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Volumn 2, Issue AUG, 2011, Pages

Estimating allele frequency from next-generation sequencing of pooled mitochondrial DNA samples

Author keywords

Allele frequency; Mitochondria DNA; Next generation sequencing; Pooled sequencing; Sequencing error

Indexed keywords


EID: 84867007629     PISSN: None     EISSN: 16648021     Source Type: Journal    
DOI: 10.3389/fgene.2011.00051     Document Type: Article
Times cited : (10)

References (40)
  • 1
    • 34250355048 scopus 로고    scopus 로고
    • Mitochondrial genetic background modifies breast cancer risk
    • Bai, R. K., Leal, S. M., Covarrubias, D., Liu, A., and Wong, L. J. (2007). Mitochondrial genetic background modifies breast cancer risk. Cancer Res. 67, 4687-4694.
    • (2007) Cancer Res , vol.67 , pp. 4687-4694
    • Bai, R.K.1    Leal, S.M.2    Covarrubias, D.3    Liu, A.4    Wong, L.J.5
  • 2
    • 25444474703 scopus 로고    scopus 로고
    • Mitochondria take center stage in aging and neurodegeneration
    • Beal, M. F. (2005). Mitochondria take center stage in aging and neurodegeneration. Ann. Neurol. 58, 495-505.
    • (2005) Ann. Neurol. , vol.58 , pp. 495-505
    • Beal, M.F.1
  • 3
    • 33750953227 scopus 로고    scopus 로고
    • Whole-genome re-sequencing
    • Bentley, D. R. (2006). Whole-genome re-sequencing. Curr. Opin. Genet. Dev. 16, 545-552.
    • (2006) Curr. Opin. Genet. Dev. , vol.16 , pp. 545-552
    • Bentley, D.R.1
  • 4
    • 44349132708 scopus 로고    scopus 로고
    • Common and rare variants in multifactorial susceptibility to common diseases
    • Bodmer, W., and Bonilla, C. (2008). Common and rare variants in multifactorial susceptibility to common diseases. Nat. Genet. 40, 695-701.
    • (2008) Nat. Genet. , vol.40 , pp. 695-701
    • Bodmer, W.1    Bonilla, C.2
  • 5
    • 24744442376 scopus 로고    scopus 로고
    • Mitochondrial DNA G10398A polymorphism and invasive breast cancer in African-American women
    • Canter, J. A., Kallianpur, A. R., Parl, F. F., and Millikan, R. C. (2005). Mitochondrial DNA G10398A polymorphism and invasive breast cancer in African-American women. Cancer Res. 65, 8028-8033.
    • (2005) Cancer Res , vol.65 , pp. 8028-8033
    • Canter, J.A.1    Kallianpur, A.R.2    Parl, F.F.3    Millikan, R.C.4
  • 7
    • 84984932946 scopus 로고    scopus 로고
    • Population genetics-making sense out of sequence
    • Chakravarti, A. (1999). Population genetics-making sense out of sequence. Nat. Genet. 21(1 Suppl.), 56-60.
    • (1999) Nat. Genet. , vol.21 , Issue.1 SUPPL. 1 , pp. 56-60
    • Chakravarti, A.1
  • 8
    • 52649175410 scopus 로고    scopus 로고
    • Mitochondrial DNA variant interactions modify breast cancer risk
    • Covarrubias, D., Bai, R. K., Wong, L. J., and Leal, S. M. (2008). Mitochondrial DNA variant interactions modify breast cancer risk. J. Hum. Genet. 53, 924-928.
    • (2008) J. Hum. Genet. , vol.53 , pp. 924-928
    • Covarrubias, D.1    Bai, R.K.2    Wong, L.J.3    Leal, S.M.4
  • 9
    • 77249134594 scopus 로고    scopus 로고
    • Rare variants create synthetic genome-wide associations
    • doi: 10.1371/journal.pbio.1000294
    • Dickson, S. P., Wang, K., Krantz, I., Hakonarson, H., and Goldstein, D. B. (2010). Rare variants create synthetic genome-wide associations. PLoS Biol. 8, e1000294. doi: 10.1371/journal.pbio.1000294
    • (2010) PLoS Biol , vol.8
    • Dickson, S.P.1    Wang, K.2    Krantz, I.3    Hakonarson, H.4    Goldstein, D.B.5
  • 10
    • 0037972522 scopus 로고    scopus 로고
    • Mitochondrial respiratory-chain diseases
    • Dimauro, S., and Schon, E. A. (2003). Mitochondrial respiratory-chain diseases. N. Engl. J. Med. 348, 2656-2668.
