The genome-wide landscape of copy number variations in the MUSGEN study provides evidence for a founder effect in the isolated Finnish population

European Journal of Human Genetics

Volumn 21, Issue 12, 2013, Pages 1411-1416

  Kanduri, Chakravarthi ^a   Ukkola Vuoti, Liisa ^a   Oikkonen, Jaana ^a   Buck, Gemma ^b   Blancher, Christine ^b   Raijas, Pirre ^c   Karma, Kai ^c   Lähdesmäki, Harri ^d   Järvelä, Irma ^a  

^a UNIVERSITY OF HELSINKI   (Finland)

^b UNIVERSITY OF OXFORD   (United Kingdom)

^c Sibelius Akatemia   (Finland)

^d AALTO UNIVERSITY   (Finland)

Author keywords

copy number variation; founder effect; Illumina HumanOmniExpress 12v.1.0 beadchip; isolated Finnish population; MUSGEN; PennCNV; QuantiSNP

Indexed keywords

ADULT; AGED; ARTICLE; CHROMOSOME 2P; CHROMOSOME 6Q; COPY NUMBER VARIATION; CYTOGENETICS; FEMALE; FINLAND; FOUNDER EFFECT; GENE DELETION; GENE FREQUENCY; GENE LOCUS; GENETIC TRAIT; GENETIC VARIABILITY; GENOME ANALYSIS; HOMOZYGOSITY; HUMAN; HUMAN EXPERIMENT; HUMAN GENOME; MALE; MUSIC; NORMAL HUMAN; PHENOTYPE; POPULATION GENETICS; PRIORITY JOURNAL;

ADOLESCENT; ADULT; AGED; AGED, 80 AND OVER; DNA COPY NUMBER VARIATIONS; FEMALE; FOUNDER EFFECT; GENETICS, POPULATION; GENOME, HUMAN; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HUMANS; MALE; MIDDLE AGED; YOUNG ADULT;

EID: 84887621488     PISSN: 10184813     EISSN: 14765438     Source Type: Journal    
DOI: 10.1038/ejhg.2013.60     Document Type: Article

References (52)

