Szabolcs Szelinger

Publications

• 15.05

  Impact points

  Enrichment of cis-regulatory gene expression SNPs and methylation quantitative trait loci among bipolar disorder susceptibility variants.

  E R Gamazon, J A Badner, L Cheng, C Zhang, D Zhang, N J Cox, E S Gershon, J R Kelsoe, T A Greenwood, C M Nievergelt, [......], J B Potash, P P Zandi, P B Mahon, M G McInnis, S Zöllner, P Zhang, D W Craig, S Szelinger, T B Barrett, C Liu

  Molecular psychiatry. 01/2012;

  We conducted a systematic study of top susceptibility variants from a genome-wide association (GWA) study of bipolar disorder to gain insight into the functional consequences of genetic variation influencing disease risk. We report here the results of experiments to explore the effects of these susc... [more] We conducted a systematic study of top susceptibility variants from a genome-wide association (GWA) study of bipolar disorder to gain insight into the functional consequences of genetic variation influencing disease risk. We report here the results of experiments to explore the effects of these susceptibility variants on DNA methylation and mRNA expression in human cerebellum samples. Among the top susceptibility variants, we identified an enrichment of cis regulatory loci on mRNA expression (eQTLs), and a significant excess of quantitative trait loci for DNA CpG methylation, hereafter referred to as methylation quantitative trait loci (mQTLs). Bipolar disorder susceptibility variants that cis regulate both cerebellar expression and methylation of the same gene are a very small proportion of bipolar disorder susceptibility variants. This finding suggests that mQTLs and eQTLs provide orthogonal ways of functionally annotating genetic variation within the context of studies of pathophysiology in brain. No lymphocyte mQTL enrichment was found, suggesting that mQTL enrichment was specific to the cerebellum, in contrast to eQTLs. Separately, we found that using mQTL information to restrict the number of single-nucleotide polymorphisms studied enhances our ability to detect a significant association. With this restriction a priori informed by the observed functional enrichment, we identified a significant association (rs12618769, P(bonferroni)<0.05) from two other GWA studies (TGen+GAIN; 2191 cases and 1434 controls) of bipolar disorder, which we replicated in an independent GWA study (WTCCC). Collectively, our findings highlight the importance of integrating functional annotation of genetic variants for gene expression and DNA methylation to advance the biological understanding of bipolar disorder.Molecular Psychiatry advance online publication, 3 January 2012; doi:10.1038/mp.2011.174.
• 1.93

  Impact points

  Induction of pluripotent stem cells from autopsy donor-derived somatic cells.

  Brooke E Hjelm, Jon B Rosenberg, Szabolcs Szelinger, Lucia I Sue, Thomas G Beach, Matthew J Huentelman, David W Craig

  Neuroscience letters. 08/2011; 502(3):219-24.

  Human induced pluripotent stem cells (iPSCs) have become an intriguing approach for neurological disease modeling, because neural lineage-specific cell types that retain the donors' complex genetics can be established in vitro. The statistical power of these iPSC-based models, however, is depend... [more] Human induced pluripotent stem cells (iPSCs) have become an intriguing approach for neurological disease modeling, because neural lineage-specific cell types that retain the donors' complex genetics can be established in vitro. The statistical power of these iPSC-based models, however, is dependent on accurate diagnoses of the somatic cell donors; unfortunately, many neurodegenerative diseases are commonly misdiagnosed in live human subjects. Postmortem histopathological examination of a donor's brain, combined with premortem clinical criteria, is often the most robust approach to correctly classify an individual as a disease-specific case or unaffected control. In this study, we describe iPSCs generated from a skin biopsy collected postmortem during the rapid autopsy of a 75-year-old male, whole body donor, defined as an unaffected neurological control by both clinical and histopathological criteria. These iPSCs were established in a feeder-free system by lentiviral transduction of the Yamanaka factors, Oct3/4, Sox2, Klf4, and c-Myc. Selected iPSC clones expressed both nuclear and surface antigens recognized as pluripotency markers of human embryonic stem cells (hESCs) and were able to differentiate in vitro into neurons and glia. Statistical analysis also demonstrated that fibroblast proliferation was significantly affected by biopsy site, but not donor age (within an elderly cohort). These results provide evidence that autopsy donor-derived fibroblasts can be successfully reprogrammed into iPSCs, and may provide an advantageous approach for generating iPSC-based neurological disease models.
• 9.53

  Impact points

  Genome-wide association of bipolar disorder suggests an enrichment of replicable associations in regions near genes.

