In-silico QTL mapping of postpubertal mammary ductal development in the mouse uncovers potential human breast cancer risk loci (original) (raw)
References
- Ambros V (2004) The functions of animal microRNAs. Nature 431:350–355
CAS PubMed Google Scholar - Andres AC, Schonenberger CA, Groner B, Hennighausen L, LeMeur M, Gerlinger P (1987) Ha-ras oncogene expression directed by a milk protein gene promoter: tissue specificity, hormonal regulation, and tumor induction in transgenic mice. Proc Natl Acad Sci USA 84:1299–1303
CAS PubMed Central PubMed Google Scholar - Apolant H (1906) Die epithelian geschwulste des maus. Arbeiten Koniglchn Ins Exp The Zu Frankfurt 1:61
Google Scholar - Atwood CS, Hovey RC, Glover JP, Chepko G, Ginsburg E, Robison WG, Vonderhaar BK (2000) Progesterone induces side-branching of the ductal epithelium in the mammary glands of peripubertal mice. J Endocrinol 167:39–52
CAS PubMed Google Scholar - Aumailley M (2013) The laminin family. Cell Adh Migr 7:48–55
PubMed Central PubMed Google Scholar - Aupperlee MD, Drolet AA, Durairaj S, Wang W, Schwartz RC, Haslam SZ (2009) Strain-specific differences in the mechanisms of progesterone regulation of murine mammary gland development. Endocrinology 150:1485–1494
CAS PubMed Central PubMed Google Scholar - Bamshad M, Lin RC, Law DJ, Watkins WC, Krakowiak PA, Moore ME, Franceschini P, Lala R, Holmes LB, Gebuhr TC, Bruneau BG, Schinzel A, Seidman JG, Seidman CE, Jorde LB (1997) Mutations in human TBX3 alter limb, apocrine and genital development in ulnar-mammary syndrome. Nat Genet 16:311–315
CAS PubMed Google Scholar - Bamshad M, Le T, Watkins WS, Dixon ME, Kramer BE, Roeder AD, Carey JC, Root S, Schinzel A, Van Maldergem L, Gardner RJ, Lin RC, Seidman CE, Seidman JG, Wallerstein R, Moran E, Sutphen R, Campbell CE, Jorde LB (1999) The spectrum of mutations in TBX3: genotype/phenotype relationship in ulnar-mammary syndrome. Am J Hum Genet 64:1550–1562
CAS PubMed Central PubMed Google Scholar - Baple EL, Chambers H, Cross HE, Fawcett H, Nakazawa Y, Chioza BA, Harlalka GV, Mansour S, Sreekantan-Nair A, Patton MA, Muggenthaler M, Rich P, Wagner K, Coblentz R, Stein CK, Last JI, Taylor AM, Jackson AP, Ogi T, Lehmann AR, Green CM, Crosby AH (2014) Hypomorphic PCNA mutation underlies a human DNA repair disorder. J Clin Invest 124:3137–3146
CAS PubMed Central PubMed Google Scholar - Bean SL, C., Swing SP, Macauley M, Neleski L (2000) C3H strains free of exongenous mmtv. JAX Notes 480, 1
- Betts MJ, Russell RB (2003) Amino acid properties and consequences of substitutions. In: Barnes MR, Gray IC (eds) Bioinformatics for geneticists. Wiley, New York
- Bhattacharya A, Ziebarth JD, Cui Y (2014) PolymiRTS Database 3.0: linking polymorphisms in microRNAs and their target sites with human diseases and biological pathways. Nucleic Acids Res 42:D86–D91
CAS PubMed Central PubMed Google Scholar - Boyle AP, Hong EL, Hariharan M, Cheng Y, Schaub MA, Kasowski M, Karczewski KJ, Park J, Hitz BC, Weng S, Cherry JM, Snyder M (2012) Annotation of functional variation in personal genomes using RegulomeDB. Genome Res 22:1790–1797
