Comprehensive DNA copy number profile and BAC library construction of an Indian individual

Gene

Volumn 500, Issue 2, 2012, Pages 186-193

  Chakrabarty, Sanjiban ^a   D'Souza, Reena R ^a   Bellampalli, Ravishankara ^a   Rotti, Harish ^a   Saadi, Abdul V ^a   Gopinath, Puthiya M ^a   Acharya, Raviraja V ^b   Govindaraj, Periyasamy ^c   Thangaraj, Kumarasamy ^c   Satyamoorthy, Kapaettu ^a  

^a MANIPAL UNIVERSITY   (India)

^b KASTURBA MEDICAL COLLEGE   (India)

^c CENTRE FOR CELLULAR AND MOLECULAR BIOLOGY   (India)

Author keywords

Array based CGH; BAC; Bacterial artificial chromosome; Copy number variation; Fluorescent in situ hybridization; Taqman assay

Indexed keywords

OLFACTOMEDIN 3 PROTEIN; PEPTIDES AND PROTEINS; SH3 AND MULTIPLE ANKYRIN REPEAT DOMAINS 3; UNCLASSIFIED DRUG;

ARTICLE; BAC LIBRARY OF AN ANONYMOUS INDIAN MALE; BACTERIAL ARTIFICIAL CHROMOSOME; COMPARATIVE GENOMIC HYBRIDIZATION; COPY NUMBER VARIATION; DNA LIBRARY; FLUORESCENCE IN SITU HYBRIDIZATION; GENE INSERTION; GENETIC SCREENING; HUMAN; HUMAN GENOME; IMBL4 GENOME; MOLECULAR CLONING; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PULSED FIELD GEL ELECTROPHORESIS; RESTRICTION MAPPING; SINGLE NUCLEOTIDE POLYMORPHISM;

CELL LINE, TRANSFORMED; CHROMOSOME MAPPING; CHROMOSOMES, ARTIFICIAL, BACTERIAL; COMPARATIVE GENOMIC HYBRIDIZATION; DNA COPY NUMBER VARIATIONS; DNA PRIMERS; ELECTROPHORESIS, GEL, PULSED-FIELD; GENOME, HUMAN; GENOMIC LIBRARY; GENOMICS; HUMANS; IN SITU HYBRIDIZATION, FLUORESCENCE; INDIA; MALE; POLYMORPHISM, SINGLE NUCLEOTIDE; REAL-TIME POLYMERASE CHAIN REACTION; REPRODUCIBILITY OF RESULTS; RESTRICTION MAPPING; SEQUENCE ANALYSIS, DNA;

BACTERIA (MICROORGANISMS);

EID: 84860439631     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2012.03.054     Document Type: Article

References (46)