  Erin N Smith, Daniel L Koller, Corrie Panganiban, Szabolcs Szelinger, Peng Zhang, Judith A Badner, Thomas B Barrett, Wade H Berrettini, Cinnamon S Bloss, William Byerley, [......], James B Potash, John Rice, Thomas G Schulze, William A Scheftner, Paul D Shilling, Peter P Zandi, Sebastian Zöllner, David W Craig, Nicholas J Schork, John R Kelsoe

  PLoS genetics. 06/2011; 7(6):e1002134.

  Although a highly heritable and disabling disease, bipolar disorder's (BD) genetic variants have been challenging to identify. We present new genotype data for 1,190 cases and 401 controls and perform a genome-wide association study including additional samples for a total of 2,191 cases and 1,4... [more] Although a highly heritable and disabling disease, bipolar disorder's (BD) genetic variants have been challenging to identify. We present new genotype data for 1,190 cases and 401 controls and perform a genome-wide association study including additional samples for a total of 2,191 cases and 1,434 controls. We do not detect genome-wide significant associations for individual loci; however, across all SNPs, we show an association between the power to detect effects calculated from a previous genome-wide association study and evidence for replication (P = 1.5×10(-7)). To demonstrate that this result is not likely to be a false positive, we analyze replication rates in a large meta-analysis of height and show that, in a large enough study, associations replicate as a function of power, approaching a linear relationship. Within BD, SNPs near exons exhibit a greater probability of replication, supporting an enrichment of reproducible associations near functional regions of genes. These results indicate that there is likely common genetic variation associated with BD near exons (±10 kb) that could be identified in larger studies and, further, provide a framework for assessing the potential for replication when combining results from multiple studies.

• Microarray-based genome-wide association studies using pooled DNA.

  Szabolcs Szelinger, John V Pearson, David W Craig

  Methods in molecular biology (Clifton, N.J.). 01/2011; 700:49-60.

  Pooling genomic DNA samples within clinical classes of disease for use in whole-genome single nucleotide polymorphism (SNP) genotyping allows for rapid and inexpensive genome-wide association studies (GWAS). We describe here a general outline for combining hundreds of genomic DNA samples prior to ge... [more] Pooling genomic DNA samples within clinical classes of disease for use in whole-genome single nucleotide polymorphism (SNP) genotyping allows for rapid and inexpensive genome-wide association studies (GWAS). We describe here a general outline for combining hundreds of genomic DNA samples prior to genotyping on commercially available high-density SNP microarrays. The pool construction approach is universal, and independent of the SNP genotyping platform utilized, and therefore provides a quick, efficient, and low-cost alternative to interrogating thousands of individual samples on singular SNP microarrays. While the strategy for pooled DNA genotyping on SNP microarrays is straightforward, the success of such studies is critically dependent upon the accuracy of allelic frequency calculations, the -ability to identify falsely positive results arising from assay variability, and the willingness to better resolve association signals through investigation of neighboring SNPs.

• Bar-coded, multiplexed sequencing of targeted DNA regions using the Illumina Genome Analyzer.

  Szabolcs Szelinger, Ahmet Kurdoglu, David W Craig

  Methods in molecular biology (Clifton, N.J.). 01/2011; 700:89-104.

  To date, genome-wide association (GWA) studies, in which thousands of markers throughout the genome are simultaneously genotyped, have identified hundreds of loci underlying disease susceptibility. These regions typically span 5-100 kb, and resequencing efforts to identify potential functional varia... [more] To date, genome-wide association (GWA) studies, in which thousands of markers throughout the genome are simultaneously genotyped, have identified hundreds of loci underlying disease susceptibility. These regions typically span 5-100 kb, and resequencing efforts to identify potential functional variants within these loci represent the next logical step in the genetic characterization pipeline. Next-generation DNA sequencing technologies are, in principle, well-suited for this task, yet despite the massive sequencing capability afforded by these platforms, the present-day reality is that it remains difficult, time-consuming, and expensive to resequence large numbers of samples across moderately sized genomic regions. To address this obstacle, we developed a generalized framework for multiplexed resequencing of targeted regions of the human genome on the Illumina Genome Analyzer using degenerate, indexed DNA sequence barcodes ligated to fragmented DNA prior to sequencing. Using this method, the DNA of multiple individuals can be simultaneously sequenced at several regions. We find that achieving adequate coverage is one of the most important factors in the design of an experiment, but other key considerations include whether the objective is to discover genetic variants for genotyping later by a separate method, to genotype all identified variants by sequencing, or to exhaustively identify all common and rare variants in the region. Given the massive bandwidth of next-generation sequencing technologies and their low inherent throughput in terms of sequencing arrays per week, multiplexed sequencing using the barcoding approach offers a clear mechanism for focusing bandwidth to a smaller region across many more individuals or samples.
• 2.43