CAS PubMed Central PubMed Google Scholar - Brewster BL, Rossiello F, French JD, Edwards SL, Wong M, Wronski A, Whiley P, Waddell N, Chen X, Bove B, Hopper JL, John EM, Andrulis I, Daly M, Volorio S, Bernard L, Peissel B, Manoukian S, Barile M, Pizzamiglio S, Verderio P, Spurdle AB, Radice P, Godwin AK, Southey MC, Brown MA, Peterlongo P (2012) Identification of fifteen novel germline variants in the BRCA1 3′UTR reveals a variant in a breast cancer case that introduces a functional miR-103 target site. Hum Mutat 33:1665–1675
CAS PubMed Google Scholar - Brunschwig H, Levi L, Ben-David E, Williams RW, Yakir B, Shifman S (2012) Fine-scale maps of recombination rates and hotspots in the mouse genome. Genetics 191:757–764
CAS PubMed Central PubMed Google Scholar - Brunskill EW, Georgas K, Rumballe B, Little MH, Potter SS (2011) Defining the molecular character of the developing and adult kidney podocyte. PLoS ONE 6:e24640
CAS PubMed Central PubMed Google Scholar - Buhler TA, Dale TC, Kieback C, Humphreys RC, Rosen JM (1993) Localization and quantification of Wnt-2 gene expression in mouse mammary development. Dev Biol 155:87–96
CAS PubMed Google Scholar - Burgess-Herbert SL, Tsaih SW, Stylianou IM, Walsh K, Cox AJ, Paigen B (2009) An experimental assessment of in silico haplotype association mapping in laboratory mice. BMC Genet 10:81
PubMed Central PubMed Google Scholar - Castellana B, Escuin D, Perez-Olabarria M, Vazquez T, Munoz J, Peiro G, Barnadas A, Lerma E (2012) Genetic up-regulation and overexpression of PLEKHA7 differentiates invasive lobular carcinomas from invasive ductal carcinomas. Hum Pathol 43:1902–1909
CAS PubMed Google Scholar - Cervino AC, Li G, Edwards S, Zhu J, Laurie C, Tokiwa G, Lum PY, Wang S, Castellini LW, Lusis AJ, Carlson S, Sachs AB, Schadt EE (2005) Integrating QTL and high-density SNP analyses in mice to identify Insig2 as a susceptibility gene for plasma cholesterol levels. Genomics 86:505–517
CAS PubMed Google Scholar - Chakravarty G, Hadsell D, Buitrago W, Settleman J, Rosen JM (2003) p190-B RhoGAP regulates mammary ductal morphogenesis. Mol Endocrinol 17:1054–1065
CAS PubMed Google Scholar - Chang SH, Jobling S, Brennan K, Headon DJ (2009) Enhanced Edar signalling has pleiotropic effects on craniofacial and cutaneous glands. PLoS ONE 4:e7591
PubMed Central PubMed Google Scholar - Chen CY, Chang IS, Hsiung CA, Wasserman WW (2014) On the identification of potential regulatory variants within genome wide association candidate SNP sets. BMC Med Genomics 7:34
PubMed Central PubMed Google Scholar - Cho KW, Kwon HJ, Shin JO, Lee JM, Cho SW, Tickle C, Jung HS (2012) Retinoic acid signaling and the initiation of mammary gland development. Dev Biol 365:259–266
CAS PubMed Google Scholar - Churchill GA, Doerge RW (1994) Empirical threshold values for quantitative trait mapping. Genetics 138:963–971
CAS PubMed Central PubMed Google Scholar - Davenport TG, Jerome-Majewska LA, Papaioannou VE (2003) Mammary gland, limb and yolk sac defects in mice lacking Tbx3, the gene mutated in human ulnar mammary syndrome. Development 130:2263–2273
CAS PubMed Google Scholar - Davis RC, van Nas A, Bennett B, Orozco L, Pan C, Rau CD, Eskin E, Lusis AJ (2013) Genome-wide association mapping of blood cell traits in mice. Mamm Genome 24:105–118
CAS PubMed Central PubMed Google Scholar - Douglas NC, Papaioannou VE (2013) The T-box transcription factors TBX2 and TBX3 in mammary gland development and breast cancer. J Mammary Gland Biol Neoplasia 18:143–147
