Table of contents


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Editorial

All in the mind p805

doi:10.1038/ng0708-805

Findings of an excess of de novo structural variants in cases of autism and schizophrenia have raised hopes that neuropsychiatric conditions may yet prove genetically tractable. Past experience suggests that success in finding causative variants will require exceptional rigor and caution.


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Correspondence

ESR1 gene amplification in breast cancer: a common phenomenon? pp806 - 807

Lindsay A Brown, Jeremy Hoog, Suet-Feung Chin, Yu Tao, Abd Alnaser Zayed, Koei Chin, Andrew E Teschendorff, John F Quackenbush, John C Marioni, Samuel Leung, Charles M Perou, Torsten O Neilsen, Matthew Ellis, Joe W Gray, Philip S Bernard, David G Huntsman & Carlos Caldas

doi:10.1038/ng0708-806

See also: News and Views by Albertson


ESR1 gene amplification in breast cancer: a common phenomenon? pp807 - 808

Hugo M Horlings, Anna Bergamaschi, Silje H Nordgard, Young H Kim, Wonshik Han, Dong-Young Noh, Keyan Salari, Simon A Joosse, Fabien Reyal, Ole Christian Lingjaerde, Vessela N Kristensen, Anne-Lise Børresen-Dale, Jonathan Pollack & Marc J van de Vijver

doi:10.1038/ng0708-807

See also: News and Views by Albertson


ESR1 gene amplification in breast cancer: a common phenomenon? p809

Anne Vincent-Salomon, Virginie Raynal, Carlo Lucchesi, Nadège Gruel & Olivier Delattre

doi:10.1038/ng0708-809a

See also: News and Views by Albertson


ESR1 gene amplification in breast cancer: a common phenomenon? pp809 - 810

Jorge S Reis-Filho, Suzanne Drury, Maryou B Lambros, Caterina Marchio, Nichola Johnson, Rachael Natrajan, Janine Salter, Pauline Levey, Olivia Fletcher, Julian Peto, Alan Ashworth & Mitch Dowsett

doi:10.1038/ng0708-809b

See also: News and Views by Albertson


Reply to "ESR1 gene amplification in breast cancer: a common phenomenon?" pp810 - 812

Frederik Holst, Phillip Stahl, Olaf Hellwinkel, Ana-Maria Dancau, Antje Krohn, Laura Wuth, Christian Heupel, Annette Lebeau, Luigi Terracciano, Khawla Al-Kuraya, Fritz Jänicke, Guido Sauter & Ronald Simon

doi:10.1038/ng0708-810

See also: News and Views by Albertson


HDAC2 deficiency and histone acetylation pp812 - 813

Anne Hansen Ree, Sigurd Folkvord & Kjersti Flatmark

doi:10.1038/ng0708-812


Reply to "HDAC2 deficiency and histone acetylation" p813

Santiago Ropero & Manel Esteller

doi:10.1038/ng0708-813


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Obituary

Giuseppe Attardi 1923–2008 p814

Douglas C Wallace

doi:10.1038/ng0708-814


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Book Review

Blood-strong love p815

Sharon F Terry reviews Spelling Love with an X: A Mother, a Son, and the Gene that Binds Them by Clare Dunsford

doi:10.1038/ng0708-815


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News and Views

Shedding light on skin cancer pp817 - 818

Paul D P Pharoah

doi:10.1038/ng0708-817

Pigmentation traits are known risk factors for skin cancer. Now, three new studies provide insights into the genetic factors underlying these effects, and the results reveal a surprisingly complex picture of the relationship between pigmentation traits and disease risk.

See also: Brief Communication by Sulem et al. | Brief Communication by Brown et al. | Letter by Gudbjartsson et al.


A new identity for the elusive intestinal stem cell pp818 - 819

Eduard Batlle

doi:10.1038/ng0708-818

The tremendous regenerative power of the intestinal epithelium has attracted considerable attention to the crypt as a model for adult stem cell biology. A new study now identifies the Polycomb group protein Bmi1 as a specific marker of intestinal stem cells in vivo.