  Impact points

  Bing: Biomedical informatics pipeline for next generation sequencing.

  Jeffrey Kriseman, Christopher Busick, Szabolcs Szelinger, Valentin Dinu

  Journal of biomedical informatics. 11/2009;

  High throughput parallel genomic sequencing (Next Generation Sequencing, NGS) shifts the bottleneck in sequencing processes from experimental data production to computationally intensive informatics-based data analysis. This manuscript introduces a Biomedical Informatics Pipeline (BING) for the anal... [more] High throughput parallel genomic sequencing (Next Generation Sequencing, NGS) shifts the bottleneck in sequencing processes from experimental data production to computationally intensive informatics-based data analysis. This manuscript introduces a Biomedical Informatics Pipeline (BING) for the analysis of NGS data that offers several novel computational approaches to 1. image alignment, 2. signal correlation, compensation, separation, and pixel-based cluster registration, 3. signal measurement and base calling, 4. quality control and accuracy measurement. These approaches address many of the informatics challenges, including image processing, computational performance, and accuracy. These new algorithms are benchmarked against the Illumina Genome Analysis Pipeline. BING is the one of the first software tools to perform pixel-based analysis of NGS data. When compared to the Illumina informatics tool, BING's pixel-based approach produces a significant increase in the number of sequence reads, while reducing the computational time per experiment and error rate (<2%). This approach has the potential of increasing the density and throughput of NGS technologies.
• 15.05

  Impact points

  Singleton deletions throughout the genome increase risk of bipolar disorder.

  D Zhang, L Cheng, Y Qian, N Alliey-Rodriguez, J R Kelsoe, T Greenwood, C Nievergelt, T B Barrett, R McKinney, N Schork, [......], P L Belmonte, P P Zandi, M G McInnis, S Zöllner, D Craig, S Szelinger, D Koller, S L Christian, C Liu, E S Gershon

  Molecular psychiatry. 01/2009;

  An overall burden of rare structural genomic variants has not been reported in bipolar disorder (BD), although there have been reports of cases with microduplication and microdeletion. Here, we present a genome-wide copy number variant (CNV) survey of 1001 cases and 1034 controls using the Affymetri... [more] An overall burden of rare structural genomic variants has not been reported in bipolar disorder (BD), although there have been reports of cases with microduplication and microdeletion. Here, we present a genome-wide copy number variant (CNV) survey of 1001 cases and 1034 controls using the Affymetrix single nucleotide polymorphism (SNP) 6.0 SNP and CNV platform. Singleton deletions (deletions that appear only once in the dataset) more than 100 kb in length are present in 16.2% of BD cases in contrast to 12.3% of controls (permutation P=0.007). This effect was more pronounced for age at onset of mania </=18 years old. Our results strongly suggest that BD can result from the effects of multiple rare structural variants.Molecular Psychiatry advance online publication, 30 December 2008; doi:10.1038/mp.2008.144.
• 9.53

  Impact points

  Resolving individuals contributing trace amounts of DNA to highly complex mixtures using high-density SNP genotyping microarrays.

  Nils Homer, Szabolcs Szelinger, Margot Redman, David Duggan, Waibhav Tembe, Jill Muehling, John V Pearson, Dietrich A Stephan, Stanley F Nelson, David W Craig

  PLoS genetics. 09/2008; 4(8):e1000167.

