem, Rany M. | Salvi, Erika | Sanna, Serena | Shi, Jianxin | Sovio, Ulla | Thompson, John R. | Turchin, Michael C. | Vandenput, Liesbeth | Verlaan, Dominique J. | Vitart, Veronique | White, Charles C. | Ziegler, Andreas | Almgren, Peter | Balmforth, Anthony J. | Campbell, Harry | Citterio, Lorena | De Grandi, Alessandro | Dominiczak, Anna | Duan, Jubao | Elliott, Paul | Elosua, Roberto | Eriksson, Johan G. | Freimer, Nelson B. | Geus, Eco J.C. | Glorioso, Nicola | Haiqing, Shen | Hartikainen, Anna-Liisa | Havulinna, Aki S. | Hicks, Andrew A. | Hui, Jennie | Igl, Wilmar | Illig, Thomas | Jula, Antti | Kajantie, Eero | Kilpeläinen, Tuomas O. | Koiranen, Markku | Kolcic, Ivana | Koskinen, Seppo | Kovacs, Peter | Laitinen, Jaana | Liu, Jianjun | Lokki, Marja-Liisa | Marusic, Ana | Maschio, Andrea | Meitinger, Thomas | Mulas, Antonella | Paré, Guillaume | Parker, Alex N. | Peden, John F. | Petersmann, Astrid | Pichler, Irene | Pietiläinen, Kirsi H. | Pouta, Anneli | Ridderstråle, Martin | Rotter, Jerome I. | Sambrook, Jennifer G. | Sanders, Alan R. | Schmidt, Carsten Oliver | Sinisalo, Juha | Smit, Jan H. | Stringham, Heather M. | Walters, G.Bragi | Widen, Elisabeth | Wild, Sarah H. | Willemsen, Gonneke | Zagato, Laura | Zgaga, Lina | Zitting, Paavo | Alavere, Helene | Farrall, Martin | McArdle, Wendy L. | Nelis, Mari | Peters, Marjolein J. | Ripatti, Samuli | van Meurs, Joyce B.J. | Aben, Katja K. | Ardlie, Kristin G | Beckmann, Jacques S. | Beilby, John P. | Bergman, Richard N. | Bergmann, Sven | Collins, Francis S. | Cusi, Daniele | den Heijer, Martin | Eiriksdottir, Gudny | Gejman, Pablo V. | Hall, Alistair S. | Hamsten, Anders | Huikuri, Heikki V. | Iribarren, Carlos | Kähönen, Mika | Kaprio, Jaakko | Kathiresan, Sekar | Kiemeney, Lambertus | Kocher, Thomas | Launer, Lenore J. | Lehtimäki, Terho | Melander, Olle | Mosley, Tom H. | Musk, Arthur W. | Nieminen, Markku S. | O'Donnell, Christopher J. | Ohlsson, Claes | Oostra, Ben | Palmer, Lyle J. | Raitakari, Olli | Ridker, Paul M. | Rioux, John D. | Rissanen, Aila | Rivolta, Carlo | Schunkert, Heribert | Shuldiner, Alan R. | Siscovick, David S. | Stumvoll, Michael | Tönjes, Anke | Tuomilehto, Jaakko | van Ommen, Gert-Jan | Viikari, Jorma | Heath, Andrew C. | Martin, Nicholas G. | Montgomery, Grant W. | Province, Michael A. | Kayser, Manfred | Arnold, Alice M. | Atwood, Larry D. | Boerwinkle, Eric | Chanock, Stephen J. | Deloukas, Panos | Gieger, Christian | Grönberg, Henrik | Hall, Per | Hattersley, Andrew T. | Hengstenberg, Christian | Hoffman, Wolfgang | Lathrop, G.Mark | Salomaa, Veikko | Schreiber, Stefan | Uda, Manuela | Waterworth, Dawn | Wright, Alan F. | Assimes, Themistocles L. | Barroso, Inês | Hofman, Albert | Mohlke, Karen L. | Boomsma, Dorret I. | Caulfield, Mark J. | Cupples, L.Adrienne | Erdmann, Jeanette | Fox, Caroline S. | Gudnason, Vilmundur | Gyllensten, Ulf | Harris, Tamara B. | Hayes, Richard B. | Jarvelin, Marjo-Riitta | Mooser, Vincent | Munroe, Patricia B. | Ouwehand, Willem H. | Penninx, Brenda W. | Pramstaller, Peter P. | Quertermous, Thomas | Rudan, Igor | Samani, Nilesh J. | Spector, Timothy D. | Völzke, Henry | Watkins, Hugh | Wilson, James F. | Groop, Leif C. | Haritunians, Talin | Hu, Frank B. | Kaplan, Robert C. | Metspalu, Andres | North, Kari E. | Schlessinger, David | Wareham, Nicholas J. | Hunter, David J. | O'Connell, Jeffrey R. | Strachan, David P. | Wichmann, H.-Erich | Borecki, Ingrid B. | van Duijn, Cornelia M. | Schadt, Eric E. | Thorsteinsdottir, Unnur | Peltonen, Leena | Uitterlinden, André | Visscher, Peter M. | Chatterjee, Nilanjan | Loos, Ruth J.F. | Boehnke, Michael | McCarthy, Mark I. | Ingelsson, Erik | Lindgren, Cecilia M. | Abecasis, Gonçalo R. | Stefansson, Kari | Frayling, Timothy M. | Hirschhorn, Joel N
Nature  2010;467(7317):832-838.
