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  • 1
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    The landscape of recombination in African Americans (2011)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2011-07-22
    Description: Recombination, together with mutation, gives rise to genetic variation in populations. Here we leverage the recent mixture of people of African and European ancestry in the Americas to build a genetic map measuring the probability of crossing over at each position in the genome, based on about 2.1 million crossovers in 30,000 unrelated African Americans. At intervals of more than three megabases it is nearly identical to a map built in Europeans. At finer scales it differs significantly, and we identify about 2,500 recombination hotspots that are active in people of West African ancestry but nearly inactive in Europeans. The probability of a crossover at these hotspots is almost fully controlled by the alleles an individual carries at PRDM9 (P value 〈 10(-245)). We identify a 17-base-pair DNA sequence motif that is enriched in these hotspots, and is an excellent match to the predicted binding target of PRDM9 alleles common in West Africans and rare in Europeans. Sites of this motif are predicted to be risk loci for disease-causing genomic rearrangements in individuals carrying these alleles. More generally, this map provides a resource for research in human genetic variation and evolution.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3154982/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3154982/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Hinch, Anjali G -- Tandon, Arti -- Patterson, Nick -- Song, Yunli -- Rohland, Nadin -- Palmer, Cameron D -- Chen, Gary K -- Wang, Kai -- Buxbaum, Sarah G -- Akylbekova, Ermeg L -- Aldrich, Melinda C -- Ambrosone, Christine B -- Amos, Christopher -- Bandera, Elisa V -- Berndt, Sonja I -- Bernstein, Leslie -- Blot, William J -- Bock, Cathryn H -- Boerwinkle, Eric -- Cai, Qiuyin -- Caporaso, Neil -- Casey, Graham -- Cupples, L Adrienne -- Deming, Sandra L -- Diver, W Ryan -- Divers, Jasmin -- Fornage, Myriam -- Gillanders, Elizabeth M -- Glessner, Joseph -- Harris, Curtis C -- Hu, Jennifer J -- Ingles, Sue A -- Isaacs, William -- John, Esther M -- Kao, W H Linda -- Keating, Brendan -- Kittles, Rick A -- Kolonel, Laurence N -- Larkin, Emma -- Le Marchand, Loic -- McNeill, Lorna H -- Millikan, Robert C -- Murphy, Adam -- Musani, Solomon -- Neslund-Dudas, Christine -- Nyante, Sarah -- Papanicolaou, George J -- Press, Michael F -- Psaty, Bruce M -- Reiner, Alex P -- Rich, Stephen S -- Rodriguez-Gil, Jorge L -- Rotter, Jerome I -- Rybicki, Benjamin A -- Schwartz, Ann G -- Signorello, Lisa B -- Spitz, Margaret -- Strom, Sara S -- Thun, Michael J -- Tucker, Margaret A -- Wang, Zhaoming -- Wiencke, John K -- Witte, John S -- Wrensch, Margaret -- Wu, Xifeng -- Yamamura, Yuko -- Zanetti, Krista A -- Zheng, Wei -- Ziegler, Regina G -- Zhu, Xiaofeng -- Redline, Susan -- Hirschhorn, Joel N -- Henderson, Brian E -- Taylor, Herman A Jr -- Price, Alkes L -- Hakonarson, Hakon -- Chanock, Stephen J -- Haiman, Christopher A -- Wilson, James G -- Reich, David -- Myers, Simon R -- 090532/Wellcome Trust/United Kingdom -- CA060691/CA/NCI NIH HHS/ -- CA092447/CA/NCI NIH HHS/ -- CA100374/CA/NCI NIH HHS/ -- CA100598/CA/NCI NIH HHS/ -- CA1116460/CA/NCI NIH HHS/ -- CA1116460S1/CA/NCI NIH HHS/ -- CA121197/CA/NCI NIH HHS/ -- CA121197S2/CA/NCI NIH HHS/ -- CA127219/CA/NCI NIH HHS/ -- CA1326792/CA/NCI NIH HHS/ -- CA140388/CA/NCI NIH HHS/ -- CA141716/CA/NCI NIH HHS/ -- CA148085/CA/NCI NIH HHS/ -- CA148127/CA/NCI NIH HHS/ -- CA22453/CA/NCI NIH HHS/ -- CA54281/CA/NCI NIH HHS/ -- CA55769/CA/NCI NIH HHS/ -- CA58223/CA/NCI NIH HHS/ -- CA63464/CA/NCI NIH HHS/ -- CA68485/CA/NCI NIH HHS/ -- CA68578/CA/NCI NIH HHS/ -- CA77305/CA/NCI NIH HHS/ -- CA87895/CA/NCI NIH HHS/ -- CA88164/CA/NCI NIH HHS/ -- ES007784/ES/NIEHS NIH HHS/ -- ES011126/ES/NIEHS NIH HHS/ -- ES06717/ES/NIEHS NIH HHS/ -- ES10126/ES/NIEHS NIH HHS/ -- GM08016/GM/NIGMS NIH HHS/ -- GM091332/GM/NIGMS NIH HHS/ -- HD33175/HD/NICHD NIH HHS/ -- HG004726/HG/NHGRI NIH HHS/ -- HHSN268200960009C/PHS HHS/ -- HL084107/HL/NHLBI NIH HHS/ -- N01-HC-65226/HC/NHLBI NIH HHS/ -- P30 ES010126/ES/NIEHS NIH HHS/ -- R01 CA052689/CA/NCI NIH HHS/ -- R01 CA092447/CA/NCI NIH HHS/ -- R01 HG006399/HG/NHGRI NIH HHS/ -- R01 HL084107-04/HL/NHLBI NIH HHS/ -- R01-CA73629/CA/NCI NIH HHS/ -- U01 HG004168/HG/NHGRI NIH HHS/ -- U01 HG004168-03/HG/NHGRI NIH HHS/ -- Intramural NIH HHS/ -- Wellcome Trust/United Kingdom -- England -- Nature. 2011 Jul 20;476(7359):170-5. doi: 10.1038/nature10336.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Wellcome Trust Centre for Human Genetics, Oxford University, Roosevelt Drive, Oxford OX3 7BN, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21775986" target="_blank"〉PubMed〈/a〉