  We use high-density single nucleotide polymorphism (SNP) genotyping microarrays to demonstrate the ability to accurately and robustly determine whether individuals are in a complex genomic DNA mixture. We first develop a theoretical framework for detecting an individual's presence within a mixtu... [more] We use high-density single nucleotide polymorphism (SNP) genotyping microarrays to demonstrate the ability to accurately and robustly determine whether individuals are in a complex genomic DNA mixture. We first develop a theoretical framework for detecting an individual's presence within a mixture, then show, through simulations, the limits associated with our method, and finally demonstrate experimentally the identification of the presence of genomic DNA of specific individuals within a series of highly complex genomic mixtures, including mixtures where an individual contributes less than 0.1% of the total genomic DNA. These findings shift the perceived utility of SNPs for identifying individual trace contributors within a forensics mixture, and suggest future research efforts into assessing the viability of previously sub-optimal DNA sources due to sample contamination. These findings also suggest that composite statistics across cohorts, such as allele frequency or genotype counts, do not mask identity within genome-wide association studies. The implications of these findings are discussed.
• 16.87

  Impact points

  Identification of genetic variants using bar-coded multiplexed sequencing.

  David W Craig, John V Pearson, Szabolcs Szelinger, Aswin Sekar, Margot Redman, Jason J Corneveaux, Traci L Pawlowski, Trisha Laub, Gary Nunn, Dietrich A Stephan, Nils Homer, Matthew J Huentelman

  Nature methods. 09/2008;

  We developed a generalized framework for multiplexed resequencing of targeted human genome regions on the Illumina Genome Analyzer using degenerate indexed DNA bar codes ligated to fragmented DNA before sequencing. Using this method, we simultaneously sequenced the DNA of multiple HapMap individuals... [more] We developed a generalized framework for multiplexed resequencing of targeted human genome regions on the Illumina Genome Analyzer using degenerate indexed DNA bar codes ligated to fragmented DNA before sequencing. Using this method, we simultaneously sequenced the DNA of multiple HapMap individuals at several Encyclopedia of DNA Elements (ENCODE) regions. We then evaluated the use of Bayes factors for discovering and genotyping polymorphisms. For polymorphisms that were either previously identified within the Single Nucleotide Polymorphism database (dbSNP) or visually evident upon re-inspection of archived ENCODE traces, we observed a false positive rate of 11.3% using strict thresholds for predicting variants and 69.6% for lax thresholds. Conversely, false negative rates were 10.8-90.8%, with false negatives at stricter cut-offs occurring at lower coverage (<10 aligned reads). These results suggest that >90% of genetic variants are discoverable using multiplexed sequencing provided sufficient coverage at the polymorphic base.
• 4.93

  Impact points

  Multimarker analysis and imputation of multiple platform pooling-based genome-wide association studies.

  Nils Homer, Waibhav D Tembe, Szabolcs Szelinger, Margot Redman, Dietrich A Stephan, John V Pearson, Stanley F Nelson, David Craig

  Bioinformatics (Oxford, England). 08/2008;

  SUMMARY: For many genome-wide association (GWA) studies individually genotyping one million or more SNPs provides a marginal increase in coverage at a substantial cost. Much of the information gained is redundant due to the correlation structure inherent in the human genome. Pooling based GWA studie... [more] SUMMARY: For many genome-wide association (GWA) studies individually genotyping one million or more SNPs provides a marginal increase in coverage at a substantial cost. Much of the information gained is redundant due to the correlation structure inherent in the human genome. Pooling based GWA studies could benefit significantly by utilizing this redundancy to reduce noise, improve the accuracy of the observations, and increase genomic coverage. We introduce a measure of correlation between individual genotyping and pooling, under the same framework that r(2) provides a measure of linkage disequilibrium between pairs of SNPs. We then report a new non-haplotype multimarker multi-loci method that leverages the correlation structure between SNPs in the human genome to increase the efficacy of pooling based GWA studies. We first give a theoretical framework and derivation of our multimarker method. Next, we evaluate simulations using this multimarker approach in comparison to single marker analysis. Finally, we experimentally evaluate our method using different pools of HapMap individuals on the Illumina 450S Duo, Illumina 550K, and Affymetrix 5.0 platforms for a combined total of 1,333,631 SNPs. Our results show that use of multimarker analysis reduces noise specific to pooling based studies, allows for efficient integration of multiple microarray platforms, and provides more accurate measures of significance than single marker analysis. Additionally, this approach can be extended to allow for imputing the association significance for SNPs not directly observed using neighboring SNPs in linkage disequilibrium. This multimarker method can now be used to cost-effectively complete pooling-based GWA studies with multiple platforms across over one million SNPs and to impute neighboring SNPs weighted for the loss of information due to pooling. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
• 12.30

  Impact points

  Identification of somatic chromosomal abnormalities in hypothalamic hamartoma tissue at the GLI3 locus.