PubMed Central PubMed Google Scholar - Eblaghie MC, Song SJ, Kim JY, Akita K, Tickle C, Jung HS (2004) Interactions between FGF and Wnt signals and Tbx3 gene expression in mammary gland initiation in mouse embryos. J Anat 205:1–13
CAS PubMed Central PubMed Google Scholar - Fernandez-Gonzalez R, Barcellos-Hoff MH, Ortiz-de-Solorzano C (2004) Quantitative image analysis in mammary gland biology. J Mammary Gland Biol Neoplasia 9:343–359
PubMed Google Scholar - Filipek A (2006) S100A6 and CacyBP/SIP—two proteins discovered in ehrlich ascites tumor cells that are potentially involved in the degradation of beta-catenin. Chemotherapy 52:32–34
CAS PubMed Google Scholar - Finlay AY, Marks R (1978) An hereditary syndrome of lumpy scalp, odd ears and rudimentary nipples. Br J Dermatol 99:423–430
CAS PubMed Google Scholar - Flux DS (1954) Growth of the mammary duct system in intact and ovariectomized mice of the CHI strain. J Endocrinol 11:223–237
CAS PubMed Google Scholar - Frazer KA, Eskin E, Kang HM, Bogue MA, Hinds DA, Beilharz EJ, Gupta RV, Montgomery J, Morenzoni MM, Nilsen GB, Pethiyagoda CL, Stuve LL, Johnson FM, Daly MJ, Wade CM, Cox DR (2007) A sequence-based variation map of 8.27 million SNPs in inbred mouse strains. Nature 448:1050–1053
CAS PubMed Google Scholar - Fuseler JW, Robichaux JP, Atiyah HI, Ramsdell AF (2014) Morphometric and fractal dimension analysis identifies early neoplastic changes in mammary epithelium of MMTV-cNeu mice. Anticancer Res 34:1171–1177
PubMed Google Scholar - Gardner WU, Strong LC (1935) The normal development of the mammary glands of virgin female mice of ten strains varying in susceptibility to spontaneous neoplasms. Am J Cancer 25:285–290
Google Scholar - Ghabrial AS, Levi BP, Krasnow MA (2011) A systematic screen for tube morphogenesis and branching genes in the Drosophila tracheal system. PLoS Genet 7:e1002087
CAS PubMed Central PubMed Google Scholar - Ghazalpour A, Rau CD, Farber CR, Bennett BJ, Orozco LD, van Nas A, Pan C, Allayee H, Beaven SW, Civelek M, Davis RC, Drake TA, Friedman RA, Furlotte N, Hui ST, Jentsch JD, Kostem E, Kang HM, Kang EY, Joo JW, Korshunov VA, Laughlin RE, Martin LJ, Ohmen JD, Parks BW, Pellegrini M, Reue K, Smith DJ, Tetradis S, Wang J, Wang Y, Weiss JN, Kirchgessner T, Gargalovic PS, Eskin E, Lusis AJ, LeBoeuf RC (2012) Hybrid mouse diversity panel: a panel of inbred mouse strains suitable for analysis of complex genetic traits. Mamm Genome 23:680–692
CAS PubMed Central PubMed Google Scholar - Ghoussaini M, Pharoah PD, Easton DF (2013) Inherited genetic susceptibility to breast cancer: the beginning of the end or the end of the beginning? Am J Pathol 183:1038–1051
CAS PubMed Google Scholar - Gibson LM (1930) A comparative study of the life history of the female mammaryg gland in two strains of albino mice. Cancer Res 14:31
Google Scholar - Gjorevski N, Nelson CM (2011) Integrated morphodynamic signalling of the mammary gland. Nat Rev Mol Cell Biol 12:581–593
CAS PubMed Google Scholar - Grupe A, Germer S, Usuka J, Aud D, Belknap JK, Klein RF, Ahluwalia MK, Higuchi R, Peltz G (2001) In silico mapping of complex disease-related traits in mice. Science 292:1915–1918
CAS PubMed Google Scholar - Haaland M (1911) Spontaneous tumors in mice. In: Bashford EF (ed) Fourth scientific report on the investigations of the imperial cancer research fund. Imperial Cancer Research Fund, London, pp 1–113
