Reply to 'Currently available bulk sequencing data do not necessarily support a model of neutral tumor evolution'.

abstract：:We conducted a genome-wide association study on 969 bladder cancer cases and 957 controls from Texas. For fast-track validation, we evaluated 60 SNPs in three additional US populations and validated the top SNP in nine European populations. A missense variant (rs2294008) in the PSCA gene showed consistent association ...

journal_title：Nature genetics

authors： Wu X,Ye Y,Kiemeney LA,Sulem P,Rafnar T,Matullo G,Seminara D,Yoshida T,Saeki N,Andrew AS,Dinney CP,Czerniak B,Zhang ZF,Kiltie AE,Bishop DT,Vineis P,Porru S,Buntinx F,Kellen E,Zeegers MP,Kumar R,Rudnai P,Gurzau

更新日期：2009-09-01 00:00:00

abstract：:Holoprosencephaly (HPE) is a developmental field defect involving the brain and face. Cytogenetic deletions in patients with HPE have localized one of the HPE genes to chromosomal region 7q36. We have characterized the 7q deletions in thirteen HPE patients. The result is the construction of a high resolution physical ...

journal_title：Nature genetics

authors： Gurrieri F,Trask BJ,van den Engh G,Krauss CM,Schinzel A,Pettenati MJ,Schindler D,Dietz-Band J,Vergnaud G,Scherer SW

更新日期：1993-03-01 00:00:00

abstract：:Breast carcinoma is the most common malignancy among women in developed countries. Because family history remains the strongest single predictor of breast cancer risk, attention has focused on the role of highly penetrant, dominantly inherited genes in cancer-prone kindreds (1). BRCA1 was localized to chromosome 17 th...

journal_title：Nature genetics

authors： Tavtigian SV,Simard J,Rommens J,Couch F,Shattuck-Eidens D,Neuhausen S,Merajver S,Thorlacius S,Offit K,Stoppa-Lyonnet D,Belanger C,Bell R,Berry S,Bogden R,Chen Q,Davis T,Dumont M,Frye C,Hattier T,Jammulapati S,Jane

更新日期：1996-03-01 00:00:00

abstract：:More than 5 million single-nucleotide polymorphisms (SNPs) with minor-allele frequency greater than 10% are expected to exist in the human genome. Some of these SNPs may be associated with risk of developing common diseases. To assess the power of currently available SNPs to detect such associations, we resequenced 50...

journal_title：Nature genetics

authors： Carlson CS,Eberle MA,Rieder MJ,Smith JD,Kruglyak L,Nickerson DA

更新日期：2003-04-01 00:00:00

abstract：:Age-related hearing loss (AHL) in common inbred mouse strains is a genetically complex quantitative trait. We found a synonymous single-nucleotide polymorphism in exon 7 of Cdh23 that shows significant association with AHL and the deafness modifier mdfw (modifer of deafwaddler). The hypomorphic Cdh23(753A) allele caus...

journal_title：Nature genetics

authors： Noben-Trauth K,Zheng QY,Johnson KR

更新日期：2003-09-01 00:00:00

abstract：:microRNAs (miRNAs) function as genetic rheostats to control gene output. Based on their role as modulators, it has been postulated that miRNAs canalize development and provide genetic robustness. Here, we uncover a previously unidentified regulatory layer of chemokine signaling by miRNAs that confers genetic robustnes...

journal_title：Nature genetics

authors： Staton AA,Knaut H,Giraldez AJ

更新日期：2011-03-01 00:00:00

abstract：:Epidemic C. difficile (027/BI/NAP1) has rapidly emerged in the past decade as the leading cause of antibiotic-associated diarrhea worldwide. However, the key events in evolutionary history leading to its emergence and the subsequent patterns of global spread remain unknown. Here, we define the global population struct...

journal_title：Nature genetics

authors： He M,Miyajima F,Roberts P,Ellison L,Pickard DJ,Martin MJ,Connor TR,Harris SR,Fairley D,Bamford KB,D'Arc S,Brazier J,Brown D,Coia JE,Douce G,Gerding D,Kim HJ,Koh TH,Kato H,Senoh M,Louie T,Michell S,Butt E,Pea

更新日期：2013-01-01 00:00:00

abstract：:The approach to annotating a genome critically affects the number and accuracy of genes identified in the genome sequence. Genome annotation based on stringent gene identification is prone to underestimate the complement of genes encoded in a genome. In contrast, over-prediction of putative genes followed by exhaustiv...

journal_title：Nature genetics

authors： Gopal S,Schroeder M,Pieper U,Sczyrba A,Aytekin-Kurban G,Bekiranov S,Fajardo JE,Eswar N,Sanchez R,Sali A,Gaasterland T

更新日期：2001-03-01 00:00:00

abstract：:An amendment to this paper has been published and can be accessed via a link at the top of the paper. ...

