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author:("Ge, tongliang")
1.  Change of Genetic Determinants of Left Ventricular Structure in Adolescence: Longitudinal Evidence from the Georgia Cardiovascular Twin Study 
American journal of hypertension  2008;21(7):10.1038/ajh.2008.178.
Genetic contribution to left ventricular (LV) structure is generally recognized, but whether and how this influence varies by ethnicity or with age is unknown.
Design and methods
Participants were 517 European American (EA) and African American (AA) twin pairs (mean age: 14.6 ± 3.0) at visit 1 and 422 EA and AA at follow-up 4.1 years later. Echocardiograms were obtained on both visits. Data were analyzed using structural equation modeling software Mx.
Body mass index (BMI) was a strong predictor for all LV measures at both visit 1 and 2, accounting for 3.5-24.2% of the total variance. Hemodynamics explained up to 4.5% additional LV measures variance. After adjusting for BMI, LV measures showed substantial heritability (range: 21%-71%). Best-fitting longitudinal models revealed considerable novel genetic effects on the interventricular septum, posterior wall and relative wall thickness (but not LV inner diameter), accounting for 32-41% of the phenotypic variance at visit 2, with no significant gender and ethnic effects. There was a gender difference for LV mass index in AA (P < 0.01), with a significant influence of novel genetic effects in males (47%), but not in females. No gender difference was seen in EA, with 34% of the phenotypic variance at visit 2 attributable to novel genetic effects.
The heritability of cardiac structure and geometry was equally substantial in both AA and EA. Significant novel genetic influences were detected for all measures but LV inner diameter and LV mass index in AA females. Further developmental genetic studies are warranted to elucidate the nature of the emerging gene effects during the transition from adolescence into adulthood.
PMCID: PMC3857089  PMID: 18443564
heritability; left ventricular mass; ethnicity
2.  Heritability of Arterial Stiffness in Black- and White American Youth and Young Adults 
American journal of hypertension  2007;20(10):1065-1072.
To examine the heritability of arterial stiffness measured as pulse wave velocity (PWV) and its dependence on ethnicity, gender and blood pressure (BP).
As part of the Georgia Cardiovascular Twin Study, we measured aortoradial (radial) and aorto-dorsalis-pedis (foot) PWV in 702 twins (41% black, 49% male) aged 12 – 30 years (mean: 17.7 ± 3.3) including monozygotic and dizygotic pairs of same- as well as opposite-gender. Ethnicity and gender effects on genetic and environmental contributions to PWV were estimated by genetic model fitting.
Diastolic BP was the most important hemodynamic predictor. Best fitting models showed no ethnicity or gender differences in estimates of genetic and environmental influence and indicated substantial heritabilities of 0.43 (95% CI: 0.30–0.54) and 0.53 (95% CI: 0.42–0.62) for radial and foot PWV, respectively. Over a quarter of these heritabilities (0.19 for radial PWV, 0.14 for foot PWV) were due to genes in common with DBP as based on multivariate models.
Individual differences in arterial stiffness of youth and young adults are substantially heritable and more than 25% of this heritability is explained by genes that also influence DBP. Heritability estimates do not show any differences between blacks and whites or males and females.
PMCID: PMC3672691  PMID: 17903689
Arterial Stiffness; Heritability; Twins; ethnicity
3.  Genome-wide association study of interferon-related cytopenia in chronic hepatitis C patients 
Journal of hepatology  2011;56(2):313-319.
Background & Aims
Interferon-alfa (IFN)-related cytopenias are common and may be dose-limiting. We performed a genome wide association study on a well-characterized genotype 1 HCV cohort to identify genetic determinants of peginterferon-α (peg-IFN)-related thrombocytopenia, neutropenia, and leukopenia.
1604/3070 patients in the IDEAL study consented to genetic testing. Trial inclusion criteria included a platelet (Pl) count ≥80 × 109/L and an absolute neutrophil count (ANC) ≥ 1500/mm3. Samples were genotyped using the Illumina Human610-quad BeadChip. The primary analyses focused on the genetic determinants of quantitative change in cell counts (Pl, ANC, lymphocytes, monocytes, eosinophils, and basophils) at week 4 in patients >80% adherent to therapy (n = 1294).
6 SNPs on chromosome 20 were positively associated with Pl reduction (top SNP rs965469, p = 10−10). These tag SNPs are in high linkage disequilibrium with 2 functional variants in the ITPA gene, rs1127354 and rs7270101, that cause ITPase deficiency and protect against ribavirin (RBV)-induced hemolytic anemia (HA). rs1127354 and rs7270101 showed strong independent associations with Pl reduction (p = 10−12, p = 10−7) and entirely explained the genome-wide significant associations. We believe this is an example of an indirect genetic association due to a reactive thrombocytosis to RBV-induced anemia: Hb decline was inversely correlated with Pl reduction (r = −0.28, p = 10−17) and Hb change largely attenuated the association between the ITPA variants and Pl reduction in regression models. No common genetic variants were associated with pegIFN-induced neutropenia or leucopenia.
