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1. Common genetic variation and the control of HIV-1 in humans.

Author

Fellay, Jacques, Ge, Dongliang, Shianna, Kevin V, Colombo, Sara, Ledergerber, Bruno, Cirulli, Elizabeth T, Urban, Thomas J, Zhang, Kunlin, Gumbs, Curtis E, Smith, Jason P, Castagna, Antonella, Cozzi-Lepri, Alessandro, De Luca, Andrea, Easterbrook, Philippa, Günthard, Huldrych F, Mallal, Simon, Mussini, Cristina, Dalmau, Judith, Martinez-Picado, Javier, Miro, José M, Obel, Niels, Wolinsky, Steven M, Martinson, Jeremy J, Detels, Roger, Margolick, Joseph B, Jacobson, Lisa P, Descombes, Patrick, Antonarakis, Stylianos E, Beckmann, Jacques S, O'Brien, Stephen J, Letvin, Norman L, McMichael, Andrew J, Haynes, Barton F, Carrington, Mary, Feng, Sheng, Telenti, Amalio, Goldstein, David B, and NIAID Center for HIV/AIDS Vaccine Immunology (CHAVI)

Subjects
NIAID Center for HIV/AIDS Vaccine Immunology, Humans, HIV-1, HIV Infections, Disease Progression, Viral Load, Major Histocompatibility Complex, Genotype, Phenotype, Polymorphism, Single Nucleotide, Alleles, Adult, Female, Male, Genetic Variation, Kaplan-Meier Estimate, Polymorphism, Single Nucleotide, Genetics, Developmental Biology
Abstract

To extend the understanding of host genetic determinants of HIV-1 control, we performed a genome-wide association study in a cohort of 2,554 infected Caucasian subjects. The study was powered to detect common genetic variants explaining down to 1.3% of the variability in viral load at set point. We provide overwhelming confirmation of three associations previously reported in a genome-wide study and show further independent effects of both common and rare variants in the Major Histocompatibility Complex region (MHC). We also examined the polymorphisms reported in previous candidate gene studies and fail to support a role for any variant outside of the MHC or the chemokine receptor cluster on chromosome 3. In addition, we evaluated functional variants, copy-number polymorphisms, epistatic interactions, and biological pathways. This study thus represents a comprehensive assessment of common human genetic variation in HIV-1 control in Caucasians.

Published
2009

2. De novo mutations in ATP1A3 cause alternating hemiplegia of childhood

Author

Heinzen, Erin L, Swoboda, Kathryn J, Hitomi, Yuki, Gurrieri, Fiorella, Nicole, Sophie, de Vries, Boukje, Tiziano, F Danilo, Fontaine, Bertrand, Walley, Nicole M, Heavin, Sinéad, Panagiotakaki, Eleni, Fiori, Stefania, Abiusi, Emanuela, Di Pietro, Lorena, Sweney, Matthew T, Newcomb, Tara M, Viollet, Louis, Huff, Chad, Jorde, Lynn B, Reyna, Sandra P, Murphy, Kelley J, Shianna, Kevin V, Gumbs, Curtis E, Little, Latasha, Silver, Kenneth, Ptáček, Louis J, Haan, Joost, Ferrari, Michel D, Bye, Ann M, Herkes, Geoffrey K, Whitelaw, Charlotte M, Webb, David, Lynch, Bryan J, Uldall, Peter, King, Mary D, Scheffer, Ingrid E, Neri, Giovanni, Arzimanoglou, Alexis, van den Maagdenberg, Arn M J M, Sisodiya, Sanjay M, Mikati, Mohamad A, and Goldstein, David B

Published
2012
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3. Rare deletions at 16p13.11 predispose to a diverse spectrum of sporadic epilepsy syndromes

