The status, quality, and expansion of the NIH full-length cDNA project: The Mammalian Gene Collection (MGC)

Daniela S. Gerhard; Lukas Wagner; Elise A. Feingold; Carolyn M. Shenmen; Lynette H. Grouse; Greg Schuler; Steven L. Klein; Susan Old; Rebekah Rasooly; Peter Good; Mark Guyer; Allison M. Peck; Jeffery G. Derge; David Lipman; Francis S. Collins; Wonhee Jang; Steven Sherry; Mike Feolo; Leonie Misquitta; Eduardo Lee; Kirill Rotmistrovsky; Susan F. Greenhut; Carl F. Schaefer; Kenneth H. Buetow; Tom I. Bonner; David Haussler; Jim Kent; Mark Diekhans; Terry Furey; Michael Brent; Christa Prange; Kirsten Schreiber; Nicole Shapiro; Narayan K. Bhat; Ralph F. Hopkins; Florence Hsie; Tom Driscoll; M. Bento Soares; Maria F. Bonaldo; Tom L. Casavant; Todd E. Scheetz; Michael J. Brownstein; Ted B. Usdin; Shiraki Toshiyuki; Piero Carninci; Yulan Piao; Dawood B. Dudekula; Minoru S.H. Ko; Koichi Kawakami; Yutaka Suzuki; Sumio Sugano; C. E. Gruber; M. R. Smith; Blake Simmons; Troy Moore; Richard Waterman; Stephen L. Johnson; Yijun Ruan; Chia Lin Wei; S. Mathavan; Preethi H. Gunaratne; Jiaqian Wu; Angela M. Garcia; Stephen W. Hulyk; Edwin Fuh; Ye Yuan; Anna Sneed; Carla Kowis; Anne Hodgson; Donna M. Muzny; John McPherson; Richard A. Gibbs; Jessica Fahey; Erin Helton; Mark Ketteman; Anuradha Madan; Stephanie Rodrigues; Amy Sanchez; Michelle Whiting; Anup Madan; Alice C. Young; Keith D. Wetherby; Steven J. Granite; Peggy N. Kwong; Charles P. Brinkley; Russell L. Pearson; Gerard G. Bouffard; Robert W. Blakesly; Eric D. Green; Mark C. Dickson; Alex C. Rodriguez; Jane Grimwood; Jeremy Schmutz; Richard M. Myers; Yaron S.N. Butterfield; Malachi Griffith; Obi L. Griffith; Martin I. Krzywinski; Nancy Liao; Ryan Morrin; Diana Palmquist; Anca S. Petrescu; Ursula Skalska; Duane E. Smailus; Jeff M. Stott; Angelique Schnerch; Jacqueline E. Schein; Steven J.M. Jones; Robert A. Holt; Agnes Baross; Marco A. Marra; Sandra Clifton; Kathryn A. Makowski; Stephanie Bosak; Joel Malek

doi:10.1101/gr.2596504

The status, quality, and expansion of the NIH full-length cDNA project: The Mammalian Gene Collection (MGC)