Two ITPA variants were associated with thrombocytopenia; this was largely explained by a thrombocytotic response to RBV-induced HA attenuating IFN-related thrombocytopenia. No genetic determinants of pegIFN-induced neutropenia were identified.
PMCID: PMC3634361  PMID: 21703177
GWAS; ITPA; Thrombocytopenia; Hepatitis C; Neutropenia; IL28B
4.  The Association of Genetic Variants with Hepatic Steatosis in Patients with Genotype 1 Chronic Hepatitis C Infection 
Digestive diseases and sciences  2012;57(8):2213-2221.
Single-nucleotide polymorphisms (SNPs) in the IL28B and PNPLA3 gene regions have been associated with hepatic steatosis in genotype 1 (G1) chronic HCV infection but their clinical impacts remain to be determined.
We sought to validate these associations and to explore their impact on treatment response to peginterferon and ribavirin therapy.
A total of 972 G1 HCV-infected Caucasian patients were genotyped for the SNPs rs12979860 (IL28B) and rs2896019 (PNPLA3). Multivariable analysis tested IL28B and PNPLA3 for association with the presence of any steatosis (>0 %); clinically significant steatosis (>5 %); steatosis severity (grade 0–3/4); and the interacting associations of the SNPs and hepatic steatosis to sustained viral response (SVR).
IL28B and PNPLA3 polymorphisms were associated with the presence of any steatosis (rs12979860, p = 1.87 × 10−7; rs2896019, p = 7.56 × 10−4); clinically significant steatosis (rs12979860, p = 1.82 × 10−3; rs2896019, p = 1.27 × 10−4); and steatosis severity (rs12979860, p = 2.05 × 10−8; rs2896019, p = 2.62 × 10−6). Obesity, hypertriglyceridemia, hyperglycemia, liver fibrosis, and liver inflammation were all independently associated with worse steatosis. Hepatic steatosis was associated with lower SVR, and this effect was attenuated by IL28B. PNPLA3 had no independent association with SVR.
IL28B and PNPLA3 are associated with hepatic steatosis prevalence and severity in Caucasians with G1 HCV, suggesting differing potential genetic risk pathways to steatosis. IL28B attenuates the association between steatosis and SVR. Remediable metabolic risk factors remain important, independently of these polymorphisms, and remain key therapeutic goals to achieve better outcomes for patients with HCV-associated hepatic steatosis.
PMCID: PMC3518927  PMID: 22543885
Polymorphism, single-nucleotide, SNP; IL28B protein, human; PNPLA3 protein, human; Adiponutrin, human; Fatty liver; Abdominal obesity metabolic syndrome
5.  The State of Genome-Wide Association Studies in Pulmonary Disease 
With rapid advances in our knowledge of the human genome and increasing availability of high-throughput investigative technology, genome-wide association (GWA) studies have recently gained marked popularity. As an unbiased approach to identifying genomic regions of importance in complex human disease, the results of such studies have the potential to illuminate novel causal pathways, guide mechanistic research, and aid in prediction of disease risk. The use of a genome-wide approach presents considerable methodological and statistical challenges, and properly conducted studies are essential to avoid false-positive results. A total of 22 GWA studies have been published in pulmonary medicine thus far, implicating several intriguing genomic regions in the determination of pulmonary function measures, onset of asthma, and susceptibility to chronic obstructive pulmonary disease. Many questions remain, however, as most identified genetic variants contribute only nominally to overall disease risk, genetic disease mechanisms remain uncertain, and disease-associated variants are not consistent across studies. Perhaps most fundamentally, the association signals identified have not yet been traced to causal variants. This perspective will review the current state of GWA studies in pulmonary disease. We begin with an introduction to the hypothesis, principles, and limitations of this type of genome-wide approach, highlight key points from available studies, and conclude by addressing future approaches to better understand the genetics of complex pulmonary disease.
PMCID: PMC3208655  PMID: 21799071
genetics; chronic obstructive pulmonary disease; asthma
6.  Personal receptor repertoires: olfaction as a model 
BMC Genomics  2012;13:414.
Information on nucleotide diversity along completely sequenced human genomes has increased tremendously over the last few years. This makes it possible to reassess the diversity status of distinct receptor proteins in different human individuals. To this end, we focused on the complete inventory of human olfactory receptor coding regions as a model for personal receptor repertoires.
