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

Research output: Contribution to journalArticle

366 Citations (Scopus)

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 languageEnglish
Pages (from-to)2121-2127
Number of pages7
JournalGenome Research
Volume14
Issue number10 B
Publication statusPublished - Oct 2004
Externally publishedYes

Fingerprint

Complementary DNA
Clone Cells
Genes
Open Reading Frames
RNA-Directed DNA Polymerase
Expressed Sequence Tags
National Institutes of Health (U.S.)
Zebrafish
Xenopus
Gene Library
Anura
Artifacts
Organism Cloning
Genome
Polymerase Chain Reaction

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

Cite this

Gerhard, D. S., Wagner, L., Feingold, E. A., Shenmen, C. M., Grouse, L. H., Schuler, G., ... 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.

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

In: Genome Research, Vol. 14, No. 10 B, 10.2004, p. 2121-2127.

Research output: Contribution to journalArticle

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.
Gerhard DS, Wagner L, Feingold EA, Shenmen CM, Grouse LH, Schuler G et al. The status, quality, and expansion of the NIH full-length cDNA project: The Mammalian Gene Collection (MGC). Genome Research. 2004 Oct;14(10 B):2121-2127.
Gerhard, Daniela S. ; Wagner, Lukas ; Feingold, Elise A. ; Shenmen, Carolyn M. ; Grouse, Lynette H. ; Schuler, Greg ; Klein, Steven L. ; Old, Susan ; Rasooly, Rebekah ; Good, Peter ; Guyer, Mark ; Peck, Allison M. ; Derge, Jeffery G. ; Lipman, David ; Collins, Francis S. ; Jang, Wonhee ; Sherry, Steven ; Feolo, Mike ; Misquitta, Leonie ; Lee, Eduardo ; Rotmistrovsky, Kirill ; Greenhut, Susan F. ; Schaefer, Carl F. ; Buetow, Kenneth H. ; Bonner, Tom I. ; Haussler, David ; Kent, Jim ; Diekhans, Mark ; Furey, Terry ; Brent, Michael ; Prange, Christa ; Schreiber, Kirsten ; Shapiro, Nicole ; Bhat, Narayan K. ; Hopkins, Ralph F. ; Hsie, Florence ; Driscoll, Tom ; Soares, M. Bento ; Bonaldo, Maria F. ; Casavant, Tom L. ; Scheetz, Todd E. ; Brownstein, Michael J. ; Usdin, Ted B. ; Toshiyuki, Shiraki ; Carninci, Piero ; Piao, Yulan ; Dudekula, Dawood B. ; Ko, Minoru S H ; Kawakami, Koichi ; Suzuki, Yutaka ; Sugano, Sumio ; Gruber, C. E. ; Smith, M. R. ; Simmons, Blake ; Moore, Troy ; Waterman, Richard ; Johnson, Stephen L. ; Ruan, Yijun ; Lin Wei, Chia ; Mathavan, S. ; Gunaratne, Preethi H. ; Wu, Jiaqian ; Garcia, Angela M. ; Hulyk, Stephen W. ; Fuh, Edwin ; Yuan, Ye ; Sneed, Anna ; Kowis, Carla ; Hodgson, Anne ; Muzny, Donna M. ; McPherson, John ; Gibbs, Richard A. ; Fahey, Jessica ; Helton, Erin ; Ketteman, Mark ; Madan, Anuradha ; Rodrigues, Stephanie ; Sanchez, Amy ; Whiting, Michelle ; Madan, Anup ; Young, Alice C. ; Wetherby, Keith D. ; Granite, Steven J. ; Kwong, Peggy N. ; Brinkley, Charles P. ; Pearson, Russell L. ; Bouffard, Gerard G. ; Blakesly, Robert W. ; Green, Eric D. ; Dickson, Mark C. ; Rodriguez, Alex C. ; Grimwood, Jane ; Schmutz, Jeremy ; Myers, Richard M. ; Butterfield, Yaron S N ; Griffith, Malachi ; Griffith, Obi L. ; Krzywinski, Martin I. ; Liao, Nancy ; Morrin, Ryan ; Palmquist, Diana ; Petrescu, Anca S. ; Skalska, Ursula ; Smailus, Duane E. ; Stott, Jeff M. ; Schnerch, Angelique ; Schein, Jacqueline E. ; Jones, Steven J M ; Holt, Robert A. ; Baross, Agnes ; Marra, Marco A. ; Clifton, Sandra ; Makowski, Kathryn A. ; Bosak, Stephanie ; Malek, Joel. / The status, quality, and expansion of the NIH full-length cDNA project : The Mammalian Gene Collection (MGC). In: Genome Research. 2004 ; Vol. 14, No. 10 B. pp. 2121-2127.
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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

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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.

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