journal_title：Nature genetics

authors： Malik R,Chauhan G,Traylor M,Sargurupremraj M,Okada Y,Mishra A,Rutten-Jacobs L,Giese AK,van der Laan SW,Gretarsdottir S,Anderson CD,Chong M,Adams HHH,Ago T,Almgren P,Amouyel P,Ay H,Bartz TM,Benavente OR,Bevan S,Bon

更新日期：2019-07-01 00:00:00

abstract：:Potato (Solanum tuberosum L.) is the most important tuber crop worldwide. Efforts are underway to transform the crop from a clonally propagated tetraploid into a seed-propagated, inbred-line-based hybrid, but this process requires a better understanding of potato genome. Here, we report the 1.67-Gb haplotype-resolved ...

journal_title：Nature genetics

authors： Zhou Q,Tang D,Huang W,Yang Z,Zhang Y,Hamilton JP,Visser RGF,Bachem CWB,Robin Buell C,Zhang Z,Zhang C,Huang S

更新日期：2020-10-01 00:00:00

abstract：:We present a new statistical test of association between a trait and genetic markers, which we theoretically and practically prove to be robust to arbitrarily complex population structure. The statistical test involves a set of parameters that can be directly estimated from large-scale genotyping data, such as those m...

journal_title：Nature genetics

authors： Song M,Hao W,Storey JD

更新日期：2015-05-01 00:00:00

abstract：:Metastasis is the leading cause of death in people with lung cancer, yet the molecular effectors underlying tumor dissemination remain poorly defined. Through the development of an in vivo spontaneous lung cancer metastasis model, we show that the developmentally regulated transcriptional repressor Capicua (CIC) suppr...

journal_title：Nature genetics

authors： Okimoto RA,Breitenbuecher F,Olivas VR,Wu W,Gini B,Hofree M,Asthana S,Hrustanovic G,Flanagan J,Tulpule A,Blakely CM,Haringsma HJ,Simmons AD,Gowen K,Suh J,Miller VA,Ali S,Schuler M,Bivona TG

更新日期：2017-01-01 00:00:00

abstract：:Reduced lung function predicts mortality and is key to the diagnosis of chronic obstructive pulmonary disease (COPD). In a genome-wide association study in 400,102 individuals of European ancestry, we define 279 lung function signals, 139 of which are new. In combination, these variants strongly predict COPD in indepe...

journal_title：Nature genetics

authors： Shrine N,Guyatt AL,Erzurumluoglu AM,Jackson VE,Hobbs BD,Melbourne CA,Batini C,Fawcett KA,Song K,Sakornsakolpat P,Li X,Boxall R,Reeve NF,Obeidat M,Zhao JH,Wielscher M,Weiss S,Kentistou KA,Cook JP,Sun BB,Zhou J,Hu

更新日期：2019-03-01 00:00:00

abstract：:Familial hyperkalemic hypertension (FHHt) is a Mendelian form of arterial hypertension that is partially explained by mutations in WNK1 and WNK4 that lead to increased activity of the Na(+)-Cl(-) cotransporter (NCC) in the distal nephron. Using combined linkage analysis and whole-exome sequencing in two families, we i...

journal_title：Nature genetics

authors： Louis-Dit-Picard H,Barc J,Trujillano D,Miserey-Lenkei S,Bouatia-Naji N,Pylypenko O,Beaurain G,Bonnefond A,Sand O,Simian C,Vidal-Petiot E,Soukaseum C,Mandet C,Broux F,Chabre O,Delahousse M,Esnault V,Fiquet B,Houillier

更新日期：2012-03-11 00:00:00

abstract：:Genome-wide association studies have identified several risk associations for ovarian carcinomas but not for mucinous ovarian carcinomas (MOCs). Our analysis of 1,644 MOC cases and 21,693 controls with imputation identified 3 new risk associations: rs752590 at 2q13 (P = 3.3 × 10(-8)), rs711830 at 2q31.1 (P = 7.5 × 10(...

journal_title：Nature genetics

authors： Kelemen LE,Lawrenson K,Tyrer J,Li Q,Lee JM,Seo JH,Phelan CM,Beesley J,Chen X,Spindler TJ,Aben KK,Anton-Culver H,Antonenkova N,Australian Cancer Study.,Australian Ovarian Cancer Study Group.,Ovarian Cancer Association Consor

更新日期：2015-08-01 00:00:00

abstract：:We defined the genetic landscape of balanced chromosomal rearrangements at nucleotide resolution by sequencing 141 breakpoints from cytogenetically interpreted translocations and inversions. We confirm that the recently described phenomenon of 'chromothripsis' (massive chromosomal shattering and reorganization) is not...

