In search of rare variants: Preliminary results from whole genome sequencing of 1,325 individuals with psychophysiological endophenotypes
dc.contributor.author | Vrieze, Scott I. | en_US |
dc.contributor.author | Malone, Stephen M. | en_US |
dc.contributor.author | Vaidyanathan, Uma | en_US |
dc.contributor.author | Kwong, Alan | en_US |
dc.contributor.author | Kang, Hyun Min | en_US |
dc.contributor.author | Zhan, Xiaowei | en_US |
dc.contributor.author | Flickinger, Matthew | en_US |
dc.contributor.author | Irons, Daniel | en_US |
dc.contributor.author | Jun, Goo | en_US |
dc.contributor.author | Locke, Adam E. | en_US |
dc.contributor.author | Pistis, Giorgio | en_US |
dc.contributor.author | Porcu, Eleonora | en_US |
dc.contributor.author | Levy, Shawn | en_US |
dc.contributor.author | Myers, Richard M. | en_US |
dc.contributor.author | Oetting, William | en_US |
dc.contributor.author | McGue, Matt | en_US |
dc.contributor.author | Abecasis, Goncalo | en_US |
dc.contributor.author | Iacono, William G. | en_US |
dc.date.accessioned | 2014-12-09T16:53:57Z | |
dc.date.available | WITHHELD_13_MONTHS | en_US |
dc.date.available | 2014-12-09T16:53:57Z | |
dc.date.issued | 2014-12 | en_US |
dc.identifier.citation | Vrieze, Scott I.; Malone, Stephen M.; Vaidyanathan, Uma; Kwong, Alan; Kang, Hyun Min; Zhan, Xiaowei; Flickinger, Matthew; Irons, Daniel; Jun, Goo; Locke, Adam E.; Pistis, Giorgio; Porcu, Eleonora; Levy, Shawn; Myers, Richard M.; Oetting, William; McGue, Matt; Abecasis, Goncalo; Iacono, William G. (2014). "In search of rare variants: Preliminary results from whole genome sequencing of 1,325 individuals with psychophysiological endophenotypes." Psychophysiology (12): 1309-1320. | en_US |
dc.identifier.issn | 0048-5772 | en_US |
dc.identifier.issn | 1469-8986 | en_US |
dc.identifier.uri | https://hdl.handle.net/2027.42/109628 | |
dc.description.abstract | Whole genome sequencing was completed on 1,325 individuals from 602 families, identifying 27 million autosomal variants. Genetic association tests were conducted for those individuals who had been assessed for one or more of 17 endophenotypes ( N range = 802–1,185). No significant associations were found. These 27 million variants were then imputed into the full sample of individuals with psychophysiological data ( N range = 3,088–4,469) and again tested for associations with the 17 endophenotypes. No association was significant. Using a gene‐based variable threshold burden test of nonsynonymous variants, we obtained five significant associations. These findings are preliminary and call for additional analysis of this rich sample. We argue that larger samples, alternative study designs, and additional bioinformatics approaches will be necessary to discover associations between these endophenotypes and genomic variation. | en_US |
dc.publisher | Wiley Periodicals, Inc. | en_US |
dc.subject.other | Whole Genome Sequencing | en_US |
dc.subject.other | Psychophysiology | en_US |
dc.subject.other | Endophenotype | en_US |
dc.subject.other | EEG | en_US |
dc.subject.other | Antisaccade | en_US |
dc.subject.other | Startle | en_US |
dc.subject.other | P300 | en_US |
dc.subject.other | Rare Variant | en_US |
dc.title | In search of rare variants: Preliminary results from whole genome sequencing of 1,325 individuals with psychophysiological endophenotypes | en_US |
dc.type | Article | en_US |
dc.rights.robots | IndexNoFollow | en_US |
dc.subject.hlbsecondlevel | Physiology | en_US |
dc.subject.hlbsecondlevel | Psychology | en_US |
dc.subject.hlbtoplevel | Health Sciences | en_US |
dc.description.peerreviewed | Peer Reviewed | en_US |
