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Items: 25

1.

Identifying, understanding, and correcting technical artifacts on the sex chromosomes in next-generation sequencing data.

Webster TH, Couse M, Grande BM, Karlins E, Phung TN, Richmond PA, Whitford W, Wilson MA.

Gigascience. 2019 Jul 1;8(7). pii: giz074. doi: 10.1093/gigascience/giz074.

2.

Blood DNA methylation and breast cancer risk: a meta-analysis of four prospective cohort studies.

Bodelon C, Ambatipudi S, Dugué PA, Johansson A, Sampson JN, Hicks B, Karlins E, Hutchinson A, Cuenin C, Chajès V, Southey MC, Romieu I, Giles GG, English D, Polidoro S, Assumma M, Baglietto L, Vineis P, Severi G, Herceg Z, Flanagan JM, Milne RL, Garcia-Closas M.

Breast Cancer Res. 2019 May 17;21(1):62. doi: 10.1186/s13058-019-1145-9.

3.

Genome-Wide Association Study in Irradiated Childhood Cancer Survivors Identifies HTR2A for Subsequent Basal Cell Carcinoma.

Sapkota Y, Turcotte LM, Ehrhardt MJ, Howell RM, Arnold MA, Wilson CL, Leisenring W, Wang Z, Sampson J, Dagnall CL, Karlins E, Li SA, Hicks BD, Weathers R, Smith SA, Shelton K, Liu Q, Tucker MA, Chanock SJ, Zhang J, Hudson MM, Neglia JP, Armstrong GT, Robison LL, Morton LM, Bhatia S, Yasui Y.

J Invest Dermatol. 2019 Sep;139(9):2042-2045.e8. doi: 10.1016/j.jid.2019.02.029. Epub 2019 Mar 22. No abstract available.

PMID:
30910758
4.

Genome-wide association study identifies multiple new loci associated with Ewing sarcoma susceptibility.

Machiela MJ, Grünewald TGP, Surdez D, Reynaud S, Mirabeau O, Karlins E, Rubio RA, Zaidi S, Grossetete-Lalami S, Ballet S, Lapouble E, Laurence V, Michon J, Pierron G, Kovar H, Gaspar N, Kontny U, González-Neira A, Picci P, Alonso J, Patino-Garcia A, Corradini N, Bérard PM, Freedman ND, Rothman N, Dagnall CL, Burdett L, Jones K, Manning M, Wyatt K, Zhou W, Yeager M, Cox DG, Hoover RN, Khan J, Armstrong GT, Leisenring WM, Bhatia S, Robison LL, Kulozik AE, Kriebel J, Meitinger T, Metzler M, Hartmann W, Strauch K, Kirchner T, Dirksen U, Morton LM, Mirabello L, Tucker MA, Tirode F, Chanock SJ, Delattre O.

Nat Commun. 2018 Aug 9;9(1):3184. doi: 10.1038/s41467-018-05537-2.

5.

Successful use of whole genome amplified DNA from multiple source types for high-density Illumina SNP microarrays.

Dagnall CL, Morton LM, Hicks BD, Li S, Zhou W, Karlins E, Teshome K, Chowdhury S, Lashley KS, Sampson JN, Robison LL, Armstrong GT, Bhatia S, Radloff GA, Davies SM, Tucker MA, Yeager M, Chanock SJ.

BMC Genomics. 2018 Mar 6;19(1):182. doi: 10.1186/s12864-018-4572-6.

6.

Genome-wide association study identifies the GLDC/IL33 locus associated with survival of osteosarcoma patients.

Koster R, Panagiotou OA, Wheeler WA, Karlins E, Gastier-Foster JM, Caminada de Toledo SR, Petrilli AS, Flanagan AM, Tirabosco R, Andrulis IL, Wunder JS, Gokgoz N, Patiño-Garcia A, Lecanda F, Serra M, Hattinger C, Picci P, Scotlandi K, Thomas DM, Ballinger ML, Gorlick R, Barkauskas DA, Spector LG, Tucker M, Belynda DH, Yeager M, Hoover RN, Wacholder S, Chanock SJ, Savage SA, Mirabello L.

Int J Cancer. 2018 Apr 15;142(8):1594-1601. doi: 10.1002/ijc.31195. Epub 2017 Dec 23.

7.

Genome-Wide Association Study to Identify Susceptibility Loci That Modify Radiation-Related Risk for Breast Cancer After Childhood Cancer.