Author

Heinzen, Erin L., Radtke, Rodney A., Urban, Thomas J., Cavalleri, Gianpiero L., Depondt, Chantal, Need, Anna C., Walley, Nicole M., Nicoletti, Paola, Dongliang Ge, Catarino, Claudia B., Duncan, John S., Kasperaviciute, Dalia, Tate, Sarah K., Caboclo, Luis O.mSander, Josemir W., Clayton, Lisa, Linney, Kristen N., Shianna, Kevin V., Gumbs, Curtis E., Smith, Jason, Cronin, Kenneth D., Maia, Jessica M., Doherty, Colin P., Pandolfo, Massimo, Leppert, David, Middleton, Lefkos T., Gibson, Rachel A., Johnson, Michael R., Matthews, Paul M., Hosford, David, Kalviainen, Reetta, Eriksson, Kai, Kantanen, Anne-Mari, Dorn, Thomas; Hansen, Jorg, Kramer, Gunter, Steinhoff, Bernhard J., Wieser, Heinz-Gregor, Zumsteg, Dominik, Ortega, Marcos, Wood, Nicholas W., Huxley-Jones, Juli, Mikati, Mohamad, Gallentine, William B., Husain, Aatif M., Buckley, Patrick G., Stallings, Ray L., Podgoreanu, Mihai V., Delanty, Norman, Sisodiya, Sanjay M., and Goldstein, David B.

Subjects
Chromosome deletion -- Research, Epilepsy -- Genetic aspects, Epilepsy -- Care and treatment, Gene expression -- Analysis, Biological sciences
Abstract

Genome-wide screens were used to identify copy number variation in 3812 patients with a diverse spectrum of epilepsy syndromes and in 1299 neurologically-normal controls to evaluate the role of 16p13.11 deletions and other structural variation in epilepsy disorders. The data implicated 16p13.11 and possibly other large deletions as risk factors for a wide range of epilepsy disorders and appear to point toward haploinsufficiency as a contributor to the pathogenicity of deletions.

Published
2010

4. ITPA gene variants protect against anaemia in patients treated for chronic hepatitis C

Author

Fellay, Jacques, Thompson, Alexander J., Ge, Dongliang, Gumbs, Curtis E., Urban, Thomas J., Shianna, Kevin V., Little, Latasha D., Qiu, Ping, Bertelsen, Arthur H., Watson, Mark, Warner, Amelia, Muir, Andrew J., Brass, Clifford, Albrecht, Janice, Sulkowski, Mark, McHutchison, John G., and Goldstein, David B.

Subjects
Anemia -- Risk factors -- Genetic aspects -- Prevention, Genetic variation -- Health aspects, Hepatitis C -- Risk factors -- Development and progression -- Genetic aspects, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Chronic infection with the hepatitis C virus (HCV) affects 170 million people worldwide and is an important cause of liver-related morbidity and mortality (1). The standard of care therapy combines pegylated interferon (pegIFN) alpha and ribavirin (RBV), and is associated with a range of treatment-limiting adverse effects (2). One of the most important of these is RBV-induced haemolytic anaemia, which affects most patients and is severe enough to require dose modification in up to 15% of patients. Here we show that genetic variants leading to inosine triphosphatase deficiency, a condition not thought to be clinically important, protect against haemolytic anaemia in hepatitis-C-infected patients receiving RBV., Using DNA from consenting participants of the IDEAL study (2),we performed a genome-wide association study (GWAS) of determinants of treatment-related anaemia in individuals with chronic genotype 1 hepatitis C. A [...]

Published
2010
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6. Exome sequencing followed by large-scale genotyping fails to identify single rare variants of large effect in idiopathic generalized epilepsy.