dc.description.bitstreamurl | http://deepblue.lib.umich.edu/bitstream/2027.42/109628/1/psyp12350.pdf | |
dc.identifier.doi | 10.1111/psyp.12350 | en_US |
dc.identifier.source | Psychophysiology | en_US |
dc.identifier.citedreference | Miller, M. B., Basu, S., Cunningham, J., Eskin, E., Malone, S. M., Oetting, W. S., … McGue, M. ( 2012 ). The Minnesota Center for Twin and Family Research genome‐wide association study. Twin Research and Human Genetics, 15, 767 – 774. | en_US |
dc.identifier.citedreference | Bevilacqua, L., Doly, S., Kaprio, J., Yuan, Q., Tikkanen, R., Paunio, T., … Goldman, D. ( 2010 ). A population‐specific HTR2B stop codon predisposes to severe impulsivity. Nature, 468, 1061 – 1066. doi: 10.1038/nature09629 | en_US |
dc.identifier.citedreference | Browning, B. L., & Browning, S. R. ( 2009 ). A unified approach to genotype imputation and haplotype‐phase inference for large data sets of trios and unrelated individuals. American Journal of Human Genetics, 84, 210 – 223. | en_US |
dc.identifier.citedreference | Cock, P. J., Fields, C. J., Goto, N., Heuer, M. L., & Rice, P. M. ( 2010 ). The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Research, 38, 1767 – 1771. | en_US |
dc.identifier.citedreference | Delaneau, O., Zagury, J. F., & Marchini, J. ( 2013 ). Improved whole‐chromosome phasing for disease and population genetic studies. Nature Methods, 10, 5 – 6. doi: 10.1038/nmeth.2307 | en_US |
dc.identifier.citedreference | ENCODE Project Consortium. ( 2012 ). An integrated encyclopedia of DNA elements in the human genome. Nature, 489, 57 – 74. doi: 10.1038/nature11247 | en_US |
dc.identifier.citedreference | Fromer, M., Pocklington, A. J., Kavanagh, D. H., Williams, H. J., Dwyer, S., Gormley, P., … O'Donovan, M. C. ( 2014 ). De novo mutations in schizophrenia implicate synaptic networks. Nature, 506, 179 – 184. doi: 10.1038/nature12929 | en_US |
dc.identifier.citedreference | Fu, W. Q., O'Connor, T. D., Jun, G., Kang, H. M., Abecasis, G., Leal, S. M., … NHLBI Exome Sequencing Project ( 2013 ). Analysis of 6,515 exomes reveals the recent origin of most human protein‐coding variants. Nature, 493, 216 – 220. doi: 10.1038/Nature11690 | en_US |
dc.identifier.citedreference | Glessner, J. T., Wang, K., Cai, G., Korvatska, O., Kim, C. E., Wood, S., Hakonarson, H. ( 2009 ). Autism genome‐wide copy number variation reveals ubiquitin and neuronal genes. Nature, 459, 569 – 573. doi: 10.1038/nature07953 | en_US |
dc.identifier.citedreference | Hirschhorn, J. N., Lohmueller, K., Byrne, E., & Hirschhorn, K. ( 2002 ). A comprehensive review of genetic association studies. Genetics in Medicine, 4, 45 – 61. | en_US |
dc.identifier.citedreference | Howie, B., Fuchsberger, C., Stephens, M., Marchini, J., & Abecasis, G. R. ( 2012 ). Fast and accurate genotype imputation in genome‐wide association studies through pre‐phasing. Nature Genetics, 44, 955 – 959. doi: 10.1038/ng.2354 | en_US |
dc.identifier.citedreference | Iacono, W. G., Malone, S. M., Vaidyanathan, U., & Vrieze, S. I. ( 2014 ). Genome‐wide scans of genetic variants for psychophysiological endophenotypes: A methodological overview. Psychophysiology, 51, 1207 – 1224. | en_US |
dc.identifier.citedreference | Insel, T. R., Cuthbert, B. N., Garvey, M., Heinssen, R., Pine, D. S., Quinn, K., … Wang, P. ( 2010 ). Research Domain Criteria (RDoC): Toward a new classification framework for research on mental disorders. American Journal of Psychiatry, 167, 748 – 751. doi: 10.1176/appi.ajp.2010.09091379 | en_US |
dc.identifier.citedreference | Visscher, P. M., Brown, M. A., McCarthy, M. I., & Yang, J. ( 2012 ). Five years of GWAS discovery. American Journal of Human Genetics, 90, 7 – 24. doi: 10.1016/j.ajhg.2011.11.029 | en_US |