journal_title：Nature genetics

authors： Chiang C,Jacobsen JC,Ernst C,Hanscom C,Heilbut A,Blumenthal I,Mills RE,Kirby A,Lindgren AM,Rudiger SR,McLaughlan CJ,Bawden CS,Reid SJ,Faull RL,Snell RG,Hall IM,Shen Y,Ohsumi TK,Borowsky ML,Daly MJ,Lee C,Morton C

更新日期：2012-03-04 00:00:00

abstract：:Many primary-tumor subregions have low levels of molecular oxygen, termed hypoxia. Hypoxic tumors are at elevated risk for local failure and distant metastasis, but the molecular hallmarks of tumor hypoxia remain poorly defined. To fill this gap, we quantified hypoxia in 8,006 tumors across 19 tumor types. In ten tumo...

journal_title：Nature genetics

authors： Bhandari V,Hoey C,Liu LY,Lalonde E,Ray J,Livingstone J,Lesurf R,Shiah YJ,Vujcic T,Huang X,Espiritu SMG,Heisler LE,Yousif F,Huang V,Yamaguchi TN,Yao CQ,Sabelnykova VY,Fraser M,Chua MLK,van der Kwast T,Liu SK,Bout

更新日期：2019-02-01 00:00:00

abstract：:Pancreatic cancer has the lowest survival rate among human cancers, and there are no effective markers for its screening and early diagnosis. To identify genetic susceptibility markers for this cancer, we carried out a genome-wide association study on 981 individuals with pancreatic cancer (cases) and 1,991 cancer-fre...

journal_title：Nature genetics

authors： Wu C,Miao X,Huang L,Che X,Jiang G,Yu D,Yang X,Cao G,Hu Z,Zhou Y,Zuo C,Wang C,Zhang X,Zhou Y,Yu X,Dai W,Li Z,Shen H,Liu L,Chen Y,Zhang S,Wang X,Zhai K,Chang J,Liu Y,Sun M,Cao W,Gao J,Ma Y,Zheng X

更新日期：2011-12-11 00:00:00

abstract：:Genetic studies of blood pressure (BP) to date have mainly analyzed common variants (minor allele frequency > 0.05). In a meta-analysis of up to ~1.3 million participants, we discovered 106 new BP-associated genomic regions and 87 rare (minor allele frequency ≤ 0.01) variant BP associations (P < 5 × 10-8), of which 32...

journal_title：Nature genetics

authors： Surendran P,Feofanova EV,Lahrouchi N,Ntalla I,Karthikeyan S,Cook J,Chen L,Mifsud B,Yao C,Kraja AT,Cartwright JH,Hellwege JN,Giri A,Tragante V,Thorleifsson G,Liu DJ,Prins BP,Stewart ID,Cabrera CP,Eales JM,Akbarov A

更新日期：2020-12-01 00:00:00

abstract：:Schwannomas are common peripheral nerve sheath tumors that can cause debilitating morbidities. We performed an integrative analysis to determine genomic aberrations common to sporadic schwannomas. Exome sequence analysis with validation by targeted DNA sequencing of 125 samples uncovered, in addition to expected NF2 d...

journal_title：Nature genetics

authors： Agnihotri S,Jalali S,Wilson MR,Danesh A,Li M,Klironomos G,Krieger JR,Mansouri A,Khan O,Mamatjan Y,Landon-Brace N,Tung T,Dowar M,Li T,Bruce JP,Burrell KE,Tonge PD,Alamsahebpour A,Krischek B,Agarwalla PK,Bi WL,Dun

更新日期：2016-11-01 00:00:00

abstract：:The hereditary breast cancer gene BRCA2 was recently cloned and is believed to account for almost half of site-specific breast cancer families and the majority of male breast cancer families. We screened 49 site-specific breast cancer families for mutations in the BRCA2 gene using single strand conformation analysis (...

journal_title：Nature genetics

authors： Phelan CM,Lancaster JM,Tonin P,Gumbs C,Cochran C,Carter R,Ghadirian P,Perret C,Moslehi R,Dion F,Faucher MC,Dole K,Karimi S,Foulkes W,Lounis H,Warner E,Goss P,Anderson D,Larsson C,Narod SA,Futreal PA

更新日期：1996-05-01 00:00:00

abstract：:We present an approximate conditional and joint association analysis that can use summary-level statistics from a meta-analysis of genome-wide association studies (GWAS) and estimated linkage disequilibrium (LD) from a reference sample with individual-level genotype data. Using this method, we analyzed meta-analysis s...

journal_title：Nature genetics

authors： Yang J,Ferreira T,Morris AP,Medland SE,Genetic Investigation of ANthropometric Traits (GIANT) Consortium.,DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) Consortium.,Madden PA,Heath AC,Martin NG,Montgomery GW,Weedon MN,Lo