    Keywords: Africa, Western/ethnology ; African Americans/*genetics ; Alleles ; Amino Acid Motifs ; Base Sequence ; Chromosome Mapping ; Crossing Over, Genetic/*genetics ; Europe/ethnology ; European Continental Ancestry Group/genetics ; Evolution, Molecular ; Female ; Gene Frequency ; Genetics, Population ; Genome, Human/*genetics ; Genomics ; Haplotypes/genetics ; Histone-Lysine N-Methyltransferase/chemistry/genetics/metabolism ; Humans ; Male ; Molecular Sequence Data ; Pedigree ; Polymorphism, Single Nucleotide/genetics ; Probability
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 2
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    Integrative genomics identifies LMO1 as a neuroblastoma oncogene (2010)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2010-12-03
    Description: Neuroblastoma is a childhood cancer of the sympathetic nervous system that accounts for approximately 10% of all paediatric oncology deaths. To identify genetic risk factors for neuroblastoma, we performed a genome-wide association study (GWAS) on 2,251 patients and 6,097 control subjects of European ancestry from four case series. Here we report a significant association within LIM domain only 1 (LMO1) at 11p15.4 (rs110419, combined P = 5.2 x 10(-16), odds ratio of risk allele = 1.34 (95% confidence interval 1.25-1.44)). The signal was enriched in the subset of patients with the most aggressive form of the disease. LMO1 encodes a cysteine-rich transcriptional regulator, and its paralogues (LMO2, LMO3 and LMO4) have each been previously implicated in cancer. In parallel, we analysed genome-wide DNA copy number alterations in 701 primary tumours. We found that the LMO1 locus was aberrant in 12.4% through a duplication event, and that this event was associated with more advanced disease (P 〈 0.0001) and survival (P = 0.041). The germline single nucleotide polymorphism (SNP) risk alleles and somatic copy number gains were associated with increased LMO1 expression in neuroblastoma cell lines and primary tumours, consistent with a gain-of-function role in tumorigenesis. Short hairpin RNA (shRNA)-mediated depletion of LMO1 inhibited growth of neuroblastoma cells with high LMO1 expression, whereas forced expression of LMO1 in neuroblastoma cells with low LMO1 expression enhanced proliferation. These data show that common polymorphisms at the LMO1 locus are strongly associated with susceptibility to developing neuroblastoma, but also may influence the likelihood of further somatic alterations at this locus, leading to malignant progression.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3320515/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3320515/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Wang, Kai -- Diskin, Sharon J -- Zhang, Haitao -- Attiyeh, Edward F -- Winter, Cynthia -- Hou, Cuiping -- Schnepp, Robert W -- Diamond, Maura -- Bosse, Kristopher -- Mayes, Patrick A -- Glessner, Joseph -- Kim, Cecilia -- Frackelton, Edward -- Garris, Maria -- Wang, Qun -- Glaberson, Wendy -- Chiavacci, Rosetta -- Nguyen, Le -- Jagannathan, Jayanti -- Saeki, Norihisa -- Sasaki, Hiroki -- Grant, Struan F A -- Iolascon, Achille -- Mosse, Yael P -- Cole, Kristina A -- Li, Hongzhe -- Devoto, Marcella -- McGrady, Patrick W -- London, Wendy B -- Capasso, Mario -- Rahman, Nazneen -- Hakonarson, Hakon -- Maris, John M -- 9024/Cancer Research UK/United Kingdom -- R00 CA151869/CA/NCI NIH HHS/ -- R01 CA124709/CA/NCI NIH HHS/ -- R01 CA124709-05/CA/NCI NIH HHS/ -- R01-CA124709/CA/NCI NIH HHS/ -- U10-CA98413/CA/NCI NIH HHS/ -- U10-CA98543/CA/NCI NIH HHS/ -- UL1-RR024134-03/RR/NCRR NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2011 Jan 13;469(7329):216-20. doi: 10.1038/nature09609. Epub 2010 Dec 1.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉The Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21124317" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Cell Line, Tumor ; Cell Proliferation ; Chromosomes, Human, Pair 11/genetics ; DNA Copy Number Variations/genetics ; DNA-Binding Proteins/*genetics ; Disease Progression ; Europe/ethnology ; Gene Duplication/genetics ; Gene Expression Regulation, Neoplastic/genetics ; Genetic Predisposition to Disease/*genetics ; Genome, Human/genetics ; *Genome-Wide Association Study ; Genomics ; Genotype ; Humans ; LIM Domain Proteins ; Neuroblastoma/*genetics/pathology ; Odds Ratio ; Oncogenes/*genetics ; Phenotype ; Polymorphism, Single Nucleotide/genetics ; Survival Rate ; Transcription Factors/*genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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