dc.identifier.citedreference | Jun, G., Flickinger, M., Hetrick, K. N., Romm, J. M., Doheny, K. F., Abecasis, G. R., … Kang, H. M. ( 2012 ). Detecting and estimating contamination of human DNA samples in sequencing and array‐based genotype data. American Journal of Human Genetics, 91, 839 – 848. | en_US |
dc.identifier.citedreference | Jun, G., Wing, M. K., Abecasis, G. R., & Kang, H. M. ( 2014 ). An efficient and scalable analysis framework for variant extraction and refinement from population scale DNA sequence data. Manuscript in preparation. | en_US |
dc.identifier.citedreference | Kang, H. M. ( 2014 ). Efficient and parallelizable association container toolbox (EPACTS). Retrieved from http://genome.sph.umich.edu/wiki/EPACTS | en_US |
dc.identifier.citedreference | Kang, H. M., Sul, J. H., Service, S. K., Zaitlen, N. A., Kong, S. Y., Freimer, N. B., … Eskin, E. ( 2010 ). Variance component model to account for sample structure in genome‐wide association studies. Nature Genetics, 42, 348 – 354. doi: 10.1038/Ng.548 | en_US |
dc.identifier.citedreference | Lander, E. S. ( 2011 ). Initial impact of the sequencing of the human genome. Nature, 470, 187 – 197. doi: 10.1038/nature09792 | en_US |
dc.identifier.citedreference | Li, H., & Durbin, R. ( 2010 ). Fast and accurate long‐read alignment with Burrows–Wheeler transform. Bioinformatics, 26, 589 – 595. | en_US |
dc.identifier.citedreference | Li, Y., Willer, C. J., Ding, J., Scheet, P., & Abecasis, G. R. ( 2010 ). MaCH: Using sequence and genotype data to estimate haplotypes and unobserved genotypes. Genetic Epidemiology, 34, 816 – 834. doi: 10.1002/Gepi.20533 | en_US |
dc.identifier.citedreference | Malone, S. M., Burwell, S. J., Vaidyanathan, U., Miller, M. B., McGue, M., & Iacono, W. G. ( 2014 ). Heritability and molecular genetic basis of resting EEG activity: A genome‐wide association study. Psychophysiology, 51, 1225 – 1245. | en_US |
dc.identifier.citedreference | Malone, S. M., Vaidyanathan, U., Basu, S., Miller, M. B., McGue, M., & Iacono, W. G. ( 2014 ). Heritability and molecular genetic basis of P3 event‐related brain potential amplitude: A genome‐wide association study. Psychophysiology, 51, 1246 – 1258. | en_US |
dc.identifier.citedreference | Maurano, M. T., Humbert, R., Rynes, E., Thurman, R. E., Haugen, E., Wang, H., … Stamatoyannopoulos, J. A. ( 2012 ). Systematic localization of common disease‐associated variation in regulatory DNA. Science, 337, 1190 – 1195. doi: 10.1126/science.1222794 | en_US |
dc.identifier.citedreference | McGue, M., Zhang, Y., Miller, M. B., Basu, S., Vrieze, S., Hicks, B., … Iacono, W. G. ( 2013 ). A genome‐wide association study of behavioral disinhibition. Behavior Genetics, 43, 363 – 373. | en_US |
dc.identifier.citedreference | Neale, B. M., Kou, Y., Liu, L., Ma'ayan, A., Samocha, K. E., Sabo, A., … Daly, M. J. ( 2012 ). Patterns and rates of exonic de novo mutations inautism spectrum disorders. Nature, 485, 242 – 245. doi: 10.1038/nature11011 | en_US |
dc.identifier.citedreference | Nelson, M. R., Wegmann, D., Ehm, M. G., Kessner, D., St Jean, P., Verzilli, C., … Mooser, V. ( 2012 ). An abundance of rare functional variants in 202 drug target genes sequenced in 14,002 people. Science, 337, 100 – 104. doi: 10.1126/science.1217876 | en_US |
dc.identifier.citedreference | O'Roak, B. J., Deriziotis, P., Lee, C., Vives, L., Schwartz, J. J., Girirajan, S., … Eichler, E. E. ( 2011 ). Exome sequencing in sporadic autism spectrum disorders identifies severe de novo mutations. Nature Genetics, 43, 585 – 589. doi: 10.1038/Ng.835 | en_US |
