In search of rare variants: Preliminary results from whole genome sequencing of 1,325 individuals with psychophysiological endophenotypes

Psychophysiology

Volumn 51, Issue 12, 2014, Pages 1309-1320

  Vrieze, Scott I ^a   Malone, Stephen M ^b   Vaidyanathan, Uma ^b   Kwong, Alan ^a   Kang, Hyun Min ^a   Zhan, Xiaowei ^a   Flickinger, Matthew ^a   Irons, Daniel ^b   Jun, Goo ^a   Locke, Adam E ^a   Pistis, Giorgio ^a   Porcu, Eleonora ^a   Levy, Shawn ^c   Myers, Richard M ^c   Oetting, William ^b   Mcgue, Matt ^b   Abecasis, Goncalo ^a   Iacono, William G ^b  

^a UNIVERSITY OF MICHIGAN   (United States)

^b UNIVERSITY OF MINNESOTA   (United States)

^c HUDSONALPHA INSTITUTE FOR BIOTECHNOLOGY   (United States)

Author keywords

Antisaccade; EEG; Endophenotype; P300; Psychophysiology; Rare variant; Startle; Whole genome sequencing

Indexed keywords

BRAIN; ELECTRODERMAL RESPONSE; ELECTROENCEPHALOGRAPHY; ENDOPHENOTYPE; EVENT RELATED POTENTIAL; GENETIC ASSOCIATION; GENETICS; GENOTYPE; HUMAN; PHYSIOLOGY; SACCADIC EYE MOVEMENT; SENSORY GATING; SINGLE NUCLEOTIDE POLYMORPHISM; STARTLE REFLEX; TWINS;

BRAIN; ELECTROENCEPHALOGRAPHY; ENDOPHENOTYPES; EVENT-RELATED POTENTIALS, P300; GALVANIC SKIN RESPONSE; GENETIC ASSOCIATION STUDIES; GENOTYPE; HUMANS; POLYMORPHISM, SINGLE NUCLEOTIDE; REFLEX, STARTLE; SACCADES; SENSORY GATING; TWINS;

EID: 84924888531     PISSN: 00485772     EISSN: 14698986     Source Type: Journal    
DOI: 10.1111/psyp.12350     Document Type: Article

References (41)

1. 1000 Genomes Project Consortium. (2012). An integrated map of genetic variation from 1, 092 human genomes. Nature, 491, 56-65. doi: 10.1038/nature11632
2. 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
3. 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.
4. 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.
5. 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
6. ENCODE Project Consortium. (2012). An integrated encyclopedia of DNA elements in the human genome. Nature, 489, 57-74. doi: 10.1038/nature11247
7. 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
8. 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
9. 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
10. Hirschhorn, J. N., Lohmueller, K., Byrne, E., & Hirschhorn, K. (2002). A comprehensive review of genetic association studies. Genetics in Medicine, 4, 45-61.
11. 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
12. 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.
13. 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
14. 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.
15. 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.
16. Kang, H. M. (2014). Efficient and parallelizable association container toolbox (EPACTS). Retrieved from http://genome.sph.umich.edu/wiki/EPACTS
17. 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
18. Lander, E. S. (2011). Initial impact of the sequencing of the human genome. Nature, 470, 187-197. doi: 10.1038/nature09792
19. Li, H., & Durbin, R. (2010). Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics, 26, 589-595.
20. 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
21. 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.
22. 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.
23. 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
24. 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.
25. 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.
26. 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
27. 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
28. 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
29. 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
30. 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
31. 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
32. 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
33. 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
34. Sullivan, P. F. (2007). Spurious genetic associations. Biological Psychiatry, 61, 1121-1126. doi: 10.1016/j.biopsych.2006.11.010
35. 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.
36. 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.
37. 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.
38. 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
39. 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
40. 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.
41. 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.