Daniela S. Gerhard, Lukas Wagner, Elise A. Feingold, Carolyn M. Shenmen, Lynette H. Grouse, Greg Schuler, Steven L. Klein, Susan Old, Rebekah Rasooly, Peter Good, Mark Guyer, Allison M. Peck, Jeffery G. Derge, David Lipman, Francis S. Collins, Wonhee Jang, Steven Sherry, Mike Feolo, Leonie Misquitta, Eduardo LeeKirill Rotmistrovsky, Susan F. Greenhut, Carl F. Schaefer, Kenneth H. Buetow, Tom I. Bonner, David Haussler, Jim Kent, Mark Diekhans, Terry Furey, Michael Brent, Christa Prange, Kirsten Schreiber, Nicole Shapiro, Narayan K. Bhat, Ralph F. Hopkins, Florence Hsie, Tom Driscoll, M. Bento Soares, Maria F. Bonaldo, Tom L. Casavant, Todd E. Scheetz, Michael J. Brownstein, Ted B. Usdin, Shiraki Toshiyuki, Piero Carninci, Yulan Piao, Dawood B. Dudekula, Minoru S.H. Ko, Koichi Kawakami, Yutaka Suzuki, Sumio Sugano, C. E. Gruber, M. R. Smith, Blake Simmons, Troy Moore, Richard Waterman, Stephen L. Johnson, Yijun Ruan, Chia Lin Wei, S. Mathavan, Preethi H. Gunaratne, Jiaqian Wu, Angela M. Garcia, Stephen W. Hulyk, Edwin Fuh, Ye Yuan, Anna Sneed, Carla Kowis, Anne Hodgson, Donna M. Muzny, John McPherson, Richard A. Gibbs, Jessica Fahey, Erin Helton, Mark Ketteman, Anuradha Madan, Stephanie Rodrigues, Amy Sanchez, Michelle Whiting, Anup Madan, Alice C. Young, Keith D. Wetherby, Steven J. Granite, Peggy N. Kwong, Charles P. Brinkley, Russell L. Pearson, Gerard G. Bouffard, Robert W. Blakesly, Eric D. Green, Mark C. Dickson, Alex C. Rodriguez, Jane Grimwood, Jeremy Schmutz, Richard M. Myers, Yaron S.N. Butterfield, Malachi Griffith, Obi L. Griffith, Martin I. Krzywinski, Nancy Liao, Ryan Morrin, Diana Palmquist, Anca S. Petrescu, Ursula Skalska, Duane E. Smailus, Jeff M. Stott, Angelique Schnerch, Jacqueline E. Schein, Steven J.M. Jones, Robert A. Holt, Agnes Baross, Marco A. Marra, Sandra Clifton, Kathryn A. Makowski, Stephanie Bosak, Joel Malek

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Abstract

The National Institutes of Health's Mammalian Gene Collection (MGC) project was designed to generate and sequence a publicly accessible cDNA resource containing a complete open reading frame (ORF) for every human and mouse gene. The project initially used a random strategy to select clones from a large number of cDNA libraries from diverse tissues. Candidate clones were chosen based on 5′-EST sequences, and then fully sequenced to high accuracy and analyzed by algorithms developed for this project. Currently, more than 11,000 human and 10,000 mouse genes are represented in MGC by at least one clone with a full ORF. The random selection approach is now reaching a saturation point, and a transition to protocols targeted at the missing transcripts is now required to complete the mouse and human collections. Comparison of the sequence of the MGC clones to reference genome sequences reveals that most cDNA clones are of very high sequence quality, although it is likely that some cDNAs may carry missense variants as a consequence of experimental artifact, such as PCR, cloning, or reverse transcriptase errors. Recently, a rat cDNA component was added to the project, and ongoing frog (Xenopus) and zebrafish (Danio) cDNA projects were expanded to take advantage of the high-throughput MGC pipeline.

Original language	English
Pages (from-to)	2121-2127
Number of pages	7
Journal	Genome research
Volume	14
Issue number	10 B
DOIs	https://doi.org/10.1101/gr.2596504
State	Published - Oct 2004

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Gerhard, D. S., Wagner, L., Feingold, E. A., Shenmen, C. M., Grouse, L. H., Schuler, G., Klein, S. L., Old, S., Rasooly, R., Good, P., Guyer, M., Peck, A. M., Derge, J. G., Lipman, D., Collins, F. S., Jang, W., Sherry, S., Feolo, M., Misquitta, L., ... Malek, J. (2004). The status, quality, and expansion of the NIH full-length cDNA project: The Mammalian Gene Collection (MGC). Genome research, 14(10 B), 2121-2127. https://doi.org/10.1101/gr.2596504

@article{5dd62c8f68924f8d8eb69c67ccc44eb1,

title = "The status, quality, and expansion of the NIH full-length cDNA project: The Mammalian Gene Collection (MGC)",

abstract = "The National Institutes of Health's Mammalian Gene Collection (MGC) project was designed to generate and sequence a publicly accessible cDNA resource containing a complete open reading frame (ORF) for every human and mouse gene. The project initially used a random strategy to select clones from a large number of cDNA libraries from diverse tissues. Candidate clones were chosen based on 5′-EST sequences, and then fully sequenced to high accuracy and analyzed by algorithms developed for this project. Currently, more than 11,000 human and 10,000 mouse genes are represented in MGC by at least one clone with a full ORF. The random selection approach is now reaching a saturation point, and a transition to protocols targeted at the missing transcripts is now required to complete the mouse and human collections. Comparison of the sequence of the MGC clones to reference genome sequences reveals that most cDNA clones are of very high sequence quality, although it is likely that some cDNAs may carry missense variants as a consequence of experimental artifact, such as PCR, cloning, or reverse transcriptase errors. Recently, a rat cDNA component was added to the project, and ongoing frog (Xenopus) and zebrafish (Danio) cDNA projects were expanded to take advantage of the high-throughput MGC pipeline.",