See also: Letter by Sangiorgi & Capecchi


Bringing age-related macular degeneration into focus pp820 - 821

Rando Allikmets & Michael Dean

doi:10.1038/ng0708-820

Genetic studies of age-related macular degeneration (AMD), the most prevalent blinding condition among the elderly, have had both great success and deep controversy. A new study now begins to resolve contradictory views over two candidate genes at a major AMD locus on chromosome 10q26 by suggesting a functional variant in one of these genes.

See also: Letter by Fritsche et al.


Conflicting evidence on the frequency of ESR1 amplification in breast cancer pp821 - 822

Donna G Albertson

doi:10.1038/ng0708-821

An earlier report of high-frequency ESR1 amplification in breast cancer is now challenged by correspondence from four groups. This discussion of whether or not there is something 'FISHy' about ESR1 amplification highlights the difficulty of validating such observations, leaving the frequency and clinical significance of ESR1 amplification in breast cancer an open question.

See also: Correspondence by Brown et al. | Correspondence by Horlings et al. | Correspondence by Vincent-Salomon et al. | Correspondence by Reis-Filho et al. | Correspondence by Holst et al.


Lung stem cells in the balance pp822 - 823

Saverio Bellusci

doi:10.1038/ng0708-822

Wnt ligands are secreted glycoproteins with critical roles in organogenesis, cancer initiation and progression, and maintenance of stem cell pluripotency. A new study strengthens considerably our understanding of the role of Wnt signaling in progenitor cells of the lung epithelium during development and injury.

See also: Article by Zhang et al.


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Research Highlights

Research highlights p825

doi:10.1038/ng0708-825


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Analysis

Systematic meta-analyses and field synopsis of genetic association studies in schizophrenia: the SzGene database pp827 - 834

Nicole C Allen, Sachin Bagade, Matthew B McQueen, John P A Ioannidis, Fotini K Kavvoura, Muin J Khoury, Rudolph E Tanzi & Lars Bertram

doi:10.1038/ng.171

Lars Bertram and colleagues report the creation of an online database, SzGene, containing all published genetic association studies for schizophrenia. A series of meta-analyses reveals 24 variants in 16 genes to be associated with the disease with nominal significance, and four of these have strong epidemiological support.


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Brief Communications

Two newly identified genetic determinants of pigmentation in Europeans pp835 - 837

Patrick Sulem, Daniel F Gudbjartsson, Simon N Stacey, Agnar Helgason, Thorunn Rafnar, Margret Jakobsdottir, Stacy Steinberg, Sigurjon A Gudjonsson, Arnar Palsson, Gudmar Thorleifsson, Snæbjörn Pálsson, Bardur Sigurgeirsson, Kristin Thorisdottir, Rafn Ragnarsson, Kristrun R Benediktsdottir, Katja K Aben, Sita H Vermeulen, Alisa M Goldstein, Margaret A Tucker, Lambertus A Kiemeney, Jon H Olafsson, Jeffrey Gulcher, Augustine Kong, Unnur Thorsteinsdottir & Kari Stefansson

doi:10.1038/ng.160

Sulem et al. report two previously unknown loci associated with variation in pigmentation in Northern Europeans. In two separate studies, Brown et al. and Gudbjartsson et al. report that some variants affecting human pigmentation, including variants on 20q11.22 near ASIP, also confer risk of cutaneous melanoma and basal cell carcinoma.

See also: News and Views by Pharoah | Brief Communication by Brown et al. | Letter by Gudbjartsson et al.


