Effective detection of rare variants in pooled DNA samples using Cross-pool tailcurve analysis

Genome Biology

Volumn 12, Issue 9, 2011, Pages

  Niranjan, Tejasvi S ^a   Adamczyk, Abby ^a   Bravo, Héctor C ^b   Taub, Margaret A ^c   Wheelan, Sarah J ^a,c   Irizarry, Rafael ^c   Wang, Tao ^a  

^a JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b University of Maryland   (United States)

^c JOHNS HOPKINS BLOOMBERG SCHOOL OF PUBLIC HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; GRIP2 PROTEIN, HUMAN; NERVE PROTEIN; SIGNAL TRANSDUCING ADAPTOR PROTEIN;

ALGORITHM; AMPLICON; ARTICLE; COHORT ANALYSIS; COMPARATIVE STUDY; COMPUTER PROGRAM; CONTROLLED STUDY; CROSS POOL TAILCURVE ANALYSIS; DNA LIBRARY; DNA SEQUENCE; EXON; GENE IDENTIFICATION; GENE POOL; GENETIC ANALYSIS; GENETIC CODE; GENETIC VARIABILITY; HUMAN; MAJOR CLINICAL STUDY; POLYMERASE CHAIN REACTION; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS; VALIDATION PROCESS; ALLELE; GENE FREQUENCY; GENETICS; GENOTYPE; HUMAN GENOME; METHODOLOGY; SEQUENCE ALIGNMENT; SINGLE NUCLEOTIDE POLYMORPHISM; STANDARD;

ADAPTOR PROTEINS, SIGNAL TRANSDUCING; ALGORITHMS; ALLELES; COHORT STUDIES; DNA; GENE FREQUENCY; GENOME, HUMAN; GENOTYPE; HUMANS; NERVE TISSUE PROTEINS; POLYMORPHISM, SINGLE NUCLEOTIDE; SENSITIVITY AND SPECIFICITY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 80052868508     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2011-12-9-r93     Document Type: Article

References (21)

