Computational and bioinformatics frameworks for next-generation whole exome and genome sequencing

The Scientific World Journal

Volumn 2013, Issue , 2013, Pages

  Dolled Filhart, Marisa P ^a   Lee, Michael ^a   Ou Yang, Chih Wen ^a   Haraksingh, Rajini Rani ^a   Lin, Jimmy Cheng Ho ^a  

^a Rare Genomics Institute   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; BIOLOGY; COMPUTER PROGRAM; EXOME; GENE DELETION; GENE INSERTION; GENE SEQUENCE; REVIEW; ALGORITHM; ANIMAL; CHROMOSOME MAP; DNA SEQUENCE; GENETIC DATABASE; GENETICS; GENOME; HUMAN; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; SEQUENCE ALIGNMENT;

ALGORITHMS; ANIMALS; BASE SEQUENCE; CHROMOSOME MAPPING; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; EXOME; GENOME; HUMANS; MOLECULAR SEQUENCE DATA; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SOFTWARE;

MLCS; MLOWN;

EID: 84873381275     PISSN: 1537744X     EISSN: 1537744X     Source Type: Journal    
DOI: 10.1155/2013/730210     Document Type: Review

References (51)

1. Mardis E. R., Next-generation DNA sequencing methods. Annual Review of Genomics and Human Genetics 2008 9 387 402 2-s2.0-52949096084 10.1146/annurev.genom.9.081307.164359
2. 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 16 2078 2079 2-s2.0-68549104404 10.1093/bioinformatics/ btp352
3. Danecek P., Auton A., Abecasis G., Albers C. A., Banks E., DePristo M. A., Handsaker R. E., Lunter G., Marth G. T., Sherry S. T., McVean G., Durbin R., The variant call format and VCFtools. Bioinformatics 2011 27 15 2156 2158 2-s2.0-79960405019 10.1093/bioinformatics/btr330 btr330
4. Day-Williams A. G., Zeggini E., The effect of next-generation sequencing technology on complex trait research. European Journal of Clinical Investigation 2011 41 5 561 567 2-s2.0-79953733858 10.1111/j.1365-2362.2010.02437.x
5. Ruffalo M., LaFramboise T., Koyuturk M., Comparative analysis of algorithms for next-generation sequencing read alignment. Bioinformatics 2011 27 20 2790 2796
6. Homer N., Nelson S. F., Improved variant discovery through local re-alignment of short-read next-generation sequencing data using SRMA. Genome Biology 2010 11 10, article R99 2-s2.0-77957579023 10.1186/gb-2010-11-10-r99
7. Langmead B., Trapnell C., Pop M., Salzberg S. L., Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 2009 10 3, article R25 2-s2.0-62349130698 10.1186/gb-2009-10-3-r25
8. Langmead B., Salzberg S. L., Fast gapped-read alignment with Bowtie 2. Nature Methods 2012 9 4 357 359
9. Li H., Durbin R., Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009 25 14 1754 1760 2-s2.0-67649884743 10.1093/bioinformatics/btp324
10. Li H., Ruan J., Durbin R., Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Research 2008 18 11 1851 1858 2-s2.0-55549097836 10.1101/gr.078212.108
11. Li H., Durbin R., Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 2010 26 5 589 595 2-s2.0-77949587649 10.1093/bioinformatics/btp698 btp698
12. Alkan C., Sajjadian S., Eichler E. E., Limitations of next-generation genome sequence assembly. Nature Methods 2011 8 1 61 65 2-s2.0-78650909427 10.1038/nmeth.1527
13. Hach F., Hormozdiari F., Alkan C., Hormozdiari F., Birol I., Eichler E. E., Sahinalp S. C., MrsFAST: a cache-oblivious algorithm for short-read mapping. Nature Methods 2010 7 8 576 577 2-s2.0-77955163329 10.1038/nmeth0810-576
14. Dinov I. D., Torri F., Macciardi F., Petrosyan P., Liu Z., Zamanyan A., Eggert P., Pierce J., Genco A., Knowles J. A., Clark A. P., Van Horn J. D., Ames J., Kesselman C., Toga A. W., Applications of the pipeline environment for visual informatics and genomics computations. BMC Bioinformatics 2011 12, article 304 2-s2.0-79960688272 10.1186/1471-2105-12-304
