The missing indels: An estimate of indel variation in a human genome and analysis of factors that impede detection

Nucleic Acids Research

Volumn 43, Issue 15, 2015, Pages 7217-7228

  Jiang, Yue ^a,b   Turinsky, Andrei L ^a   Brudno, Michael ^a,c  

^a HOSPITAL FOR SICK CHILDREN   (Canada)

^b HARBIN INSTITUTE OF TECHNOLOGY   (China)

^c UNIVERSITY OF TORONTO   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

DIMER;

ARTICLE; CONTROLLED STUDY; GENE DELETION; GENE INSERTION; GENE SEQUENCE; GENETIC ANALYSIS; HETEROZYGOSITY; HIGH THROUGHPUT SEQUENCING; HUMAN; HUMAN GENOME; INDEL MUTATION; NEXT GENERATION SEQUENCING; PRIORITY JOURNAL; SEQUENCE ALIGNMENT; SHORT INTERSPERSED REPEAT; SINGLE NUCLEOTIDE POLYMORPHISM; ALU SEQUENCE; ANIMAL; DNA BASE COMPOSITION; MOLECULAR EVOLUTION; NUCLEOTIDE REPEAT; NUCLEOTIDE SEQUENCE; PRIMATE; PROCEDURES;

ALU ELEMENTS; ANIMALS; BASE COMPOSITION; DNA MUTATIONAL ANALYSIS; EVOLUTION, MOLECULAR; GENOME, HUMAN; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; INDEL MUTATION; PRIMATES; REPETITIVE SEQUENCES, NUCLEIC ACID;

EID: 84941254075     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkv677     Document Type: Article

References (35)

