A novel application of pattern recognition for accurate SNP and indel discovery from high-throughput data: Targeted resequencing of the glucocorticoid receptor co-chaperone FKBP5 in a Caucasian population

Molecular Genetics and Metabolism

Volumn 104, Issue 4, 2011, Pages 457-469

  Pelleymounter, Linda L ^a   Moon, Irene ^a   Johnson, Julie A ^a   Laederach, Alain ^b   Halvorsen, Matt ^b   Eckloff, Bruce ^c   Abo, Ryan ^a   Rossetti, Sandro ^a  

^a MAYO CLINIC   (United States)

^b UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

^c MAYO GRADUATE SCHOOL   (United States)

Author keywords

FKBP5; HLA; Indels; Next generation sequencing analysis; Pattern recognition; Rare variants

Indexed keywords

GLUCOCORTICOID RECEPTOR; MESSENGER RNA; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR FKBP5; UNCLASSIFIED DRUG;

ADULT; ARTICLE; AUTOMATED PATTERN RECOGNITION; BINDING SITE; BIOINFORMATICS; CAUCASIAN; CONTROLLED STUDY; FALSE POSITIVE RESULT; GENE DELETION; GENE SEQUENCE; GENETIC VARIABILITY; GENOTYPE; HUMAN; MEDICAL RESEARCH; METHODOLOGY; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN BINDING; RNA STABILITY; SENSITIVITY ANALYSIS; SENSITIVITY AND SPECIFICITY; SINGLE NUCLEOTIDE POLYMORPHISM; VALIDATION STUDY;

3' UNTRANSLATED REGIONS; ALGORITHMS; BASE SEQUENCE; COMPUTER SIMULATION; EUROPEAN CONTINENTAL ANCESTRY GROUP; GENETIC VARIATION; HAPLOTYPES; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; INDEL MUTATION; LINKAGE DISEQUILIBRIUM; MODELS, GENETIC; NUCLEIC ACID CONFORMATION; PATTERN RECOGNITION, AUTOMATED; POLYMORPHISM, SINGLE NUCLEOTIDE; RESPONSE ELEMENTS; RNA STABILITY; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS, DNA; TACROLIMUS BINDING PROTEINS;

EID: 82255174930     PISSN: 10967192     EISSN: 10967206     Source Type: Journal    
DOI: 10.1016/j.ymgme.2011.08.019     Document Type: Article

References (62)