By performing data-mining from public and private sources we scored genetic variations in 413 intact OR loci, for which one or more individuals had an intact open reading frame. Using 1000 Genomes Project haplotypes, we identified a total of 4069 full-length polypeptide variants encoded by these OR loci, average of ~10 per locus, constituting a lower limit for the effective human OR repertoire. Each individual is found to harbor as many as 600 OR allelic variants, ~50% higher than the locus count. Because OR neuronal expression is allelically excluded, this has direct effect on smell perception diversity of the species. We further identified 244 OR segregating pseudogenes (SPGs), loci showing both intact and pseudogene forms in the population, twenty-six of which are annotatively “resurrected” from a pseudogene status in the reference genome. Using a custom SNP microarray we validated 150 SPGs in a cohort of 468 individuals, with every individual genome averaging 36 disrupted sequence variations, 15 in homozygote form. Finally, we generated a multi-source compendium of 63 OR loci harboring deletion Copy Number Variations (CNVs). Our combined data suggest that 271 of the 413 intact OR loci (66%) are affected by nonfunctional SNPs/indels and/or CNVs.
These results portray a case of unusually high genetic diversity, and suggest that individual humans have a highly personalized inventory of functional olfactory receptors, a conclusion that might apply to other receptor multigene families.
PMCID: PMC3462693  PMID: 22908908
Olfactory receptor; Genetic polymorphism; Haplotypes; Single nucleotide polymorphism; Copy number variation; Olfaction; Gene family
8.  Copy Number Variation of KIR Genes Influences HIV-1 Control 
PLoS Biology  2011;9(11):e1001208.
The authors that the number of activating and inhibitory KIR genes varies between individuals and plays a role in the regulation of immune mechanisms that determine HIV-1 control.
A genome-wide screen for large structural variants showed that a copy number variant (CNV) in the region encoding killer cell immunoglobulin-like receptors (KIR) associates with HIV-1 control as measured by plasma viral load at set point in individuals of European ancestry. This CNV encompasses the KIR3DL1-KIR3DS1 locus, encoding receptors that interact with specific HLA-Bw4 molecules to regulate the activation of lymphocyte subsets including natural killer (NK) cells. We quantified the number of copies of KIR3DS1 and KIR3DL1 in a large HIV-1 positive cohort, and showed that an increase in KIR3DS1 count associates with a lower viral set point if its putative ligand is present (p = 0.00028), as does an increase in KIR3DL1 count in the presence of KIR3DS1 and appropriate ligands for both receptors (p = 0.0015). We further provide functional data that demonstrate that NK cells from individuals with multiple copies of KIR3DL1, in the presence of KIR3DS1 and the appropriate ligands, inhibit HIV-1 replication more robustly, and associated with a significant expansion in the frequency of KIR3DS1+, but not KIR3DL1+, NK cells in their peripheral blood. Our results suggest that the relative amounts of these activating and inhibitory KIR play a role in regulating the peripheral expansion of highly antiviral KIR3DS1+ NK cells, which may determine differences in HIV-1 control following infection.
Author Summary
There is marked intrinsic variation in the extent to which individuals are able to control HIV-1. We have identified a genetic copy number variable region (CNV) in humans that plays a significant role in the control of HIV-1. This CNV is located in the genomic region that encodes the killer cell immunoglobulin-like receptors (KIRs) and specifically affects the KIR3DS1 and KIR3DL1 genes, encoding two KIRs that interact with human leukocyte antigen B (HLA-B) ligands. KIRs are expressed on the surface of natural killer (NK) cells, which serve as important players in the innate immune response, and are involved in the recognition of infected and malignant cells through a loss or alteration in “self” ligands. We use both genetic association and functional evidence to show a strong interaction between KIR3DL1 and KIR3DS1, indicating that increasing gene counts for KIR3DL1 confer increasing levels of protection against HIV-1, but only in the presence of at least one copy of KIR3DS1. This effect was associated with a dramatic increase in the abundance of KIR3DS1+ NK cells in the peripheral blood, and strongly associated with a more robust capacity of peripheral NK cells to suppress HIV-1 replication in vitro. This work provides one of the few examples of an association between a relatively common CNV and a human complex trait.
PMCID: PMC3226550  PMID: 22140359
9.  Genetic variation in IL28B and spontaneous clearance of hepatitis C virus 
Nature  2009;461(7265):798-801.
Hepatitis C virus (HCV) infection is the most common blood borne infection in the U.S. with estimates of 4 million HCV-infected individuals in the U.S. and 170 million worldwide1. The majority (70%–80%) of HCV infections persist and about 30% of individuals with persistent infection develop chronic liver disease, including cirrhosis and hepatocellular carcinoma2. Epidemiological, viral, and host factors have been associated with the differences in HCV clearance or persistence and studies have demonstrated that a strong host immune response against HCV favors viral clearance3,4. Thus, variation in genes involved in the immune response may contribute to the ability to clear the virus. In a recent genome-wide association study, a single nucleotide polymorphism (rs12979860) 3kb upstream of the IL28B gene, which encodes the type III interferon IFN-λ3, was shown to associate strongly with more than a 2-fold difference in response to HCV drug treatment5. To determine the potential effect of rs12979860 variation on outcome to HCV infection in a natural history setting, we genotyped this variant in HCV cohorts comprised of individuals who spontaneously cleared the virus (N = 388) or had persistent infection (N = 620). We show that the C/C genotype strongly enhances resolution of HCV infection amongst individuals of both European and African ancestry (European: OR = 0.38, p = 10−7; African: OR = 0.32, p = 10−4; combined: OR = 0.33, p <10−12). To date, this is the strongest and most significant genetic effect associated with natural clearance of HCV, and these results implicate a primary role for IL28B in resolution of HCV infection.