    • (2003) N. Engl. J. Med. , vol.348 , pp. 2656-2668
    • Dimauro, S.1    Schon, E.A.2
  • 13
    • 60749100685 scopus 로고    scopus 로고
    • SNP frequency estimation using massively parallel sequencing of pooled DNA
    • Ingman, M., and Gyllensten, U. (2009). SNP frequency estimation using massively parallel sequencing of pooled DNA. Eur. J. Hum. Genet. 17, 383-386.
    • (2009) Eur. J. Hum. Genet. , vol.17 , pp. 383-386
    • Ingman, M.1    Gyllensten, U.2
  • 14
    • 0037320552 scopus 로고    scopus 로고
    • Estimation of haplotype frequencies, linkage-disequilibrium measures, and combination of haplotype copies in each pool by use of pooled DNA data
    • Ito, T., Chiku, S., Inoue, E., Tomita, M., Morisaki, T., Morisaki, H., and Kamatani, N. (2003). Estimation of haplotype frequencies, linkage-disequilibrium measures, and combination of haplotype copies in each pool by use of pooled DNA data. Am. J. Hum. Genet. 72, 384-398.
    • (2003) Am. J. Hum. Genet. , vol.72 , pp. 384-398
    • Ito, T.1    Chiku, S.2    Inoue, E.3    Tomita, M.4    Morisaki, T.5    Morisaki, H.6    Kamatani, N.7
  • 15
    • 0030221371 scopus 로고    scopus 로고
    • Cellular activation mediated by nitric oxide
    • Lander, H. M. (1996). Cellular activation mediated by nitric oxide. Methods 10, 15-20.
    • (1996) Methods , vol.10 , pp. 15-20
    • Lander, H.M.1
  • 16
    • 0347988090 scopus 로고    scopus 로고
    • Pyrosequencing-based SNP allele frequency estimation in DNA pools
    • Lavebratt, C., Sengul, S., Jansson, M., and Schalling, M. (2004). Pyrosequencing-based SNP allele frequency estimation in DNA pools. Hum. Mutat. 23, 92-97.
    • (2004) Hum. Mutat. , vol.23 , pp. 92-97
    • Lavebratt, C.1    Sengul, S.2    Jansson, M.3    Schalling, M.4
  • 17
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • Li, H., and Durbin, R. (2009). Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754-1760.
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 19
    • 12344305124 scopus 로고    scopus 로고
    • Mitochondrial dysfunction and type 2 diabetes
    • Lowell, B. B., and Shulman, G. I. (2005). Mitochondrial dysfunction and type 2 diabetes. Science 307, 384-387.
    • (2005) Science , vol.307 , pp. 384-387
    • Lowell, B.B.1    Shulman, G.I.2
  • 22
    • 44849122207 scopus 로고    scopus 로고
    • Power and SNP tagging in whole mitochondrial genome association studies
    • Mcrae, A. F., Byrne, E. M., Zhao, Z. Z., Montgomery, G. W., and Visscher, P. M. (2008). Power and SNP tagging in whole mitochondrial genome association studies. Genome Res. 18, 911-917.
    • (2008) Genome Res , vol.18 , pp. 911-917
    • Mcrae, A.F.1    Byrne, E.M.2    Zhao, Z.Z.3    Montgomery, G.W.4    Visscher, P.M.5
  • 23
    • 0038268052 scopus 로고    scopus 로고
    • Precise determination of mitochondrial DNA copy number in human skeletal and cardiac muscle by a PCR-based assay: lack of change of copy number with age
    • Miller, F. J., Rosenfeldt, F. L., Zhang, C., Linnane, A. W., and Nagley, P. (2003). Precise determination of mitochondrial DNA copy number in human skeletal and cardiac muscle by a PCR-based assay: lack of change of copy number with age. Nucleic Acids Res. 31, e61.
    • (2003) Nucleic Acids Res , vol.31
    • Miller, F.J.1    Rosenfeldt, F.L.2    Zhang, C.3    Linnane, A.W.4    Nagley, P.5
  • 24
    • 0020406173 scopus 로고
    • Molecular clock of silent substitution: at least six-fold preponderance of silent changes in mitochondrial genes over those in nuclear genes
    • Miyata, T., Hayashida, H., Kikuno, R., Hasegawa, M., Kobayashi, M., and Koike, K. (1982). Molecular clock of silent substitution: at least six-fold preponderance of silent changes in mitochondrial genes over those in nuclear genes. J. Mol. Evol. 19, 28-35.