1. Chakravarti A. Population genetics - making sense out of sequence. Nat. Genet. 1999, 21:56-60.
2. Sabeti P.C., Schaffner S.F., Fry B., Lohmueller J., Varilly P., Shamovsky O., Palma A., Mikkelsen T.S., Altshuler D., Lander E.S. Positive natural selection in the human lineage. Science 2006, 312:1614-1620.
3. Lieberman-Aiden E., van Berkum N.L., Williams L., Imakaev M., Ragoczy T., Telling A., Amit I., Lajoie B.R., Sabo P.J., Dorschner M.O., Sandstrom R., Bernstein B., Bender M.A., Groudine M., Gnirke A., Stamatoyannopoulos J., Mirny L.A., Lander E.S., Dekker J. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 2009, 326:289-293.
4. Marguerat S., Wilhelm B.T., Bähler J. Next-generation sequencing: applications beyond genomes. Biochem. Soc. Trans. 2008, 36(Pt5):1091-1096.
5. Kidd J.M., Sampas N., Antonacci F., Graves T., Fulton R., Hayden H.S., Alkan C., Malig M., Ventura M., Giannuzzi G., Kallicki J., Anderson P., Tsalenko A., Yamada N.A., Tsang P., Kaul R., Wilson R.K., Bruhn L., Eichler E.E. Characterization of missing human genome sequences and copy-number polymorphic insertions. Nat. Methods 2010, 7:365-371.
6. Chen Y., Cicciarelli J., Pravica V., Hutchinson I.V. Long-range linkage on chromosome 6p of VEGF, FKBP5, HLA and TNF alleles associated with transplant rejection. Mol. Immunol. 2009, 47:96-100.
7. Pratt W.B., Toft D.O. Steroid receptor interactions with heat shock protein and immunophilin chaperones. Endocr. Rev. 1997, 18:306-360.
8. Hubler T.R., Scammell J.G. Intronic hormone response elements mediate regulation of FKBP5 by progestins and glucocorticoids. Cell Stress Chaperones 2004, 9:243-252.
9. Binder E.B. The role of FKBP5, a co-chaperone of the glucocorticoid receptor in the pathogenesis and therapy of affective and anxiety disorders. Psychoneuroendocrinology 2009, 34:S186-S195.
10. Bao H., Guo H., Wang J., Zhou R., Lu X., Shi S. MapView: visualization of short reads alignment on a desktop computer. Bioinformatics 2009, 25:1554-1555.
11. Bell C.J., Dinwiddie D.L., Miller N.A., Hateley S.L., Ganusova E.E., Mudge J., Langley R.J., Zhang L., Lee C.C., Schilkey F.D., Sheth V., Woodward J.E., Peckham H.E., Schroth G.P., Kim R.W., Kingsmore S.F. Carrier testing for severe childhood recessive diseases by next-generation sequencing. Sci. Transl. Med. 2011, 3:65ra64.
12. Carver T., Böhme U., Otto T.D., Parkhill J., Berriman M. BamView: viewing mapped read alignment data in the context of the reference sequence. Bioinformatics 2010, 26:676-677.
13. Robinson J.T., Thorvaldsdóttir H., Winckler W., Guttman M., Lander E.S., Getz G., Mesirov J.P. Integrative genomics viewer. Nat. Biotechnol. 2011, 29:24-26.
14. Mills R.E., Luttig C.T., Larkins C.E., Beauchamp A., Tsui C., Pittard W.S., Devine S.E. An initial map of insertion and deletion (INDEL) variation in the human genome. Genome Res. 2006, 16:1182-1190.
15. Chuzhanova N.A., Anassis E.J., Ball E.V., Krawczak M., Cooper D.N. Meta-analysis of indels causing human genetic disease: mechanisms of mutagenesis and the role of local DNA sequence complexity. Hum. Mutat. 2003, 21:28-44.
16. Li H., Ruan J., Durbin R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res. 2008, 18:1851-1858.
17. Mullaney J.M., Mills R.E., Pittard W.S., Devine S.E. Small insertions and deletions (INDELs) in human genomes. Hum. Mol. Genet. 2010, 19:R131-R136.
18. Paakinaho V., Makkonen H., Jaaskelainen T., Palvimo J.J. Glucocorticoid receptor activates poised FKBP51 locus through long-distance interactions. Mol. Endocrinol. 2010, 24:511-525.