PMCID: PMC3172006  PMID: 19759533
11.  Common genetic variation and performance on standardized cognitive tests 
One surprising feature of the recently completed waves of genome-wide association studies is the limited impact of common genetic variation in individually detectable polymorphisms on many human traits. This has been particularly pronounced for studies on psychiatric conditions, which have failed to produce clear, replicable associations for common variants. One popular explanation for these negative findings is that many of these traits may be genetically heterogeneous, leading to the idea that relevant endophenotypes may be more genetically tractable. Aspects of cognition may be the most important endophenotypes for psychiatric conditions such as schizophrenia, leading many researchers to pursue large-scale studies on the genetic contributors of cognitive performance in the normal population as a surrogate for aspects of liability to disease. Here, we perform a genome-wide association study with two tests of executive function, Digit Symbol and Stroop Color-Word, in 1086 healthy volunteers and with an expanded cognitive battery in 514 of these volunteers. We show that, consistent with published studies of the psychiatric conditions themselves, no single common variant has a large effect (explaining >4–8% of the population variation) on the performance of healthy individuals on standardized cognitive tests. Given that these are important endophenotypes, our work is consistent with the idea that identifying rare genetic causes of psychiatric conditions may be more important for future research than identifying genetically homogenous endophenotypes.
PMCID: PMC2987367  PMID: 20125193
endophenotypes; genome-wide association; cognition; psychiatric conditions; common variants
12.  SVA: software for annotating and visualizing sequenced human genomes 
Bioinformatics  2011;27(14):1998-2000.
Summary: Here we present Sequence Variant Analyzer (SVA), a software tool that assigns a predicted biological function to variants identified in next-generation sequencing studies and provides a browser to visualize the variants in their genomic contexts. SVA also provides for flexible interaction with software implementing variant association tests allowing users to consider both the bioinformatic annotation of identified variants and the strength of their associations with studied traits. We illustrate the annotation features of SVA using two simple examples of sequenced genomes that harbor Mendelian mutations.
Availability and implementation: Freely available on the web at
Supplementary information: Supplementary data are available at Bioinformatics online.
PMCID: PMC3129530  PMID: 21624899
13.  Variants in the ITPA Gene Protect Against Ribavirin-Induced Hemolytic Anemia and Decrease the Need for Ribavirin Dose Reduction 
Gastroenterology  2010;139(4):1181-1189.
In a genome-wide association study of patients being treated for chronic hepatitis C, 2 functional variants in ITPA that cause inosine triphosphatase (ITPase) deficiency were shown to protect against ribavirin (RBV)-induced hemolytic anemia during early stages of treatment. We aimed to replicate this finding in an independent cohort from the Study of Viral Resistance to Antiviral Therapy of Chronic Hepatitis C and to investigate the effects of these variants beyond week 4.
Genetic material was available from 318 patients. The ITPA variants, rs1127354 (exon 2, P32T) and rs7270101 (intron 2, splice altering), were genotyped and tested for association with hemoglobin (Hb) reduction at week 4. An ITPase deficiency variable was defined that combined both ITPA variants according to documented effect on ITPase activity. We investigated the impact of ITPA variants on Hb levels over the course of therapy and on the need for RBV dose reduction.
The final analysis included 304 patients with genotype 1 hepatitis C virus (167 white patients and 137 black patients). The polymorphisms rs1127354 and rs7270101 were associated with Hb reduction at week 4 (P = 3.1 × 10−13 and 1.3 × 10−3, respectively). The minor alleles of each variant protected against Hb reduction. Combining the variants into the ITPase deficiency variable strengthened the association (P = 2.4 × 10−18). The ITPase deficiency variable was associated with lower rates of anemia over the entire treatment period (48 weeks), as well as a lower rate of anemia-related RBV dose reduction (hazard ratio, 0.52; P = .0037). No association with sustained virological response was observed.
Two polymorphisms that cause ITPase deficiency are strongly associated with protection from RBV-induced hemolytic anemia and decrease the need for RBV dose reduction.
PMCID: PMC3086671  PMID: 20547162
Pharmacogenomics; Genome-Wide Association Study; Polymorphism; Single Nucleotide Polymorphism; HCV; Adverse Event
14.  Host determinants of HIV-1 control in African Americans 
The Journal of infectious diseases  2010;201(8):1141-1149.