author = "Gerhard, {Daniela S.} and Lukas Wagner and Feingold, {Elise A.} and Shenmen, {Carolyn M.} and Grouse, {Lynette H.} and Greg Schuler and Klein, {Steven L.} and Susan Old and Rebekah Rasooly and Peter Good and Mark Guyer and Peck, {Allison M.} and Derge, {Jeffery G.} and David Lipman and Collins, {Francis S.} and Wonhee Jang and Steven Sherry and Mike Feolo and Leonie Misquitta and Eduardo Lee and Kirill Rotmistrovsky and Greenhut, {Susan F.} and Schaefer, {Carl F.} and Buetow, {Kenneth H.} and Bonner, {Tom I.} and David Haussler and Jim Kent and Mark Diekhans and Terry Furey and Michael Brent and Christa Prange and Kirsten Schreiber and Nicole Shapiro and Bhat, {Narayan K.} and Hopkins, {Ralph F.} and Florence Hsie and Tom Driscoll and Soares, {M. Bento} and Bonaldo, {Maria F.} and Casavant, {Tom L.} and Scheetz, {Todd E.} and Brownstein, {Michael J.} and Usdin, {Ted B.} and Shiraki Toshiyuki and Piero Carninci and Yulan Piao and Dudekula, {Dawood B.} and Ko, {Minoru S.H.} and Koichi Kawakami and Yutaka Suzuki and Sumio Sugano and Gruber, {C. E.} and Smith, {M. R.} and Blake Simmons and Troy Moore and Richard Waterman and Johnson, {Stephen L.} and Yijun Ruan and {Lin Wei}, Chia and S. Mathavan and Gunaratne, {Preethi H.} and Jiaqian Wu and Garcia, {Angela M.} and Hulyk, {Stephen W.} and Edwin Fuh and Ye Yuan and Anna Sneed and Carla Kowis and Anne Hodgson and Muzny, {Donna M.} and John McPherson and Gibbs, {Richard A.} and Jessica Fahey and Erin Helton and Mark Ketteman and Anuradha Madan and Stephanie Rodrigues and Amy Sanchez and Michelle Whiting and Anup Madan and Young, {Alice C.} and Wetherby, {Keith D.} and Granite, {Steven J.} and Kwong, {Peggy N.} and Brinkley, {Charles P.} and Pearson, {Russell L.} and Bouffard, {Gerard G.} and Blakesly, {Robert W.} and Green, {Eric D.} and Dickson, {Mark C.} and Rodriguez, {Alex C.} and Jane Grimwood and Jeremy Schmutz and Myers, {Richard M.} and Butterfield, {Yaron S.N.} and Malachi Griffith and Griffith, {Obi L.} and Krzywinski, {Martin I.} and Nancy Liao and Ryan Morrin and Diana Palmquist and Petrescu, {Anca S.} and Ursula Skalska and Smailus, {Duane E.} and Stott, {Jeff M.} and Angelique Schnerch and Schein, {Jacqueline E.} and Jones, {Steven J.M.} and Holt, {Robert A.} and Agnes Baross and Marra, {Marco A.} and Sandra Clifton and Makowski, {Kathryn A.} and Stephanie Bosak and Joel Malek",