Author

Heinzen, Erin, Depondt, Chantal, Cavalleri, Gianpiero L, Ruzzo, Elizabeth K, Walley, Nicole M, Need, Anna C, Ge, Dongliang, He, Min, Cirulli, Elizabeth T, Zhao, Qian, Cronin, Kenneth D, Gumbs, Curtis E, Campbell, C Ryan, Hong, Linda K, Maia, Jessica M, Shianna, Kevin V, McCormack, Mark, Radtke, Rodney A, O'Conner, Gerard D, Mikati, Mohamad A, Gallentine, William B, Husain, Aatif M, Sinha, Saurabh R, Chinthapalli, Krishna, Puranam, Ram S, McNamara, James O, Ottman, Ruth, Sisodiya, Sanjay M, Delanty, Norman, Goldstein, David B, Heinzen, Erin, Depondt, Chantal, Cavalleri, Gianpiero L, Ruzzo, Elizabeth K, Walley, Nicole M, Need, Anna C, Ge, Dongliang, He, Min, Cirulli, Elizabeth T, Zhao, Qian, Cronin, Kenneth D, Gumbs, Curtis E, Campbell, C Ryan, Hong, Linda K, Maia, Jessica M, Shianna, Kevin V, McCormack, Mark, Radtke, Rodney A, O'Conner, Gerard D, Mikati, Mohamad A, Gallentine, William B, Husain, Aatif M, Sinha, Saurabh R, Chinthapalli, Krishna, Puranam, Ram S, McNamara, James O, Ottman, Ruth, Sisodiya, Sanjay M, Delanty, Norman, and Goldstein, David B

Abstract

Idiopathic generalized epilepsy (IGE) is a complex disease with high heritability, but little is known about its genetic architecture. Rare copy-number variants have been found to explain nearly 3% of individuals with IGE; however, it remains unclear whether variants with moderate effect size and frequencies below what are reliably detected with genome-wide association studies contribute significantly to disease risk. In this study, we compare the exome sequences of 118 individuals with IGE and 242 controls of European ancestry by using next-generation sequencing. The exome-sequenced epilepsy cases include study subjects with two forms of IGE, including juvenile myoclonic epilepsy (n = 93) and absence epilepsy (n = 25). However, our discovery strategy did not assume common genetic control between the subtypes of IGE considered. In the sequence data, as expected, no variants were significantly associated with the IGE phenotype or more specific IGE diagnoses. We then selected 3,897 candidate epilepsy-susceptibility variants from the sequence data and genotyped them in a larger set of 878 individuals with IGE and 1,830 controls. Again, no variant achieved statistical significance. However, 1,935 variants were observed exclusively in cases either as heterozygous or homozygous genotypes. It is likely that this set of variants includes real risk factors. The lack of significant association evidence of single variants with disease in this two-stage approach emphasizes the high genetic heterogeneity of epilepsy disorders, suggests that the impact of any individual single-nucleotide variant in this disease is small, and indicates that gene-based approaches might be more successful for future sequencing studies of epilepsy predisposition., Journal Article, Research Support, N.I.H. Extramural, Research Support, Non-U.S. Gov't, SCOPUS: ar.j, info:eu-repo/semantics/published

Published
2012

7. Exome Sequencing Followed by Large-Scale Genotyping Fails to Identify Single Rare Variants of Large Effect in Idiopathic Generalized Epilepsy

Author

Heinzen, Erin L., primary, Depondt, Chantal, additional, Cavalleri, Gianpiero L., additional, Ruzzo, Elizabeth K., additional, Walley, Nicole M., additional, Need, Anna C., additional, Ge, Dongliang, additional, He, Min, additional, Cirulli, Elizabeth T., additional, Zhao, Qian, additional, Cronin, Kenneth D., additional, Gumbs, Curtis E., additional, Campbell, C. Ryan, additional, Hong, Linda K., additional, Maia, Jessica M., additional, Shianna, Kevin V., additional, McCormack, Mark, additional, Radtke, Rodney A., additional, O'Conner, Gerard D., additional, Mikati, Mohamad A., additional, Gallentine, William B., additional, Husain, Aatif M., additional, Sinha, Saurabh R., additional, Chinthapalli, Krishna, additional, Puranam, Ram S., additional, McNamara, James O., additional, Ottman, Ruth, additional, Sisodiya, Sanjay M., additional, Delanty, Norman, additional, and Goldstein, David B., additional

Published
2012
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8. Exome Sequencing Followed by Large-Scale Genotyping Suggests a Limited Role for Moderately Rare Risk Factors of Strong Effect in Schizophrenia