19. Kent W.J., Sugnet C.W., Furey T.S., Roskin K.M., Pringle T.H., Zahler A.M., Haussler D. The human genome browser at UCSC. Genome Res. 2002, 12:996-1006.
20. Zhao Z., Boerwinkle E. Neighboring-nucleotide effects on single nucleotide polymorphisms: a study of 2.6million polymorphisms across the human genome. Genome Res. 2002, 12:1679-1686.
21. Mungall A.J., Palmer S.A., Sims S.K., Edwards C.A., Ashurst J.L., Wilming L., Jones M.C., Horton R., Hunt S.E., Scott C.E., Gilbert J.G., Clamp M.E., Bethel G., Milne S., Ainscough R., Almeida J.P., Ambrose K.D., Andrews T.D., Babbage A., Ashwell R.I., Bagguley C.L., Bailey J., Banerjee R., Barker D.J., Barlow K.F., Bates K., Beare D.M., Beasley H., Beasley O., Bird C.P., Blakey S., Bray-Allen S., Brook J., Brown A.J., Brown J.Y., Burford D.C., Burrill W., Burton J., Carder C., Carter N.P., Chapman J.C., Clark S.Y., Clark G., Clee C.M., Clegg S., Cobley V., Collier R.E., Collins J.E., Colman L.K., Corby N.R., Coville G.J., Culley K.M., Dhami P., Davies J., Dunn M., Earthrowl M.E., Ellington A.E., Evans K.A., Faulkner L., Francis M.D., Frankish A., Frankland J., French L., Garner P., Garnett J., Ghori M.J., Gilby L.M., Gillson C.J., Glithero R.J., Grafham D.V., Grant M., Gribble S., Griffiths C., Griffiths M., Hall R., Halls K.S., Hammond S., Harley J.L., Hart E.A., Heath P.D., Heathcott R., Holmes S.J., Howden P.J., Howe K.L., Howell G.R., Huckle E., Humphray S.J., Humphries M.D., Hunt A.R., Johnson C.M., Joy A.A., Kay M., Keenan S.J., Kimberley A.M., King A., Laird G.K., Langford C., Lawlor S., Leongamornlert D.A., Leversha M., Lloyd C.R., Lloyd D.M., Loveland J.E., Lovell J., Martin S., Mashreghi-Mohammadi M., Maslen G.L., Matthews L., McCann O.T., McLaren S.J., McLay K., McMurray A., Moore M.J., Mullikin J.C., Niblett D., Nickerson T., Novik K.L., Oliver K., Overton-Larty E.K., Parker A., Patel R., Pearce A.V., Peck A.I., Phillimore B., Phillips S., Plumb R.W., Porter K.M., Ramsey Y., Ranby S.A., Rice C.M., Ross M.T., Searle S.M., Sehra H.K., Sheridan E., Skuce C.D., Smith S., Smith M., Spraggon L., Squares S.L., Steward C.A., Sycamore N., Tamlyn-Hall G., Tester J., Theaker A.J., Thomas D.W., Thorpe A., Tracey A., Tromans A., Tubby B., Wall M., Wallis J.M., West A.P., White S.S., Whitehead S.L., Whittaker H., Wild A., Willey D.J., Wilmer T.E., Wood J.M., Wray P.W., Wyatt J.C., Young L., Younger R.M., Bentley D.R., Coulson A., Durbin R., Hubbard T., Sulston J.E., Dunham I., Rogers J., Beck S. The DNA sequence and analysis of human chromosome 6. Nature 2003, 425:805-811.
22. Raca G., Jackson C., Warman B., Bair T., Schimmenti L.A. Next generation sequencing in research and diagnostics of ocular birth defects. Mol. Genet. Metab. 2010, 100:184-192.
23. Chou L.S., Liu C.S., Boese B., Zhang X., Mao R. DNA sequence capture and enrichment by microarray followed by next-generation sequencing for targeted resequencing: neurofibromatosis type 1 gene as a model. Clin. Chem. 2010, 56:62-72.
24. Mitchell A.A., Zwick M.E., Chakravarti A., Cutler D.J. Discrepancies in dbSNP confirmation rates and allele frequency distributions from varying genotyping error rates and patterns. Bioinformatics 2004, 20:1022-1032.
25. Cirulli E.T., Goldstein D.B. Uncovering the roles of rare variants in common disease through whole-genome sequencing. Nat. Rev. Genet. 2010, 11:415-425.
26. Harismendy O., Frazer K. Method for improving sequence coverage uniformity of targeted genomic intervals amplified by LR-PCR using Illumina GA sequencing-by-synthesis technology. Biotechniques 2009, 46:229-231.