year = "2004",

month = oct,

doi = "10.1101/gr.2596504",

language = "English",

volume = "14",

pages = "2121--2127",

journal = "Genome research",

issn = "1088-9051",

number = "10 B",

}

Gerhard, DS, Wagner, L, Feingold, EA, Shenmen, CM, Grouse, LH, Schuler, G, Klein, SL, Old, S, Rasooly, R, Good, P, Guyer, M, Peck, AM, Derge, JG, Lipman, D, Collins, FS, Jang, W, Sherry, S, Feolo, M, Misquitta, L, Lee, E, Rotmistrovsky, K, Greenhut, SF, Schaefer, CF, Buetow, KH, Bonner, TI, Haussler, D, Kent, J, Diekhans, M, Furey, T, Brent, M, Prange, C, Schreiber, K, Shapiro, N, Bhat, NK, Hopkins, RF, Hsie, F, Driscoll, T, Soares, MB, Bonaldo, MF, Casavant, TL, Scheetz, TE, Brownstein, MJ, Usdin, TB, Toshiyuki, S, Carninci, P, Piao, Y, Dudekula, DB, Ko, MSH, Kawakami, K, Suzuki, Y, Sugano, S, Gruber, CE, Smith, MR, Simmons, B, Moore, T, Waterman, R, Johnson, SL, Ruan, Y, Lin Wei, C, Mathavan, S, Gunaratne, PH, Wu, J, Garcia, AM, Hulyk, SW, Fuh, E, Yuan, Y, Sneed, A, Kowis, C, Hodgson, A, Muzny, DM, McPherson, J, Gibbs, RA, Fahey, J, Helton, E, Ketteman, M, Madan, A, Rodrigues, S, Sanchez, A, Whiting, M, Madan, A, Young, AC, Wetherby, KD, Granite, SJ, Kwong, PN, Brinkley, CP, Pearson, RL, Bouffard, GG, Blakesly, RW, Green, ED, Dickson, MC, Rodriguez, AC, Grimwood, J, Schmutz, J, Myers, RM, Butterfield, YSN, Griffith, M , Griffith, OL, Krzywinski, MI, Liao, N, Morrin, R, Palmquist, D, Petrescu, AS, Skalska, U, Smailus, DE, Stott, JM, Schnerch, A, Schein, JE, Jones, SJM, Holt, RA, Baross, A, Marra, MA, Clifton, S, Makowski, KA, Bosak, S & Malek, J 2004, 'The status, quality, and expansion of the NIH full-length cDNA project: The Mammalian Gene Collection (MGC)', Genome research, vol. 14, no. 10 B, pp. 2121-2127. https://doi.org/10.1101/gr.2596504

TY - JOUR

T1 - The status, quality, and expansion of the NIH full-length cDNA project

T2 - The Mammalian Gene Collection (MGC)

AU - Gerhard, Daniela S.

AU - Wagner, Lukas

AU - Feingold, Elise A.

AU - Shenmen, Carolyn M.

AU - Grouse, Lynette H.

AU - Schuler, Greg

AU - Klein, Steven L.

AU - Old, Susan

AU - Rasooly, Rebekah

AU - Good, Peter

AU - Guyer, Mark

AU - Peck, Allison M.

AU - Derge, Jeffery G.

AU - Lipman, David

AU - Collins, Francis S.

AU - Jang, Wonhee

AU - Sherry, Steven

AU - Feolo, Mike

AU - Misquitta, Leonie

AU - Lee, Eduardo

AU - Rotmistrovsky, Kirill

AU - Greenhut, Susan F.

AU - Schaefer, Carl F.

AU - Buetow, Kenneth H.

AU - Bonner, Tom I.

AU - Haussler, David

AU - Kent, Jim

AU - Diekhans, Mark

AU - Furey, Terry

AU - Brent, Michael

AU - Prange, Christa

AU - Schreiber, Kirsten

AU - Shapiro, Nicole

AU - Bhat, Narayan K.

AU - Hopkins, Ralph F.

AU - Hsie, Florence

AU - Driscoll, Tom

AU - Soares, M. Bento

AU - Bonaldo, Maria F.

AU - Casavant, Tom L.

AU - Scheetz, Todd E.

AU - Brownstein, Michael J.

AU - Usdin, Ted B.

AU - Toshiyuki, Shiraki

AU - Carninci, Piero

AU - Piao, Yulan

AU - Dudekula, Dawood B.

AU - Ko, Minoru S.H.

AU - Kawakami, Koichi

AU - Suzuki, Yutaka

AU - Sugano, Sumio

AU - Gruber, C. E.

AU - Smith, M. R.

AU - Simmons, Blake

AU - Moore, Troy

AU - Waterman, Richard

AU - Johnson, Stephen L.

AU - Ruan, Yijun

AU - Lin Wei, Chia

AU - Mathavan, S.

AU - Gunaratne, Preethi H.

AU - Wu, Jiaqian

AU - Garcia, Angela M.

AU - Hulyk, Stephen W.

AU - Fuh, Edwin

AU - Yuan, Ye

AU - Sneed, Anna

AU - Kowis, Carla

AU - Hodgson, Anne

AU - Muzny, Donna M.

