Evaluation of microsatellite variation in the 1000 Genomes Project pilot studies is indicative of the quality and utility of the raw data and alignments

Genomics

Volumn 97, Issue 4, 2011, Pages 193-199

  McIver, L J ^a   Fondon, J W ^b   Skinner, M A ^c,d   Garner, H R ^a  

^a VIRGINIA BIOINFORMATICS INSTITUTE   (United States)

^b UNIVERSITY OF TEXAS AT ARLINGTON   (United States)

^c UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

^d CHILDREN S MEDICAL CENTER   (United States)

Author keywords

1000 Genomes Project; Genomics; Microsatellites; Repetitive DNA

Indexed keywords

MICROSATELLITE DNA;

ARTICLE; CONTROLLED STUDY; FEMALE; GENE FREQUENCY; GENETIC VARIABILITY; HUMAN; HUMAN GENOME PROJECT; INHERITANCE; MALE; PHENOTYPE; PILOT STUDY; PRIORITY JOURNAL; PROTEIN MOTIF; SEQUENCE ALIGNMENT; SINGLE NUCLEOTIDE POLYMORPHISM;

FEMALE; GENETIC VARIATION; GENOME, HUMAN; HUMANS; MALE; MICROSATELLITE REPEATS; PEDIGREE; PILOT PROJECTS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

EID: 79952815580     PISSN: 08887543     EISSN: 10898646     Source Type: Journal    
DOI: 10.1016/j.ygeno.2011.01.001     Document Type: Article

References (40)

