publication . Preprint . 2015

SSCM: A method to analyze and predict the pathogenicity of sequence variants

Sharad Vikram; Matthew D Rasmussen; Eric A Evans; Imran S Haque;
Open Access English
  • Published: 26 Jun 2015
  • Publisher: Cold Spring Harbor Laboratory
Abstract
<jats:p>The advent of cost-effective DNA sequencing has provided clinics with high-resolution information about patients' genetic variants, which has resulted in the need for efficient interpretation of this genomic data. Traditionally, variant interpretation has been dominated by many manual, time-consuming processes due to the disparate forms of relevant information in clinical databases and literature. Computational techniques promise to automate much of this, and while they currently play only a supporting role, their continued improvement for variant interpretation is necessary to tackle the problem of scaling genetic sequencing to ever larger populations. ...
34 references, page 1 of 3

[1] 1000 Genomes Project Consortium, R. M. Durbin, G. R. Abecasis, D. L. Altshuler, A. Auton, L. D. Brooks, R. M. Durbin, R. A. Gibbs, M. E. Hurles, and G. A. McVean. A map of human genome variation from population-scale sequencing. Nature, 467(7319):1061{1073, Oct 2010.

[2] G. R. Abecasis, A. Auton, L. D. Brooks, M. A. DePristo, R. M. Durbin, R. E. Handsaker, H. M. Kang, G. T. Marth, and G. A. McVean. An integrated map of genetic variation from 1,092 human genomes. Nature, 491(7422):56{65, Nov. 2012.

[3] I. A. Adzhubei, S. Schmidt, L. Peshkin, V. E. Ramensky, A. Gerasimova, P. Bork, A. S. Kondrashov, and S. R. Sunyaev. A method and server for predicting damaging missense mutations. Nature methods, 7(4):248{9, Apr. 2010.

[4] M. Baker. One-stop shop for disease genes. Nature, 491(7423):171, Nov. 2012.

[5] B. E. Bernstein, E. Birney, I. Dunham, E. D. Green, C. Gunter, and M. Snyder. An integrated encyclopedia of DNA elements in the human genome. Nature, 489(7414):57{ 74, Sept. 2012.

[6] Y. Choi, G. E. Sims, S. Murphy, J. R. Miller, and A. P. Chan. Predicting the Functional E ect of Amino Acid Substitutions and Indels. PLoS ONE, 7(10), 2012. [OpenAIRE]

[7] S. Chun and J. C. Fay. Identi cation of deleterious mutations within three human genomes. Genome research, 19(9):1553{61, Sept. 2009.

[8] E. V. Davydov, D. L. Goode, M. Sirota, G. M. Cooper, A. Sidow, and S. Batzoglou. Identifying a high fraction of the human genome to be under selective constraint using GERP++. PLoS computational biology, 6(12):e1001025, Jan. 2010.

[9] F. O. Desmet, D. Hamroun, M. Lalande, G. Collod-Beroud, M. Claustres, and C. Beroud. Human Splicing Finder: an online bioinformatics tool to predict splicing signals. Nucleic Acids Res., 37(9):e67, May 2009. [OpenAIRE]

[10] P. L. Devers, A. Cronister, K. E. Ormond, F. Facio, C. K. Brasington, and P. Flodman. Noninvasive prenatal testing/noninvasive prenatal diagnosis: the position of the National Society of Genetic Counselors. J Genet Couns, 22(3):291{295, Jun 2013. [OpenAIRE]

[11] F. E. Dewey, M. E. Grove, C. Pan, B. A. Goldstein, J. A. Bernstein, H. Chaib, J. D. Merker, R. L. Goldfeder, G. M. Enns, S. P. David, N. Pakdaman, K. E. Ormond,

[15] A. R. Gregg, S. J. Gross, R. G. Best, K. G. Monaghan, K. Bajaj, B. G. Skotko, B. H. Thompson, and M. S. Watson. ACMG statement on noninvasive prenatal screening for fetal aneuploidy. Genet. Med., 15(5):395{398, May 2013.

[16] B. Gulko, M. J. Hubisz, I. Gronau, and A. Siepel. A method for calculating probabilities of tness consequences for point mutations across the human genome. Nat. Genet., 47(3):276{283, Mar 2015.

[17] M. M. Ho man, O. J. Buske, J. Wang, Z. Weng, J. A. Bilmes, and W. S. Noble. Unsupervised pattern discovery in human chromatin structure through genomic segmentation. Nature methods, 9(5):473{6, May 2012.