  David W Craig, Abraham Itty, Corrie Panganiban, Szabolcs Szelinger, Michael C Kruer, Aswin Sekar, David Reiman, Vinodh Narayanan, Dietrich A Stephan, John F Kerrigan

  American journal of human genetics. 03/2008; 82(2):366-74.

  Hypothalamic hamartomas (HH) are rare, benign congenital tumors associated with intractable epilepsy. Most cases are sporadic and nonsyndromic. Approximately 5% of HH cases are associated with Pallister-Hall syndrome (PHS), which is caused by haploinsufficiency of GLI3. We have investigated the poss... [more] Hypothalamic hamartomas (HH) are rare, benign congenital tumors associated with intractable epilepsy. Most cases are sporadic and nonsyndromic. Approximately 5% of HH cases are associated with Pallister-Hall syndrome (PHS), which is caused by haploinsufficiency of GLI3. We have investigated the possibility that HH pathogenesis in sporadic cases is due to a somatic (tumor-only) mutation in GLI3. We isolated genomic DNA from peripheral blood and surgically resected HH tissue in 55 patients with sporadic HH and intractable epilepsy. A genome-wide screen for loss of heterozygosity (LOH) and chromosomal abnormalities was performed with parallel analysis of blood and HH tissue with Affymetrix 10K SNP microarrays. Additionally, resequencing and fine mapping with SNP genotyping were completed for the GLI3 gene with comparisons between peripheral blood and HH tissue pairs. By analyzing chromosomal copy-number data for paired samples on the Affymetrix 10K array, we identified a somatic chromosomal abnormality on chromosome 7p in one HH tissue sample. Resequencing of GLI3 did not identify causative germline mutations but did identify LOH within the GLI3 gene in the HH tissue samples of three patients. Further genotyping of 28 SNPs within and surrounding GLI3 identified five additional patients exhibiting LOH. Together, these data provide evidence that the development of chromosomal abnormalities within GLI3 is associated with the pathogenesis of HH lesions in sporadic, nonsyndromic patients with HH and intractable epilepsy. Chromosomal abnormalities including the GLI3 locus were seen in 8 of 55 (15%) of the resected HH tissue samples. These somatic mutations appear to be highly variable.
• 47.05

  Impact points

  Whole-genome analysis of sporadic amyotrophic lateral sclerosis.

  Travis Dunckley, Matthew J Huentelman, David W Craig, John V Pearson, Szabolcs Szelinger, Keta Joshipura, Rebecca F Halperin, Chelsea Stamper, Kendall R Jensen, David Letizia, [......], Richard Crook, Henrik Ryberg, Michael Hutton, Jonathan Katz, Ericka P Simpson, Hiroshi Mitsumoto, Robert Bowser, Robert G Miller, Stanley H Appel, Dietrich A Stephan

  The New England journal of medicine. 08/2007; 357(8):775-88.

  BACKGROUND: Approximately 90% of persons with amyotrophic lateral sclerosis (ALS) have the sporadic form, which may be caused by the interaction of multiple environmental factors and previously unknown genes. METHODS: We performed a genomewide association analysis using 766,955 single-nucleotide pol... [more] BACKGROUND: Approximately 90% of persons with amyotrophic lateral sclerosis (ALS) have the sporadic form, which may be caused by the interaction of multiple environmental factors and previously unknown genes. METHODS: We performed a genomewide association analysis using 766,955 single-nucleotide polymorphisms (SNPs) found in 386 white patients with sporadic ALS and 542 neurologically normal white controls (the discovery series). Associations of SNPs with sporadic ALS were confirmed in two independent replication populations: replication series 1, with 766 case patients with the disease and 750 neurologically normal controls, and replication series 2, with 135 case patients and 275 controls. RESULTS: We identified 10 genetic loci that are significantly associated (P<0.05) with sporadic ALS in three independent series of case patients and controls and an additional 41 loci that had significant associations in two of the three series. The most significant association with disease in white case patients as compared with controls was found for a SNP near an uncharacterized gene known as FLJ10986 (P=3.0x10(-4); odds ratio for having the genotype in patients vs. controls, 1.35; 95% confidence interval, 1.13 to 1.62). The FLJ10986 protein was found to be expressed in the spinal cord and cerebrospinal fluid of patients and of controls. Specific SNPs seem to be associated with sex, age at onset, and site of onset of sporadic ALS. CONCLUSIONS: Variants of FLJ10986 may confer susceptibility to sporadic ALS. FLJ10986 and 50 other candidate loci warrant further investigation for their potential role in conferring susceptibility to the disease.
• 12.30

  Impact points

  Identification of a novel risk locus for progressive supranuclear palsy by a pooled genomewide scan of 500,288 single-nucleotide polymorphisms.