Morton LM, Sampson JN, Armstrong GT, Chen TH, Hudson MM, Karlins E, Dagnall CL, Li SA, Wilson CL, Srivastava DK, Liu W, Kang G, Oeffinger KC, Henderson TO, Moskowitz CS, Gibson TM, Merino DM, Wong JR, Hammond S, Neglia JP, Turcotte LM, Miller J, Bowen L, Wheeler WA, Leisenring WM, Whitton JA, Burdette L, Chung C, Hicks BD, Jones K, Machiela MJ, Vogt A, Wang Z, Yeager M, Neale G, Lear M, Strong LC, Yasui Y, Stovall M, Weathers RE, Smith SA, Howell R, Davies SM, Radloff GA, Onel K, Berrington de González A, Inskip PD, Rajaraman P, Fraumeni JF Jr, Bhatia S, Chanock SJ, Tucker MA, Robison LL.

J Natl Cancer Inst. 2017 Nov 1;109(11). doi: 10.1093/jnci/djx058.

8.

Evaluating the Causal Link Between Malaria Infection and Endemic Burkitt Lymphoma in Northern Uganda: A Mendelian Randomization Study.

Legason ID, Pfeiffer RM, Udquim KI, Bergen AW, Gouveia MH, Kirimunda S, Otim I, Karlins E, Kerchan P, Nabalende H, Bayanjargal A, Emmanuel B, Kagwa P, Talisuna AO, Bhatia K, Yeager M, Biggar RJ, Ayers LW, Reynolds SJ, Goedert JJ, Ogwang MD, Fraumeni JF Jr, Prokunina-Olsson L, Mbulaiteye SM.

EBioMedicine. 2017 Nov;25:58-65. doi: 10.1016/j.ebiom.2017.09.037. Epub 2017 Oct 3.

9.

Higher-than-expected population prevalence of potentially pathogenic germline TP53 variants in individuals unselected for cancer history.

de Andrade KC, Mirabello L, Stewart DR, Karlins E, Koster R, Wang M, Gapstur SM, Gaudet MM, Freedman ND, Landi MT, Lemonnier N, Hainaut P, Savage SA, Achatz MI.

Hum Mutat. 2017 Dec;38(12):1723-1730. doi: 10.1002/humu.23320. Epub 2017 Sep 21.

10.

Whole exome sequencing in 75 high-risk families with validation and replication in independent case-control studies identifies TANGO2, OR5H14, and CHAD as new prostate cancer susceptibility genes.

Karyadi DM, Geybels MS, Karlins E, Decker B, McIntosh L, Hutchinson A, Kolb S, McDonnell SK, Hicks B, Middha S, FitzGerald LM, DeRycke MS, Yeager M, Schaid DJ, Chanock SJ, Thibodeau SN, Berndt SI, Stanford JL, Ostrander EA.

Oncotarget. 2017 Jan 3;8(1):1495-1507. doi: 10.18632/oncotarget.13646.

11.

Female chromosome X mosaicism is age-related and preferentially affects the inactivated X chromosome.

Machiela MJ, Zhou W, Karlins E, Sampson JN, Freedman ND, Yang Q, Hicks B, Dagnall C, Hautman C, Jacobs KB, Abnet CC, Aldrich MC, Amos C, Amundadottir LT, Arslan AA, Beane-Freeman LE, Berndt SI, Black A, Blot WJ, Bock CH, Bracci PM, Brinton LA, Bueno-de-Mesquita HB, Burdett L, Buring JE, Butler MA, Canzian F, Carreón T, Chaffee KG, Chang IS, Chatterjee N, Chen C, Chen C, Chen K, Chung CC, Cook LS, Crous Bou M, Cullen M, Davis FG, De Vivo I, Ding T, Doherty J, Duell EJ, Epstein CG, Fan JH, Figueroa JD, Fraumeni JF, Friedenreich CM, Fuchs CS, Gallinger S, Gao YT, Gapstur SM, Garcia-Closas M, Gaudet MM, Gaziano JM, Giles GG, Gillanders EM, Giovannucci EL, Goldin L, Goldstein AM, Haiman CA, Hallmans G, Hankinson SE, Harris CC, Henriksson R, Holly EA, Hong YC, Hoover RN, Hsiung CA, Hu N, Hu W, Hunter DJ, Hutchinson A, Jenab M, Johansen C, Khaw KT, Kim HN, Kim YH, Kim YT, Klein AP, Klein R, Koh WP, Kolonel LN, Kooperberg C, Kraft P, Krogh V, Kurtz RC, LaCroix A, Lan Q, Landi MT, Marchand LL, Li D, Liang X, Liao LM, Lin D, Liu J, Lissowska J, Lu L, Magliocco AM, Malats N, Matsuo K, McNeill LH, McWilliams RR, Melin BS, Mirabello L, Moore L, Olson SH, Orlow I, Park JY, Patiño-Garcia A, Peplonska B, Peters U, Petersen GM, Pooler L, Prescott J, Prokunina-Olsson L, Purdue MP, Qiao YL, Rajaraman P, Real FX, Riboli E, Risch HA, Rodriguez-Santiago B, Ruder AM, Savage SA, Schumacher F, Schwartz AG, Schwartz KL, Seow A, Wendy Setiawan V, Severi G, Shen H, Sheng X, Shin MH, Shu XO, Silverman DT, Spitz MR, Stevens VL, Stolzenberg-Solomon R, Stram D, Tang ZZ, Taylor PR, Teras LR, Tobias GS, Van Den Berg D, Visvanathan K, Wacholder S, Wang JC, Wang Z, Wentzensen N, Wheeler W, White E, Wiencke JK, Wolpin BM, Wong MP, Wu C, Wu T, Wu X, Wu YL, Wunder JS, Xia L, Yang HP, Yang PC, Yu K, Zanetti KA, Zeleniuch-Jacquotte A, Zheng W, Zhou B, Ziegler RG, Perez-Jurado LA, Caporaso NE, Rothman N, Tucker M, Dean MC, Yeager M, Chanock SJ.