1. Druley TE, Vallania FL, Wegner DJ, Varley KE, Knowles OL, Bonds JA, Robison SW, Doniger SW, Hamvas A, Cole FS, Fay JC, Mitra RD. Quantification of rare allelic variants from pooled genomic DNA. Nat Methods 2009, 6:263-265. 10.1038/nmeth.1307, 2776647, 19252504.
2. Out AA, van Minderhout IJ, Goeman JJ, Ariyurek Y, Ossowski S, Schneeberger K, Weigel D, van Galen M, Taschner PE, Tops CM, Breuning MH, van Ommen GJ, den Dunnen JT, Devilee P, Hes FJ. Deep sequencing to reveal new variants in pooled DNA samples. Hum Mutat 2009, 30:1703-1712. 10.1002/humu.21122, 19842214.
3. Calvo SE, Tucker EJ, Compton AG, Kirby DM, Crawford G, Burtt NP, Rivas M, Guiducci C, Bruno DL, Goldberger OA, Redman MC, Wiltshire E, Wilson CJ, Altshuler D, Gabriel SB, Daly MJ, Thorburn DR, Mootha VK. High-throughput, pooled sequencing identifies mutations in NUBPL and FOXRED1 in human complex I deficiency. Nat Genet 2010, 42:851-858. 10.1038/ng.659, 2977978, 20818383.
4. McClellan J, King M-C. Genetic heterogeneity in human disease. Cell 2010, 141:210-217. 10.1016/j.cell.2010.03.032, 20403315.
5. Hamady M, Walker JJ, Harris JK, Gold NJ, Knight R. Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex. Nat Methods 2008, 5:235-237. 10.1038/nmeth.1184, 18264105.
6. Craig DW, Pearson JV, Szelinger S, Sekar A, Redman M, Corneveaux JJ, Pawlowski TL, Laub T, Nunn G, Stephan DA, Homer N, Huentelman MJ. Identification of genetic variants using bar-coded multiplexed sequencing. Nat Methods 2008, 5:887-893. 10.1038/nmeth.1251, 3171277, 18794863.
7. Bravo HC, Irizarry RA. Model-based quality assessment and base-calling for second-generation sequencing data. Biometrics 2009, 66:665-674. 2888717, 19912177.
8. Thomas AJ, Molla MN, Muzny DM, Nazareth L, Wheeler D, Song X, Richmond TA, Middle CM, Rodesch MJ, Packard CJ, Weinstock GM, Gibbs RA. Direct selection of human genomic loci by microarray hybridization. Nat Methods 2007, 4:903-905. 10.1038/nmeth1111, 17934467.
9. Bainbridge MN, Wang M, Burgess DL, Kovar C, Rodesch MJ, D'Ascenzo M, Kitzman J, Wu YQ, Newsham I, Richmond TA, Jeddeloh JA, Muzny D, Albert TJ, Gibbs RA. Whole exome capture in solution with 3 Gbp of data. Genome Biol 2010, 11:R62. 10.1186/gb-2010-11-6-r62, 2911110, 20565776.
10. Okou DT, Steinberg KM, Middle C, Cutler DJ, Albert TJ, Zwick ME. Microarray- based genomic selection for high-throughput resequencing. Nat Methods 2007, 4:907-909. 10.1038/nmeth1109, 17934469.
11. Porreca GJ, Zhang K, Li JB, Xie B, Austin D, Vassallo SL, LeProust EM, Peck BJ, Emig CJ, Dahl F, Gao Y, Church GM, Shendure J. Multiplex amplification of large sets of human exons. Nat Methods 2007, 4:931-936. 10.1038/nmeth1110, 17934468.
12. Markoulatos P, Siafakas N, Moncany M. Multiplex polymerase chain reaction: a practical approach. J Clin Lab Anal 2002, 16:47-51. 10.1002/jcla.2058, 11835531.
13. Quail MA, Kozarewa I, Smith F, Scally A, Stephens PJ, Durbin R, Swerdlow H, Turner DJ. A large genome center's improvements to the Illumina sequencing system. Nat Methods 2008, 5:1005-1010. 10.1038/nmeth.1270, 2610436, 19034268.
14. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009, 10:R25. 10.1186/gb-2009-10-3-r25, 2690996, 19261174.
15. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. The Sequence Alignment/Map (SAM) format and SAMtools. Bioinformatics 2009, 25:2078-2079. 10.1093/bioinformatics/btp352, 2723002, 19505943.
16. Rousseeuw PJ. Silhouettes: a graphical aid to the interpretation and validation of cluster analysis. J Comput Appl Math 1987, 20:53-65.
17. Bansal V. A statistical method for the detection of variants from next-generation resequencing of DNA pools. Bioinformatics 2010, 26:i318-i324. 10.1093/bioinformatics/btq214, 2881398, 20529923.
18. Vallania FLM, Druley TE, Ramos E, Wang J, Borecki I, Province M, Mitra RD. High-throughput discovery of rare insertions and deletions in large cohorts. Genome Res 2010, 20:1711-1718. 10.1101/gr.109157.110, 2989997, 21041413.
19. Rivas M, Daly M. Syzygy Documentation Release 0.9. , http://www.broadinstitute.org/software/syzygy/sites/default/files/Syzygy.pdf
20. Mejias R, Adamczyk A, Anggono V, Niranjan T, Thomas GM, Sharma K, Skinner C, Schwartz CE, Stevenson RE, Fallin MD, Kaufmann W, Pletnikov M, Valle D, Huganir RL, Wang T. Gain-of-function glutamate receptor interacting protein 1 variants alter GluA2 recycling and surface distribution in patients with autism. Proc Natl Acad Sci USA 2011, 108:4920-495. 10.1073/pnas.1102233108, 3064362, 21383172.
21. Niranjan T, Bravo HC. Download Links for SRFIM and SERVIC4E scripts. , http://www.cbcb.umd.edu/~hcorrada/secgen