Multi-sample pooling and illumina genome analyzer sequencing methods to determine gene sequence variation for database development.
作者： Karl V. Voelkerding , Jacob D. Durtschi , David C. Pattison , Rong Mao , Rebecca L. Margraf
DOI:
关键词:
摘要: Determination of sequence variation within a genetic locus to develop clinically relevant databases is critical for molecular assay design and clinical test interpretation, so multisample pooling Illumina genome analyzer (GA) sequencing was investigated using the RET proto-oncogene as model. Samples were Sanger-sequenced exons 10, 11, 13–16. Ten samples with 13 known unique variants (“singleton variants” pool) seven common changes amplified then equimolar-pooled before on single flow cell lane, generating 36 base reads. For comparison, “control” sample run in different lane. After alignment, 24-base quality score-screening threshold 3` read end trimming three bases yielded low background error rates 27% decrease aligned coverage. Sequencing data evaluated an established variant detection method (percent reads), by presented subtractive correction method, SNPSeeker software. In total, 41 (of which 23 singleton variants) detected 10 pool data, included all Sanger-identified variants. The near expected 5% allele frequency (average 5.17%±0.90% well above highest (1.25%). Based rates, coverage, simulated 30, 40, 50 frequencies pools, methods; ≥30 (which demonstrated minimum 1% reads singletons) could be pooled reliably detect GA sequencing.
参考文章(25)
Steve Rozen, Helen Skaletsky, Primer3 on the WWW for general users and for biologist programmers. Methods of Molecular Biology. ,vol. 132, pp. 365- 386 ,(2000) , 10.1385/1-59259-192-2:365
David W Craig, John V Pearson, Szabolcs Szelinger, Aswin Sekar, Margot Redman, Jason J Corneveaux, Traci L Pawlowski, Trisha Laub, Gary Nunn, Dietrich A Stephan, Nils Homer, Matthew J Huentelman, None, Identification of genetic variants using bar-coded multiplexed sequencing Nature Methods. ,vol. 5, pp. 887- 893 ,(2008) , 10.1038/NMETH.1251
Richard T. Kloos (Chair), Charis Eng, Douglas B. Evans, Gary L. Francis, Robert F. Gagel, Hossein Gharib, Jeffrey F. Moley, Furio Pacini, Matthew D. Ringel, Martin Schlumberger, Samuel A. Wells, Medullary thyroid cancer: management guidelines of the American Thyroid Association. Thyroid. ,vol. 19, pp. 565- 612 ,(2009) , 10.1089/THY.2008.0403
David R Bentley, Shankar Balasubramanian, Harold P Swerdlow, Geoffrey P Smith, John Milton, Clive G Brown, Kevin P Hall, Dirk J Evers, Colin L Barnes, Helen R Bignell, Jonathan M Boutell, Jason Bryant, Richard J Carter, R Keira Cheetham, Anthony J Cox, Darren J Ellis, Michael R Flatbush, Niall A Gormley, Sean J Humphray, Leslie J Irving, Mirian S Karbelashvili, Scott M Kirk, Heng Li, Xiaohai Liu, Klaus S Maisinger, Lisa J Murray, Bojan Obradovic, Tobias Ost, Michael L Parkinson, Mark R Pratt, Isabelle MJ Rasolonjatovo, Mark T Reed, Roberto Rigatti, Chiara Rodighiero, Mark T Ross, Andrea Sabot, Subramanian V Sankar, Aylwyn Scally, Gary P Schroth, Mark E Smith, Vincent P Smith, Anastassia Spiridou, Peta E Torrance, Svilen S Tzonev, Eric H Vermaas, Klaudia Walter, Xiaolin Wu, Lu Zhang, Mohammed D Alam, Carole Anastasi, Ify C Aniebo, David MD Bailey, Iain R Bancarz, Saibal Banerjee, Selena G Barbour, Primo A Baybayan, Vincent A Benoit, Kevin F Benson, Claire Bevis, Phillip J Black, Asha Boodhun, Joe S Brennan, John A Bridgham, Rob C Brown, Andrew A Brown, Dale H Buermann, Abass A Bundu, James C Burrows, Nigel P Carter, Nestor Castillo, Maria Chiara E. Catenazzi, Simon Chang, R