1. Ahn S.M., et al. The first Korean genome sequence and analysis: full genome sequencing for a socio-ethnic group. Genome Res. 2009, 19:1622-1629.
2. Asakawa S., et al. Human BAC library: construction and rapid screening. Gene 1997, 191:69-79.
3. Bastian B.C., et al. Chromosomal gains and losses in primary cutaneous melanomas detected by comparative genomic hybridization. Cancer Res. 1998, 58:2170-2175.
4. Beatty B., et al. FISH: A Practical Approach 2002, Oxford University Press, New York.
5. Becker K.G., et al. The genetic association database. Nat. Genet. 2004, 36:431-432.
6. Bonaglia M.C., et al. Molecular mechanisms generating and stabilizing terminal 22q13 deletions in 44 subjects with Phelan/McDermid syndrome. PLoS Genet. 2011, 7:e1002173.
7. Boone P.M., et al. Detection of clinically relevant exonic copy-number changes by array CGH. Hum. Mutat. 2010, 31:1326-1342.
8. Brunet A., et al. BAC array CGH in patients with velocardiofacial syndrome-like features reveals genomic aberrations on chromosome region 1q21.1. BMC Med. Genet. 2009, 10:144.
9. Collins F.S. Reengineering translational science: the time is right. Sci. Transl. Med. 2011, 3. 90cm17.
10. Conrad D.F., et al. Origins and functional impact of copy number variation in the human genome. Nature 2010, 464:704-712.
11. De Preter K., et al. Low-cost dedicated mini-arrays for high-throughput analysis of DNA copy-number alterations in neuroblastoma. Cancer Lett. 2008, 269:111-116.
12. Dhar S.U., et al. 22q13.3 deletion syndrome: clinical and molecular analysis using array CGH. Am. J. Med. Genet. A 2010, 152A:573-581.
13. Ferreira I.D., et al. Real-time quantitative PCR with SYBR Green I detection for estimating copy numbers of nine drug resistance candidate genes in Plasmodium falciparum. Malar. J. 2006, 5:1.
14. Gautam P., et al. Spectrum of large copy number variations in 26 diverse Indian populations: potential involvement in phenotypic diversity. Hum. Genet. 2011, 131:1-13.
15. Herschleb J., et al. Pulsed-field gel electrophoresis. Nat. Protoc. 2007, 2:677-684.
16. Hester S.D., et al. Comparison of comparative genomic hybridization technologies across microarray platforms. J. Biomol. Tech. 2009, 20:135-151.
17. Hoebeeck J., et al. Real-time quantitative PCR as an alternative to Southern blot or fluorescence in situ hybridization for detection of gene copy number changes. Methods Mol. Biol. 2007, 353:205-226.
18. Huang da W., et al. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 2009, 4:44-57.
19. Kim U.J., et al. Characterization of a human chromosome 22 enriched bacterial artificial chromosome sublibrary. Genet. Anal. 1995, 12:73-79.
20. Kim U.J., et al. Construction and characterization of a human bacterial artificial chromosome library. Genomics 1996, 34:213-218.
21. Kim J.I., et al. A highly annotated whole-genome sequence of a Korean individual. Nature 2009, 460:1011-1015.
22. Kumar D. The personalised medicine. A paradigm of evidence-based medicine. Ann. Ist. Super. Sanita 2011, 47:31-40.
23. Lee H.S., Tomarev S.I. Optimedin induces expression of N-cadherin and stimulates aggregation of NGF-stimulated PC12 cells. Exp. Cell Res. 2007, 313:98-108.
24. Ligon A.H., et al. Simultaneous, multilocus FISH analysis for detection of microdeletions in the diagnostic evaluation of developmental delay and mental retardation. Am. J. Hum. Genet. 1997, 61:51-59.
25. McKernan K.J., et al. Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding. Genome Res. 2009, 19:1527-1541.
26. Miller G. Immortalization of human lymphocytes by Epstein-Barr virus. Yale J. Biol. Med. 1982, 55:305-310.
27. Neill N.J., et al. Comparative analysis of copy number detection by whole-genome BAC and oligonucleotide array CGH. Mol. Cytogenet. 2010, 3:11.
28. Osoegawa K., et al. A bacterial artificial chromosome library for sequencing the complete human genome. Genome Res. 2001, 11:483-496.
29. Pang A.W., et al. Towards a comprehensive structural variation map of an individual human genome. Genome Biol. 2010, 11:R52.
30. Park M.H., et al. Korean BAC library construction and characterization of HLA-DRA, HLA-DRB3. J. Biochem. Mol. Biol. 2006, 39:418-425.
31. Park J.H., et al. Application of a target array comparative genomic hybridization to prenatal diagnosis. BMC Med. Genet. 2010, 11:102.
32. Pinkel D., et al. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat. Genet. 1998, 20:207-211.
33. Sambrook J., Russell D.W. Molecular Cloning: A Laboratory Manual 2001, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
34. Sarasua S.M., et al. Association between deletion size and important phenotypes expands the genomic region of interest in Phelan-McDermid syndrome (22q13 deletion syndrome). J. Med. Genet. 2011, 48:761-766.
35. Shizuya H., Kouros-Mehr H. The development and applications of the bacterial artificial chromosome cloning system. Keio J. Med. 2001, 50:26-30.
36. Shizuya H., et al. Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector. Proc. Natl. Acad. Sci. U. S. A. 1992, 89:8794-8797.
37. Stankiewicz P., et al. Challenges in clinical interpretation of microduplications detected by array CGH analysis. Am. J. Med. Genet. A 2010, 152A:1089-1100.
38. Strong S.J., et al. Marked improvement of PAC and BAC cloning is achieved using electroelution of pulsed-field gel-separated partial digests of genomic DNA. Nucleic Acids Res. 1997, 25:3959-3961.
39. Terabayashi Y., et al. Construction of Japanese BAC library Yamato-2 (JY2): a set of 330K clone resources of damage-minimized DNA taken from a genetically established Japanese individual. Hum. Cell 2011, 1-11.
40. Weise A., et al. POD-FISH: a new technique for parental origin determination based on copy number variation polymorphism. Methods Mol. Biol. 2010, 659:291-298.
41. Wicker N., et al. A new look towards BAC-based array CGH through a comprehensive comparison with oligo-based array CGH. BMC Genomics 2007, 8:84.
42. Ylstra B., et al. BAC to the future! or oligonucleotides: a perspective for micro array comparative genomic hybridization (array CGH). Nucleic Acids Res. 2006, 34:445-450.
43. Yu S., et al. Validation of the Agilent 244K oligonucleotide array-based comparative genomic hybridization platform for clinical cytogenetic diagnosis. Am. J. Clin. Pathol. 2009, 132:349-360.
44. Zhang B., et al. WebGestalt: an integrated system for exploring gene sets in various biological contexts. Nucleic Acids Res. 2005, 33:W741-W748.
45. Zhang J., et al. Development of bioinformatics resources for display and analysis of copy number and other structural variants in the human genome. Cytogenet. Genome Res. 2006, 115:205-214.
46. Krzywinski M., et al. Circos: an information aesthetic for comparative genomics. Genome Res. 2009, 19:1639-1645.