Author

Need, Anna C., primary, McEvoy, Joseph P., additional, Gennarelli, Massimo, additional, Heinzen, Erin L., additional, Ge, Dongliang, additional, Maia, Jessica M., additional, Shianna, Kevin V., additional, He, Min, additional, Cirulli, Elizabeth T., additional, Gumbs, Curtis E., additional, Zhao, Qian, additional, Campbell, C. Ryan, additional, Hong, Linda, additional, Rosenquist, Peter, additional, Putkonen, Anu, additional, Hallikainen, Tero, additional, Repo-Tiihonen, Eila, additional, Tiihonen, Jari, additional, Levy, Deborah L., additional, Meltzer, Herbert Y., additional, and Goldstein, David B., additional

Published
2012
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10. The Characterization of Twenty Sequenced Human Genomes

Author

Pelak, Kimberly, primary, Shianna, Kevin V., additional, Ge, Dongliang, additional, Maia, Jessica M., additional, Zhu, Mingfu, additional, Smith, Jason P., additional, Cirulli, Elizabeth T., additional, Fellay, Jacques, additional, Dickson, Samuel P., additional, Gumbs, Curtis E., additional, Heinzen, Erin L., additional, Need, Anna C., additional, Ruzzo, Elizabeth K., additional, Singh, Abanish, additional, Campbell, C. Ryan, additional, Hong, Linda K., additional, Lornsen, Katharina A., additional, McKenzie, Alexander M., additional, Sobreira, Nara L. M., additional, Hoover-Fong, Julie E., additional, Milner, Joshua D., additional, Ottman, Ruth, additional, Haynes, Barton F., additional, Goedert, James J., additional, and Goldstein, David B., additional

Published
2010
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11. Whole-Genome Sequencing of a Single Proband Together with Linkage Analysis Identifies a Mendelian Disease Gene

Author

Sobreira, Nara L. M., primary, Cirulli, Elizabeth T., additional, Avramopoulos, Dimitrios, additional, Wohler, Elizabeth, additional, Oswald, Gretchen L., additional, Stevens, Eric L., additional, Ge, Dongliang, additional, Shianna, Kevin V., additional, Smith, Jason P., additional, Maia, Jessica M., additional, Gumbs, Curtis E., additional, Pevsner, Jonathan, additional, Thomas, George, additional, Valle, David, additional, Hoover-Fong, Julie E., additional, and Goldstein, David B., additional

Published
2010
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12. Common genetic variation and the control of HIV-1 in humans

Author

Barton F. Haynes, Antonella Castagna, Kevin V. Shianna, Andrew J. McMichael, Simon Mallal, Curtis Gumbs, Steven M. Wolinsky, Huldrych F. Günthard, Joseph B. Margolick, Stylianos E. Antonarakis, Norman L. Letvin, Jacques S. Beckmann, Lisa P. Jacobson, David Goldstein, Jeremy J. Martinson, Andrea De Luca, Amalio Telenti, Stephen J. O'Brien, Roger Detels, Mary Carrington, Patrick Descombes, Sara Colombo, Kunlin Zhang, José M. Miró, Judith Dalmau, Niels Obel, Cristina Mussini, Bruno Ledergerber, Javier Martinez-Picado, Alessandro Cozzi-Lepri, Thomas J. Urban, Elizabeth T. Cirulli, Dongliang Ge, Jason Smith, Jacques Fellay, Philippa J. Easterbrook, Sheng Feng, University of Zurich, Fellay, J, McCarthy, Mark I, Universitat de Barcelona, NIAID Center for HIV/AIDS Vaccine Immunology (CHAVI), Fellay, Jacque, Ge, Dongliang, Shianna Kevin, V., Colombo, Sara, Ledergerber, Bruno, Cirulli Elizabeth, T., Urban Thomas, J., Zhang, Kunlin, Gumbs Curtis, E., Smith Jason, P., Castagna, Antonella, Cozzi Lepri, Alessandro, De Luca, Andrea, Easterbrook, Philippa, Guenthard Huldrych, F., Mallal, Simon, Mussini, Cristina, Dalmau, Judith, Martinez Picado, Javier, Miro Jose, M., Obel, Niel, Wolinsky Steven, M., Martinson Jeremy, J., Detels, Roger, Margolick Joseph, B., Jacobson Lisa, P., Descombes, Patrick, Antonarakis Stylianos, E., Beckmann Jacques, S., O'Brien Stephen, J., Letvin Norman, L., McMichael Andrew, J., Haynes Barton, F., Carrington, Mary, Feng, Sheng, Telenti, Amalio, Goldstein David, B., and Antonarakis, Stylianos