  Stacey Melquist, David W Craig, Matthew J Huentelman, Richard Crook, John V Pearson, Matt Baker, Victoria L Zismann, Jennifer Gass, Jennifer Adamson, Szabolcs Szelinger, [......], Ryan J Uitti, Zbigniew K Wszolek, Lawrence I Golbe, Richard J Caselli, Neill Graff-Radford, Irene Litvan, Matthew J Farrer, Dennis W Dickson, Mike Hutton, Dietrich A Stephan

  American journal of human genetics. 04/2007; 80(4):769-78.

  To date, only the H1 MAPT haplotype has been consistently associated with risk of developing the neurodegenerative disease progressive supranuclear palsy (PSP). We hypothesized that additional genetic loci may be involved in conferring risk of PSP that could be identified through a pooling-based gen... [more] To date, only the H1 MAPT haplotype has been consistently associated with risk of developing the neurodegenerative disease progressive supranuclear palsy (PSP). We hypothesized that additional genetic loci may be involved in conferring risk of PSP that could be identified through a pooling-based genomewide association study of >500,000 SNPs. Candidate SNPs with large differences in allelic frequency were identified by ranking all SNPs by their probe-intensity difference between cohorts. The MAPT H1 haplotype was strongly detected by this methodology, as was a second major locus on chromosome 11p12-p11 that showed evidence of association at allelic (P<.001), genotypic (P<.001), and haplotypic (P<.001) levels and was narrowed to a single haplotype block containing the DNA damage-binding protein 2 (DDB2) and lysosomal acid phosphatase 2 (ACP2) genes. Since DNA damage and lysosomal dysfunction have been implicated in aging and neurodegenerative processes, both genes are viable candidates for conferring risk of disease.
• 12.30

  Impact points

  Identification of the genetic basis for complex disorders by use of pooling-based genomewide single-nucleotide-polymorphism association studies.

  John V Pearson, Matthew J Huentelman, Rebecca F Halperin, Waibhav D Tembe, Stacey Melquist, Nils Homer, Marcel Brun, Szabolcs Szelinger, Keith D Coon, Victoria L Zismann, [......], Reinhard Heun, Frank Jessen, Heike Kolsch, Magdalini Tsolaki, Makrina Daniilidou, Eric M Reiman, Andreas Papassotiropoulos, Michael L Hutton, Dietrich A Stephan, David W Craig

  American journal of human genetics. 02/2007; 80(1):126-39.

  We report the development and validation of experimental methods, study designs, and analysis software for pooling-based genomewide association (GWA) studies that use high-throughput single-nucleotide-polymorphism (SNP) genotyping microarrays. We first describe a theoretical framework for establishi... [more] We report the development and validation of experimental methods, study designs, and analysis software for pooling-based genomewide association (GWA) studies that use high-throughput single-nucleotide-polymorphism (SNP) genotyping microarrays. We first describe a theoretical framework for establishing the effectiveness of pooling genomic DNA as a low-cost alternative to individually genotyping thousands of samples on high-density SNP microarrays. Next, we describe software called "GenePool," which directly analyzes SNP microarray probe intensity data and ranks SNPs by increased likelihood of being genetically associated with a trait or disorder. Finally, we apply these methods to experimental case-control data and demonstrate successful identification of published genetic susceptibility loci for a rare monogenic disease (sudden infant death with dysgenesis of the testes syndrome), a rare complex disease (progressive supranuclear palsy), and a common complex disease (Alzheimer disease) across multiple SNP genotyping platforms. On the basis of these theoretical calculations and their experimental validation, our results suggest that pooling-based GWA studies are a logical first step for determining whether major genetic associations exist in diseases with high heritability.

• Analysis Software for High-density Pooled Genotyping Data.