    • (1982) J. Mol. Evol. , vol.19 , pp. 28-35
    • Miyata, T.1    Hayashida, H.2    Kikuno, R.3    Hasegawa, M.4    Kobayashi, M.5    Koike, K.6
  • 25
    • 65249131713 scopus 로고    scopus 로고
    • Rare variants of IFIH1, a gene implicated in antiviral responses, protect against type 1 diabetes
    • Nejentsev, S., Walker, N., Riches, D., Egholm, M., and Todd, J. A. (2009). Rare variants of IFIH1, a gene implicated in antiviral responses, protect against type 1 diabetes. Science 324, 387-389.
    • (2009) Science , vol.324 , pp. 387-389
    • Nejentsev, S.1    Walker, N.2    Riches, D.3    Egholm, M.4    Todd, J.A.5
  • 27
    • 0036433069 scopus 로고    scopus 로고
    • The presence of a common mitochondrial DNA variant is associated with fasting insulin levels in Europeans in Auckland
    • Poulton, J., Bednarz, A. L., Scott-Brown, M., Thompson, C., Macaulay, V. A., and Simmons, D. (2002). The presence of a common mitochondrial DNA variant is associated with fasting insulin levels in Europeans in Auckland. Diabet. Med. 19, 969-971.
    • (2002) Diabet. Med. , vol.19 , pp. 969-971
    • Poulton, J.1    Bednarz, A.L.2    Scott-Brown, M.3    Thompson, C.4    Macaulay, V.A.5    Simmons, D.6
  • 28
    • 15644370476 scopus 로고    scopus 로고
    • A common mitochondrial DNA variant is associated with insulin resistance in adult life
    • Poulton, J., Brown, M. S., Cooper, A., Marchington, D. R., and Phillips, D. I. (1998). A common mitochondrial DNA variant is associated with insulin resistance in adult life. Diabetologia 41, 54-58.
    • (1998) Diabetologia , vol.41 , pp. 54-58
    • Poulton, J.1    Brown, M.S.2    Cooper, A.3    Marchington, D.R.4    Phillips, D.I.5
  • 29
    • 0035451780 scopus 로고    scopus 로고
    • On the allelic spectrum of human disease
    • Reich, D. E., and Lander, E. S. (2001). On the allelic spectrum of human disease. Trends Genet. 17, 502-510.
    • (2001) Trends Genet , vol.17 , pp. 502-510
    • Reich, D.E.1    Lander, E.S.2
  • 30
    • 0347356538 scopus 로고    scopus 로고
    • Effects of purifying and adaptive selection on regional variation in human mtDNA
    • Ruiz-Pesini, E., Mishmar, D., Brandon, M., Procaccio, V., and Wallace, D. C. (2004). Effects of purifying and adaptive selection on regional variation in human mtDNA. Science 303, 223-226.
    • (2004) Science , vol.303 , pp. 223-226
    • Ruiz-Pesini, E.1    Mishmar, D.2    Brandon, M.3    Procaccio, V.4    Wallace, D.C.5
  • 31
    • 18244372432 scopus 로고    scopus 로고
    • Mechanisms of insulin resistance in humans and possible links with inflammation
    • Savage, D. B., Petersen, K. F., and Shulman, G. I. (2005). Mechanisms of insulin resistance in humans and possible links with inflammation. Hypertension 45, 828-833.
    • (2005) Hypertension , vol.45 , pp. 828-833
    • Savage, D.B.1    Petersen, K.F.2    Shulman, G.I.3
  • 32
    • 0033032999 scopus 로고    scopus 로고
    • Mitochondrial involvement in Parkinson's disease, Huntington's disease, hereditary spastic paraplegia and Friedreich's ataxia
    • Schapira, A. H. (1999). Mitochondrial involvement in Parkinson's disease, Huntington's disease, hereditary spastic paraplegia and Friedreich's ataxia. Biochim. Biophys. Acta 1410, 159-170.
    • (1999) Biochim. Biophys. Acta , vol.1410 , pp. 159-170
    • Schapira, A.H.1
  • 33
    • 0031889566 scopus 로고    scopus 로고
    • Allele frequency distributions in pooled DNA samples: applications to mapping complex disease genes
    • Shaw, S. H., Carrasquillo, M. M., Kashuk, C., Puffenberger, E. G., and Chakravarti, A. (1998). Allele frequency distributions in pooled DNA samples: applications to mapping complex disease genes. Genome Res. 8, 111-123.