Google Scholar - Heckman BM, Chakravarty G, Vargo-Gogola T, Gonzales-Rimbau M, Hadsell DL, Lee AV, Settleman J, Rosen JM (2007) Crosstalk between the p190-B RhoGAP and IGF signaling pathways is required for embryonic mammary bud development. Dev Biol 309:137–149
CAS PubMed Central PubMed Google Scholar - Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, Cheng JX, Murre C, Singh H, Glass CK (2010) Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell 38:576–589
CAS PubMed Central PubMed Google Scholar - Højsgaard S, Halekoh U, Robinson-Cox J, Wright K, Leidi AA (2013) doBy—groupwise summary statistics, general linerar constrasts, population means (least-squares-means), and other utilities, R package version 4.5-8. http://CRAN.R-project.org/package=doBy
- Hong H, Yen HY, Brockmeyer A, Liu Y, Chodankar R, Pike MC, Stanczyk FZ, Maxson R, Dubeau L (2010) Changes in the mouse estrus cycle in response to BRCA1 inactivation suggest a potential link between risk factors for familial and sporadic ovarian cancer. Cancer Res 70:221–228
CAS PubMed Central PubMed Google Scholar - Howard BA, Gusterson BA (2000a) The characterization of a mouse mutant that displays abnormal mammary gland development. Mamm Genome 11:234–237
CAS PubMed Google Scholar - Howard BA, Gusterson BA (2000b) Mammary gland patterning in the AXB/BXA recombinant inbred strains of mouse. Mech Dev 91:305–309
CAS PubMed Google Scholar - Howard B, Panchal H, McCarthy A, Ashworth A (2005) Identification of the scaramanga gene implicates Neuregulin3 in mammary gland specification. Genes Dev 19:2078–2090
CAS PubMed Central PubMed Google Scholar - Hunter KW (2004) Host genetics and tumour metastasis. Br J Cancer 90:752–755
CAS PubMed Central PubMed Google Scholar - Hunter KW (2012) Mouse models of cancer: does the strain matter? Nat Rev Cancer 12:144–149
CAS PubMed Google Scholar - Huseby RA, Bittner JJ (1946) A comparative morphological study of the mammary glands with reference to the known factors influencing the development of mammary carcinoma in mice. Cancer Res 6:240–255
CAS PubMed Google Scholar - Kamikawa A, Ichii O, Yamaji D, Imao T, Suzuki C, Okamatsu-Ogura Y, Terao A, Kon Y, Kimura K (2009) Diet-induced obesity disrupts ductal development in the mammary glands of nonpregnant mice. Dev Dyn 238:1092–1099
CAS PubMed Google Scholar - Kang HM, Zaitlen NA, Wade CM, Kirby A, Heckerman D, Daly MJ, Eskin E (2008) Efficient control of population structure in model organism association mapping. Genetics 178:1709–1723
PubMed Central PubMed Google Scholar - Kendrick H, Regan JL, Magnay FA, Grigoriadis A, Mitsopoulos C, Zvelebil M, Smalley MJ (2008) Transcriptome analysis of mammary epithelial subpopulations identifies novel determinants of lineage commitment and cell fate. BMC Genom 9:591
Google Scholar - Kessler JD, Kahle KT, Sun T, Meerbrey KL, Schlabach MR, Schmitt EM, Skinner SO, Xu Q, Li MZ, Hartman ZC, Rao M, Yu P, Dominguez-Vidana R, Liang AC, Solimini NL, Bernardi RJ, Yu B, Hsu T, Golding I, Luo J, Osborne CK, Creighton CJ, Hilsenbeck SG, Schiff R, Shaw CA, Elledge SJ, Westbrook TF (2012) A SUMOylation-dependent transcriptional subprogram is required for Myc-driven tumorigenesis. Science 335:348–353