Most common human traits and diseases have a polygenic pattern of inheritance: DNA sequence variants at many genetic loci influence phenotype. Genome-wide association (GWA) studies have identified >600 variants associated with human traits1, but these typically explain small fractions of phenotypic variation, raising questions about the utility of further studies. Here, using 183,727 individuals, we show that hundreds of genetic variants, in at least 180 loci, influence adult height, a highly heritable and classic polygenic trait2,3. The large number of loci reveals patterns with important implications for genetic studies of common human diseases and traits. First, the 180 loci are not random, but instead are enriched for genes that are connected in biological pathways (P=0.016), and that underlie skeletal growth defects (P<0.001). Second, the likely causal gene is often located near the most strongly associated variant: in 13 of 21 loci containing a known skeletal growth gene, that gene was closest to the associated variant. Third, at least 19 loci have multiple independently associated variants, suggesting that allelic heterogeneity is a frequent feature of polygenic traits, that comprehensive explorations of already-discovered loci should discover additional variants, and that an appreciable fraction of associated loci may have been identified. Fourth, associated variants are enriched for likely functional effects on genes, being over-represented amongst variants that alter amino acid structure of proteins and expression levels of nearby genes. Our data explain ∼10% of the phenotypic variation in height, and we estimate that unidentified common variants of similar effect sizes would increase this figure to ∼16% of phenotypic variation (∼20% of heritable variation). Although additional approaches are needed to fully dissect the genetic architecture of polygenic human traits, our findings indicate that GWA studies can identify large numbers of loci that implicate biologically relevant genes and pathways.
doi:10.1038/nature09410
PMCID: PMC2955183  PMID: 20881960
7.  Proteome-wide identification of poly(ADP-ribose) binding proteins and poly(ADP-ribose)-associated protein complexes 
Nucleic Acids Research  2008;36(22):6959-6976.
Poly(ADP-ribose) (pADPr) is a polymer assembled from the enzymatic polymerization of the ADP-ribosyl moiety of NAD by poly(ADP-ribose) polymerases (PARPs). The dynamic turnover of pADPr within the cell is essential for a number of cellular processes including progression through the cell cycle, DNA repair and the maintenance of genomic integrity, and apoptosis. In spite of the considerable advances in the knowledge of the physiological conditions modulated by poly(ADP-ribosyl)ation reactions, and notwithstanding the fact that pADPr can play a role of mediator in a wide spectrum of biological processes, few pADPr binding proteins have been identified so far. In this study, refined in silico prediction of pADPr binding proteins and large-scale mass spectrometry-based proteome analysis of pADPr binding proteins were used to establish a comprehensive repertoire of pADPr-associated proteins. Visualization and modeling of these pADPr-associated proteins in networks not only reflect the widespread involvement of poly(ADP-ribosyl)ation in several pathways but also identify protein targets that could shed new light on the regulatory functions of pADPr in normal physiological conditions as well as after exposure to genotoxic stimuli.
doi:10.1093/nar/gkn771
PMCID: PMC2602769  PMID: 18981049

Results 1-7 (7)