  Waibhav Tembe, Nils Homer, Sotiris Mitropanopoulos, Mitchell Storey, Szabolcs Szelinger, Marcel Brun, Matthew J. Huentelman, Edward Suh, Dietrich A. Stephan, James Lowey, John V. Pearson, David W. Craig

  International Conference on Bioinformatics & Computational Biology, BIOCOMP 2007, Volume I, June 25-28, 2007, Las Vegas Nevada, USA; 01/2007

• Comparison of ecdysteroid concentration in different morphs of aphids.

  L A Polgár, B Darvas, W Völkl, P Porcheron, A Székács, S Szelinger

  Comparative biochemistry and physiology. Part C, Pharmacology, toxicology & endocrinology. 11/1996; 115(2):179-83.

  The amounts of ecdysteroids were determined in different morphs of holocyclic monoecious aphids (Acyrthosiphon pisum Harris, Dysaphis devecta Walk., Lachnus roboris L., Schizolachnus pineti F.) and holocyclic heteroecious aphids (Aphis sambuci L., Rhopalosiphum padi L.) by means enzyme immunoassay. ... [more] The amounts of ecdysteroids were determined in different morphs of holocyclic monoecious aphids (Acyrthosiphon pisum Harris, Dysaphis devecta Walk., Lachnus roboris L., Schizolachnus pineti F.) and holocyclic heteroecious aphids (Aphis sambuci L., Rhopalosiphum padi L.) by means enzyme immunoassay. Among the parthenogenetic morphs (fundatrices, virginoparae, and oviparae), the fundatrices have consistently higher amounts of ecdysteroids than those of other morphs of the same species. Alate and apterous virginoparae showed slight differences in their ecdysteroid titer both in heteroecious and monoecious aphids. The migrant morphs (i.e., alate fundatrices and gynoparae) have the lowest amounts of ecdysteroids within a species. With the exception of D. devecta, the oviparae of both heteroecious and monoecious aphids have the second greatest amounts of ecdysteroids among the morphs living on same host plant. Polyphenism, dispersal behavior, and fecundity in connection with weight, ovariole number, and ecdysteroid concentration of different morphs of aphids are discussed.

• Genome-wide association of bipolar disorder suggests an enrichment of replicable associations in regions near genes

  E. N. Smith, D. L. Koller, C. Panganiban, S. Szelinger, P. Zhang, J. A. Badner, T. B. Barrett, W. H. Berrettini, C. S. Bloss, W. Byerley, [......], J. B. Potash, J. Rice, T. G. Schulze, W. A. Scheftner, P. D. Shilling, P. P. Zandi, S. Zollner, D. W. Craig, N. J. Schork, J. R. Kelsoe

  PLoS genetics. 7(6):e1002134.

  Although a highly heritable and disabling disease, bipolar disorder's (BD) genetic variants have been challenging to identify. We present new genotype data for 1,190 cases and 401 controls and perform a genome-wide association study including additional samples for a total of 2,191 cases and 1,4... [more] Although a highly heritable and disabling disease, bipolar disorder's (BD) genetic variants have been challenging to identify. We present new genotype data for 1,190 cases and 401 controls and perform a genome-wide association study including additional samples for a total of 2,191 cases and 1,434 controls. We do not detect genome-wide significant associations for individual loci; however, across all SNPs, we show an association between the power to detect effects calculated from a previous genome-wide association study and evidence for replication (P = 1.5x10(-7)). To demonstrate that this result is not likely to be a false positive, we analyze replication rates in a large meta-analysis of height and show that, in a large enough study, associations replicate as a function of power, approaching a linear relationship. Within BD, SNPs near exons exhibit a greater probability of replication, supporting an enrichment of reproducible associations near functional regions of genes. These results indicate that there is likely common genetic variation associated with BD near exons (+/-10 kb) that could be identified in larger studies and, further, provide a framework for assessing the potential for replication when combining results from multiple studies.

• Large-scale genome-wide association analysis of bipolar disorder identifies a new susceptibility locus near ODZ4

  P. Sklar, S. Ripke, L. J. Scott, O. A. Andreassen, S. Cichon, N. Craddock, H. J. Edenberg, J. I. Nurnberger, M. Rietschel, D. Blackwood, [......], G. W. Montgomery, M. Lathrop, H. Oskarsson, M. Bauer, A. Wright, P. B. Mitchell, M. Hautzinger, A. Reif, J. R. Kelsoe, S. M. Purcell

  Nature genetics. 43(10):977-83.