CAS PubMed Central PubMed Google Scholar - Kirby A, Kang HM, Wade CM, Cotsapas CJ, Kostem E, Han B, Furlotte N, Kang EY, Rivas M, Bogue MA, Frazer KA, Johnson FM, Beilharz EJ, Cox DR, Eskin E, Daly MJ (2010) Fine mapping in 94 inbred mouse strains using a high-density haplotype resource. Genetics 185(3):1081–1095
- Klinowska TC, Soriano JV, Edwards GM, Oliver JM, Valentijn AJ, Montesano R, Streuli CH (1999) Laminin and beta1 integrins are crucial for normal mammary gland development in the mouse. Dev Biol 215:13–32
CAS PubMed Google Scholar - Kohl M (2011) MKmisc: miscellaneous functions from M. Kohl, R package version 0.9. http://www.stamats.de
- Kouros-Mehr H, Werb Z (2006) Candidate regulators of mammary branching morphogenesis identified by genome-wide transcript analysis. Dev Dyn 235:3404–3412
CAS PubMed Central PubMed Google Scholar - Kurita S, Yamada T, Rikitsu E, Ikeda W, Takai Y (2013) Binding between the junctional proteins afadin and PLEKHA7 and implication in the formation of adherens junction in epithelial cells. J Biol Chem 288:29356–29368
CAS PubMed Central PubMed Google Scholar - Lain AR, Creighton CJ, Conneely OM (2013) Research resource: progesterone receptor targetome underlying mammary gland branching morphogenesis. Mol Endocrinol 27:1743–1761
CAS PubMed Central PubMed Google Scholar - Larive RM, Abad A, Cardaba CM, Hernandez T, Canamero M, de Alava E, Santos E, Alarcon B, Bustelo XR (2012) The Ras-like protein R-Ras2/TC21 is important for proper mammary gland development. Mol Biol Cell 23:2373–2387
CAS PubMed Central PubMed Google Scholar - Li MJ, Wang P, Liu X, Lim EL, Wang Z, Yeager M, Wong MP, Sham PC, Chanock SJ, Wang J (2012) GWASdb: a database for human genetic variants identified by genome-wide association studies. Nucleic Acids Res 40:D1047–D1054
CAS PubMed Central PubMed Google Scholar - Lifsted T, Le Voyer T, Williams M, Muller W, Klein-Szanto A, Buetow KH, Hunter KW (1998) Identification of inbred mouse strains harboring genetic modifiers of mammary tumor age of onset and metastatic progression. Int J Cancer 77:640–644
CAS PubMed Google Scholar - Lydon JP, Ge G, Kittrell FS, Medina D, O’Malley BW (1999) Murine mammary gland carcinogenesis is critically dependent on progesterone receptor function. Cancer Res 59:4276–4284
CAS PubMed Google Scholar - Macintyre G, Bailey J, Haviv I, Kowalczyk A (2010) is-rSNP: a novel technique for in silico regulatory SNP detection. Bioinformatics 26:i524–i530
CAS PubMed Central PubMed Google Scholar - Maurano MT, Humbert R, Rynes E, Thurman RE, Haugen E, Wang H, Reynolds AP, Sandstrom R, Qu H, Brody J, Shafer A, Neri F, Lee K, Kutyavin T, Stehling-Sun S, Johnson AK, Canfield TK, Giste E, Diegel M, Bates D, Hansen RS, Neph S, Sabo PJ, Heimfeld S, Raubitschek A, Ziegler S, Cotsapas C, Sotoodehnia N, Glass I, Sunyaev SR, Kaul R, Stamatoyannopoulos JA (2012) Systematic localization of common disease-associated variation in regulatory DNA. Science 337:1190–1195
CAS PubMed Central PubMed Google Scholar - McCleland ML, Kallio MJ, Barrett-Wilt GA, Kestner CA, Shabanowitz J, Hunt DF, Gorbsky GJ, Stukenberg PT (2004) The vertebrate Ndc80 complex contains Spc24 and Spc25 homologs, which are required to establish and maintain kinetochore-microtubule attachment. Curr Biol 14:131–137