We performed a whole-genome association study on HIV-1 viral load setpoint in an African American cohort (n=515), and an intronic SNP in the HLA-B gene showed one of the strongest associations. Using a subset of patients, we show that this SNP reflects the effect of the HLA-B*5703 allele, which shows a genome-wide significant association with HIV-1 VL setpoint (p=5.6×10−10). These analyses therefore confirm a member of the HLA-B*57 group of alleles as the most important common variant influencing viral load variation in African Americans, consistent with what is observed in individuals of European ancestry in which the most important common variant is HLA-B*5701.
PMCID: PMC2838940  PMID: 20205591
HIV; viral load setpoint; host genetics; association study; HLA
15.  Common variants conferring risk of schizophrenia 
Stefansson, Hreinn | Ophoff, Roel A. | Steinberg, Stacy | Andreassen, Ole A. | Cichon, Sven | Rujescu, Dan | Werge, Thomas | Pietiläinen, Olli P. H. | Mors, Ole | Mortensen, Preben B. | Sigurdsson, Engilbert | Gustafsson, Omar | Nyegaard, Mette | Tuulio-Henriksson, Annamari | Ingason, Andres | Hansen, Thomas | Suvisaari, Jaana | Lonnqvist, Jouko | Paunio, Tiina | Børglum, Anders D. | Hartmann, Annette | Fink-Jensen, Anders | Nordentoft, Merete | Hougaard, David | Norgaard-Pedersen, Bent | Böttcher, Yvonne | Olesen, Jes | Breuer, René | Möller, Hans-Jürgen | Giegling, Ina | Rasmussen, Henrik B. | Timm, Sally | Mattheisen, Manuel | Bitter, István | Réthelyi, János M. | Magnusdottir, Brynja B. | Sigmundsson, Thordur | Olason, Pall | Masson, Gisli | Gulcher, Jeffrey R. | Haraldsson, Magnus | Fossdal, Ragnheidur | Thorgeirsson, Thorgeir E. | Thorsteinsdottir, Unnur | Ruggeri, Mirella | Tosato, Sarah | Franke, Barbara | Strengman, Eric | Kiemeney, Lambertus A. | Melle, Ingrid | Djurovic, Srdjan | Abramova, Lilia | Kaleda, Vasily | Sanjuan, Julio | de Frutos, Rosa | Bramon, Elvira | Vassos, Evangelos | Fraser, Gillian | Ettinger, Ulrich | Picchioni, Marco | Walker, Nicholas | Toulopoulou, Timi | Need, Anna C. | Ge, Dongliang | Yoon, Joeng Lim | Shianna, Kevin V. | Freimer, Nelson B. | Cantor, Rita M. | Murray, Robin | Kong, Augustine | Golimbet, Vera | Carracedo, Angel | Arango, Celso | Costas, Javier | Jönsson, Erik G. | Terenius, Lars | Agartz, Ingrid | Petursson, Hannes | Nöthen, Markus M. | Rietschel, Marcella | Matthews, Paul M. | Muglia, Pierandrea | Peltonen, Leena | St Clair, David | Goldstein, David B. | Stefansson, Kari | Collier, David A.
Nature  2009;460(7256):744-747.
Schizophrenia is a complex disorder, caused by both genetic and environmental factors and their interactions. Research on pathogenesis has traditionally focused on neurotransmitter systems in the brain, particularly those involving dopamine. Schizophrenia has been considered a separate disease for over a century, but in the absence of clear biological markers, diagnosis has historically been based on signs and symptoms. A fundamental message emerging from genome-wide association studies of copy number variations (CNVs) associated with the disease is that its genetic basis does not necessarily conform to classical nosological disease boundaries. Certain CNVs confer not only high relative risk of schizophrenia but also of other psychiatric disorders1–3. The structural variations associated with schizophrenia can involve several genes and the phenotypic syndromes, or the ‘genomic disorders’, have not yet been characterized4. Single nucleotide polymorphism (SNP)-based genome-wide association studies with the potential to implicate individual genes in complex diseases may reveal underlying biological pathways. Here we combined SNP data from several large genome-wide scans and followed up the most significant association signals. We found significant association with several markers spanning the major histocompatibility complex (MHC) region on chromosome 6p21.3-22.1, a marker located upstream of the neurogranin gene (NRGN) on 11q24.2 and a marker in intron four of transcription factor 4 (TCF4) on 18q21.2. Our findings implicating the MHC region are consistent with an immune component to schizophrenia risk, whereas the association with NRGN and TCF4 points to perturbation of pathways involved in brain development, memory and cognition.
PMCID: PMC3077530  PMID: 19571808
16.  A genome-wide study of common SNPs and CNVs in cognitive performance in the CANTAB 
Human Molecular Genetics  2009;18(23):4650-4661.