Common sequence variants on 20q11.22 confer melanoma susceptibility pp838 - 840

Kevin M Brown, Stuart MacGregor, Grant W Montgomery, David W Craig, Zhen Zhen Zhao, Kelly Iyadurai, Anjali K Henders, Nils Homer, Megan J Campbell, Mitchell Stark, Shane Thomas, Helen Schmid, Elizabeth A Holland, Elizabeth M Gillanders, David L Duffy, Judith A Maskiell, Jodie Jetann, Megan Ferguson, Dietrich A Stephan, Anne E Cust, David Whiteman, Adele Green, Håkan Olsson, Susana Puig, Paola Ghiorzo, Johan Hansson, Florence Demenais, Alisa M Goldstein, Nelleke A Gruis, David E Elder, Julia Newton Bishop, Richard F Kefford, Graham G Giles, Bruce K Armstrong, Joanne F Aitken, John L Hopper, Nicholas G Martin, Jeffrey M Trent, Graham J Mann & Nicholas K Hayward

doi:10.1038/ng.163

Brown et al. report results of a genome-wide association study for melanoma. Their screen, which used a pooling strategy, identified common variants on 20q11.22 associated with melanoma susceptibility. In two separate studies, Sulem et al. and Gudbjartsson et al. report that the same region on 20q11.22, near ASIP, influences pigmentation and confers risk of cutaneous melanoma and basal cell carcinoma.

See also: News and Views by Pharoah | Brief Communication by Sulem et al. | Letter by Gudbjartsson et al.


Estimating coverage and power for genetic association studies using near-complete variation data pp841 - 843

Tushar R Bhangale, Mark J Rieder & Deborah A Nickerson

doi:10.1038/ng.180

Tushar Bhangale, Mark Reider, and Deborah Nickerson report estimates of coverage and power by commercial genotyping arrays using a variation dataset for 76 genes resequenced as part of the SeattleSNPs program.


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Articles

NAD(P)H:quinone oxidoreductase 1 NQO1*2 genotype (P187S) is a strong prognostic and predictive factor in breast cancer pp844 - 853

Rainer Fagerholm, Barbara Hofstetter, Johanna Tommiska, Kirsimari Aaltonen, Radek Vrtel, Kirsi Syrjäkoski, Anne Kallioniemi, Outi Kilpivaara, Arto Mannermaa, Veli-Matti Kosma, Matti Uusitupa, Matti Eskelinen, Vesa Kataja, Kristiina Aittomäki, Karl von Smitten, Päivi Heikkilä, Jiri Lukas, Kaija Holli, Jirina Bartkova, Carl Blomqvist, Jiri Bartek & Heli Nevanlinna

doi:10.1038/ng.155

Jiri Bartek and colleagues find that a common variant reducing NAD(P)H:quinone oxidoreductase 1 activity is a potential predictor of response to epirubicin chemotherapy in women with breast cancer. Cell-based assays suggest three modes of action for the enzyme via the p53 and TNF–NF-kappaB pathways and by direct detoxification of reactive oxygen species.


Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks pp854 - 861

Jun Zhu, Bin Zhang, Erin N Smith, Becky Drees, Rachel B Brem, Leonid Kruglyak, Roger E Bumgarner & Eric E Schadt

doi:10.1038/ng.167

Eric Schadt and colleagues report the construction of yeast regulatory networks from multiple sources of large-scale functional genomic data, and show that a network constructed from the integration of genotypic, transcription factor binding site, and protein–protein interaction data is the most predictive.


A Gata6-Wnt pathway required for epithelial stem cell development and airway regeneration pp862 - 870

Yuzhen Zhang, Ashley M Goss, Ethan David Cohen, Rachel Kadzik, John J Lepore, Karthika Muthukumaraswamy, Jifu Yang, Francesco J DeMayo, Jeffrey A Whitsett, Michael S Parmacek & Edward E Morrisey

doi:10.1038/ng.157

Edward Morrisey and colleagues show that mice lacking the transcription factor Gata6 in the lung epithelium have an increased number of bronchioalveolar stem cells during development and in the context of lung regeneration. Additional evidence suggests that a Gata6-Wnt pathway regulates the balance of stem cell expansion and epithelial differentiation in the lung.