CAS PubMed Google Scholar - McNally S, Martin F (2011) Molecular regulators of pubertal mammary gland development. Ann Med 43:212–234
PubMed Google Scholar - Medina D (2010) Of mice and women: a short history of mouse mammary cancer research with an emphasis on the paradigms inspired by the transplantation method. Cold Spring Harb Perspect Biol 2:a004523
CAS PubMed Central PubMed Google Scholar - Megarbane H, Cluzeau C, Bodemer C, Fraitag S, Chababi-Atallah M, Megarbane A, Smahi A (2008) Unusual presentation of a severe autosomal recessive anhydrotic ectodermal dysplasia with a novel mutation in the EDAR gene. Am J Med Genet A 146A:2657–2662
CAS PubMed Google Scholar - Metzger RJ, Klein OD, Martin GR, Krasnow MA (2008) The branching programme of mouse lung development. Nature 453:745–750
CAS PubMed Central PubMed Google Scholar - Miller BH, Schultz LE, Gulati A, Su AI, Pletcher MT (2010) Phenotypic characterization of a genetically diverse panel of mice for behavioral despair and anxiety. PLoS ONE 5:e14458
CAS PubMed Central PubMed Google Scholar - Miller TW, Rexer BN, Garrett JT, Arteaga CL (2011) Mutations in the phosphatidylinositol 3-kinase pathway: role in tumor progression and therapeutic implications in breast cancer. Breast Cancer Res 13:224
CAS PubMed Central PubMed Google Scholar - Morris JS, Stein T, Pringle MA, Davies CR, Weber-Hall S, Ferrier RK, Bell AK, Heath VJ, Gusterson BA (2006) Involvement of axonal guidance proteins and their signaling partners in the developing mouse mammary gland. J Cell Physiol 206:16–24
CAS PubMed Google Scholar - Mulac-Jericevic B, Lydon JP, DeMayo FJ, Conneely OM (2003) Defective mammary gland morphogenesis in mice lacking the progesterone receptor B isoform. Proc Natl Acad Sci USA 100:9744–9749
CAS PubMed Central PubMed Google Scholar - Naylor MJ, Ormandy CJ (2002) Mouse strain-specific patterns of mammary epithelial ductal side branching are elicited by stromal factors. Dev Dyn 225:100–105
CAS PubMed Google Scholar - Neuwirth E (2007) RColorBrewer: ColorBrewer palettes. R package version 1.0-2
- Ochoa-Espinosa A, Affolter M (2012) Branching morphogenesis: from cells to organs and back. Cold Spring Harb Perspect Biol 4:1–14
- Ohta K, Takagi S, Asou H, Fujisawa H (1992) Involvement of neuronal cell surface molecule B2 in the formation of retinal plexiform layers. Neuron 9:151–161
CAS PubMed Google Scholar - Okazaki M, Kishida S, Murai H, Hinoi T, Kikuchi A (1996) Ras-interacting domain of Ral GDP dissociation stimulator like (RGL) reverses v-Ras-induced transformation and Raf-1 activation in NIH3T3 cells. Cancer Res 56:2387–2392
CAS PubMed Google Scholar - Olson LK, Tan Y, Zhao Y, Aupperlee MD, Haslam SZ (2010) Pubertal exposure to high fat diet causes mouse strain-dependent alterations in mammary gland development and estrogen responsiveness. Int J Obes (Lond) 34:1415–1426
CAS Google Scholar - Owen BM, Bookout AL, Ding X, Lin VY, Atkin SD, Gautron L, Kliewer SA, Mangelsdorf DJ (2013) FGF21 contributes to neuroendocrine control of female reproduction. Nat Med 19:1153–1156
CAS PubMed Central PubMed Google Scholar - Paul DS, Albers CA, Rendon A, Voss K, Stephens J, van der Harst P, Chambers JC, Soranzo N, Ouwehand WH, Deloukas P (2013) Maps of open chromatin highlight cell type-restricted patterns of regulatory sequence variation at hematological trait loci. Genome Res 23:1130–1141