Nat Commun. 2016 Jun 13;7:11843. doi: 10.1038/ncomms11843.

12.

Biallelic BRCA2 Mutations Shape the Somatic Mutational Landscape of Aggressive Prostate Tumors.

Decker B, Karyadi DM, Davis BW, Karlins E, Tillmans LS, Stanford JL, Thibodeau SN, Ostrander EA.

Am J Hum Genet. 2016 May 5;98(5):818-829. doi: 10.1016/j.ajhg.2016.03.003. Epub 2016 Apr 14.

13.

Comparison against 186 canid whole-genome sequences reveals survival strategies of an ancient clonally transmissible canine tumor.

Decker B, Davis BW, Rimbault M, Long AH, Karlins E, Jagannathan V, Reiman R, Parker HG, Drögemüller C, Corneveaux JJ, Chapman ES, Trent JM, Leeb T, Huentelman MJ, Wayne RK, Karyadi DM, Ostrander EA.

Genome Res. 2015 Nov;25(11):1646-55. doi: 10.1101/gr.190314.115. Epub 2015 Jul 31.

14.

Homologous Mutation to Human BRAF V600E Is Common in Naturally Occurring Canine Bladder Cancer--Evidence for a Relevant Model System and Urine-Based Diagnostic Test.

Decker B, Parker HG, Dhawan D, Kwon EM, Karlins E, Davis BW, Ramos-Vara JA, Bonney PL, McNiel EA, Knapp DW, Ostrander EA.

Mol Cancer Res. 2015 Jun;13(6):993-1002. doi: 10.1158/1541-7786.MCR-14-0689. Epub 2015 Mar 12.

15.

A copy number variant at the KITLG locus likely confers risk for canine squamous cell carcinoma of the digit.

Karyadi DM, Karlins E, Decker B, vonHoldt BM, Carpintero-Ramirez G, Parker HG, Wayne RK, Ostrander EA.

PLoS Genet. 2013 Mar;9(3):e1003409. doi: 10.1371/journal.pgen.1003409. Epub 2013 Mar 28.

16.

Fine scale mapping of the breast cancer 16q12 locus.

Udler MS, Ahmed S, Healey CS, Meyer K, Struewing J, Maranian M, Kwon EM, Zhang J, Tyrer J, Karlins E, Platte R, Kalmyrzaev B, Dicks E, Field H, Maia AT, Prathalingam R, Teschendorff A, McArthur S, Doody DR, Luben R, Caldas C, Bernstein L, Kolonel LK, Henderson BE, Wu AH, Le Marchand L, Ursin G, Press MF, Lindblom A, Margolin S, Shen CY, Yang SL, Hsiung CN, Kang D, Yoo KY, Noh DY, Ahn SH, Malone KE, Haiman CA, Pharoah PD, Ponder BA, Ostrander EA, Easton DF, Dunning AM.

Hum Mol Genet. 2010 Jun 15;19(12):2507-15. doi: 10.1093/hmg/ddq122. Epub 2010 Mar 23.

17.

No evidence of BRCA2 mutations in chromosome 13q-linked Utah high-risk prostate cancer pedigrees.

Allen-Brady K, Farnham JM, Camp NJ, Karlins E, Ostrander EA, Cannon-Albright LA.

BMC Res Notes. 2009 May 28;2:94. doi: 10.1186/1756-0500-2-94.

18.

FGFR2 variants and breast cancer risk: fine-scale mapping using African American studies and analysis of chromatin conformation.