[18] J. Hu and P. C. Ng. SIFT Indel: predictions for the functional e ects of amino acid insertions/deletions in proteins. PloS one, 8(10):e77940, Jan. 2013.

34 references, page 1 of 3
Abstract
<jats:p>The advent of cost-effective DNA sequencing has provided clinics with high-resolution information about patients' genetic variants, which has resulted in the need for efficient interpretation of this genomic data. Traditionally, variant interpretation has been dominated by many manual, time-consuming processes due to the disparate forms of relevant information in clinical databases and literature. Computational techniques promise to automate much of this, and while they currently play only a supporting role, their continued improvement for variant interpretation is necessary to tackle the problem of scaling genetic sequencing to ever larger populations. ...
34 references, page 1 of 3

[1] 1000 Genomes Project Consortium, R. M. Durbin, G. R. Abecasis, D. L. Altshuler, A. Auton, L. D. Brooks, R. M. Durbin, R. A. Gibbs, M. E. Hurles, and G. A. McVean. A map of human genome variation from population-scale sequencing. Nature, 467(7319):1061{1073, Oct 2010.

[2] G. R. Abecasis, A. Auton, L. D. Brooks, M. A. DePristo, R. M. Durbin, R. E. Handsaker, H. M. Kang, G. T. Marth, and G. A. McVean. An integrated map of genetic variation from 1,092 human genomes. Nature, 491(7422):56{65, Nov. 2012.

[3] I. A. Adzhubei, S. Schmidt, L. Peshkin, V. E. Ramensky, A. Gerasimova, P. Bork, A. S. Kondrashov, and S. R. Sunyaev. A method and server for predicting damaging missense mutations. Nature methods, 7(4):248{9, Apr. 2010.

[4] M. Baker. One-stop shop for disease genes. Nature, 491(7423):171, Nov. 2012.

[5] B. E. Bernstein, E. Birney, I. Dunham, E. D. Green, C. Gunter, and M. Snyder. An integrated encyclopedia of DNA elements in the human genome. Nature, 489(7414):57{ 74, Sept. 2012.

[6] Y. Choi, G. E. Sims, S. Murphy, J. R. Miller, and A. P. Chan. Predicting the Functional E ect of Amino Acid Substitutions and Indels. PLoS ONE, 7(10), 2012. [OpenAIRE]

[7] S. Chun and J. C. Fay. Identi cation of deleterious mutations within three human genomes. Genome research, 19(9):1553{61, Sept. 2009.

[8] E. V. Davydov, D. L. Goode, M. Sirota, G. M. Cooper, A. Sidow, and S. Batzoglou. Identifying a high fraction of the human genome to be under selective constraint using GERP++. PLoS computational biology, 6(12):e1001025, Jan. 2010.

[9] F. O. Desmet, D. Hamroun, M. Lalande, G. Collod-Beroud, M. Claustres, and C. Beroud. Human Splicing Finder: an online bioinformatics tool to predict splicing signals. Nucleic Acids Res., 37(9):e67, May 2009. [OpenAIRE]

[10] P. L. Devers, A. Cronister, K. E. Ormond, F. Facio, C. K. Brasington, and P. Flodman. Noninvasive prenatal testing/noninvasive prenatal diagnosis: the position of the National Society of Genetic Counselors. J Genet Couns, 22(3):291{295, Jun 2013. [OpenAIRE]

[11] F. E. Dewey, M. E. Grove, C. Pan, B. A. Goldstein, J. A. Bernstein, H. Chaib, J. D. Merker, R. L. Goldfeder, G. M. Enns, S. P. David, N. Pakdaman, K. E. Ormond,

[15] A. R. Gregg, S. J. Gross, R. G. Best, K. G. Monaghan, K. Bajaj, B. G. Skotko, B. H. Thompson, and M. S. Watson. ACMG statement on noninvasive prenatal screening for fetal aneuploidy. Genet. Med., 15(5):395{398, May 2013.

[16] B. Gulko, M. J. Hubisz, I. Gronau, and A. Siepel. A method for calculating probabilities of tness consequences for point mutations across the human genome. Nat. Genet., 47(3):276{283, Mar 2015.

[17] M. M. Ho man, O. J. Buske, J. Wang, Z. Weng, J. A. Bilmes, and W. S. Noble. Unsupervised pattern discovery in human chromatin structure through genomic segmentation. Nature methods, 9(5):473{6, May 2012.

[18] J. Hu and P. C. Ng. SIFT Indel: predictions for the functional e ects of amino acid insertions/deletions in proteins. PloS one, 8(10):e77940, Jan. 2013.

34 references, page 1 of 3
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