Solution-based targeted genomic enrichment for precious DNA samples

BMC Biotechnology

Richard JH Smith²  Michael S Hildebrand¹  Aiden Eliot Shearer³ 

[1]Department of Otolaryngology—Head & Neck Surgery, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA

[2]Interdepartmental PhD Program in Genetics, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA

[3]Department of Molecular Physiology & Biophysics, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA

关键词: Illumina;    Massively parallel sequencing;    Sequence capture;    Targeted genomic enrichment;   

Others  :  1135189
DOI  :  10.1186/1472-6750-12-20

 received in 2011-12-13, accepted in 2012-05-04,  发布年份 2012

【 摘 要 】

Background

Solution-based targeted genomic enrichment (TGE) protocols permit selective sequencing of genomic regions of interest on a massively parallel scale. These protocols could be improved by: 1) modifying or eliminating time consuming steps; 2) increasing yield to reduce input DNA and excessive PCR cycling; and 3) enhancing reproducible.

Results

We developed a solution-based TGE method for downstream Illumina sequencing in a non-automated workflow, adding standard Illumina barcode indexes during the post-hybridization amplification to allow for sample pooling prior to sequencing. The method utilizes Agilent SureSelect baits, primers and hybridization reagents for the capture, off-the-shelf reagents for the library preparation steps, and adaptor oligonucleotides for Illumina paired-end sequencing purchased directly from an oligonucleotide manufacturing company.

Conclusions

This solution-based TGE method for Illumina sequencing is optimized for small- or medium-sized laboratories and addresses the weaknesses of standard protocols by reducing the amount of input DNA required, increasing capture yield, optimizing efficiency, and improving reproducibility.

【 授权许可】

   
2012 Shearer et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

【 参考文献 】

• [1]Ng SB, Nickerson DA, Bamshad MJ, Shendure J: Massively parallel sequencing and rare disease. Hum Mol Genet 2010, 19(R2):R119-R124.
• [2]Bamshad MJ, Ng SB, Bigham AW, Tabor HK, Emond MJ, Nickerson DA, Shendure J: Exome sequencing as a tool for Mendelian disease gene discovery. Nat Rev Genet 2011, 12(11):745-755.
• [3]Shearer AE, DeLuca AP, Hildebrand MS, Taylor KR, Gurrola J, Scherer S, Scheetz TE, Smith RJH: Comprehensive genetic testing for hereditary hearing loss using massively parallel sequencing. Proc Natl Acad Sci USA 2010, 107(49):21104-21109.
• [4]Walsh T, Lee MK, Casadei S, Thornton AM, Stray SM, Pennil C, Nord AS, Mandell JB, Swisher EM, King M: Detection of inherited mutations for breast and ovarian cancer using genomic capture and massively parallel sequencing. Proc Natl Acad Sci USA 2010, 107(28):12629-12633.
• [5]Gnirke A, Melnikov A, Maguire J, Rogov P, LeProust EM, Brockman W, Fennell T, Giannoukos G, Fisher S, Russ C, Gabriel S, Jaffe DB, Lander ES, Nusbaum C: Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol 2009, 27(2):182-189.
• [6]Albert TJ, 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(11):903-905.
• [7]Kiialainen A, Karlberg O, Ahlford A, Sigurdsson S, Lindblad-Toh K, Syvanen A: Performance of Microarray and Liquid Based Capture Methods for Target Enrichment for Massively Parallel Sequencing and SNP Discovery. PLoS One 2011, 6(2):e16486.
• [8]Clark MJ, Chen R, Lam HYK, Karczewski KJ, Chen R, Euskirchen G, Butte AJ, Snyder M: Performance comparison of exome DNA sequencing technologies. Nat Biotechnol 2011, 29(10):908-914.
• [9]Mamanova L, Coffey AJ, Scott CE, Kozarewa I, Turner EH, Kumar A, Howard E, Shendure J, Turner DJ: Target-enrichment strategies for next-generation sequencing. Nat Meth 2010, 7(2):111-118.
• [10]Fisher S, Barry A, Abreu J, Minie B, Nolan J, Delorey TM, Young G, Fennell TJ, Allen A, Ambrogio L, Berlin AM, Blumenstiel B, Cibulskis K, Friedrich D, Johnson R, Juhn F, Reilly B, Shammas R, Stalker J, Sykes SM, Thompson J, Walsh J, Zimmer A, Zwirko Z, Gabriel S, Nicol R, Nusbaum C: A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries. Genome Biol 2011, 12(1):R1. BioMed Central Full Text
• [11]Harakalova M, Mokry M, Hrdlickova B, Renkens I, Duran K, van Roekel H, Lansu N, van Roosmalen M, de Bruijn E, Nijman IJ, Kloosterman WP, Cuppen E: Multiplexed array-based and in-solution genomic enrichment for flexible and cost-effective targeted next-generation sequencing. Nat Prot 2011, 6(12):1870-1886.
• [12]Nijman I, Mokry M, van Boxtel R, Toonen P, de Bruijn E, Cuppen E: Mutation discovery by targeted genomic enrichment of multiplexed barcoded samples. Nat Meth 2010, 7(11):913-915.
• [13]Wesolowska A, Dalgaard M, Borst L, Gautier L, Bak M, Weinhold N, Nielsen B, Helt L, Audouze K, Nersting J, Tommerup N, Brunak S, Sicheritz-Ponten T, Leffers H, Schmiegelow K, Gupta R: Cost-effective multiplexing before capture allows screening of 25,000 clinically relevant SNPs in childhood acute lymphoblastic leukemia. Leukemia 2011, 6:1001-1006.
• [14]Natsoulis G, Bell JM, Xu H, Buenrostro JD, Ordonez H, Grimes S, Newburger D, Jensen M, Zahn JM, Zhang N, Ji HP: A flexible approach for highly multiplexed candidate gene targeted resequencing. PLoS One 2011, 6(6):e21088.