15. Alkan C., Kidd J. M., Marques-Bonet T., Aksay G., Antonacci F., Hormozdiari F., Kitzman J. O., Baker C., Malig M., Mutlu O., Sahinalp S. C., Gibbs R. A., Eichler E. E., Personalized copy number and segmental duplication maps using next-generation sequencing. Nature Genetics 2009 41 10 1061 1067 2-s2.0-70349556543 10.1038/ng.437
16. Rumble S. M., Lacroute P., Dalca A. V., Fiume M., Sidow A., Brudno M., SHRiMP: accurate mapping of short color-space reads. PLoS Computational Biology 2009 5 5 2-s2.0-67049159825 10.1371/journal.pcbi.1000386 e1000386
17. David M., Dzamba M., Lister D., Ilie L., Brudno M., SHRiMP2: sensitive yet practical short read mapping. Bioinformatics 2011 27 7 1011 1012 2-s2.0-79953310937 10.1093/bioinformatics/btr046 btr046
18. Li R., Li Y., Kristiansen K., Wang J., SOAP: short oligonucleotide alignment program. Bioinformatics 2008 24 5 713 714 2-s2.0-40049104732 10.1093/bioinformatics/btn025 (Pubitemid 351321217)
19. Li R., Yu C., Li Y., Lam T. W., Yiu S. M., Kristiansen K., Wang J., SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 2009 25 15 1966 1967 2-s2.0-67650711615 10.1093/bioinformatics/btp336
20. Liu C. M., Wong K. F., Wu E. M. K., SOAP3: ultra-fast GPU-based parallel alignment tool for short reads. Bioinformatics 2012 28 6 878 879
21. Nielsen R., Paul J. S., Albrechtsen A., Song Y. S., Genotype and SNP calling from next-generation sequencing data. Nature Reviews Genetics 2011 12 6 443 451 2-s2.0-79956314887 10.1038/nrg2986
22. 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 Research 2010 20 9 1297 1303 2-s2.0-77956295988 10.1101/gr.107524.110
23. Cancer Genome Atlas Network, Comprehensive molecular portraits of human breast tumours. Nature 2012 490 7418 61 70
24. Altshuler D. L., Durbin R. M., Abecasis G. R., Bentley D. R., Chakravarti A., Clark A. G., Collins F. S., De La Vega F. M., Donnelly P., Egholm M., Flicek P., Gabriel S. B., Gibbs R. A., Knoppers B. M., Lander E. S., Lehrach H., Mardis E. R., McVean G. A., Nickerson D. A., Peltonen L., Schafer A. J., Sherry S. T., Wang J., Wilson R. K., Deiros D., Metzker M., Muzny D., Reid J., Wheeler D., Wang S. J., Li J., Jian M., Li G., Li R., Liang H., Tian G., Wang B., Wang J., Wang W., Yang H., Zhang X., Zheng H., Ambrogio L., Bloom T., Cibulskis K., Fennell T. J., Jaffe D. B., Shefler E., Sougnez C. L., Bentley I. D. R., Gormley N., Humphray S., Kingsbury Z., Koko-Gonzales P., Stone J., Mc Kernan K. J., Costa G. L., Ichikawa J. K., Lee C. C., Sudbrak R., Borodina T. A., Dahl A., Davydov A. N., Marquardt P., Mertes F., Nietfeld W., Rosenstiel P., Schreiber S., Soldatov A. V., Timmermann B., Tolzmann M., Affourtit J., Ashworth D., Attiya S., Bachorski M., Buglione E., Burke A., Caprio A., Celone C., Clark S., Conners D., Desany B., Gu L., Guccione L., Kao K., Kebbel A., Knowlton J., Labrecque M., McDade L., Mealmaker C., Minderman M., Nawrocki A., Niazi F., Pareja K., Ramenani R., Riches D., Song W., Turcotte C., Wang S., Dooling D., Fulton L., Fulton R., Weinstock G., Burton J., Carter D. M., Churcher C., Coffey A., Cox A., Palotie A., Quail M., Skelly T., Stalker J., Swerdlow H. P., Turner D., De Witte A., Giles S., Bainbridge M., Challis D., Sabo A., Yu F., Yu J., Fang X., Guo X., Li Y., Luo R., Tai S., Wu H., Zheng H., Zheng X., Zhou Y., Marth G. T., Garrison E. P., Huang W., Indap A., Kural D., Lee W. P., Leong W. F., Quinlan A. R., Stewart C., Stromberg M. P., Ward A. N., Wu J., Lee C., Mills R. E., Shi X., Daly M. J., DePristo M. A., Ball A. D., Banks E., Browning B. L., Garimella K. V., Grossman S. R., Handsaker R. E., Hanna M., Hartl C., Kernytsky A. M., Korn J. M., Li H., Maguire J. R., McKenna A., Nemesh J. C., Philippakis A. A., Poplin R. E., Price A., Rivas M. A., Sabeti P. C., Schaffner S. F., Shlyakhter I. A., Cooper D. N., Ball E. V., Mort M., Phillips A. D., Stenson