1. Mills,R.E., Luttig,C.T., Larkins,C.E., Beauchamp,A., Tsui,C., Pittard,W.S. and Devine,S.E. (2006) An initial map of insertion and deletion (INDEL) variation in the human genome. Genome Res., 16, 1182-1190.
2. Kidd,J.M., Cooper,G.M., Donahue,W.F., Hayden,H.S., Sampas,N., Graves,T., Hansen,N., Teague,B., Alkan,C., Antonacci,F. et al. (2008) Mapping and sequencing of structural variation from eight human genomes. Nature, 453, 56-64.
3. Mills,R.E., Pittard,W.S., Mullaney,J.M., Farooq,U., Creasy,T.H., Mahurkar,A.A., Kemeza,D.M., Strassler,D.S., Ponting,C.P., Webber,C. et al. (2011) Natural genetic variation caused by small insertions and deletions in the human genome. Genome Res., 21, 830-839.
4. Bamshad,M.J., Ng,S.B., Bigham,A.W., Tabor,H.K., Emond,M.J., Nickerson,D.A. and Shendure,J. (2011) Exome sequencing as a tool for Mendelian disease gene discovery. Nat. Rev. Genet., 12, 745-755.
5. Saunders,C.J., Miller,N.A., Soden,S.E., Dinwiddie,D.L., Noll,A., Alnadi,N.A., Andraws,N., Patterson,M.L., Krivohlavek,L.A., Fellis,J. et al. (2012) Rapid whole-genome sequencing for genetic disease diagnosis in neonatal intensive care units. Sci. Transl. Med., 4, 154ra135.
6. Rehm,H.L. (2013) Disease-targeted sequencing: a cornerstone in the clinic. Nat. Rev. Genet., 14, 295-300.
7. Gilissen,C., Hoischen,A., Brunner,H.G. and Veltman,J.A. (2011) Unlocking Mendelian disease using exome sequencing. Genome Biol., 12, 228.
8. Levy,S., Sutton,G., Ng,P.C., Feuk,L., Halpern,A.L., Walenz,B.P., Axelrod,N., Huang,J., Kirkness,E.F., Denisov,G. et al. (2007) The diploid genome sequence of an individual human. PLoS Biol., 5, e254.
9. Sanger,F., Nicklen,S. and Coulson,A.R. (1977) DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. U.S.A., 74, 5463-5467.
10. Wheeler,D.A., Srinivasan,M., Egholm,M., Shen,Y., Chen,L., McGuire,A., He,W., Chen,Y.J., Makhijani,V., Roth,G.T. et al. (2008) The complete genome of an individual by massively parallel DNA sequencing. Nature, 452, 872-876.
11. Voelkerding,K.V., Dames,S.A. and Durtschi,J.D. (2009) Next-generation sequencing: from basic research to diagnostics. Clin. Chem., 55, 641-658.
12. 1000 Genomes Project Consortium, Abecasis,G.R., Altshuler,D., Auton,A., Brooks,L.D., Durbin,R.M., Gibbs,R.A., Hurles,M.E. and McVean,G.A. (2010) A map of human genome variation from population-scale sequencing. Nature, 467, 1061-1073.
13. Jiang,Y.,Wang,Y. and Brudno,M. (2012) PRISM: pair-read informed split-read mapping for base-pair level detection of insertion, deletion and structural variants. Bioinformatics, 28, 2576-2583.
14. Mullaney,J.M.,Mills,R.E., Pittard,W.S. and Devine,S.E. (2010) Small insertions and deletions (INDELs) in human genomes. Hum. Mol. Genet., 19, R131-R136.
15. Dawson,E., Chen,Y., Hunt,S., Smink,L.J., Hunt,A., Rice,K., Livingston,S., Bumpstead,S., Bruskiewich,R., Sham,P. et al. (2001) A SNP resource for human chromosome 22: extracting dense clusters of SNPs from the genomic sequence. Genome Res., 11, 170-178.
16. Chen,J.Q., Wu,Y., Yang,H., Bergelson,J., Kreitman,M. and Tian,D. (2009) Variation in the ratio of nucleotide substitution and indel rates across genomes in mammals and bacteria. Mol. Biol. Evol., 26, 1523-1531.
17. Wang,J., Wang,W., Li,R., Li,Y., Tian,G., Goodman,L., Fan,W., Zhang,J., Li,J., Guo,Y. et al. (2008) The diploid genome sequence of an Asian individual. Nature, 456, 60-65.
18. Bentley,D.R., Balasubramanian,S., Swerdlow,H.P., Smith,G.P., Milton,J., Brown,C.G., Hall,K.P., Evers,D.J., Barnes,C.L., Bignell,H.R. et al. (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature, 456, 53-59.
19. Zhang,Z.D., Du,J., Lam,H., Abyzov,A., Urban,A.E., Snyder,M. and Gerstein,M. (2011) Identification of genomic indels and structural variations using split reads. BMC Genomics, 12, 375.
20. Kircher,M. and Kelso,J. (2010) High-throughput DNA sequencing-concepts and limitations. Bioessays, 32, 524-536.
21. Li,H. and Homer,N. (2010) A survey of sequence alignment algorithms for next-generation sequencing. Brief. Bioinform., 11, 473-483.
22. O'Rawe,J., Jiang,T., Sun,G., Wu,Y., Wang,W., Hu,J., Bodily,P., Tian,L., Hakonarson,H., Johnson,W.E. et al. (2013) Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing. Genome Med., 5, 28.
23. Ghoneim,D.H., Myers,J.R., Tuttle,E. and Paciorkowski,A.R. (2014) Comparison of insertion/deletion calling algorithms on human next-generation sequencing data. BMC Res. Notes, 7, 864.
24. Krawitz,P., Rodelsperger,C., Jager,M., Jostins,L., Bauer,S. and Robinson,P.N. (2010) Microindel detection in short-read sequence data. Bioinformatics, 26, 722-729.
25. Neuman,J.A., Isakov,O. and Shomron,N. (2013) Analysis of insertion-deletion from deep-sequencing data: software evaluation for optimal detection. Brief. Bioinform., 14, 46-55.
26. Porter,J., Berkhahn,J. and Zhang,L. (2014) A Comparative Analysis of Computational Indel Calling Pipelines for Next Generation Sequencing Data. Proceedings of the International Conference on Bioinformatics and Computational Biology (BIOCOMP'14). Las Vegas.
27. Narzisi,G., O'Rawe,J.A., Iossifov,I., Fang,H., Lee,Y.H., Wang,Z., Wu,Y., Lyon,G.J., Wigler,M. and Schatz,M.C. (2014) Accurate de novo and transmitted indel detection in exome-capture data using microassembly. Nat. Methods, 11, 1033-1036.
28. Fang,H., Wu,Y., Narzisi,G., O'Rawe,J.A., Barron,L.T., Rosenbaum,J., Ronemus,M., Iossifov,I., Schatz,M.C. and Lyon,G.J. (2014) Reducing INDEL calling errors in whole genome and exome sequencing data. Genome Med., 6, 89.
29. McKenna,A., Hanna,M., Banks,E., Sivachenko,A., Cibulskis,K., Kernytsky,A., Garimella,K., Altshuler,D., Gabriel,S., Daly,M. et al. (2010) The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res., 20, 1297-1303.
30. Albers,C.A., Lunter,G., MacArthur,D.G., McVean,G., Ouwehand,W.H. and Durbin,R. (2011) Dindel: accurate indel calls from short-read data. Genome Res., 21, 961-973.
31. Li,H. and Durbin,R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760.
32. Homer,N., Merriman,B. and Nelson,S.F. (2009) BFAST: an alignment tool for large scale genome resequencing. PloS One, 4, e7767.
33. Li,H. and Durbin,R. (2010) Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics, 26, 589-595.
34. Rosenbloom,K.R., Armstrong,J., Barber,G.P., Casper,J., Clawson,H., Diekhans,M., Dreszer,T.R., Fujita,P.A., Guruvadoo,L., Haeussler,M. et al. (2014) The UCSC Genome Browser database: 2015 update. Nucleic Acids Res., 43, D670-D681.
35. Benjamini,Y. and Speed,T.P. (2012) Summarizing and correcting the GC content bias in high-throughput sequencing. Nucleic Acids Res., 40, e72.