Subjects
Male, Cancer Research, Candidate gene, genetic control, Genome-wide association study, HIV Infections, Human genetic variation, Kaplan-Meier Estimate, Major Histocompatibility Complex/genetics, 10234 Clinic for Infectious Diseases, Major Histocompatibility Complex, 2.1 Biological and endogenous factors, ddc:576.5, 1306 Cancer Research, Molecular genetics, Aetiology, Genetics (clinical), Genetics and Genomics/Genetics of Disease, Genetics, HIV-1/ physiology, Single Nucleotide, Infectious Diseases/HIV Infection and AIDS, Viral Load, Polymorphism, Single Nucleotide/genetics, HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 (HIV-1), CD4(+) cells, Infectious Diseases, Phenotype, Adult, Alleles, Disease Progression, Female, Genetic Variation, Genotype, HIV Infections/virology, HIV-1/physiology, Humans, HIV/AIDS, Infection, Research Article, medicine.medical_specialty, 2716 Genetics (clinical), lcsh:QH426-470, Single-nucleotide polymorphism, 610 Medicine & health, Biology, Genetics and Genomics/Complex Traits, Polymorphism, Single Nucleotide, Genètica molecular, 1311 Genetics, Clinical Research, Genetic variation, medicine, VIH (Virus), 1312 Molecular Biology, Allele, Polymorphism, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Kaplan-Meiers Estimate, HIV (Viruses), Haplotype, Human Genome, HIV, Virology/Mechanisms of Resistance and Susceptibility, including Host Genetics, NIAID Center for HIV/AIDS Vaccine Immunology, lcsh:Genetics, 1105 Ecology, Evolution, Behavior and Systematics, HIV-1, Immunology/Genetics of the Immune System, Developmental Biology
Abstract

To extend the understanding of host genetic determinants of HIV-1 control, we performed a genome-wide association study in a cohort of 2,554 infected Caucasian subjects. The study was powered to detect common genetic variants explaining down to 1.3% of the variability in viral load at set point. We provide overwhelming confirmation of three associations previously reported in a genome-wide study and show further independent effects of both common and rare variants in the Major Histocompatibility Complex region (MHC). We also examined the polymorphisms reported in previous candidate gene studies and fail to support a role for any variant outside of the MHC or the chemokine receptor cluster on chromosome 3. In addition, we evaluated functional variants, copy-number polymorphisms, epistatic interactions, and biological pathways. This study thus represents a comprehensive assessment of common human genetic variation in HIV-1 control in Caucasians., Author Summary The ability to spontaneously control HIV-1 upon infection is highly variable between individuals. To evaluate the contribution of variation in human genes to differences in plasma viral load and in disease progression rates, we performed a genome-wide association study in >2,500 HIV–infected individuals. This study achieved two goals: it completed the analysis of common variation influencing viral control, and it re-assessed the majority of previously reported genetic associations. We show that genetic variants located near the HLA-B and HLA-C genes are the strongest determinants of viral control, and that other independent associations exist in the same region of chromosome 6, the Major Histocompatibility Complex, known to contain a large number of genes involved in immune defense. We could not replicate most of the previously published associations with HIV candidate genes in this large, well-characterized cohort. Overall, common human genetic variation, together with demographic variables, explains up to 22% of the variability in viral load in the Caucasian population.

Published
2009

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