A systematic, large-scale resequencing screen of X-chromosome coding exons in mental retardation

Patrick S Tarpey; Raffaella Smith; Erin Pleasance; Annabel Whibley; Sarah Edkins; Claire Hardy; Sarah O'meara; Calli Latimer; Ed Dicks; Andrew Menzies; Phil Stephens; Matt Blow; Christopher Greenman; Yali Xue; Chris Tyler-smith; Deborah Thompson; Kristian Gray; Jenny Andrews; Syd Barthorpe; Gemma Buck; Jennifer Cole; Rebecca Dunmore; David Jones; Mark Maddison; Tatiana Mironenko; Rachel Turner; Kelly Turrell; Jennifer Varian; Sofie West; Sara Widaa; Paul Wray; Jon Teague; Adam Butler; Andrew Jenkinson; Mingming Jia; David Richardson; Rebecca Shepherd; Richard Wooster; M Isabel Tejada; Francisco Martinez; Gemma Carvill; Rene Goliath; Arjan P M De Brouwer; Hans Van Bokhoven; Hilde Van Esch; Jamel Chelly; Martine Raynaud; Hans-hilger Ropers; Fatima E Abidi; Anand K Srivastava; James Cox; Ying Luo; Uma Mallya; Jenny Moon; Josef Parnau; Shehla Mohammed; John L Tolmie; Cheryl Shoubridge; Mark Corbett; Alison Gardner; Eric Haan; Sinitdhorn Rujirabanjerd; Marie Shaw; Lucianne Vandeleur; Tod Fullston; Douglas F Easton; Jackie Boyle; Michael Partington; Anna Hackett; Michael Field; Cindy Skinner; Roger E Stevenson; Martin Bobrow; Gillian Turner; Charles E Schwartz; Jozef Gecz; F Lucy Raymond; P Andrew Futreal; Michael R Stratton

doi:10.1038/ng.367

A systematic, large-scale resequencing screen of X-chromosome coding exons in mental retardation

Patrick S Tarpey, Raffaella Smith, Erin Pleasance, Annabel Whibley, Sarah Edkins, Claire Hardy, Sarah O'meara, Calli Latimer, Ed Dicks, Andrew Menzies, Phil Stephens, Matt Blow, Christopher Greenman, Yali Xue, Chris Tyler-smith, Deborah Thompson, Kristian Gray, Jenny Andrews, Syd Barthorpe, Gemma BuckJennifer Cole, Rebecca Dunmore, David Jones, Mark Maddison, Tatiana Mironenko, Rachel Turner, Kelly Turrell, Jennifer Varian, Sofie West, Sara Widaa, Paul Wray, Jon Teague, Adam Butler, Andrew Jenkinson, Mingming Jia, David Richardson, Rebecca Shepherd, Richard Wooster, M Isabel Tejada, Francisco Martinez, Gemma Carvill, Rene Goliath, Arjan P M De Brouwer, Hans Van Bokhoven, Hilde Van Esch, Jamel Chelly, Martine Raynaud, Hans-hilger Ropers, Fatima E Abidi, Anand K Srivastava, James Cox, Ying Luo, Uma Mallya, Jenny Moon, Josef Parnau, Shehla Mohammed, John L Tolmie, Cheryl Shoubridge, Mark Corbett, Alison Gardner, Eric Haan, Sinitdhorn Rujirabanjerd, Marie Shaw, Lucianne Vandeleur, Tod Fullston, Douglas F Easton, Jackie Boyle, Michael Partington, Anna Hackett, Michael Field, Cindy Skinner, Roger E Stevenson, Martin Bobrow, Gillian Turner, Charles E Schwartz, Jozef Gecz, F Lucy Raymond, P Andrew Futreal, Michael R Stratton

Research output: Contribution to journal › Article

426 Citations (Scopus)

Abstract

Large-scale systematic resequencing has been proposed as the key future strategy for the discovery of rare, disease-causing sequence variants across the spectrum of human complex disease. We have sequenced the coding exons of the X chromosome in 208 families with X-linked mental retardation (XLMR), the largest direct screen for constitutional disease-causing mutations thus far reported. The screen has discovered nine genes implicated in XLMR, including SYP, ZNF711 and CASK reported here, confirming the power of this strategy. The study has, however, also highlighted issues confronting whole-genome sequencing screens, including the observation that loss of function of 1% or more of X-chromosome genes is compatible with apparently normal existence.

