Closing gaps in the human genome using sequencing by synthesis

Genome Biology

Volumn 10, Issue 6, 2009, Pages

  Garber, Manuel ^a   Zody, Michael C ^a,b   Arachchi, Harindra M ^a   Berlin, Aaron ^a   Gnerre, Sante ^a   Green, Lisa M ^a   Lennon, Niall ^a   Nusbaum, Chad ^a  

^a BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^b UPPSALA UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA;

ANALYTIC METHOD; ARTICLE; CHROMOSOME 15; DNA BASE COMPOSITION; DNA CONFORMATION; GENE AMPLIFICATION; GENE INSERTION; GENE SEQUENCE; HUMAN; HUMAN GENOME; MOLECULAR CLONING; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS; CELL LINE; DNA SEQUENCE; GENETICS; METHODOLOGY;

BASE SEQUENCE; CELL LINE; CHROMOSOMES, HUMAN, PAIR 15; GENOME, HUMAN; HUMANS; SEQUENCE ANALYSIS, DNA;

EID: 67649659820     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2009-10-6-r60     Document Type: Article

References (22)

1. Zody MC Garber M Sharpe T Young SK Rowen L O'Neill K Whittaker CA Kamal M Chang JL Cuomo CA Dewar K FitzGerald MG Kodira CD Madan A Qin S Yang X Abbasi N Abouelleil A Arachchi HM Baradarani L Birditt B Bloom S Bloom T Borowsky ML Burke J Butler J Cook A DeArellano K DeCaprio D Dorris L et al. Analysis of the DNA sequence and duplication history of human chromosome 15. Nature 2006, 440:671-675. 10.1038/nature04601 16572171
2. Makoff AJ Flomen RH Detailed analysis of 15q11-q14 sequence corrects errors and gaps in the public access sequence to fully reveal large segmental duplications at breakpoints for Prader-Willi, Angelman, and inv dup(15) syndromes. Genome Biol 2007, 8:R114. 2394762 17573966 10.1186/gb-2007-8-6-r114
3. Bovee D Zhou Y Haugen E Wu Z Hayden HS Gillett W Cooper GM Sampas N Phelps K Levy R Morrison VA Sprague J Jewett D Buckely D Subramaniam S Chang J Smith DR Olson MZV Eichler EE Kayl R Closing gaps in the human genome with fosmid resources generated from multiple individuals. Nat Genet 2008, 40:96-101. 10.1038/ng.2007.34 18157130
4. Istrail S Sutton GG Florea L Halpern AL Mobarry CM Lippert R Walenz B Shatkay H Dew I Miller JR Flanigan MJ Edwards NJ Bolanos R Fasulo D Halldorsson BV Hannenhalli S Turner R Yooseph S Lu F Nusskern DR Shue BC Zheng XH Zhong F Dlecher AL Huson DH Kravitz SA Mouchard L Reinert K Remington KA Clark AG et al. Whole-genome shotgun assembly and comparison of human genome assemblies. Proc Natl Acad Sci USA 2004, 101:1916-1921. 357027 14769938 10.1073/pnas.0307971100
5. Levy S Sutton G Ng PC Feuk L Halpern AL Walenz BP Axelrod N Huang J Kirkness EF Denisov G Lin Y MacDonald JR Pang AWC Shago M Stockwell TB Tsiamouri A Bafna V Bansal V Kravitz SA Busam DA Beeson KY McIntosh TC Remington KA Abril JF Gill J Borman J Rogers JH Frazier ME Scherer SW Strausberg RL Venter JC The diploid genome sequence of an individual human. PLoS Biol 2007, 5:e254. 1964779 17803354 10.1371/ journal.pbio.0050254
6. Rhesus Macaque Genome Sequencing and Analysis Consortium Evolutionary and biomedical insights from the rhesus macaque genome. Science 2007, 316:222-234. 10.1126/science.1139247 17431167
7. McMurray AA Sulston JE Quail MA Short-insert libraries as a method of problem solving in genome sequencing. Genome Res 1998, 8:562-566. 310723 9582200