P. D., Sebat J., Makarov V., Ye K., Yoon S. C., Bustamante C. D., Boyko A., Degenhardt J., Gravel S., Gutenkunst R. N., Kaganovich M., Keinan A., Lacroute P., Ma X., Reynolds A., Clarke L., Cunningham F., Herrero J., Keenen S., Kulesha E., Leinonen R., McLaren W. M., Radhakrishnan R., Smith R. E., Zalunin V., Korbel J. O., Stütz A. M., Humphray I. S., Bauer M., Cheetham R. K., Cox T., Eberle M., James T., Kahn S., Murray L., Ye K., Fu Y., Hyland F. C. L., Manning J. M., Stephen F. M., Peckham H. E., Sakarya O., Sun Y. A., Tsung E. F., Mark A. B., Konkel M. K., Walker J. A., Albrecht M. W., Amstislavskiy V. S., Herwig R., Parkhomchuk D. V., Agarwala R., Khouri H. M., Morgulis A. O., Paschall J. E., Phan L. D., Rotmistrovsky K. E., Sanders R. D., Shumway M. F., Xiao C., Gil A. M., Auton A., Iqbal Z., Lunter G., Marchini J. L., Moutsianas L., Myers S., Tumian A., Knight J., Winer R., Craig D. W., Beckstrom-Sternberg S. M., Christoforides A., Kurdoglu A. A., Pearson J. V., Sinari S. A., Tembe W. D., Haussler D., Hinrichs A. S., Katzman S. J., Kern A., Kuhn R. M., Przeworski M., Hernandez R. D., Howie B., Kelley J. L., Melton S. C., Li Y., Anderson P., Blackwell T., Chen W., Cookson W. O., Ding J., Kang H. M., Lathrop M., Liang L., Moffatt M. F., Scheet P., Sidore C., Snyder M., Zhan X., Zöllner S., Awadalla P., Casals F., Idaghdour Y., Keebler J., Stone E. A., Zilversmit M., Jorde L., Xing J., Eichler E. E., Aksay G., Alkan C., Hajirasouliha I., Hormozdiari F., Kidd J. M., CenkSahinalp S., Sudmant P. H., Chen K., Chinwalla A., Ding L., Koboldt D. C., McLellan M. D., Wallis J. W., Wendl M. C., Zhang Q., Albers C. A., Ayub Q., Balasubramaniam S., Barrett J. C., Chen Y., Conrad D. F., Danecek P., Dermitzakis E. T., Hu M., Huang N., Matt E. H., Jin H., Jostins L., Keane T. M., Quang Le S., Lindsay S., Long Q., MacArthur D. G., Montgomery S. B., Parts L., Chris Tyler-Smith, Walter K., Zhang Y., Gerstein M. B., Snyder M., Abyzov A., Balasubramanian S., Bjornson R., Grubert F., Habegger L., Haraksingh R., Khurana E., Lam H. Y. K., Leng J., Mu X. J., Urban A. E., Zhang Z., McCarroll S. A., Zheng-Bradley X., Batzer M. A., Hurles M. E., Du J., Jee J., Coafra C., Dinh H., Kovar C., Lee S., Nazareth L., Wilkinson J., Coffey A., Scott C., Tyler-Smith C., Gharani N., Kaye J. S., Kent A., Li T., McGuire A. L., Ossorio P. N., Rotimi C. N., Su Y., Toji L. H., Felsenfeld A. L., McEwen J. E., Abdallah A., Juenger C. R., Clemm N. C., Duncanson A., Green E. D., Guyer M. S., Peterson J. L., A map of human genome variation from population-scale sequencing. Nature 2010 467 7319 1061 1073 2-s2.0-78049390036 10.1038/nature09534
25. Koboldt D. C., Chen K., Wylie T., Larson D. E., McLellan M. D., Mardis E. R., Weinstock G. M., Wilson R. K., Ding L., VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics 2009 25 17 2283 2285 2-s2.0-69949122158 10.1093/bioinformatics/btp373
26. Koboldt D. C., Zhang Q., Larson D. E., VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Research 2012 22 3 568 576
27. Challis D., Yu J., Evani U. S., An integrative variant analysis suite for whole exome next-generation sequencing data. BMC Bioinformatics 2012 13, article 8
28. Hillman-Jackson J., Clements D., Blankenberg D., Taylor J., Nekrutenko A., Using Galaxy to perform large-scale interactive data analyses. Current Protocols in Bioinformatics 2012 chapter 10, unit 10.5
29. Ji H. P., Improving bioinformatic pipelines for exome variant calling. Genome Medicine 2012 4 1, article 7
30. Lemos R. R., Souza M. B., Oliveira J. R., Exploring the implications of INDELs in neuropsychiatric genetics: challenges and perspectives. Journal of Molecular Neuroscience 2012 47 3 419 424