1. Iafrate AJ, Feuk L, Rivera MN et al: Detection of large-scale variation in the human genome. Nat Genet 2004; 36: 949-951.
2. Sebat J, Lakshmi B, Troge J et al: Large-scale copy number polymorphism in the human genome. Science 2004; 305: 525-528.
3. Feuk L, Carson AR, Scherer SW: Structural variation in the human genome. Nat Rev Genet 2006; 7: 85-97.
4. Redon R, Ishikawa S, Fitch KR et al: Global variation in copy number in the human genome. Nature 2006; 444: 444-454.
5. Lupski JR: Genomic rearrangements and sporadic disease. Nat Genet 2007; 39: S43-S47.
6. Henrichsen CN, Chaignat E, Reymond A: Copy number variants, diseases and gene expression. Hum Mol Genet 2009; 18: R1-R8.
7. Zhang F, Gu W, Hurles ME, Lupski JR: Copy number variation in human health, disease, and evolution. Annu Rev Genomics Hum Genet 2009; 10: 451-481.
8. Scherer SW, Lee C, Birney E et al: Challenges and standards in integrating surveys of structural variation. Nat Genet 2007; 39: S7-S15.
9. Eichler EE, Flint J, Gibson G et al: Missing heritability and strategies for finding the underlying causes of complex disease. Nat Rev Genet 2010; 11: 446-450.
10. White SJ, Vissers LE, Geurts van Kessel A et al: Variation of CNV distribution in five different ethnic populations. Cytogenet Genome Res 2007; 118: 19-30.
11. Zogopoulos G, Ha KC, Naqib F et al: Germ-line DNA copy number variation frequencies in a large North American population. Hum Genet 2007; 122: 345-353.
12. Itsara A, Cooper GM, Baker C et al: Population analysis of large copy number variants and hotspots of human genetic disease. Am J Hum Genet 2009; 84: 148-161.
13. Li J, Yang T, Wang L et al: Whole genome distribution and ethnic differentiation of copy number variation in Caucasian and Asian populations. PLoS ONE 2009; 4: e7958.
14. Shaikh TH, Gai X, Perin JC et al: High-resolution mapping and analysis of copy number variations in the human genome: a data resource for clinical and research applications. Genome Res 2009; 19: 1682-1690.
15. Park H, Kim JI, Ju YS et al: Discovery of common Asian copy number variants using integrated high-resolution array CGH and massively parallel DNA sequencing. Nat Genet 2010; 42: 400-405.
16. Vogler C, Gschwind L, Rothlisberger B et al: Microarray-based maps of copy-number variant regions in European and sub-Saharan populations. PLoS ONE 2010; 5: e15246.
17. Yim SH, Kim TM, Hu HJ et al: Copy number variations in East-Asian population and their evolutionary and functional implications. Hum Mol Genet 2010; 19: 1001-1008.
18. Teo SM, Ku CS, Naidoo N et al: A population-based study of copy number variants and regions of homozygosity in healthy Swedish individuals. J Hum Genet 2011; 56: 524-533.
19. Xu H, Poh WT, Sim X et al: SgD-CNV, a database for common and rare copy number variants in three Asian populations. Hum Mutat 2011; 32: 1341-1349.
20. Lou H, Li S, Yang Y et al: A map of copy number variations in Chinese populations. PLoS ONE 2011; 6: e27341.
21. Wineinger NE, Pajewski NM, Kennedy RE et al: Characterization of autosomal copynumber variation in African Americans: the HyperGEN Study. Eur J Hum Genet 2011; 19: 1271-1275.
22. Moon S, Kim YJ, Hong CB, Kim DJ, Lee JY, Kim BJ: Data-driven approach to detect common copy-number variations and frequency profiles in a population-based Korean cohort. Eur J Hum Genet 2011; 19: 1167-1172.
23. Yeo RA, Gangestad SW, Liu J, Calhoun VD, Hutchison KE: Rare copy number deletions predict individual variation in intelligence. PLoS ONE 2011; 6: e16339.
24. Dauber A, Yu Y, Turchin MC et al: Genome-wide association of copy-number variation reveals an association between short stature and the presence of low-frequency genomic deletions. Am J Hum Genet 2011; 89: 751-759.
25. Kim YK, Moon S, Hwang MY et al: Gene-based copy number variation study reveals a microdeletion at 12q24 that influences height in the Korean population. Genomics 2013; 101: 134-138.
26. Macleod AK, Davies G, Payton A et al: Genetic copy number variation and general cognitive ability. PLoS ONE 2012; 7: e37385.
27. Pulli K, Karma K, Norio R, Sistonen P, Goring HH, Jarvela I: Genome-wide linkage scan for loci of musical aptitude in Finnish families: evidence for a major locus at 4q22. J Med Genet 2008; 45: 451-456.
28. Peltonen L, Jalanko A, Varilo T: Molecular genetics of the Finnish disease heritage. Hum Mol Genet 1999; 8: 1913-1923.
29. Norio R: Finnish Disease Heritage II: population prehistory and genetic roots of Finns. Hum Genet 2003; 112: 457-469.
30. Wang K, Li M, Hadley D et al: PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Res 2007; 17: 1665-1674.
31. Colella S, Yau C, Taylor JM et al: QuantiSNP: an objective Bayes hidden-Markov model to detect and accurately map copy number variation using SNP genotyping data. Nucleic Acids Res 2007; 35: 2013-2025.
32. Forsberg LA, Rasi C, Razzaghian HR et al: Age-related somatic structural changes in the nuclear genome of human blood cells. Am J Hum Genet 2012; 90: 217-228.
33. Backes C, Keller A, Kuentzer J et al: GeneTrail-advanced gene set enrichment analysis. Nucleic Acids Res 2007; 35: W186-W192.
34. Kasowski M, Grubert F, Heffelfinger C et al: Variation in transcription factor binding among humans. Science 2010; 328: 232-235.
35. Schlattl A, Anders S, Waszak SM, Huber W, Korbel JO: Relating CNVs to transcriptome data at fine resolution: assessment of the effect of variant size, type, and overlap with functional regions. Genome Res 2011; 21: 2004-2013.
36. Katori S, Hamada S, Noguchi Y et al: Protocadherin-alpha family is required for serotonergic projections to appropriately innervate target brain areas. J Neurosci 2009; 29: 9137-9147.
37. Ukkola-Vuoti L, Kanduri C, Oikkonen J et al: Genome-wide copy number variation analysis in extended families and unrelated individuals characterized for musical aptitude and creativity in music. PLoS ONE 2013; 8: e56356. doi:10.1371/ journal.pone.0056356.
38. Liu X, Cannon DM, Akula N et al: A non-synonymous polymorphism in galactose mutarotase (GALM) is associated with serotonin transporter binding potential in the human thalamus: results of a genome-wide association study. Mol Psychiatry 2011; 16: 584-585.
39. Paul C, Schoberl F, Weinmeister P et al: Signaling through cGMP-dependent protein kinase I in the amygdala is critical for auditory-cued fear memory and long-term potentiation. J Neurosci 2008; 28: 14202-14212.
40. Stefansson H, Rujescu D, Cichon S et al: Large recurrent microdeletions associated with schizophrenia. Nature 2008; 455: 232-236.
41. Pinto D, Pagnamenta AT, Klei L et al: Functional impact of global rare copy number variation in autism spectrum disorders. Nature 2010; 466: 368-372.
42. Cooper GM, Coe BP, Girirajan S et al: A copy number variation morbidity map of developmental delay. Nat Genet 2011; 43: 838-846.
43. Conrad DF, Pinto D, Redon R et al: Origins and functional impact of copy number variation in the human genome. Nature 2010; 464: 704-712.
44. Wang J, Jiang J, Fu W et al: A genome-wide detection of copy number variations using SNP genotyping arrays in swine. BMC Genomics 2012; 13: 273.
45. Noonan JP, Grimwood J, Schmutz J, Dickson M, Myers RM: Gene conversion and the evolution of protocadherin gene cluster diversity. Genome Res 2004; 14: 354-366.
46. Perry GH, Dominy NJ, Claw KG et al: Diet and the evolution of human amylase gene copy number variation. Nat Genet 2007; 39: 1256-1260.
47. Young JM, Endicott RM, Parghi SS, Walker M, Kidd JM, Trask BJ: Extensive copynumber variation of the human olfactory receptor gene family. Am J Hum Genet 2008; 83: 228-242.
48. Winchester L, Yau C, Ragoussis J: Comparing CNV detection methods for SNP arrays. Brief Funct Genomic Proteomic 2009; 8: 353-366.
49. Dellinger AE, Saw SM, Goh LK, Seielstad M, Young TL, Li YJ: Comparative analyses of seven algorithms for copy number variant identification from single nucleotide polymorphism arrays. Nucleic Acids Res 2010; 38: e105.
50. Pinto D, Darvishi K, Shi X et al: Comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants. Nat Biotechnol 2011; 29: 512-520.
51. Haraksingh RR, Abyzov A, Gerstein M, Urban AE, Snyder M: Genome-wide mapping of copy number variation in humans: comparative analysis of high resolution array platforms. PLoS ONE 2011; 6: e27859.
52. Poptsova M, Banerjee S, Gokcumen O, Rubin MA, Demichelis F: Impact of constitutional copy number variants on biological pathway evolution. BMC Evol Biol 2013; 13: 19.