Page 19 - Read Online
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Gottlieb et al. J Cancer Metastasis Treat 2018;4:37  I  http://dx.doi.org/10.20517/2394-4722.2018.26                        Page 13 of 14

                   Cancer 2014;21:T161-81.
               24.  Gottlieb B, Beitel LK, Nadarajah A, Paliouras M, Trifiro M. The androgen receptor gene mutations database (ARDB): 2012 update. Hum
                   Mutat 2012;33:887-94.
               25.  Brockman W, Alvarez P. Young S, Garber M, Gainnoukos G, Lee WI, Russ C, Lander ES, Nusbaum C, Jaffe DB. Quality scores and SNP
                   detection in sequencing-by-sequencing systems. Genome Res 2008;19:767-70.
               26.  Shao W, Boltz VF, Spindler JE, Kearney MF, Maldarelli F, Mellors JW, Stewart C, Volfovsky N, Levitsky A, Stephens RM, Coffin JM.
                   Analysis of 454 sequencing error rate, error sources, and artifact recombination for detection of low-frequency drug resistance mutations in
                   HIV-1 DNA. Retrovirology 2013;10:18.
               27.  Behjati S, Huch M, van Boxtel R, Karthaus W, Wedge DC, Tamuri AU, Martincorena I, Petljak M, Alexandrov LB, Gundem G, Patrick
                   S, Tarpey PS, Roerink S, Blokker J, Maddison M, Mudie L, Robinson B, Nik-Zainal S, Campbell P, Goldman N, van de Wetering M,
                   Cuppen E, Clevers H, Stratton MR. Genome sequencing of normal cells reveals developmental lineages and mutational processes. Nature
                   2014;513:422-5.
               28.  Gulukota K, Helseth DL Jr, Khadekar JD. Direct observation of genomic heterogeneity through local haplotyping analysis. BMC Genomics
                   2014;15:418.
               29.  Makohon-Moore AP, Zhang M, Reiter JG, Bozic I, Allen B, Kundu D, Chatterjee K, Wong F, Jiao Y, Kohutek ZA, Hong J, Attiyeh M,
                   Javier B, Wood LD, Hruban RH, Nowak MA, Papadopoulos N, Kinzler KW, Vogelstein B, Iacobuzio-Donahue CA. Limited heterogeneity
                   of known driver gene mutations among the metastases of individual patients with pancreatic cancer. Nat Genet 2017;49:358-66.
               30.  Chen L, Liu P, Evans TC Jr, Ettwiller L. DNA damage is a major cause of sequencing errors, directly confounding variant identification.
                   Science 2017;355:752-6.
               31.  Lander ES, Waterman MS. Genomic mapping by fingerprinting random clones: a mathematical analysis. Genomics 1988;2:231-9.
               32.  Sims D, Sudbery I, Ilott NE, Heger A, Ponting CP. Sequencing depth and coverage: key considerations in genomic analysis. Nat Rev Genet
                   2014;15:121-32.
               33.  Hatem A, Bozdag D, Toland AE, Catalyurek UV. Benchmarking short sequence mapping tools. BMC Bioinformatics 2013;14:184.
               34.  Flaherty P, Natsoulis G, Muralidharan O, Winters M, Buenrostro J, Bell J, Brown S, Holodniy M, Zhang N, Ji HP. Ultrasensitive detection
                   of rare mutations using next-generation targeted sequencing. Nucleic Acids Res 2012;40:e2.
               35.  Cibulskis K, Lawrence MS, Carter SL, Sivachenko A, Jaffe D, Sougnez C, Gabriel S, Meyerson M, Lander ES, Getz G. Sensitive detection
                   of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotech 2013;31:213-9.
               36.  Ostrow SL, Barshir R, DeGregori J, Yeger-Lotem E, Hershberg R. Cancer evolution is associated with pervasive positive selection on
                   globally expressed genes. PLoS Genet 2014;10:e1004239.
               37.  Thomas F, Ujvan B, Renaud F, Vincent M. Cancer adaptations: atavism, de novo selection, or something in between? Bioessays
                   2017;39:1700039.
               38.  Polyak K. Tumor heterogeneity confounds and illuminates: a case of Darwinian tumor evolution. Nature Med 2014;20:344-6.