AU - McPherson, John

AU - Gibbs, Richard A.

AU - Fahey, Jessica

AU - Helton, Erin

AU - Ketteman, Mark

AU - Madan, Anuradha

AU - Rodrigues, Stephanie

AU - Sanchez, Amy

AU - Whiting, Michelle

AU - Madan, Anup

AU - Young, Alice C.

AU - Wetherby, Keith D.

AU - Granite, Steven J.

AU - Kwong, Peggy N.

AU - Brinkley, Charles P.

AU - Pearson, Russell L.

AU - Bouffard, Gerard G.

AU - Blakesly, Robert W.

AU - Green, Eric D.

AU - Dickson, Mark C.

AU - Rodriguez, Alex C.

AU - Grimwood, Jane

AU - Schmutz, Jeremy

AU - Myers, Richard M.

AU - Butterfield, Yaron S.N.

AU - Griffith, Malachi

AU - Griffith, Obi L.

AU - Krzywinski, Martin I.

AU - Liao, Nancy

AU - Morrin, Ryan

AU - Palmquist, Diana

AU - Petrescu, Anca S.

AU - Skalska, Ursula

AU - Smailus, Duane E.

AU - Stott, Jeff M.

AU - Schnerch, Angelique

AU - Schein, Jacqueline E.

AU - Jones, Steven J.M.

AU - Holt, Robert A.

AU - Baross, Agnes

AU - Marra, Marco A.

AU - Clifton, Sandra

AU - Makowski, Kathryn A.

AU - Bosak, Stephanie

AU - Malek, Joel

PY - 2004/10

Y1 - 2004/10

N2 - The National Institutes of Health's Mammalian Gene Collection (MGC) project was designed to generate and sequence a publicly accessible cDNA resource containing a complete open reading frame (ORF) for every human and mouse gene. The project initially used a random strategy to select clones from a large number of cDNA libraries from diverse tissues. Candidate clones were chosen based on 5′-EST sequences, and then fully sequenced to high accuracy and analyzed by algorithms developed for this project. Currently, more than 11,000 human and 10,000 mouse genes are represented in MGC by at least one clone with a full ORF. The random selection approach is now reaching a saturation point, and a transition to protocols targeted at the missing transcripts is now required to complete the mouse and human collections. Comparison of the sequence of the MGC clones to reference genome sequences reveals that most cDNA clones are of very high sequence quality, although it is likely that some cDNAs may carry missense variants as a consequence of experimental artifact, such as PCR, cloning, or reverse transcriptase errors. Recently, a rat cDNA component was added to the project, and ongoing frog (Xenopus) and zebrafish (Danio) cDNA projects were expanded to take advantage of the high-throughput MGC pipeline.

AB - The National Institutes of Health's Mammalian Gene Collection (MGC) project was designed to generate and sequence a publicly accessible cDNA resource containing a complete open reading frame (ORF) for every human and mouse gene. The project initially used a random strategy to select clones from a large number of cDNA libraries from diverse tissues. Candidate clones were chosen based on 5′-EST sequences, and then fully sequenced to high accuracy and analyzed by algorithms developed for this project. Currently, more than 11,000 human and 10,000 mouse genes are represented in MGC by at least one clone with a full ORF. The random selection approach is now reaching a saturation point, and a transition to protocols targeted at the missing transcripts is now required to complete the mouse and human collections. Comparison of the sequence of the MGC clones to reference genome sequences reveals that most cDNA clones are of very high sequence quality, although it is likely that some cDNAs may carry missense variants as a consequence of experimental artifact, such as PCR, cloning, or reverse transcriptase errors. Recently, a rat cDNA component was added to the project, and ongoing frog (Xenopus) and zebrafish (Danio) cDNA projects were expanded to take advantage of the high-throughput MGC pipeline.

UR - http://www.scopus.com/inward/record.url?scp=7444262496&partnerID=8YFLogxK

U2 - 10.1101/gr.2596504

DO - 10.1101/gr.2596504

M3 - Article

C2 - 15489334

AN - SCOPUS:7444262496

SN - 1088-9051

VL - 14

SP - 2121

EP - 2127

JO - Genome research

JF - Genome research

IS - 10 B

ER -

The status, quality, and expansion of the NIH full-length cDNA project: The Mammalian Gene Collection (MGC)

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