    • (1998) Genome Res , vol.8 , pp. 111-123
    • Shaw, S.H.1    Carrasquillo, M.M.2    Kashuk, C.3    Puffenberger, E.G.4    Chakravarti, A.5
  • 34
    • 17744393686 scopus 로고    scopus 로고
    • Mitochondrial DNA mutations in human disease
    • Taylor, R. W., and Turnbull, D. M. (2005). Mitochondrial DNA mutations in human disease. Nat. Rev. Genet. 6, 389-402.
    • (2005) Nat. Rev. Genet. , vol.6 , pp. 389-402
    • Taylor, R.W.1    Turnbull, D.M.2
  • 35
    • 23844558266 scopus 로고    scopus 로고
    • A mitochondrial paradigm of metabolic and degenerative diseases, aging, and cancer: a dawn for evolutionary medicine
    • Wallace, D. C. (2005). A mitochondrial paradigm of metabolic and degenerative diseases, aging, and cancer: a dawn for evolutionary medicine. Annu. Rev. Genet. 39, 359-407.
    • (2005) Annu. Rev. Genet. , vol.39 , pp. 359-407
    • Wallace, D.C.1
  • 36
    • 0023240790 scopus 로고
    • Sequence analysis of cDNAs for the human and bovine ATP synthase beta subunit: mitochondrial DNA genes sustain seventeen times more mutations
    • Wallace, D. C., Ye, J. H., Neckelmann, S. N., Singh, G., Webster, K. A., and Greenberg, B. D. (1987). Sequence analysis of cDNAs for the human and bovine ATP synthase beta subunit: mitochondrial DNA genes sustain seventeen times more mutations. Curr. Genet. 12, 81-90.
    • (1987) Curr. Genet. , vol.12 , pp. 81-90
    • Wallace, D.C.1    Ye, J.H.2    Neckelmann, S.N.3    Singh, G.4    Webster, K.A.5    Greenberg, B.D.6
  • 37
    • 77954194389 scopus 로고    scopus 로고
    • Resequencing of pooled DNA for detecting disease associations with rare variants
    • Wang, T., Lin, C. Y., Rohan, T. E., and Ye, K. (2010). Resequencing of pooled DNA for detecting disease associations with rare variants. Genet. Epidemiol. 34, 492-501.
    • (2010) Genet. Epidemiol. , vol.34 , pp. 492-501
    • Wang, T.1    Lin, C.Y.2    Rohan, T.E.3    Ye, K.4
  • 38
    • 54049140995 scopus 로고    scopus 로고
    • Association of mitochondrial DNA displacement loop (CA)n dinucleotide repeat polymorphism with breast cancer risk and survival among Chinese women
    • Ye, C., Gao, Y. T., Wen, W., Breyer, J. P., Shu, X. O., Smith, J. R., Zheng, W., and Cai, Q. (2008). Association of mitochondrial DNA displacement loop (CA)n dinucleotide repeat polymorphism with breast cancer risk and survival among Chinese women. Cancer Epidemiol. Biomarkers Prev. 17, 2117-2122.
    • (2008) Cancer Epidemiol. Biomarkers Prev. , vol.17 , pp. 2117-2122
    • Ye, C.1    Gao, Y.T.2    Wen, W.3    Breyer, J.P.4    Shu, X.O.5    Smith, J.R.6    Zheng, W.7    Cai, Q.8
  • 39
    • 77957925524 scopus 로고    scopus 로고
    • Mitochondrial DNA variant discovery and evaluation in human cardiomyopathies through next-generation sequencing
    • doi: 10.1371/journal.pone.0012295
    • Zaragoza, M. V., Fass, J., Diegoli, M., Lin, D., and Arbustini, E. (2010). Mitochondrial DNA variant discovery and evaluation in human cardiomyopathies through next-generation sequencing. PLoS ONE 5, e12295. doi: 10.1371/journal.pone.0012295
    • (2010) PLoS ONE , vol.5
    • Zaragoza, M.V.1    Fass, J.2    Diegoli, M.3    Lin, D.4    Arbustini, E.5
  • 40
    • 11144314695 scopus 로고    scopus 로고
    • Estimating haplotype-disease associations with pooled genotype data
    • Zeng, D., and Lin, D. Y. (2005). Estimating haplotype-disease associations with pooled genotype data. Genet. Epidemiol. 28, 70-82.
    • (2005) Genet. Epidemiol. , vol.28 , pp. 70-82
    • Zeng, D.1    Lin, D.Y.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.