               39.  Adjiri A. DNA mutations may not be the cause of cancer. Oncol Ther 2017;5:85-101.
               40.  Zhu T, Ye j, Han I, Qiu QW, Zhang H, Liang L, Gu X. Variations in genotype-phenotype correlations in phenylalanine hydroxylate
                   deficiency in Chinese Han population. Gene 2013;529:80-7.
               41.  Cooper DN, Krawczak M, Polychronakos C, Tyler-Smith C, Kehrer-Sawatzki H. Where genotype is not predictive of phenotype: towards
                   an understanding of the molecular basis of reduced penetrance in human inherited disease. Hum Genet 2013;132:1077-130.
               42.  Chen R, Shi L, Hakenberg J, Naughton B, Sklar P, Zhang J, Zhou H, Tian L, Prakash O, Lemire M, Sleiman P, Cheng WH, Chen W, Shah
                   H, Shen Y, Fromer M, Omberg L, Deardorff MA, Zackai E, Bobe JR, Levin E, Hudson TJ, Groop L, Wang J, Hakonarson H, Wojcicki A,
                   Diaz GA, Edelmann L, Schadt EE, Friend SH. Analysis of 589,306 genomes identifies individuals resilient to severe Mendelian childhood
                   diseases. Nat Biotechnol 2016;34:531-8.
               43.  Youseef O, Knuuttila A, Piirla P, Bohling T, Sargadi V, Knuutila S. Presence of cancer-associated mutations in exhaled breath condensates
                   of healthy individuals by next generation sequencing. Oncotarget 2017;8:18166-76.
               44.  Calado F, Siva-Santos B, Norell H. Intra-tumor heterogeneity going beyond genetics. FEBS J 2016;283:2245-58.
               45.  Gottlieb B, Beitel LK, Trifiro M. Changing genetic paradigms: creating next-generation genetic databases as tools to understand the
                   emerging complexities of genotype/phenotype relationships. Hum Genomics 2014;8:9.
               46.  Gottlieb B, Beitel LK, Alvarado C, Trifiro MA. Selection and mutation in the “new” genetics: an emerging hypothesis. Hum Genet
                   2010;127:491-501.
               47.  Ju YS, Martincorena I, Gerstung M, Petljak M, Alexandrov LB, Rahbari R, Wedge DC, Davies HR, Ramakrishna M, Fullam A, Martin
                   S, Alder C, Patel N, Gamble S, O’Meara S, Giri DD, Sauer T, Pinder SE, Purdie CA, Borg Å, Stunnenberg H, van de Vijver M, Tan BK,
                   Caldas C, Tutt A, Ueno NT, van ‘t Veer LJ, Martens JW, Sotiriou C, Knappskog S, Span PN, Lakhani SR, Eyfjörd JE, Børresen-Dale AL,
                   Richardson A, Thompson AM, Viari A, Hurles ME, Nik-Zainal S, Campbell PJ, Stratton MR. Somatic mutations reveal asymmetric cellular
                   dynamics in the early human embryo. Nature 2017;543:714-8.
               48.  Liggett LA, DeGregori J. Changing mutational and adaptive landscapes and the genesis of cancer. Biochem Biophys Acta 2017;1867:84-94.
               49.  Scott J, Marusyk A. Somatic clonal evolution: a selection-centric perspective. Biochem Biophys Acta 2017;1867:139-50.
               50.  Kerr J, Anderson C, Lippman SM. Physical activity, sedentary behavior, diet and cancer: an update and emerging new evidence. Lancet
                   Oncol 2017;18:e457-71.
               51.  Hochberg ME, Noble RJ. A framework for how environment contributes to cancer risk. Ecology Letters 2017;20:117-34.
               52.  Wang M, Zhao J, Zhang L, Wei F, Lian Y, Wu Y, Gong Z, Zhang S, Zhou J, Cao K, Li X, Xiong W, Li G, Zeng Z. Role of tumor
                   microenvironment in tumorigenesis. J Cancer 2017;8:761-73.
               53.  Hirata E, Sahai E. Tumor microenvironment and differential responses to therapy. Cold Spring Harb Perspect Med 2017;7:a026781.
               54.  Jorba I, Uriarte JJ, Campillo N, Farre R, Navajas D. Probing micromechanical properties of the extracellular matrix of soft tissues by atomic
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