更新日期：2012-03-18 00:00:00

abstract：:Gene therapy strategies designed to combat haemophilia B, caused by defects in clotting factor IX, have so far concentrated on ex vivo approaches. We have now evaluated adenoviral vector-mediated expression of human factor IX in vivo. Injection of the vector Av1H9B, which encodes human factor IX cDNA, into the tail ve...

journal_title：Nature genetics

authors： Smith TA,Mehaffey MG,Kayda DB,Saunders JM,Yei S,Trapnell BC,McClelland A,Kaleko M

更新日期：1993-12-01 00:00:00

abstract：:Testicular germ cell tumor (TGCT) is the most common cancer in young men and is notable for its high familial risks. So far, six loci associated with TGCT have been reported. From genome-wide association study (GWAS) analysis of 307,291 SNPs in 986 TGCT cases and 4,946 controls, we selected for follow-up 694 SNPs, whi...

journal_title：Nature genetics

authors： Ruark E,Seal S,McDonald H,Zhang F,Elliot A,Lau K,Perdeaux E,Rapley E,Eeles R,Peto J,Kote-Jarai Z,Muir K,Nsengimana J,Shipley J,UK Testicular Cancer Collaboration (UKTCC).,Bishop DT,Stratton MR,Easton DF,Huddart RA,R

更新日期：2013-06-01 00:00:00

abstract：:The GM2 gangliosidoses, Tay-Sachs and Sandhoff diseases, are caused by mutations in the HEXA (alpha-subunit) and HEXB (beta-subunit) genes, respectively. Each gene encodes a subunit for the heterodimeric lysosomal enzyme, beta-hexosaminidase A (alpha beta), as well as for the homodimers beta-hexosaminidase B (beta bet...

journal_title：Nature genetics

authors： Sango K,McDonald MP,Crawley JN,Mack ML,Tifft CJ,Skop E,Starr CM,Hoffmann A,Sandhoff K,Suzuki K,Proia RL

更新日期：1996-11-01 00:00:00

abstract：:Through whole-genome sequencing of 2,230 Icelanders, we detected a rare nonsynonymous SNP (minor allele frequency = 0.55%) in the C3 gene encoding a p.Lys155Gln substitution in complement factor 3, which, following imputation into a set of Icelandic cases with age-related macular degeneration (AMD) and controls, assoc...

journal_title：Nature genetics

authors： Helgason H,Sulem P,Duvvari MR,Luo H,Thorleifsson G,Stefansson H,Jonsdottir I,Masson G,Gudbjartsson DF,Walters GB,Magnusson OT,Kong A,Rafnar T,Kiemeney LA,Schoenmaker-Koller FE,Zhao L,Boon CJ,Song Y,Fauser S,Pei M,

更新日期：2013-11-01 00:00:00

abstract：:Enchondromas are common benign cartilage tumors of bone. They can occur as solitary lesions or as multiple lesions in enchondromatosis (Ollier and Maffucci diseases). Clinical problems caused by enchondromas include skeletal deformity and the potential for malignant change to chondrosarcoma. The extent of skeletal inv...

journal_title：Nature genetics

authors： Hopyan S,Gokgoz N,Poon R,Gensure RC,Yu C,Cole WG,Bell RS,Jüppner H,Andrulis IL,Wunder JS,Alman BA

更新日期：2002-03-01 00:00:00

abstract：:Microarray analysis has become a widely used tool for the generation of gene expression data on a genomic scale. Although many significant results have been derived from microarray studies, one limitation has been the lack of standards for presenting and exchanging such data. Here we present a proposal, the Minimum In...

journal_title：Nature genetics

authors： Brazma A,Hingamp P,Quackenbush J,Sherlock G,Spellman P,Stoeckert C,Aach J,Ansorge W,Ball CA,Causton HC,Gaasterland T,Glenisson P,Holstege FC,Kim IF,Markowitz V,Matese JC,Parkinson H,Robinson A,Sarkans U,Schulze-Krem

更新日期：2001-12-01 00:00:00

abstract：:New genetic data has enabled scientists to re-examine the relationship between human genetic variation and 'race'. We review the results of genetic analyses that show that human genetic variation is geographically structured, in accord with historical patterns of gene flow and genetic drift. Analysis of many loci now ...

journal_title：Nature genetics

authors： Jorde LB,Wooding SP

更新日期：2004-11-01 00:00:00

abstract：:Communication between distal chromosomal elements is essential for control of many nuclear processes. For example, genes in higher eukaryotes often require distant enhancer sequences for high-level expression. The mechanisms proposed for long-range enhancer action fall into two basic categories. Non-contact models pro...

journal_title：Nature genetics

authors： Carter D,Chakalova L,Osborne CS,Dai YF,Fraser P

更新日期：2002-12-01 00:00:00