Neil Cooley, Natasha R Crake, Olubunmi O Dada, Konstantinos D Diakoumakos, Belen Dominguez-Fernandez, David J Earnshaw, Ugonna C Egbujor, David W Elmore, Sergey S Etchin, Mark R Ewan, Milan Fedurco, Louise J Fraser, Karin V Fuentes Fajardo, W Scott Furey, David George, Kimberley J Gietzen, Colin P Goddard, George S Golda, Philip A Granieri, David E Green, David L Gustafson, Nancy F Hansen, Kevin Harnish, Christian D Haudenschild, Narinder I Heyer, Matthew M Hims, Johnny T Ho, Adrian M Horgan, Katya Hoschler, Steve Hurwitz, Denis V Ivanov, Maria Q Johnson, Terena James, TA Huw Jones, Gyoung-Dong Kang, Tzvetana H Kerelska, Alan D Kersey, Irina Khrebtukova, Alex P Kindwall, Zoya Kingsbury, Paula I Kokko-Gonzales, Anil Kumar, Marc A Laurent, Cynthia T Lawley, Sarah E Lee, Xavier Lee, Arnold K Liao, Jennifer A Loch, Mitch Lok, Shujun Luo, Radhika M Mammen, John W Martin, Patrick G McCauley, Paul McNitt, Parul Mehta, Keith W Moon, Joe W Mullens, Taksina Newington, Zemin Ning, Bee Ling Ng, Sonia M Novo, Michael J O’Neill, Mark A Osborne, Andrew Osnowski, Omead Ostadan, Lambros L Paraschos, Lea Pickering, Andrew C Pike, Alger C Pike, D Chris Pinkard, Daniel P Pliskin, Joe Podhasky, Victor J Quijano, Come Raczy, Vicki H Rae, Stephen R Rawlings, Ana Chiva Rodriguez, Phyllida M Roe, None, Accurate whole human genome sequencing using reversible terminator chemistry Nature. ,vol. 456, pp. 53- 59 ,(2008) , 10.1038/NATURE07517
Michael A Quail, Iwanka Kozarewa, Frances Smith, Aylwyn Scally, Philip J Stephens, Richard Durbin, Harold Swerdlow, Daniel J Turner, A large genome center's improvements to the Illumina sequencing system Nature Methods. ,vol. 5, pp. 1005- 1010 ,(2008) , 10.1038/NMETH.1270
Fernanda R.O. Calderon, Amit R. Phansalkar, David K. Crockett, Martin Miller, Rong Mao, Mutation database for the galactose-1-phosphate uridyltransferase (GALT) gene. Human Mutation. ,vol. 28, pp. 939- 943 ,(2007) , 10.1002/HUMU.20544
S. Ossowski, K. Schneeberger, R. M. Clark, C. Lanz, N. Warthmann, D. Weigel, Sequencing of natural strains of Arabidopsis thaliana with short reads Genome Research. ,vol. 18, pp. 2024- 2033 ,(2008) , 10.1101/GR.080200.108
Rebecca L. Margraf, David K. Crockett, Patti M.F. Krautscheid, Ryan Seamons, Fernanda R.O. Calderon, Carl T. Wittwer, Rong Mao, Multiple endocrine neoplasia type 2 RET protooncogene database: repository of MEN2-associated RET sequence variation and reference for genotype/phenotype correlations. Human Mutation. ,vol. 30, pp. 548- 556 ,(2009) , 10.1002/HUMU.20928
V. Bansal, O. Harismendy, R. Tewhey, S. S. Murray, N. J. Schork, E. J. Topol, K. A. Frazer, Accurate detection and genotyping of SNPs utilizing population sequencing data Genome Research. ,vol. 20, pp. 537- 545 ,(2010) , 10.1101/GR.100040.109
Charis Eng, David Clayton, Isabelle Schuffenecker, Gilbert Lenoir, Gilbert Cote, Robert F Gagel, Hans Kristian Ploos Van Amstel, Cornelis JM Lips, Isamu Nishisho, Shin-Ichiro Takai, Debbie J Marsh, Bruce G Robinson, Karin Frank-Raue, Friedhelm Raue, Feiyu Xue, Walter W Noll, Cristina Romei, Furio Pacini, Monika Fink, Bruno Niederle, Jan Zedenius, Magnus Nordenskjöld, Paul Komminoth, Geoffrey N Hendy, Hossein Gharib, Stephen N Thibodeau, André Lacroix, Andrea Frilling, Bruce AJ Ponder, Lois M Mulligan, The relationship between specific RET proto-oncogene mutations and disease phenotype in multiple endocrine neoplasia type 2. International RET mutation consortium analysis JAMA: The Journal of the American Medical Association. ,vol. 276, pp. 1575- 1579 ,(1996) , 10.1001/JAMA.276.19.1575