A bioinformatics approach for determining sample identity from different lanes of high-throughput sequencing data

PLoS ONE

Volumn 6, Issue 8, 2011, Pages

  Goldfeder, Rachel L ^a   Parker, Stephen C J ^a   Ajay, Subramanian S ^a   Abaan, Hatice ^a   Margulies, Elliott H ^a,b  

^a NATIONAL HUMAN GENOME RESEARCH INSTITUTE   (United States)

^b ILLUMINA INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANALYTIC METHOD; ARTICLE; BIOINFORMATICS; CONTROLLED STUDY; DATA ANALYSIS; DATA BASE; DATA COLLECTION METHOD; DNA BARCODING; DNA MODIFICATION; FEMALE; GENE SEQUENCE; GENETIC ANALYSIS; GENOTYPE; HIGH THROUGHPUT SEQUENCING; HISEQ 2000 INSTRUMENT; HUMAN; INSTRUMENT; MALE; QUALITY CONTROL; READ CODING; SEQUENCE ANALYSIS; SEX DETERMINATION; BIOLOGY; DNA SEQUENCE; GENETIC POLYMORPHISM; GENETICS; GENOMICS; HUMAN GENOME; METHODOLOGY; REPRODUCIBILITY;

MAMMALIA;

COMPUTATIONAL BIOLOGY; FEMALE; GENOME, HUMAN; GENOMICS; GENOTYPE; HUMANS; MALE; POLYMORPHISM, GENETIC; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS, DNA;

EID: 80051758437     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0023683     Document Type: Article

References (11)

1. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, et al. (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456: 53-59 doi:10.1038/nature07517.
2. Valouev A, Ichikawa J, Tonthat T, Stuart J, Ranade S, et al. (2008) A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Res 18: 1051-1063 doi:10.1101/gr.076463.108.
3. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437: 376-380 doi:10.1038/nature03959.
4. Parameswaran P, Jalili R, Tao L, Shokralla S, Gharizadeh B, et al. (2007) A pyrosequencing-tailored nucleotide barcode design unveils opportunities for large-scale sample multiplexing. Nucleic Acids Res 35: e130-e130 doi:10.1093/nar/gkm760.
5. Smith AM, Heisler LE, St. Onge RP, Farias-Hesson E, Wallace IM, et al. (2010) Highly-multiplexed barcode sequencing: an efficient method for parallel analysis of pooled samples. Nucleic Acids Res 38: e142 doi:10.1093/nar/gkq368.
6. Craig DW, Pearson JV, Szelinger S, Sekar A, Redman M, et al. (2008) Identification of genetic variants using bar-coded multiplexed sequencing. Nat. Methods 5: 887-893 doi:10.1038/nmeth.1251.
7. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms (2001) Nature 409: 928-933 doi:10.1038/35057149.
8. Lander ES, Waterman MS, (1988) Genomic mapping by fingerprinting random clones: A mathematical analysis. Genomics 2: 231-239 doi:16/0888-7543(88)90007-9.
9. Li H, Durbin R, (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760 doi:10.1093/bioinformatics/btp324.
10. Teer JK, Bonnycastle LL, Chines PS, Hansen NF, Aoyama N, et al. (2010) Systematic comparison of three genomic enrichment methods for massively parallel DNA sequencing. Genome Res 20: 1420-1431 doi:10.1101/gr.106716.110.
11. Ajay SS, Parker SCJ, Ozel Abaan H, Fuentes Fajardo KV, Margulies EH, (2011) Accurate and comprehensive sequencing of personal genomes. Genome Res In press.