8. Margulies M Egholm M Altman WE Attiya S Bader JS Bemben LA Berka J Braverman MS Chen YJ Chen Z Dewell SB Du L Fierro JM Gomes XV Godwin BC He W Helgesen S Ho CH Irzyk GP Jando SC Alenquer MLI Jarvie TP Jirage KB Kim JB Knight JR Lanza JR Leamon JH Lefkowitz SM Lei M Li J Lohman KL Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005, 437:376-380. 1464427 16056220
9. Jaffe DB Butler J Gnerre S Mauceli E Lindblad-Toh K Mesirov JP Zody MC Lander ES Whole-genome sequence assembly for mammalian genomes: Arachne 2. Genome Res 2003, 13:91-96. 430950 12529310 10.1101/gr.828403
10. International Human Genome Consortium Finishing the euchromatic sequence of the human genome. Nature 2004, 431:931-945. 10.1038/nature03001 15496913
11. Wheeler DA Srinivasan M Egholm M Shen Y Chen L McGuire A He W Chen YJ Makhijani V Roth GT Gomes X Tartaro K Niazi F Turcotte CL Irzyk GP Lupski JR Chinault G Song XZ Liu Y Yuan Y Nazareth L Qin X Muzny DM Margulies M Weinstock GM Gibbs RA Rothberg JM The complete genome of an individual by massively parallel DNA sequencing. Nature 2008, 452:872-876. 10.1038/nature06884 18421352.
12. Konopka AK Reiter J Jung M Zarling DA Jovin TM Concordance of experimentally mapped or predicted Z-DNA sites with positions of selected alternating purine-pyrimidine tracts. Nucleic Acids Res 1985, 13:1683-1701. 341105 4000942 10.1093/nar/13.5.1683
13. Kouprina N Leem SH Solomon G Ly A Koriabine M Otstot J Pak E Dutra A Zhao S Barrett JC Larionov V Segments missing from the draft human genome sequence can be isolated by transformation-associated recombination cloning in yeast. EMBO Rep 2003, 4:257-262. 1315894 12634842 10.1038/sj.embor.embor766
14. Eichler EE Clark RA She X An assessment of the sequence gaps: Unfinished business in a finished human genome. Nat Rev Genet 2004, 5:345-354. 10.1038/nrg1322 15143317
15. Leem SH Kouprina N Grimwood J Kim JH Mullokandov M Yoon YH Chae JY Morgan J Lucas S Richardson P Detter C Glavina T Rubin E Barrett JC Larionov V Closing the gaps on human chromosome 19 revealed genes with a high density of repetitive tandemly arrayed elements. Genome Res 2004, 14:239-246. 327099 14718380 10.1101/gr.1929904
16. Pruitt KD Tatusova T Maglott DR NCBI reference sequences (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 2007, 35:D61-D65. 1716718 17130148 10.1093/ nar/gkl842
17. Mouse Genome Sequencing Consortium Initial sequencing and comparative analysis of the mouse genome. Nature 2002, 420:520-562. 10.1038/ nature01262 12466850
18. Lindblad-Toh K Wade CM Mikkelsen TS Karlsson EK Jaffe DB Kamal M Clamp M J Chang JL Kulbokas EJ Zody MC Mauceli E Xie X Breen M Wayne RK Ostrander EA Ponting CP Galibert F Smith DR deJong PJ Kirkness E Alvarez P Biagi T Brockman W Butler J Chin CW Cook A Cuff J Daly MJ DeCaprio D Sante Gnerre Manfred Grabherr Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature 2005, 438:803-819. 10.1038/nature04338 16341006
19. Corriell Institute for Medical Research http://www.coriell.org/
20. Source code for the assembly program used in this work ftp://ftp.broadinstitute.org/pub/papers/uncloneable_gaps/
21. Rozen S Skaletsky H Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 2000, 132:365-386. 10547847
22. NCBI Short Read Archive http://www.ncbi.nlm.nih.gov/Traces/sra