See also: News and Views by Bellusci


Dishevelled controls apical docking and planar polarization of basal bodies in ciliated epithelial cells pp871 - 879

Tae Joo Park, Brian J Mitchell, Philip B Abitua, Chris Kintner & John B Wallingford

doi:10.1038/ng.104

Using Xenopus epidermis as a model, John Wallingford and colleagues show that the planar cell polarity protein Dishevelled, acting in concert with Inturned and Rho, controls the apical positioning of basal bodies. Subsequently, Dvl and Rho are also required for directional ciliary beating, suggesting that a common signaling apparatus governs both apical docking and planar polarization of basal bodies.


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Letters

Strong association of de novo copy number mutations with sporadic schizophrenia pp880 - 885

Bin Xu, J Louw Roos, Shawn Levy, E J van Rensburg, Joseph A Gogos & Maria Karayiorgou

doi:10.1038/ng.162

Maria Karayiorgou and colleagues report that de novo mutations in DNA copy number are strongly associated with nonfamilial cases of schizophrenia. The authors observed no such enrichment among familial cases, suggesting that this type of mutation contributes primarily to sporadic forms of the disease.


ASIP and TYR pigmentation variants associate with cutaneous melanoma and basal cell carcinoma pp886 - 891

Daniel F Gudbjartsson, Patrick Sulem, Simon N Stacey, Alisa M Goldstein, Thorunn Rafnar, Bardur Sigurgeirsson, Kristrun R Benediktsdottir, Kristin Thorisdottir, Rafn Ragnarsson, Steinunn G Sveinsdottir, Veronica Magnusson, Annika Lindblom, Konstantinos Kostulas, Rafael Botella-Estrada, Virtudes Soriano, Pablo Juberías, Matilde Grasa, Berta Saez, Raquel Andres, Dominique Scherer, Peter Rudnai, Eugene Gurzau, Kvetoslava Koppova, Lambertus A Kiemeney, Margret Jakobsdottir, Stacy Steinberg, Agnar Helgason, Solveig Gretarsdottir, Margaret A Tucker, José I Mayordomo, Eduardo Nagore, Rajiv Kumar, Johan Hansson, Jon H Olafsson, Jeffrey Gulcher, Augustine Kong, Unnur Thorsteinsdottir & Kari Stefansson

doi:10.1038/ng.161

Gudbjartsson et al. report that variants near two genes, ASIP and TYR, are associated with risk of cutaneous melanoma and basal cell carcinoma. These loci are among several loci initially discovered for their role in human pigmentation, as reported by Sulem et al. In a separate study, Brown et al. independently discover an association between variants near ASIP and melanoma risk.

See also: News and Views by Pharoah | Brief Communication by Sulem et al. | Brief Communication by Brown et al.


Age-related macular degeneration is associated with an unstable ARMS2 (LOC387715) mRNA pp892 - 896

Lars G Fritsche, Thomas Loenhardt, Andreas Janssen, Sheila A Fisher, Andrea Rivera, Claudia N Keilhauer & Bernhard H F Weber

doi:10.1038/ng.170

Bernhard Weber and colleagues identify a previously unknown insertion-deletion polymorphism in ARMS2 (LOC387715), a gene associated with age-related macular degeneration. The variant leads to rapid mRNA turnover of the ARMS2 transcript, suggesting a role for this gene in AMD.

See also: News and Views by Allikmets & Dean


Combinatorial patterns of histone acetylations and methylations in the human genome pp897 - 903

Zhibin Wang, Chongzhi Zang, Jeffrey A Rosenfeld, Dustin E Schones, Artem Barski, Suresh Cuddapah, Kairong Cui, Tae-Young Roh, Weiqun Peng, Michael Q Zhang & Keji Zhao

doi:10.1038/ng.154

Keji Zhao and colleagues report genome-wide maps of 18 histone lysine acetylations in human CD4+ T cells as detected by ChIP-sequencing. Analysis of the data along with genome-wide maps of histone lysine methylations revealed a common module of 17 modifications associated with 25% of genes.