Original language	English
Pages (from-to)	535-543
Number of pages	9
Journal	Nature Genetics
Volume	41
Issue number	5
DOIs	https://doi.org/10.1038/ng.367
Publication status	Published - 1 May 2009

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10.1038/ng.367

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Tarpey, P. S., Smith, R., Pleasance, E., Whibley, A., Edkins, S., Hardy, C., O'meara, S., Latimer, C., Dicks, E., Menzies, A., Stephens, P., Blow, M., Greenman, C., Xue, Y., Tyler-smith, C., Thompson, D., Gray, K., Andrews, J., Barthorpe, S., ... Stratton, M. R. (2009). A systematic, large-scale resequencing screen of X-chromosome coding exons in mental retardation. Nature Genetics, 41(5), 535-543. https://doi.org/10.1038/ng.367

Tarpey, Patrick S ; Smith, Raffaella ; Pleasance, Erin ; Whibley, Annabel ; Edkins, Sarah ; Hardy, Claire ; O'meara, Sarah ; Latimer, Calli ; Dicks, Ed ; Menzies, Andrew ; Stephens, Phil ; Blow, Matt ; Greenman, Christopher ; Xue, Yali ; Tyler-smith, Chris ; Thompson, Deborah ; Gray, Kristian ; Andrews, Jenny ; Barthorpe, Syd ; Buck, Gemma ; Cole, Jennifer ; Dunmore, Rebecca ; Jones, David ; Maddison, Mark ; Mironenko, Tatiana ; Turner, Rachel ; Turrell, Kelly ; Varian, Jennifer ; West, Sofie ; Widaa, Sara ; Wray, Paul ; Teague, Jon ; Butler, Adam ; Jenkinson, Andrew ; Jia, Mingming ; Richardson, David ; Shepherd, Rebecca ; Wooster, Richard ; Tejada, M Isabel ; Martinez, Francisco ; Carvill, Gemma ; Goliath, Rene ; De Brouwer, Arjan P M ; Van Bokhoven, Hans ; Van Esch, Hilde ; Chelly, Jamel ; Raynaud, Martine ; Ropers, Hans-hilger ; Abidi, Fatima E ; Srivastava, Anand K ; Cox, James ; Luo, Ying ; Mallya, Uma ; Moon, Jenny ; Parnau, Josef ; Mohammed, Shehla ; Tolmie, John L ; Shoubridge, Cheryl ; Corbett, Mark ; Gardner, Alison ; Haan, Eric ; Rujirabanjerd, Sinitdhorn ; Shaw, Marie ; Vandeleur, Lucianne ; Fullston, Tod ; Easton, Douglas F ; Boyle, Jackie ; Partington, Michael ; Hackett, Anna ; Field, Michael ; Skinner, Cindy ; Stevenson, Roger E ; Bobrow, Martin ; Turner, Gillian ; Schwartz, Charles E ; Gecz, Jozef ; Raymond, F Lucy ; Futreal, P Andrew ; Stratton, Michael R. / A systematic, large-scale resequencing screen of X-chromosome coding exons in mental retardation. In: Nature Genetics. 2009 ; Vol. 41, No. 5. pp. 535-543.