Udler MS, Meyer KB, Pooley KA, Karlins E, Struewing JP, Zhang J, Doody DR, MacArthur S, Tyrer J, Pharoah PD, Luben R, Bernstein L, Kolonel LN, Henderson BE, Le Marchand L, Ursin G, Press MF, Brennan P, Sangrajrang S, Gaborieau V, Odefrey F, Shen CY, Wu PE, Wang HC, Kang D, Yoo KY, Noh DY, Ahn SH, Ponder BA, Haiman CA, Malone KE, Dunning AM, Ostrander EA, Easton DF; SEARCH Collaborators.

Hum Mol Genet. 2009 May 1;18(9):1692-703. doi: 10.1093/hmg/ddp078. Epub 2009 Feb 17.

19.

Association of FGFR4 genetic polymorphisms with prostate cancer risk and prognosis.

FitzGerald LM, Karlins E, Karyadi DM, Kwon EM, Koopmeiners JS, Stanford JL, Ostrander EA.

Prostate Cancer Prostatic Dis. 2009;12(2):192-7. doi: 10.1038/pcan.2008.46. Epub 2008 Sep 2.

20.

Rare germline mutations in the BRCA2 gene are associated with early-onset prostate cancer.

Agalliu I, Karlins E, Kwon EM, Iwasaki LM, Diamond A, Ostrander EA, Stanford JL.

Br J Cancer. 2007 Sep 17;97(6):826-31. Epub 2007 Aug 14.

21.

A single IGF1 allele is a major determinant of small size in dogs.

Sutter NB, Bustamante CD, Chase K, Gray MM, Zhao K, Zhu L, Padhukasahasram B, Karlins E, Davis S, Jones PG, Quignon P, Johnson GS, Parker HG, Fretwell N, Mosher DS, Lawler DF, Satyaraj E, Nordborg M, Lark KG, Wayne RK, Ostrander EA.

Science. 2007 Apr 6;316(5821):112-5. Erratum in: Science. 2007 Jun 1;316(5829):1284.

22.

Frequency of LRRK2 mutations in early- and late-onset Parkinson disease.

Clark LN, Wang Y, Karlins E, Saito L, Mejia-Santana H, Harris J, Louis ED, Cote LJ, Andrews H, Fahn S, Waters C, Ford B, Frucht S, Ottman R, Marder K.

Neurology. 2006 Nov 28;67(10):1786-91. Epub 2006 Oct 18.

PMID:
17050822
23.

Case-control study of the parkin gene in early-onset Parkinson disease.

Clark LN, Afridi S, Karlins E, Wang Y, Mejia-Santana H, Harris J, Louis ED, Cote LJ, Andrews H, Fahn S, Waters C, Ford B, Frucht S, Ottman R, Marder K.

Arch Neurol. 2006 Apr;63(4):548-52.

PMID:
16606767
24.

An intermediate grade of finished genomic sequence suitable for comparative analyses.

Blakesley RW, Hansen NF, Mullikin JC, Thomas PJ, McDowell JC, Maskeri B, Young AC, Benjamin B, Brooks SY, Coleman BI, Gupta J, Ho SL, Karlins EM, Maduro QL, Stantripop S, Tsurgeon C, Vogt JL, Walker MA, Masiello CA, Guan X; NISC Comparative Sequencing Program, Bouffard GG, Green ED.

Genome Res. 2004 Nov;14(11):2235-44. Epub 2004 Oct 12.

25.

Comparative analyses of multi-species sequences from targeted genomic regions.

Thomas JW, Touchman JW, Blakesley RW, Bouffard GG, Beckstrom-Sternberg SM, Margulies EH, Blanchette M, Siepel AC, Thomas PJ, McDowell JC, Maskeri B, Hansen NF, Schwartz MS, Weber RJ, Kent WJ, Karolchik D, Bruen TC, Bevan R, Cutler DJ, Schwartz S, Elnitski L, Idol JR, Prasad AB, Lee-Lin SQ, Maduro VV, Summers TJ, Portnoy ME, Dietrich NL, Akhter N, Ayele K, Benjamin B, Cariaga K, Brinkley CP, Brooks SY, Granite S, Guan X, Gupta J, Haghighi P, Ho SL, Huang MC, Karlins E, Laric PL, Legaspi R, Lim MJ, Maduro QL, Masiello CA, Mastrian SD, McCloskey JC, Pearson R, Stantripop S, Tiongson EE, Tran JT, Tsurgeon C, Vogt JL, Walker MA, Wetherby KD, Wiggins LS, Young AC, Zhang LH, Osoegawa K, Zhu B, Zhao B, Shu CL, De Jong PJ, Lawrence CE, Smit AF, Chakravarti A, Haussler D, Green P, Miller W, Green ED.

Nature. 2003 Aug 14;424(6950):788-93.

PMID:
12917688

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