CAS PubMed Central PubMed Google Scholar - Perala N, Sariola H, Immonen T (2012) More than nervous: the emerging roles of plexins. Differentiation 83:77–91
PubMed Google Scholar - Peto J, Mack TM (2000) High constant incidence in twins and other relatives of women with breast cancer. Nat Genet 26:411–414
CAS PubMed Google Scholar - Pletcher MT, McClurg P, Batalov S, Su AI, Barnes SW, Lagler E, Korstanje R, Wang X, Nusskern D, Bogue MA, Mural RJ, Paigen B, Wiltshire T (2004) Use of a dense single nucleotide polymorphism map for in silico mapping in the mouse. PLoS Biol 2:e393
PubMed Central PubMed Google Scholar - Propper AY, Howard BA, Veltmaat JM (2013) Prenatal morphogenesis of mammary glands in mouse and rabbit. J Mammary Gland Biol Neoplasia 18:93–104
PubMed Central PubMed Google Scholar - Rasmussen SBY, Young LJT, Smith GH (2000) Preparing mammary gland whole mounts from mice. In: Ip BB, Asch MM (eds) Methods in mammary gland biology and breast cancer research. Kluwer Academic/Plenum Publishers, New York
Google Scholar - Richert MM, Schwertfeger KL, Ryder JW, Anderson SM (2000) An atlas of mouse mammary gland development. J Mammary Gland Biol Neoplasia 5:227–241
CAS PubMed Google Scholar - Rijnkels M, Freeman-Zadrowski C, Hernandez J, Potluri V, Wang L, Li W, Lemay DG (2013) Epigenetic modifications unlock the milk protein gene loci during mouse mammary gland development and differentiation. PLoS ONE 8:e53270
CAS PubMed Central PubMed Google Scholar - Robichaux JP, Hallett RM, Fuseler JW, Hassell JA, Ramsdell AF (2014) Mammary glands exhibit molecular laterality and undergo left-right asymmetric ductal epithelial growth in MMTV-cNeu mice*. Oncogene. doi:10.1038/onc.2014.149
- Rogozin IB, Basu MK, Jordan IK, Pavlov YI, Koonin EV (2005) APOBEC4, a new member of the AID/APOBEC family of polynucleotide (deoxy)cytidine deaminases predicted by computational analysis. Cell Cycle 4:1281–1285
CAS PubMed Google Scholar - Sakakura T, Suzuki Y, Shiurba R (2013) Mammary stroma in development and carcinogenesis. J Mammary Gland Biol Neoplasia 18:189–197
PubMed Google Scholar - Sethupathy P, Collins FS (2008) MicroRNA target site polymorphisms and human disease. Trends Genet 24:489–497
CAS PubMed Google Scholar - Short K, Hodson M, Smyth I (2013) Spatial mapping and quantification of developmental branching morphogenesis. Development 140:471–478
CAS PubMed Google Scholar - Short KM, Combes AN, Lefevre J, Ju AL, Georgas KM, Lamberton T, Cairncross O, Rumballe BA, McMahon AP, Hamilton NA, Smyth IM, Little MH (2014) Global quantification of tissue dynamics in the developing mouse kidney. Dev Cell 29:188–202
CAS PubMed Google Scholar - Silberstein GB (2001) Postnatal mammary gland morphogenesis. Microsc Res Tech 52:155–162
CAS PubMed Google Scholar - Sternlicht MD (2006) Key stages in mammary gland development: the cues that regulate ductal branching morphogenesis. Breast Cancer Res 8:201
PubMed Central PubMed Google Scholar - Stover BC, Muller KF (2010) TreeGraph 2: combining and visualizing evidence from different phylogenetic analyses. BMC Bioinformatics 11:7