Psychiatric disorders such as schizophrenia are commonly accompanied by cognitive impairments that are treatment resistant and crucial to functional outcome. There has been great interest in studying cognitive measures as endophenotypes for psychiatric disorders, with the hope that their genetic basis will be clearer. To investigate this, we performed a genome-wide association study involving 11 cognitive phenotypes from the Cambridge Neuropsychological Test Automated Battery. We showed these measures to be heritable by comparing the correlation in 100 monozygotic and 100 dizygotic twin pairs. The full battery was tested in ∼750 subjects, and for spatial and verbal recognition memory, we investigated a further 500 individuals to search for smaller genetic effects. We were unable to find any genome-wide significant associations with either SNPs or common copy number variants. Nor could we formally replicate any polymorphism that has been previously associated with cognition, although we found a weak signal of lower than expected P-values for variants in a set of 10 candidate genes. We additionally investigated SNPs in genomic loci that have been shown to harbor rare variants that associate with neuropsychiatric disorders, to see if they showed any suggestion of association when considered as a separate set. Only NRXN1 showed evidence of significant association with cognition. These results suggest that common genetic variation does not strongly influence cognition in healthy subjects and that cognitive measures do not represent a more tractable genetic trait than clinical endpoints such as schizophrenia. We discuss a possible role for rare variation in cognitive genomics.
PMCID: PMC2773267  PMID: 19734545
17.  HLA-C cell surface expression and control of HIV/AIDS correlate with a variant upstream of HLA-C 
Nature genetics  2009;41(12):1290-1294.
A variant 35 kb upstream of the HLA-C gene (-35C/T) was previously shown to associate with HLA-C mRNA expression level and steady-state plasma HIV RNA levels. We genotyped this variant in 1,698 patients of European ancestry with HIV. Individuals with known seroconversion dates were used for disease progression analysis and those with longitudinal viral load data were used for viral load analysis. We further tested cell surface expression of HLA-C in normal donors using an HLA-C-specific antibody. We show that the -35C allele is a proxy for high HLA-C cell surface expression, and that individuals with high-expressing HLA-C alleles progress more slowly to AIDS and control viremia significantly better than individuals with low HLA-C expressing alleles. These data strongly implicate high HLA-C expression levels in more effective control of HIV-1, potentially through better antigen presentation to cytotoxic T lymphocytes or recognition and killing of infected cells by natural killer cells.
PMCID: PMC2887091  PMID: 19935663
18.  The Characterization of Twenty Sequenced Human Genomes 
PLoS Genetics  2010;6(9):e1001111.
We present the analysis of twenty human genomes to evaluate the prospects for identifying rare functional variants that contribute to a phenotype of interest. We sequenced at high coverage ten “case” genomes from individuals with severe hemophilia A and ten “control” genomes. We summarize the number of genetic variants emerging from a study of this magnitude, and provide a proof of concept for the identification of rare and highly-penetrant functional variants by confirming that the cause of hemophilia A is easily recognizable in this data set. We also show that the number of novel single nucleotide variants (SNVs) discovered per genome seems to stabilize at about 144,000 new variants per genome, after the first 15 individuals have been sequenced. Finally, we find that, on average, each genome carries 165 homozygous protein-truncating or stop loss variants in genes representing a diverse set of pathways.
Author Summary
We report here the nearly complete genomic sequence of 20 different individuals, determined using “next-generation” sequencing technologies. We use these data to characterize the type of genetic variation carried by humans in a sample of this size, which is to our knowledge the largest set of unrelated genomic sequences that have been reported. We summarize different categories of variation in each genome, and in total across all 20 of the genomes, finding a surprising number of variants predicted to reduce or remove the proteins encoded by many different genes. This work provides important fundamental information about the scope of human genetic variation, and suggests ways to further explore the relationship between these genetic variants and human disease.
PMCID: PMC2936541  PMID: 20838461
19.  Ethnic differences in the association of Birth Weight and Blood Pressure -the Georgia Cardiovascular Twin Study 
American journal of hypertension  2007;20(12):1235-1241.
African Americans (AA) not only have higher blood pressure levels, but also an increased risk of low weight at birth, compared to European Americans (EA). In light of fetal programming theories it has been suggested that ethnic differences in blood pressure originate in utero. However, most previous studies in bi-ethnic samples have not found a significant inverse association between birth weight and blood pressure in AAs.
In 562 EA and 465 AA adolescent twins of the Georgia Cardiovascular Twin Study we investigated the potential ethnic difference in blood pressure - birth weight association, with the ability to control for potential confounding by familial factors.
Blood pressure levels were significantly higher in AAs compared to EAs, independent of birth weight (p<0.01). After adjustment for parental factors and BMI, the difference in systolic blood pressure per kg birth weight was -1.1 mm Hg (95% confidence interval -2.7, 0.48, p=0.17) in EAs and -2.5 mm Hg (95% CI -4.7, -0.40, p=0.02) in AAs. A significant ethnic interaction was revealed in paired analysis where the inverse association remained in AAs, but not in EAs. Associations with diastolic blood pressure were generally weaker and non significant.
