Uniparental disomy analysis in trios using genome-wide SNP array and whole-genome sequencing data imply segmental uniparental isodisomy in general populations

Gene

Volumn 512, Issue 2, 2013, Pages 267-274

  Sasaki, Kensaku ^a   Mishima, Hiroyuki ^a   Miura, Kiyonori ^a   Yoshiura, Koh ichiro ^a  

^a NAGASAKI UNIVERSITY   (Japan)

Author keywords

1000 Genomes Project; DNA repair; Gene conversion; Genomic integrity; Human genome; International HapMap Project

Indexed keywords

DOUBLE STRANDED DNA;

ADULT; ARTICLE; AUTOSOME; BIOINFORMATICS; BIRTH; CHROMOSOME; CHROMOSOME PAIRING; CLINICAL ARTICLE; DNA STRAND BREAKAGE; FEMALE; GENE SEQUENCE; GENETIC ANALYSIS; GENOTYPE; HOMOLOGOUS RECOMBINATION; HUMAN; MALE; MICROARRAY ANALYSIS; PHENOTYPE; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; UNIPARENTAL DISOMY;

CHROMOSOME MAPPING; FEMALE; GENOME, HUMAN; GENOME-WIDE ASSOCIATION STUDY; HUMANS; MALE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA;

EID: 84870355345     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2012.10.035     Document Type: Article

References (53)