1. Markoff J. I.B.M. Joins Pursuit of the $1,000 Personal Genome 2009, The New York Times.
2. Biology 2.0, The Economist. A Special Report on the Human Genome 2010, 3-5.
3. M. Herper, Your Genome is Coming, Journal, (2010).
4. Siva N. 1000 Genomes project. Nat. Biotechnol. 2008, 26:256.
5. Wellcome Trust Sanger Institute Press Release: 1,000 Genomes Project releases data from pilot projects on path to providing database for 2,500 human genomes June 21, 2010, http://www.sanger.ac.uk/about/press/2010/100621.html.
6. Durbin R.M., Abecasis G.R., Altshuler D.L., Auton A., Brooks L.D., Gibbs R.A., Hurles M.E., McVean G.A. A map of human genome variation from population-scale sequencing. Nature 2010, 467:1061-1073.
7. Brown T.A. Genomes 2002, BIOS Scientific Publisher, Ltd., Manchester, UK.
8. Forgacs E., Wren J.D., Kamibayashi C., Kondo M., Xu X.L., Markowitz S., Tomlinson G.E., Muller C.Y., Gazdar A.F., Garner H.R., Minna J.D. Searching for microsatellite mutations in coding regions in lung, breast, ovarian and colorectal cancers. Oncogene 2001, 20:1005-1009.
9. Fondon J.W., Hammock E.A., Hannan A.J., King D.G. Simple sequence repeats: genetic modulators of brain function and behavior. Trends Neurosci. 2008, 31:328-334.
10. Fondon J.W., Garner H.R. Detection of length-dependent effects of tandem repeat alleles by 3-D geometric decomposition of craniofacial variation. Dev. Genes Evol. 2007, 217:79-85.
11. Brouwer J.R., Willemsen R., Oostra B.A. Microsatellite repeat instability and neurological disease. Bioessays 2009, 31:71-83.
12. Kadouri L., Kote-Jarai Z., Easton D.F., Hubert A., Hamoudi R., Glaser B., Abeliovich D., Peretz T., Eeles R.A. Polyglutamine repeat length in the AIB1 gene modifies breast cancer susceptibility in BRCA1 carriers. Int. J. Cancer 2004, 108:399-403.
13. Cummings C.J., Zoghbi H.Y. Fourteen and counting: unraveling trinucleotide repeat diseases. Hum. Mol. Genet. 2000, 9:909-916.
14. Chandok G.S., Kapoor K.K., Brick R.M., Sidorova J.M., Krasilnikova M.M. A distinct first replication cycle of DNA introduced in mammalian cells. Nucleic Acids Res. 2010.
15. Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999, 27:573-580.
16. Valon C.L. New developments in mutation reserach 2006, Nova Science Publishers, New York.
17. Butler J.M. Genetics and genomics of core short tandem repeat loci used in human identity testing. J. Forensic Sci. 2006, 51:253-265.
18. Rasmussen-Torvik L.J., Pankow J.S., Peacock J.M., Borecki I.B., Hixson J.E., Tsai M.Y., Kabagambe E.K., Arnett D.K. Suggestion for linkage of chromosome 1p35.2 and 3q28 to plasma adiponectin concentrations in the GOLDN Study. BMC Med. Genet. 2009, 10:39.
19. Koorey D.J., Bishop G.A., McCaughan G.W. Allele non-amplification: a source of confusion in linkage studies employing microsatellite polymorphisms. Hum. Mol. Genet. 1993, 2:289-291.
20. Ewen K.R., Bahlo M., Treloar S.A., Levinson D.F., Mowry B., Barlow J.W., Foote S.J. Identification and analysis of error types in high-throughput genotyping. Am. J. Hum. Genet. 2000, 67:727-736.
21. Simpson A.J. The natural somatic mutation frequency and human carcinogenesis. Adv. Cancer Res. 1997, 71:209-240.
22. Veeriah S., Brennan C., Meng S., Singh B., Fagin J.A., Solit D.B., Paty P.B., Rohle D., Vivanco I., Chmielecki J., Pao W., Ladanyi M., Gerald W.L., Liau L., Cloughesy T.C., Mischel P.S., Sander C., Taylor B., Schultz N., Major J., Heguy A., Fang F., Mellinghoff I.K., Chan T.A. The tyrosine phosphatase PTPRD is a tumor suppressor that is frequently inactivated and mutated in glioblastoma and other human cancers. Proc. Natl Acad. Sci. USA 2009, 106:9435-9440.
23. Mokarram P., Kumar K., Brim H., Naghibalhossaini F., Saberi-firoozi M., Nouraie M., Green R., Lee E., Smoot D.T., Ashktorab H. Distinct high-profile methylated genes in colorectal cancer. PLoS ONE 2009, 4:e7012.
24. Duan D. From the smallest virus to the biggest gene: marching towards gene therapy for duchenne muscular dystrophy. Discov. Med. 2006, 6:103-108.
25. Oudet C., Heilig R., Hanauer A., Mandel J.L. Nonradioactive assay for new microsatellite polymorphisms at the 5' end of the dystrophin gene, and estimation of intragenic recombination. Am. J. Hum. Genet. 1991, 49:311-319.
26. Maheshwari M., Vijaya R., Kabra M., Arora S., Shastri S.S., Deka D., Kriplani A., Menon P.S. Prenatal diagnosis of Duchenne muscular dystrophy. Natl Med. J. India 2000, 13:129-131.
27. Smith D.I., Zhu Y., McAvoy S., Kuhn R. Common fragile sites, extremely large genes, neural development and cancer. Cancer Lett. 2006, 232:48-57.
28. Ma C., Quesnelle K.M., Sparano A., Rao S., Park M.S., Cohen M.A., Wang Y., Samanta M., Kumar M.S., Aziz M.U., Naylor T.L., Weber B.L., Fakharzadeh S.S., Weinstein G.S., Vachani A., Feldman M.D., Brose M.S. Characterization CSMD1 in a large set of primary lung, head and neck, breast and skin cancer tissues. Cancer Biol. Ther. 2009, 8:907-916.
29. Toomes C., Jackson A., Maguire K., Wood J., Gollin S., Ishwad C., Paterson I., Prime S., Parkinson K., Bell S., Woods G., Markham A., Oliver R., Woodward R., Sloan P., Dixon M., Read A., Thakker N. The presence of multiple regions of homozygous deletion at the CSMD1 locus in oral squamous cell carcinoma question the role of CSMD1 in head and neck carcinogenesis. Genes Chromosom. Cancer 2003, 37:132-140.
30. Sebat J., Lakshmi B., Malhotra D., Troge J., Lese-Martin C., Walsh T., Yamrom B., Yoon S., Krasnitz A., Kendall J., Leotta A., Pai D., Zhang R., Lee Y.H., Hicks J., Spence S.J., Lee A.T., Puura K., Lehtimaki T., Ledbetter D., Gregersen P.K., Bregman J., Sutcliffe J.S., Jobanputra V., Chung W., Warburton D., King M.C., Skuse D., Geschwind D.H., Gilliam T.C., Ye K., Wigler M. Strong association of de novo copy number mutations with autism. Science 2007, 316:445-449.
31. Martin C.L., Duvall J.A., Ilkin Y., Simon J.S., Arreaza M.G., Wilkes K., Alvarez-Retuerto A., Whichello A., Powell C.M., Rao K., Cook E., Geschwind D.H. Cytogenetic and molecular characterization of A2BP1/FOX1 as a candidate gene for autism. Am. J. Med. Genet. B Neuropsychiatr. Genet. 2007, 144B:869-876.
32. Ellegren H. Microsatellites: simple sequences with complex evolution. Nat. Rev. Genet. 2004, 5:435-445.
33. 1,000 Genomes Project May 1, 2010, http://www.1000genomes.org/.
34. NCBI Human Reference Genome, Build 36.1 March 1, 2009, ftp://ftp.ncbi.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.36.1/.
35. Rhead B., Karolchik D., Kuhn R.M., Hinrichs A.S., Zweig A.S., Fujita P.A., Diekhans M., Smith K.E., Rosenbloom K.R., Raney B.J., Pohl A., Pheasant M., Meyer L.R., Learned K., Hsu F., Hillman-Jackson J., Harte R.A., Giardine B., Dreszer T.R., Clawson H., Barber G.P., Haussler D., Kent W.J. The UCSC Genome Browser database: update 2010. Nucleic Acids Res. 2010, 38:D613-D619.
36. Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R. The sequence alignment/map format and SAMtools. Bioinformatics 2009, 25:2078-2079.
37. Altschul S.F., Gish W., Miller W., Myers E.W., Lipman D.J. Basic local alignment search tool. J. Mol. Biol. 1990, 215:403-410.
38. Galindo C.L., McIver L.J., McCormick J.F., Skinner M.A., Xie Y., Gelhausen R.A., Ng K., Kumar N.M., Garner H.R. Global microsatellite content distinguishes humans, primates, animals, and plants. Mol. Biol. Evol. 2009, 26:2809-2819.
39. Li H., Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009, 25:1754-1760.
40. Schuler G.D. Sequence mapping by electronic PCR. Genome Res. 1997, 7:541-550.