  We conducted a combined genome-wide association study (GWAS) of 7,481 individuals with bipolar disorder (cases) and 9,250 controls as part of the Psychiatric GWAS Consortium. Our replication study tested 34 SNPs in 4,496 independent cases with bipolar disorder and 42,422 independent controls and fou... [more] We conducted a combined genome-wide association study (GWAS) of 7,481 individuals with bipolar disorder (cases) and 9,250 controls as part of the Psychiatric GWAS Consortium. Our replication study tested 34 SNPs in 4,496 independent cases with bipolar disorder and 42,422 independent controls and found that 18 of 34 SNPs had P < 0.05, with 31 of 34 SNPs having signals with the same direction of effect (P = 3.8 x 10(-7)). An analysis of all 11,974 bipolar disorder cases and 51,792 controls confirmed genome-wide significant evidence of association for CACNA1C and identified a new intronic variant in ODZ4. We identified a pathway comprised of subunits of calcium channels enriched in bipolar disorder association intervals. Finally, a combined GWAS analysis of schizophrenia and bipolar disorder yielded strong association evidence for SNPs in CACNA1C and in the region of NEK4-ITIH1-ITIH3-ITIH4. Our replication results imply that increasing sample sizes in bipolar disorder will confirm many additional loci.

• Singleton deletions throughout the genome increase risk of bipolar disorder

  D. Zhang, L. Cheng, Y. Qian, N. Alliey-Rodriguez, J. R. Kelsoe, T. Greenwood, C. Nievergelt, T. B. Barrett, R. McKinney, N. Schork, [......], P. L. Belmonte, P. P. Zandi, M. G. McInnis, S. Zollner, D. Craig, S. Szelinger, D. Koller, S. L. Christian, C. Liu, E. S. Gershon

  Molecular psychiatry. 14(4):376-80.

  An overall burden of rare structural genomic variants has not been reported in bipolar disorder (BD), although there have been reports of cases with microduplication and microdeletion. Here, we present a genome-wide copy number variant (CNV) survey of 1001 cases and 1034 controls using the Affymetri... [more] An overall burden of rare structural genomic variants has not been reported in bipolar disorder (BD), although there have been reports of cases with microduplication and microdeletion. Here, we present a genome-wide copy number variant (CNV) survey of 1001 cases and 1034 controls using the Affymetrix single nucleotide polymorphism (SNP) 6.0 SNP and CNV platform. Singleton deletions (deletions that appear only once in the dataset) more than 100 kb in length are present in 16.2% of BD cases in contrast to 12.3% of controls (permutation P=0.007). This effect was more pronounced for age at onset of mania <or=18 years old. Our results strongly suggest that BD can result from the effects of multiple rare structural variants.

• Comparison of ecdysteroid concentration in different morphs of aphids

  L.A. Polgár, B. Darvas, W. Völkl, P. Porcheron, A. Székács, S. Szelinger

  Comparative Biochemistry and Physiology Part C: Pharmacology, Toxicology and Endocrinology.

  The amounts of ecdysteroids were determined in different morphs of holocyclic monoecious aphids (Acyrthosiphon pisum Harris, Dysaphis devecta Walk., Lachnus roboris L., Schizolachnus pineti F.) and holocyclic heteroecious aphids (Aphis sambuci L., Rhopalosiphum padi L.) by means enzyme immunoassay. ... [more] The amounts of ecdysteroids were determined in different morphs of holocyclic monoecious aphids (Acyrthosiphon pisum Harris, Dysaphis devecta Walk., Lachnus roboris L., Schizolachnus pineti F.) and holocyclic heteroecious aphids (Aphis sambuci L., Rhopalosiphum padi L.) by means enzyme immunoassay. Among the parthenogenetic morphs (fundatrices, virginoparae, and oviparae), the fundatrices have consistently higher amounts of ecdysteroids than those of other morphs of the same species. Alate and apterous virginoparae showed slight differences in their ecdysteroid titer both in heteroecious and monoecious aphids. The migrant morphs (i.e., alate fundatrices and gynoparae) have the lowest amounts of ecdysteroids within a species. With the exception of D. devecta, the oviparae of both heteroecious and monoecious aphids have the second greatest amounts of ecdysteroids among the morphs living on same host plant. Polyphenism dispersal behavior, and fecundity in connection with weight, ovariole number, and ecdysteroid concentration of different morphs of aphids are discussed.