We could show that low birth weight was associated with an elevated systolic blood pressure in AAs, independent of familial factors. The results also suggest that the association between birth weight and blood pressure may be more pronounced in AAs in adolescence.
PMCID: PMC2924638  PMID: 18047911
Birth Weight; Blood Pressure; Fetal Programming; Ethnicity; Twins
20.  Whole-Genome Sequencing of a Single Proband Together with Linkage Analysis Identifies a Mendelian Disease Gene 
PLoS Genetics  2010;6(6):e1000991.
Although more than 2,400 genes have been shown to contain variants that cause Mendelian disease, there are still several thousand such diseases yet to be molecularly defined. The ability of new whole-genome sequencing technologies to rapidly indentify most of the genetic variants in any given genome opens an exciting opportunity to identify these disease genes. Here we sequenced the whole genome of a single patient with the dominant Mendelian disease, metachondromatosis (OMIM 156250), and used partial linkage data from her small family to focus our search for the responsible variant. In the proband, we identified an 11 bp deletion in exon four of PTPN11, which alters frame, results in premature translation termination, and co-segregates with the phenotype. In a second metachondromatosis family, we confirmed our result by identifying a nonsense mutation in exon 4 of PTPN11 that also co-segregates with the phenotype. Sequencing PTPN11 exon 4 in 469 controls showed no such protein truncating variants, supporting the pathogenicity of these two mutations. This combination of a new technology and a classical genetic approach provides a powerful strategy to discover the genes responsible for unexplained Mendelian disorders.
Author Summary
Metachondromatosis (MC) is an autosomal dominant condition characterized by exostoses (osteochondromas), commonly of the hands and feet, and enchondromas of long bone metaphyses and iliac crests. MC exostoses may regress or even resolve over time, and short stature is not characteristic of MC. Here, we sequenced the whole genome of a single patient with MC and used partial linkage data from her small family to focus our search for the responsible variant. In the proband, we identified an 11 bp deletion in exon four of PTPN11, which results in premature translation termination and co-segregates with the phenotype. In a second metachondromatosis family, we identified a nonsense mutation in exon 4 of PTPN11 that also co-segregates with the phenotype. Germline gain-of-function missense mutations in PTPN11 cause an overlapping but distinct group of dominant disorders with involvement of the face, heart, skeleton, skin, and brain, including Noonan syndrome (OMIM 163950), Noonan-like disorder with multiple giant cell lesion syndrome (OMIM 163955), and LEOPARD syndrome (OMIM 151100). Nonsense mutations in PTPN11 have not been described in humans and the loss-of-function PTPN11 mutations we report here are the first to be described in human disease.
PMCID: PMC2887469  PMID: 20577567
21.  Screening the human exome: a comparison of whole genome and whole transcriptome sequencing 
Genome Biology  2010;11(5):R57.
There is considerable interest in the development of methods to efficiently identify all coding variants present in large sample sets of humans. There are three approaches possible: whole-genome sequencing, whole-exome sequencing using exon capture methods, and RNA-Seq. While whole-genome sequencing is the most complete, it remains sufficiently expensive that cost effective alternatives are important.
Here we provide a systematic exploration of how well RNA-Seq can identify human coding variants by comparing variants identified through high coverage whole-genome sequencing to those identified by high coverage RNA-Seq in the same individual. This comparison allowed us to directly evaluate the sensitivity and specificity of RNA-Seq in identifying coding variants, and to evaluate how key parameters such as the degree of coverage and the expression levels of genes interact to influence performance. We find that although only 40% of exonic variants identified by whole genome sequencing were captured using RNA-Seq; this number rose to 81% when concentrating on genes known to be well-expressed in the source tissue. We also find that a high false positive rate can be problematic when working with RNA-Seq data, especially at higher levels of coverage.
We conclude that as long as a tissue relevant to the trait under study is available and suitable quality control screens are implemented, RNA-Seq is a fast and inexpensive alternative approach for finding coding variants in genes with sufficiently high expression levels.
PMCID: PMC2898068  PMID: 20598109
22.  The Duffy Antigen Receptor for Chemokines Null Promoter Variant Does Not Influence HIV-1 Acquisition Or Disease Progression 
Cell host & microbe  2009;5(5):408-419.
Ma’am – We read with great interest the article by He et al. [2008] describing the effects on HIV acquisition and disease progression of a single-nucleotide polymorphism (SNP, rs2814778, -46T→C) that disrupts the promoter region of the Duffy antigen receptor for chemokines (DARC) gene and abolishes gene expression in red blood cells. He et al. reported that HIV-infected African Americans have a frequency of the null homozygous genotype (-46C/C) of 70% while non-HIV infected individuals have a null genotype frequency of 60%. Based on this frequency difference they argued that the null allele confers susceptibility to infection with HIV-1. They also reported that the null genotype is associated with better outcomes amongst those who do become infected, including longer survival, slower loss of CD4+ T-lymphocytes, and delayed progression to HIV-associated dementia.