Genomic surveys by methylation-sensitive SNP analysis identify sequence-dependent allele-specific DNA methylation pp904 - 908

Kristi Kerkel, Alexandra Spadola, Eric Yuan, Jolanta Kosek, Le Jiang, Eldad Hod, Kerry Li, Vundavalli V Murty, Nicole Schupf, Eric Vilain, Mitzi Morris, Fatemeh Haghighi & Benjamin Tycko

doi:10.1038/ng.174

Ben Tycko and colleagues report the identification of genotype-dependent allele-specific methylation at many loci through the use of genomic methylation-sensitive SNP array analysis. Using independent assays, they confirm allele-specific methylation at 16 SNP-tagged loci on various chromosomes.


Mouse segmental duplication and copy number variation pp909 - 914

Xinwei She, Ze Cheng, Sebastian Zöllner, Deanna M Church & Evan E Eichler

doi:10.1038/ng.172

Evan Eichler and colleagues assess copy number variation of the C57BL/6J duplicated regions in 15 mouse strains used for genetic association studies. They report that mice show comparable copy number polymorphism when compared to humans, but that it is more locally restricted, specifically to regions containing gene families associated with spermatogenesis, pregnancy, viviparity, pheromone signaling and the immune response.


Bmi1 is expressed in vivo in intestinal stem cells pp915 - 920

Eugenio Sangiorgi & Mario R Capecchi

doi:10.1038/ng.165

Eugenio Sangiorgi and Mario Capecchi use lineage tracing in mice to identify Bmi1 as a specific marker of a stem cell population located at the +4 position of the small intestinal crypt. Their findings address a long-standing debate in the field and support the existence of two distinct intestinal stem cell populations near the crypt base.

See also: News and Views by Batlle


Ras-MAPK signaling promotes trophectoderm formation from embryonic stem cells and mouse embryos pp921 - 926

Chi-Wei Lu, Akiko Yabuuchi, Lingyi Chen, Srinivas Viswanathan, Kitai Kim & George Q Daley

doi:10.1038/ng.173

George Daley and colleagues show that ectopic Ras activation diverts embryonic stem cells towards trophoblastic fates, and conversely, that inhibition of MAPK signaling reduces trophectoderm outgrowth from embryo explants. These results implicate Ras-MAPK signaling in this early and critical cell fate decision.


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Corrigenda

Corrigendum: Prolyl 3-hydroxylase 1 deficiency causes a recessive metabolic bone disorder resembling lethal/severe osteogenesis imperfecta p927

Wayne A Cabral, Weizhong Chang, Aileen M Barnes, MaryAnn Weis, Melissa A Scott, Sergey Leikin, Elena Makareeva, Natalia V Kuznetsova, Kenneth N Rosenbaum, Cynthia J Tifft, Dorothy I Bulas, Chahira Kozma, Peter A Smith, David R Eyre & Joan C Marini

doi:10.1038/ng0708-927a


Corrigendum: Hypomorphic mutations in syndromic encephalocele genes are associated with Bardet-Biedl syndrome p927

Carmen C Leitch, Norann A Zaghloul, Erica E Davis, Corinne Stoetzel, Anna Diaz-Font, Suzanne Rix, Majid Al-Fadhel, Richard Alan Lewis, Wafaa Eyaid, Eyal Banin, Helene Dollfus, Philip L Beales, Jose L Badano & Nicholas Katsanis

doi:10.1038/ng0708-927b


Corrigendum: Mutations in 15-hydroxyprostaglandin dehydrogenase cause primary hypertrophic osteoarthropathy p927

Sandeep Uppal, Christine P Diggle, Ian M Carr, Colin W G Fishwick, Mushtaq Ahmed, Gamal H Ibrahim, Philip S Helliwell, Anna Latos-Bielen acuteska, Simon E V Phillips, Alexander F Markham, Christopher P Bennett & David T Bonthron

doi:10.1038/ng0708-927c


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