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abstract = "Large-scale systematic resequencing has been proposed as the key future strategy for the discovery of rare, disease-causing sequence variants across the spectrum of human complex disease. We have sequenced the coding exons of the X chromosome in 208 families with X-linked mental retardation (XLMR), the largest direct screen for constitutional disease-causing mutations thus far reported. The screen has discovered nine genes implicated in XLMR, including SYP, ZNF711 and CASK reported here, confirming the power of this strategy. The study has, however, also highlighted issues confronting whole-genome sequencing screens, including the observation that loss of function of 1% or more of X-chromosome genes is compatible with apparently normal existence.",

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Tarpey, PS, Smith, R, Pleasance, E, Whibley, A, Edkins, S, Hardy, C, O'meara, S, Latimer, C, Dicks, E, Menzies, A, Stephens, P, Blow, M, Greenman, C, Xue, Y, Tyler-smith, C, Thompson, D, Gray, K, Andrews, J, Barthorpe, S, Buck, G, Cole, J, Dunmore, R, Jones, D, Maddison, M, Mironenko, T, Turner, R, Turrell, K, Varian, J, West, S, Widaa, S, Wray, P, Teague, J, Butler, A, Jenkinson, A, Jia, M, Richardson, D, Shepherd, R, Wooster, R, Tejada, MI, Martinez, F, Carvill, G, Goliath, R, De Brouwer, APM, Van Bokhoven, H, Van Esch, H, Chelly, J, Raynaud, M, Ropers, H, Abidi, FE, Srivastava, AK, Cox, J, Luo, Y, Mallya, U, Moon, J, Parnau, J, Mohammed, S, Tolmie, JL, Shoubridge, C, Corbett, M, Gardner, A, Haan, E, Rujirabanjerd, S, Shaw, M, Vandeleur, L, Fullston, T, Easton, DF, Boyle, J, Partington, M, Hackett, A, Field, M, Skinner, C, Stevenson, RE, Bobrow, M, Turner, G, Schwartz, CE, Gecz, J, Raymond, FL, Futreal, PA & Stratton, MR 2009, 'A systematic, large-scale resequencing screen of X-chromosome coding exons in mental retardation', Nature Genetics, vol. 41, no. 5, pp. 535-543. https://doi.org/10.1038/ng.367

A systematic, large-scale resequencing screen of X-chromosome coding exons in mental retardation. / Tarpey, Patrick S; Smith, Raffaella; Pleasance, Erin; Whibley, Annabel; Edkins, Sarah; Hardy, Claire; O'meara, Sarah; Latimer, Calli; Dicks, Ed; Menzies, Andrew; Stephens, Phil; Blow, Matt; Greenman, Christopher; Xue, Yali; Tyler-smith, Chris; Thompson, Deborah; Gray, Kristian; Andrews, Jenny; Barthorpe, Syd; Buck, Gemma; Cole, Jennifer; Dunmore, Rebecca; Jones, David; Maddison, Mark; Mironenko, Tatiana; Turner, Rachel; Turrell, Kelly; Varian, Jennifer; West, Sofie; Widaa, Sara; Wray, Paul; Teague, Jon; Butler, Adam; Jenkinson, Andrew; Jia, Mingming; Richardson, David; Shepherd, Rebecca; Wooster, Richard; Tejada, M Isabel; Martinez, Francisco; Carvill, Gemma; Goliath, Rene; De Brouwer, Arjan P M; Van Bokhoven, Hans; Van Esch, Hilde; Chelly, Jamel; Raynaud, Martine; Ropers, Hans-hilger; Abidi, Fatima E; Srivastava, Anand K; Cox, James; Luo, Ying; Mallya, Uma; Moon, Jenny; Parnau, Josef; Mohammed, Shehla; Tolmie, John L; Shoubridge, Cheryl; Corbett, Mark; Gardner, Alison; Haan, Eric; Rujirabanjerd, Sinitdhorn; Shaw, Marie; Vandeleur, Lucianne; Fullston, Tod; Easton, Douglas F; Boyle, Jackie; Partington, Michael; Hackett, Anna; Field, Michael; Skinner, Cindy; Stevenson, Roger E; Bobrow, Martin; Turner, Gillian; Schwartz, Charles E; Gecz, Jozef; Raymond, F Lucy; Futreal, P Andrew; Stratton, Michael R.