PMCID: PMC2720554  PMID: 19454339
23.  Genome-Wide mRNA Expression Correlates of Viral Control in CD4+ T-Cells from HIV-1-Infected Individuals 
PLoS Pathogens  2010;6(2):e1000781.
There is great interindividual variability in HIV-1 viral setpoint after seroconversion, some of which is known to be due to genetic differences among infected individuals. Here, our focus is on determining, genome-wide, the contribution of variable gene expression to viral control, and to relate it to genomic DNA polymorphism. RNA was extracted from purified CD4+ T-cells from 137 HIV-1 seroconverters, 16 elite controllers, and 3 healthy blood donors. Expression levels of more than 48,000 mRNA transcripts were assessed by the Human-6 v3 Expression BeadChips (Illumina). Genome-wide SNP data was generated from genomic DNA using the HumanHap550 Genotyping BeadChip (Illumina). We observed two distinct profiles with 260 genes differentially expressed depending on HIV-1 viral load. There was significant upregulation of expression of interferon stimulated genes with increasing viral load, including genes of the intrinsic antiretroviral defense. Upon successful antiretroviral treatment, the transcriptome profile of previously viremic individuals reverted to a pattern comparable to that of elite controllers and of uninfected individuals. Genome-wide evaluation of cis-acting SNPs identified genetic variants modulating expression of 190 genes. Those were compared to the genes whose expression was found associated with viral load: expression of one interferon stimulated gene, OAS1, was found to be regulated by a SNP (rs3177979, p = 4.9E-12); however, we could not detect an independent association of the SNP with viral setpoint. Thus, this study represents an attempt to integrate genome-wide SNP signals with genome-wide expression profiles in the search for biological correlates of HIV-1 control. It underscores the paradox of the association between increasing levels of viral load and greater expression of antiviral defense pathways. It also shows that elite controllers do not have a fully distinctive mRNA expression pattern in CD4+ T cells. Overall, changes in global RNA expression reflect responses to viral replication rather than a mechanism that might explain viral control.
Author Summary
There has been recent progress in understanding the genetic factors that modulate susceptibility to HIV-1 infection. Genetic variation explains to a certain extent differences in disease progression among individuals. Less is known regarding the contribution of differences in gene expression to viral control. The present study evaluated, genome-wide, gene expression levels in CD4+ T cell, the main target of HIV-1. Thereafter, it searched for genetic variants that would modify gene expression. Specific expression profiles associated with high levels of viremia—in particular, the upregulation of genes of the antiviral defense. In contrast, no expression profile associated with effective viral control. Multiple genetic variants modulated gene expression in CD4+ T cells; however, none had a strong influence on viral control. This integrated genome-wide assessment suggests that viral replication drives gene expression rather than expression pointing to mechanisms of viral control.
PMCID: PMC2829051  PMID: 20195503
24.  Stress-Induced Sodium Excretion, a New Intermediate Phenotype to Study the Early Genetic Etiology of Hypertension? 
Hypertension  2008;53(2):262-269.
Impaired stress-induced pressure natriuresis, i.e., an inadequate increase in urinary sodium excretion (UNaV) in response to a stress-induced blood pressure increase, may lead to the premature development of essential hypertension. To assess the heritability of baseline UNaV, stress UNaV, and the UNaV response to stress (ΔUNaV = stress UNaV – baseline UNaV), we studied 396 African American (AA) and 494 European American (EA) twins, including monozygotic and dizygotic of same- as well as opposite-sex (mean age: 17.6 ± 3.3; range: 11.9–30.0). Bivariate genetic model fitting was performed to examine the extent to which genetic and environmental factors are common or specific to baseline and stress UNaV. Heritability estimates for ΔUNaV can be derived from these bivariate models. All bivariate analyses were performed separately in EAs and AAs, because univariate models for baseline UNaV showed significant ethnic differences in heritability estimates. Best fitting models showed that the heritability of stress UNaV was 0.42 in EAs and 0.58 in AAs. Only 15% and 11% of the total variance could be attributed to genetic factors common to baseline and stress UNaV in EAs and AAs, respectively. After removal of all shared influences with baseline UNaV, heritabilities for stress UNaV were 0.32 in EAs and 0.57 in AAs. Heritability estimates for ΔUNaV were 0.36 in EAs and 0.39 in AAs. In summary, this study establishes ΔUNaV and stress UNaV as heritable phenotypes that may be used to study the genetic etiology of early hypertension development.
PMCID: PMC2719844  PMID: 19104006
natriuresis; blood pressure; risk factors; genetics; twin study; African American
25.  Common Genetic Variation and the Control of HIV-1 in Humans 
PLoS Genetics  2009;5(12):e1000791.
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.
PMCID: PMC2791220  PMID: 20041166

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