31. Lee S. A., Mun H. S., Kim H., Lee H. K., Kim B. J., Hwang E. S., Kook Y. H., Kim B. J., Naturally occurring hepatitis B virus X deletions and insertions among Korean chronic patients. Journal of Medical Virology 2011 83 1 65 70 2-s2.0-78649537401 10.1002/jmv.21938
32. Väli U., Brandström M., Johansson M., Ellegren H., Insertion-deletion polymorphisms (indels) as genetic markers in natural populations. BMC Genetics 2008 9, article 8 2-s2.0-40949091938 10.1186/1471-2156-9-8
33. Lunter G., Probabilistic whole-genome alignments reveal high indel rates in the human and mouse genomes. Bioinformatics 2007 23 13 i289 i296 2-s2.0-34547830856 10.1093/bioinformatics/btm185 (Pubitemid 47244412)
34. Krawitz P., Rödelsperger C., Jäger M., Jostins L., Bauer S., Robinson P. N., Microindel detection in short-read sequence data. Bioinformatics 2010 26 6 722 729 2-s2.0-77951939888 10.1093/bioinformatics/btq027 btq027
35. Ye K., Schulz M. H., Long Q., Apweiler R., Ning Z., Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics 2009 25 21 2865 2871 2-s2.0-70350694443 10.1093/bioinformatics/btp394
36. MacArthur D. G., Balasubramanian S., Frankish A., A systematic survey of loss-of-function variants in human protein-coding genes. Science 2012 335 6070 823 828
37. Albers C. A., Lunter G., MacArthur D. G., McVean G., Ouwehand W. H., Durbin R., Dindel: accurate indel calls from short-read data. Genome Research 2011 21 6 961 973 2-s2.0-79957932376 10.1101/gr.112326.110
38. Neuman J. A., Isakov O., Shomron N., Analysis of insertion-deletion from deep-sequencing data: software evaluation for optimal detection. Briefings in Bioinformatics. In press 10.1093/bib/bbs013
39. Cooper G. M., Shendure J., Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data. Nature Reviews Genetics 2011 12 9 628 640
40. Lander E. S., Initial impact of the sequencing of the human genome. Nature 2011 470 7333 187 197 2-s2.0-79951481957 10.1038/nature09792
41. Hindorff L. A., Sethupathy P., Junkins H. A., Ramos E. M., Mehta J. P., Collins F. S., Manolio T. A., Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proceedings of the National Academy of Sciences of the United States of America 2009 106 23 9362 9367 2-s2.0-67249117049 10.1073/pnas.0903103106
42. Kumar P., Henikoff S., Ng P. C., Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nature Protocols 2009 4 7 1073 1081 2-s2.0-68149165614 10.1038/nprot.2009.86
43. Adzhubei I. A., Schmidt S., Peshkin L., Ramensky V. E., Gerasimova A., Bork P., Kondrashov A. S., Sunyaev S. R., A method and server for predicting damaging missense mutations. Nature Methods 2010 7 4 248 249 2-s2.0-77951640946 10.1038/nmeth0410-248
44. Nair P. S., Vihinen M., VariBench: A benchmark database for variations. Human Mutation. In press
45. Cingolani P., Platts A., Wang le L., A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118, iso-2, iso-3. Fly 2012 6 2 80 92
46. De Baets G., Van Durme J., Reumers J., SNPeffect 4.0: on-line prediction of molecular and structural effects of protein-coding variants. Nucleic Acids Research 2012 40 D935 D939
47. Wang K., Li M., Hakonarson H., ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Research 2010 38 16 e164 2-s2.0-77956534324 10.1093/nar/gkq603 gkq603
48. Yandell M., Huff C. D., Hu H., A probabilistic disease-gene finder for personal genomes. Genome Research 2011 21 9 1529 1542
49. Habegger L., Balasubramanian S., Chen D. Z., VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment. Bioinformatics 2012 28 17 2267 2269
50. MacArthur D. G., Balasubramanian S., Frankish A., A systematic survey of loss-of-function variants in human protein-coding genes. Science 2012 335 6070 823 828
51. Sincan M., Simeonov D. R., Adams D., VAR-MD: a tool to analyze whole exome-genome variants in small human pedigrees with mendelian inheritance. Human Mutation 2012 33 4 593 598