27. Sachidanandam R., Weissman D., Schmidt S.C., Kakol J.M., Stein L.D., Marth G., Sherry S., Mullikin J.C., Mortimore B.J., Willey D.L., Hunt S.E., Cole C.G., Coggill P.C., Rice C.M., Ning Z., Rogers J., Bentley D.R., Kwok P.Y., Mardis E.R., Yeh R.T., Schultz B., Cook L., Davenport R., Dante M., Fulton L., Hillier L., Waterston R.H., McPherson J.D., Gilman B., Schaffner S., Van Etten W.J., Reich D., Higgins J., Daly M.J., Blumenstiel B., Baldwin J., Stange-Thomann N., Zody M.C., Linton L., Lander E.S., Altshuler D. A map of human genome sequence variation containing 1.42million single nucleotide polymorphisms. Nature 2001, 409:928-933. I.S.M.W. Group.
28. Weinberg C.R., Morris R.W. Invited commentary: testing for Hardy-Weinberg disequilibrium using a genome single-nucleotide polymorphism scan based on cases only. Am. J. Epidemiol. 2003, 158:401-403. discussion 404-405.
29. Wigginton J.E., Cutler D.J., Abecasis G.R. A note on exact tests of Hardy-Weinberg equilibrium. Am. J. Hum. Genet. 2005, 76:887-893.
30. Consortium T.I.H. A haplotype map of the human genome. Nature 2005, 437:1299-1320.
31. Clement N.L., Snell Q., Clement M.J., Hollenhorst P.C., Purwar J., Graves B.J., Cairns B.R., Johnson W.E. The GNUMAP algorithm: unbiased probabilistic mapping of oligonucleotides from next-generation sequencing. Bioinformatics 2010, 26:38-45.
32. Bansal V., Harismendy O., Tewhey R., Murray S.S., Schork N.J., Topol E.J., Frazer K.A. Accurate detection and genotyping of SNPs utilizing population sequencing data. Genome Res. 2010, 20:537-545.
33. Ahn S.M., Kim T.H., Lee S., Kim D., Ghang H., Kim D.S., Kim B.C., Kim S.Y., Kim W.Y., Kim C., Park D., Lee Y.S., Kim S., Reja R., Jho S., Kim C.G., Cha J.Y., Kim K.H., Lee B., Bhak J., Kim S.J. The first Korean genome sequence and analysis: full genome sequencing for a socio-ethnic group. Genome Res. 2009, 19:1622-1629.
34. The 1000 Genomes Project Consortium A map of human genome variation from population-scale sequencing. Nature 2010, 467:1061-1073.
35. 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. G.P.D.P. Subgroup.
36. McKenna A., Hanna M., Banks E., Sivachenko A., Cibulskis K., Kernytsky A., Garimella K., Altshuler D., Gabriel S., Daly M., DePristo M.A. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010, 20:1297-1303.
37. Nackley A.G., Shabalina S.A., Tchivileva I.E., Satterfield K., Korchynskyi O., Makarov S.S., Maixner W., Diatchenko L. Human catechol-O-methyltransferase haplotypes modulate protein expression by altering mRNA secondary structure. Science 2006, 314:1930-1933.
38. Duan J., Wainwright M.S., Comeron J.M., Saitou N., Sanders A.R., Gelernter J., Gejman P.V. Synonymous mutations in the human dopamine receptor D2 (DRD2) affect mRNA stability and synthesis of the receptor. Hum. Mol. Genet. 2003, 12:205-216.
39. Hunt R., Sauna Z.E., Ambudkar S.V., Gottesman M.M., Kimchi-Sarfaty C. Silent (synonymous) SNPs: should we care about them?. Methods Mol. Biol. 2009, 578:23-39.
40. Sauna Z.E., Kimchi-Sarfaty C., Ambudkar S.V., Gottesman M.M. Silent polymorphisms speak: how they affect pharmacogenomics and the treatment of cancer. Cancer Res. 2007, 67:9609-9612.
41. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003, 31:3406-3415.
42. Halvorsen M., Martin J.S., Broadaway S., Laederach A. Disease-associated mutations that alter the RNA structural ensemble. PLoS Genet. 2010, 6:e1001074.