In: Nature Genetics, Vol. 41, No. 5, 01.05.2009, p. 535-543.

Research output: Contribution to journal › Article

TY - JOUR

T1 - A systematic, large-scale resequencing screen of X-chromosome coding exons in mental retardation

AU - Tarpey, Patrick S

AU - Smith, Raffaella

AU - Pleasance, Erin

AU - Whibley, Annabel

AU - Edkins, Sarah

AU - Hardy, Claire

AU - O'meara, Sarah

AU - Latimer, Calli

AU - Dicks, Ed

AU - Menzies, Andrew

AU - Stephens, Phil

AU - Blow, Matt

AU - Greenman, Christopher

AU - Xue, Yali

AU - Tyler-smith, Chris

AU - Thompson, Deborah

AU - Gray, Kristian

AU - Andrews, Jenny

AU - Barthorpe, Syd

AU - Buck, Gemma

AU - Cole, Jennifer

AU - Dunmore, Rebecca

AU - Jones, David

AU - Maddison, Mark

AU - Mironenko, Tatiana

AU - Turner, Rachel

AU - Turrell, Kelly

AU - Varian, Jennifer

AU - West, Sofie

AU - Widaa, Sara

AU - Wray, Paul

AU - Teague, Jon

AU - Butler, Adam

AU - Jenkinson, Andrew

AU - Jia, Mingming

AU - Richardson, David

AU - Shepherd, Rebecca

AU - Wooster, Richard

AU - Tejada, M Isabel

AU - Martinez, Francisco

AU - Carvill, Gemma

AU - Goliath, Rene

AU - De Brouwer, Arjan P M

AU - Van Bokhoven, Hans

AU - Van Esch, Hilde

AU - Chelly, Jamel

AU - Raynaud, Martine

AU - Ropers, Hans-hilger

AU - Abidi, Fatima E

AU - Srivastava, Anand K

AU - Cox, James

AU - Luo, Ying

AU - Mallya, Uma

AU - Moon, Jenny

AU - Parnau, Josef

AU - Mohammed, Shehla

AU - Tolmie, John L

AU - Shoubridge, Cheryl

AU - Corbett, Mark

AU - Gardner, Alison

AU - Haan, Eric

AU - Rujirabanjerd, Sinitdhorn

AU - Shaw, Marie

AU - Vandeleur, Lucianne

AU - Fullston, Tod

AU - Easton, Douglas F

AU - Boyle, Jackie

AU - Partington, Michael

AU - Hackett, Anna

AU - Field, Michael

AU - Skinner, Cindy

AU - Stevenson, Roger E

AU - Bobrow, Martin

AU - Turner, Gillian

AU - Schwartz, Charles E

AU - Gecz, Jozef

AU - Raymond, F Lucy

AU - Futreal, P Andrew

AU - Stratton, Michael R

PY - 2009/5/1

Y1 - 2009/5/1

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AB - Large-scale systematic resequencing has been proposed as the key future strategy for the discovery of rare, disease-causing sequence variants across the spectrum of human complex disease. We have sequenced the coding exons of the X chromosome in 208 families with X-linked mental retardation (XLMR), the largest direct screen for constitutional disease-causing mutations thus far reported. The screen has discovered nine genes implicated in XLMR, including SYP, ZNF711 and CASK reported here, confirming the power of this strategy. The study has, however, also highlighted issues confronting whole-genome sequencing screens, including the observation that loss of function of 1% or more of X-chromosome genes is compatible with apparently normal existence.

U2 - 10.1038/ng.367

DO - 10.1038/ng.367

M3 - Article

VL - 41

SP - 535

EP - 543

JO - Nature Genetics

JF - Nature Genetics

SN - 1061-4036

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ER -