1. Altshuler D., et al. A map of human genome variation from population-scale sequencing. Nature 2010, 467:1061-1073.
2. Altug-Teber O., et al. A rapid microarray based whole genome analysis for detection of uniparental disomy. Hum. Mutat. 2005, 26:153-159.
3. Amor D.J., Halliday J. A review of known imprinting syndromes and their association with assisted reproduction technologies. Hum. Reprod. 2008, 23:2826-2834.
4. Baumer A., et al. A novel MSP/DHPLC method for the investigation of the methylation status of imprinted genes enables the molecular detection of low cell mosaicisms. Hum. Mutat. 2001, 17:423-430.
5. Chen J.M., et al. Gene conversion: mechanisms, evolution and human disease. Nat. Rev. Genet. 2007, 8:762-775.
6. Conrad D.F., et al. Origins and functional impact of copy number variation in the human genome. Nature 2010, 464:704-712.
7. Conrad D.F., et al. Variation in genome-wide mutation rates within and between human families. Nat. Genet. 2011, 43:712-714.
8. D'haene B., et al. Accurate and objective copy number profiling using real-time quantitative PCR. Methods 2010, 50:262-270.
9. DePristo M.A., et al. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat. Genet. 2011, 43:491-498.
10. Engel E. A new genetic concept: uniparental disomy and its potential effect, isodisomy. Am. J. Med. Genet. 1980, 6:137-143.
11. Hannula K., et al. A narrow segment of maternal uniparental disomy of chromosome 7q31-qter in Silver-Russell syndrome delimits a candidate gene region. Am. J. Hum. Genet. 2000, 68:247-253.
12. Hartlerode A.J., Scully R. Mechanisms of double-strand break repair in somatic mammalian cells. Biochem. J. 2009, 423:157-168.
13. Jacobs K.B., et al. Detectable clonal mosaicism and its relationship to aging and cancer. Nat. Genet. 2012, 44:651-658.
14. Jaroudi S., SenGupta S. DNA repair in mammalian embryos. Mutat. Res. 2006, 635:53-77.
15. Kidd J.M., et al. Mapping and sequencing of structural variation from eight human genomes. Nature 2008, 453:56-64.
16. Kotzot D. Complex and segmental uniparental disomy (UPD): review and lessons from rare chromosomal complements. J. Med. Genet. 2001, 38:497-507.
17. Kotzot D. Complex and segmental uniparental disomy updated. J. Med. Genet. 2008, 45:545-556.
18. Kotzot D., Utermann G. Uniparental disomy (UPD) other than 15: phenotypes and bibliography updated. Am. J. Med. Genet. A 2005, 136:287-305.
19. Laurie C.C., et al. Detectable clonal mosaicism from birth to old age and its relationship to cancer. Nat. Genet. 2012, 44:642-650.
20. Liehr T. Cytogenetic contribution to uniparental disomy (UPD). Mol. Cytogenet. 2010, 3:8.
21. McCarroll S.A., et al. Integrated detection and population-genetic analysis of SNPs and copy number variation. Nat. Genet. 2008, 40:1166-1174.
22. McKenna A., et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010, 20:1297-1303.
23. Mills R.E., et al. Mapping copy number variation by population-scale genome sequencing. Nature 2011, 470:59-65.
24. Moynahan M.E., Jasin M. Loss of heterozygosity induced by a chromosomal double-strand break. Proc. Natl. Acad. Sci. U. S. A. 1997, 94:8988-8993.
25. Moynahan M.E., Jasin M. Mitotic homologous recombination maintains genomic stability and suppresses tumorigenesis. Nat. Rev. Mol. Cell Biol. 2010, 11:196-207.
26. Pérez B., et al. Segmental uniparental disomy leading to homozygosity for a pathogenic mutation in three recessive metabolic diseases. Mol. Genet. Metab. 2011, 105:270-271.
27. Pop R., et al. A homozygous nonsense mutation in SOX9 in the dominant disorder campomelic dysplasia: a case of mitotic gene conversion. Hum. Genet. 2005, 117:43-53.
28. Quinlan A.R., Hall I.M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 2010, 26:841-842.
29. Redon R., et al. Global variation in copy number in the human genome. Nature 2006, 444:444-454.
30. Robinson W.P. Mechanisms leading to uniparental disomy and their clinical consequences. Bioessays 2000, 22:452-459.
31. Rodríguez-Santiago B., et al. Mosaic uniparental disomies and aneuploidies as large structural variants of the human genome. Am. J. Hum. Genet. 2010, 87:129-138.
32. Sonoda E., et al. Differential usage of non-homologous end-joining and homologous recombination in double strand break repair. DNA Repair (Amst) 2006, 5:1021-1029.
33. Stark J.M., Jasin M. Extensive loss of heterozygosity is suppressed during homologous repair of chromosomal breaks. Mol. Cell. Biol. 2003, 23:733-743.
34. Tichy E.D. Mechanisms maintaining genomic integrity in embryonic stem cells and induced pluripotent stem cells. Exp. Biol. Med. (Maywood) 2011, 236:987-996.
35. Tichy E.D., Stambrook P.J. DNA repair in murine embryonic stem cells and differentiated cells. Exp. Cell Res. 2008, 314:1929-1936.
36. Ting J.C., et al. Visualization of uniparental inheritance, Mendelian inconsistencies, deletions, and parent of origin effects in single nucleotide polymorphism trio data with SNPtrio. Hum. Mutat. 2007, 28:1225-1235.
37. Tsai M.F., et al. PrimerZ: streamlined primer design for promoters, exons and human SNPs. Nucleic Acids Res. 2007, 35(Web Server issue):W63-5.
38. Untergasser A., et al. Primer3Plus, an enhanced web interface to Primer3. Nucleic Acids Res. 2007, 35(Web Server issue):W71-4.
39. Vinson R.K., Hales B.F. DNA repair during organogenesis. Mutat. Res. 2002, 509:79-91.
40. Wang K., et al. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 2010, 38:e164.
41. Wyman C., Kanaar R. DNA double-strand break repair: all's well that ends well. Annu. Rev. Genet. 2006, 40:363-383.
42. 1000 Genomes Project pilot 2 data ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/pilot_data/data/.
43. 1000 Genomes Project http://www.1000genomes.org/.
44. Best Practice Variant Detection with the GATK v2 http://www.broadinstitute.org/gsa/wiki/index.php/Best_Practice_Variant_Detection_with_the_GATK_v2.
45. Coriell Institute http://ccr.coriell.org/sections/collections/NHGRI/?SsId=11.
46. Geneimprint http://www.geneimprint.com/site/genes-by-species.Homo+sapiens.imprinted-All.
47. HapMap 3 raw data ftp://ftp.ncbi.nlm.nih.gov/hapmap/raw_data/hapmap3_affy6.0/.
48. Liehr T. Cases with uniparental disomy http://www.fish.uniklinikum-jena.de/UPD.html.
49. Picard (version 1.38) http://picard.sourceforge.net/.
50. Primer3Plus http://www.bioinformatics.nl/cgi-bin/primer3plus/primer3plus.cgi.
51. PrimerZ http://genepipe.ngc.sinica.edu.tw/primerz/beginDesign.do.
52. The National Center for Biotechnology Information (NCBI) http://www.ncbi.nlm.nih.gov/.
53. The University of California Santa Cruz (UCSC) http://genome.ucsc.edu/.