PubMed Central PubMed Google Scholar - Tang PL, Cheung CL, Sham PC, McClurg P, Lee B, Chan SY, Smith DK, Tanner JA, Su AI, Cheah KS, Kung AW, Song YQ (2009) Genome-wide haplotype association mapping in mice identifies a genetic variant in CER1 associated with BMD and fracture in southern Chinese women. J Bone Miner Res 24:1013–1021
CAS PubMed Google Scholar - Team RDC (2010) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna
Google Scholar - Thomas-Chollier M, Hufton A, Heinig M, O’Keeffe S, Masri NE, Roider HG, Manke T, Vingron M (2011) Transcription factor binding predictions using TRAP for the analysis of ChIP-seq data and regulatory SNPs. Nat Protoc 6:1860–1869
CAS PubMed Google Scholar - van Bokhoven H, Hamel BC, Bamshad M, Sangiorgi E, Gurrieri F, Duijf PH, Vanmolkot KR, van Beusekom E, van Beersum SE, Celli J, Merkx GF, Tenconi R, Fryns JP, Verloes A, Newbury-Ecob RA, Raas-Rotschild A, Majewski F, Beemer FA, Janecke A, Chitayat D, Crisponi G, Kayserili H, Yates JR, Neri G, Brunner HG (2001) p63 Gene mutations in eec syndrome, limb-mammary syndrome, and isolated split hand-split foot malformation suggest a genotype-phenotype correlation. Am J Hum Genet 69:481–492
PubMed Central PubMed Google Scholar - van Genderen C, Okamura RM, Farinas I, Quo RG, Parslow TG, Bruhn L, Grosschedl R (1994) Development of several organs that require inductive epithelial-mesenchymal interactions is impaired in LEF-1-deficient mice. Genes Dev 8:2691–2703
PubMed Google Scholar - van Steensel MA, Celli J, van Bokhoven JH, Brunner HG (1999) Probing the gene expression database for candidate genes. Eur J Hum Genet 7:910–919
PubMed Google Scholar - Vargo-Gogola T, Heckman BM, Gunther EJ, Chodosh LA, Rosen JM (2006) P190-B Rho GTPase-activating protein overexpression disrupts ductal morphogenesis and induces hyperplastic lesions in the developing mammary gland. Mol Endocrinol 20:1391–1405
CAS PubMed Google Scholar - Ward LD, Kellis M (2012) HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants. Nucleic Acids Res 40:D930–D934
CAS PubMed Central PubMed Google Scholar - Warnes GR, Bolker B, Bonebakker L, Gentleman R, Liaw WHA, Lumley T, Maechler M, Magnusson A, Moeller S, Schwartz M, Venables B (2011) gplots: Various R programming tools for plotting data, R package version 2.10.1. http://CRAN.R-project.org/package=gplots
- Yamaji D, Kang K, Robinson GW, Hennighausen L (2013) Sequential activation of genetic programs in mouse mammary epithelium during pregnancy depends on STAT5A/B concentration. Nucleic Acids Res 41:1622–1636
CAS PubMed Central PubMed Google Scholar - Yant J, Gusterson B, Kamalati T (1998) Induction of strain-specific mouse mammary gland ductal architecture. The Breast 7:4
Google Scholar - Yuan R, Meng Q, Nautiyal J, Flurkey K, Tsaih SW, Krier R, Parker MG, Harrison DE, Paigen B (2012) Genetic coregulation of age of female sexual maturation and lifespan through circulating IGF1 among inbred mouse strains. Proc Natl Acad Sci USA 109:8224–8229
CAS PubMed Central PubMed Google Scholar
Video S1. Mammary ductal reconstruction in 3D illustrating local patterning in the CZECHII/EiJ stain at 6 week of age. This video is representative of independent samples from at least 6 animals. (MOV 5418 kb) Video S2. Mammary ductal reconstruction in 3D illustrating local patterning in the KK/HlJ stain at 6 week of age. This video is representative of independent samples from at least 6 animals. (MOV 5878 kb)