dc.identifier.citedreference | Pickrell, J. K. ( 2014 ). Joint analysis of functional genomic data and genome‐wide association studies of 18 human traits. American Journal of Human Genetics, 94, 559 – 573. doi: 10.1016/j.ajhg.2014.03.004 | en_US |
dc.identifier.citedreference | Poduri, A., Evrony, G. D., Cai, X., & Walsh, C. A. ( 2013 ). Somatic mutation, genomic variation, and neurological disease. Science, 341, 1237758. doi: 10.1126/science.1237758 | en_US |
dc.identifier.citedreference | Price, A. L., Kryukov, G. V., de Bakker, P. I., Purcell, S. M., Staples, J., Wei, L. J., & Sunyaev, S. R. ( 2010 ). Pooled association tests for rare variants in exon‐resequencing studies. American Journal of Human Genetics, 86, 832 – 838. doi: 10.1016/j.ajhg.2010.04.005 | en_US |
dc.identifier.citedreference | Purcell, S. M., Moran, J. L., Fromer, M., Ruderfer, D., Solovieff, N., Roussos, P., … Sklar, P. ( 2014 ). A polygenic burden of rare disruptive mutations in schizophrenia. Nature, 506, 185 – 190. doi: 10.1038/nature12975 | en_US |
dc.identifier.citedreference | Rees, E., Walters, J. T., Chambert, K. D., O'Dushlaine, C., Szatkiewicz, J., Richards, A. L., … Kirov, G. ( 2014 ). CNV analysis in a large schizophrenia sample implicates deletions at 16p12.1 and SLC1A1 and duplications at 1p36.33 and CGNL1. Human Molecular Genetics, 23, 1669 – 1676. doi: 10.1093/hmg/ddt540 | en_US |
dc.identifier.citedreference | Sullivan, P. F. ( 2007 ). Spurious genetic associations. Biological Psychiatry, 61, 1121 – 1126. doi: 10.1016/j.biopsych.2006.11.010 | en_US |
dc.identifier.citedreference | Vaidyanathan, U., Isen, J. D., Malone, S. M., Miller, M. B., McGue, M., & Iacono, W. G. ( 2014 ). Heritability and molecular genetic basis of electrodermal activity: A genome‐wide association study. Psychophysiology, 51, 1259 – 1271. | en_US |
dc.identifier.citedreference | Vaidyanathan, U., Malone, S. M., Donnelly, J. M., Hammer, M. A., Miller, M. B., McGue, M., & Iacono, W. G. ( 2014 ). Heritability and molecular genetic basis of antisaccade eye tracking error rate: A genome‐wide association study. Psychophysiology, 51, 1272 – 1284. | en_US |
dc.identifier.citedreference | Vaidyanathan, U., Malone, S. M., Miller, M. B., McGue, M., & Iacono, W. G. ( 2014 ). Heritability and molecular genetic basis of acoustic startle eye blink and affectively modulated startle response: A genome‐wide association study. Psychophysiology, 51, 1285 – 1299. | en_US |
dc.identifier.citedreference | Vrieze, S. I., Iacono, W. G., & McGue, M. ( 2012 ). Confluence of genes, environment, development, and behavior in a post genome‐wide association study world. Development and Psychopathology, 24, 1195 – 1214. doi: 10.1017/S0954579412000648 | en_US |
dc.identifier.citedreference | Vrieze, S. I., Malone, S. M., Pankratz, N., Vaidyanathan, U., Miller, M. B., Kang, H. M., … Iacono, W. G. ( 2014 ). Genetic associations of nonsynonymous exonic variants with psychophysiological endophenotypes. Psychophysiology, 51, 1300 – 1308. | en_US |
dc.identifier.citedreference | Wu, M. C., Lee, S., Cai, T., Li, Y., Boehnke, M., & Lin, X. ( 2011 ). Rare‐variant association testing for sequencing data with the sequence kernel association test. American Journal of Human Genetics, 89, 82 – 93. | en_US |
dc.identifier.citedreference | 1000 Genomes Project Consortium. ( 2012 ). An integrated map of genetic variation from 1,092 human genomes. Nature, 491, 56 – 65. doi: 10.1038/nature11632 | en_US |
dc.owningcollname | Interdisciplinary and Peer-Reviewed |
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