43. Owens-Grillo J.K., Stancato L.F., Hoffmann K., Pratt W.B., Krishna P. Binding of immunophilins to the 90kDa heat shock protein (hsp90) via a tetratricopeptide repeat domain is a conserved protein interaction in plants. Biochemistry 1996, 35:15249-15255.
44. Hafner M., Landthaler M., Burger L., Khorshid M., Hausser J., Berninger P., Rothballer A., Ascano M., Jungkamp A.-C., Munschauer M., Ulrich A., Wardle G.S., Dewell S., Zavolan M., Tuschl T. Transcriptome-wide identification of RNA-binding protein and MicroRNA target sites by PAR-CLIP. Cell 2010, 141:129-141.
45. Chen C.-Y.A., Zheng D., Xia Z., Shyu A.-B. Ago-TNRC6 triggers microRNA-mediated decay by promoting two deadenylation steps. Nat. Struct. Mol. Biol. 2009, 16:1160-1166.
46. Lagos-Quintana M., Rauhut R., Yalcin A., Meyer J., Lendeckel W., Tuschl T. Identification of tissue-specific MicroRNAs from mouse. Curr. Biol. 2002, 12:735-739.
47. Kreitman M., Di Rienzo A. Balancing claims for balancing selection. Trends Genet. 2004, 20:300-304.
48. Zan Q., Wen B., He Y., Wang Y., Xu S., Qian J., Lu D., Jin L. Complete sequence data support lack of balancing selection on PRNP in a natural Chinese population. J. Hum. Genet. 2006, 51:451-454.
49. Lee Y.-H., Kang E.S., Kim S.H., Han S.J., Kim C.H., Kim H.J., Ahn C.W., Cha B.S., Nam M., Nam C.M., Lee H.C. Association between polymorphisms in SLC30A8, HHEX, CDKN2A/B, IGF2BP2, FTO, WFS1, CDKAL1, KCNQ1 and type 2 diabetes in the Korean population. J. Hum. Genet. 2008, 53:991-998.
50. Guryev V., Smits B.M.G., de Belt J.v., Verheul M., Hubner N., Cuppen E. Haplotype block structure is conserved across mammals. PLoS Genet. 2006, 2:e121.
51. Kimchi-Sarfaty C., Oh J.M., Kim I.-W., Sauna Z.E., Calcagno A.M., Ambudkar S.V., Gottesman M.M. A "silent" polymorphism in the MDR1 gene changes substrate specificity. Science 2007, 315:525-528.
52. Fung K.L., Gottesman M.M. A synonymous polymorphism in a common MDR1 (ABCB1) haplotype shapes protein function. Biochim. Biophys. Acta 2009, 1794:860-871.
53. Frazier B., Hsiao C.W., Deuster P., Poth M. African Americans and Caucasian Americans: differences in glucocorticoid-induced insulin resistance. Horm. Metab. Res. 2010, 42:887-891.
54. Devil in the details. Nature 2011, 470:305-306.
55. Mamanova L., Coffey A.J., Scott C.E., Kozarewa I., Turner E.H., Kumar A., Howard E., Shendure J., Turner D.J. Target-enrichment strategies for next-generation sequencing. Nat. Methods 2010, 7:111-118.
56. Chaisson M.J., Brinza D., Pevzner P.A. De novo fragment assembly with short mate-paired reads: does the read length matter?. Genome Res. 2009, 19:336-346.
57. Quail M.A., Kozarewa I., Smith F., Scally A., Stephens P.J., Durbin R., Swerdlow H., Turner D.J. A large genome center's improvements to the Illumina sequencing system. Nat. Methods 2008, 5:1005-1010.
58. Morgan J.E., Carr I.M., Sheridan E., Chu C.E., Hayward B., Camm N., Lindsay H.A., Mattocks C.J., Markham A.F., Bonthron D.T., Taylor G.R. Genetic diagnosis of familial breast cancer using clonal sequencing. Hum. Mutat. 2010, 31:484-491.
59. McPherson J.D. Next-generation gap. Nat. Methods 2009, 6:2-5.
60. Rossetti S., Chauveau D., Walker D., Saggar-Malik A., Winearls C.G., Torres V.E., Harris P.C. A complete mutation screen of the ADPKD genes by DHPLC. Kidney Int. 2002, 61:1588-1599.
61. Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 1989, 123:585-595.
62. Ball E.V., Stenson P.D., Abeysinghe S.S., Krawczak M., Cooper D.N., Chuzhanova N.A. Microdeletions and microinsertions causing human genetic disease: common mechanisms of mutagenesis and the role of local DNA sequence complexity. Hum. Mutat. 2005, 26:205-213.