Tang, J. et al. The genomic landscapes of individual melanocytes from human skin. Nature 586, 600–605 (2020).
Google Scholar
Fowler, J. C. et al. Selection of oncogenic mutant clones in normal human skin varies with body site. Cancer Discov. 11, 340–361 (2020).
Google Scholar
Reed, R. In New Concepts in Surgical Pathology of the Skin 89–90 (Wiley, 1976).
Wang, K. C., Helms, J. A. & Chang, H. Y. Regeneration, repair and remembering identity: the three Rs of Hox gene expression. Trends Cell Biol. 19, 268–275 (2009).
Google Scholar
Curtin, J. A. et al. Distinct sets of genetic alterations in melanoma. N. Engl. J. Med. 353, 2135–2147 (2005).
Google Scholar
Hayward, N. K. et al. Whole-genome landscapes of major melanoma subtypes. Nature 545, 175–180 (2017).
Google Scholar
Petrelli, F. et al. Prognostic survival associated with left-sided vs right-sided colon cancer: a systematic review and meta-analysis. JAMA Oncol. 3, 211–219 (2017).
Google Scholar
Rabbie, R., Ferguson, P., Molina-Aguilar, C., Adams, D. J. & Robles-Espinoza, C. D. Melanoma subtypes: genomic profiles, prognostic molecular markers and therapeutic possibilities. J. Pathol. 247, 539–551 (2019).
Google Scholar
Belote, R. L. et al. Human melanocyte development and melanoma dedifferentiation at single-cell resolution. Nat. Cell Biol. 23, 1035–1047 (2021).
Google Scholar
Moon, H. et al. Melanocyte stem cell activation and translocation initiate cutaneous melanoma in response to UV exposure. Cell Stem Cell 21, 665–678.e666 (2017).
Google Scholar
Kohler, C. et al. Mouse cutaneous melanoma induced by mutant Braf arises from expansion and dedifferentiation of mature pigmented melanocytes. Cell Stem Cell 21, 679–693.e676 (2017).
Google Scholar
Newell, F. et al. Whole-genome sequencing of acral melanoma reveals genomic complexity and diversity. Nat. Commun. 11, 5259 (2020).
Google Scholar
Yeh, I. et al. Targeted genomic profiling of acral melanoma. J. Natl Cancer Inst. 111, 1068–1077 (2019).
Google Scholar
Liang, W. S. et al. Integrated genomic analyses reveal frequent TERT aberrations in acral melanoma. Genome Res. 27, 524–532 (2017).
Google Scholar
Klemen, N. D. et al. Survival after checkpoint inhibitors for metastatic acral, mucosal and uveal melanoma. J. Immunother. Cancer 8, e000341 (2020).
Google Scholar
Shoushtari, A. N. et al. The efficacy of anti-PD-1 agents in acral and mucosal melanoma. Cancer 122, 3354–3362 (2016).
Google Scholar
Cerami, E. et al. The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov. 2, 401–404 (2012).
Google Scholar
Zehir, A. et al. Mutational landscape of metastatic cancer revealed from prospective clinical sequencing of 10,000 patients. Nat. Med. 23, 703–713 (2017).
Google Scholar
Luo, L. Y. & Hahn, W. C. Oncogenic signaling adaptor proteins. J. Genet. Genomics 42, 521–529 (2015).
Google Scholar
Bentires-Alj, M. et al. A role for the scaffolding adapter GAB2 in breast cancer. Nat. Med. 12, 114–121 (2006).
Google Scholar
Cheung, H. W. et al. Amplification of CRKL induces transformation and epidermal growth factor receptor inhibitor resistance in human non-small cell lung cancers. Cancer Discov. 1, 608–625 (2011).
Google Scholar
Hemmeryckx, B. et al. Crkl enhances leukemogenesis in BCR/ABL P190 transgenic mice. Cancer Res. 61, 1398–1405 (2001).
Google Scholar
Chernoff, K. A. et al. GAB2 amplifications refine molecular classification of melanoma. Clin. Cancer Res. 15, 4288–4291 (2009).
Google Scholar
Horst, B. et al. Gab2-mediated signaling promotes melanoma metastasis. Am. J. Pathol. 174, 1524–1533 (2009).
Google Scholar
Eshiba, S. et al. Stem cell spreading dynamics intrinsically differentiate acral melanomas from nevi. Cell Rep. 36, 109492 (2021).
Google Scholar
Nakamura, T., Gehrke, A. R., Lemberg, J., Szymaszek, J. & Shubin, N. H. Digits and fin rays share common developmental histories. Nature 537, 225–228 (2016).
Google Scholar
Shubin, N. H., Daeschler, E. B. & Jenkins, F. A. Jr The pectoral fin of Tiktaalik roseae and the origin of the tetrapod limb. Nature 440, 764–771 (2006).
Google Scholar
Xu, B., Feng, X. & Burdine, R. D. Categorical data analysis in experimental biology. Dev. Biol. 348, 3–11 (2010).
Google Scholar
Philippidou, P. & Dasen, J. S. Hox genes: choreographers in neural development, architects of circuit organization. Neuron 80, 12–34 (2013).
Google Scholar
Petit, F., Sears, K. E. & Ahituv, N. Limb development: a paradigm of gene regulation. Nat. Rev. Genet. 18, 245–258 (2017).
Google Scholar
Sheth, R. et al. Distal limb patterning requires modulation of cis-regulatory activities by HOX13. Cell Rep. 17, 2913–2926 (2016).
Google Scholar
Li, S. et al. Cistrome-GO: a web server for functional enrichment analysis of transcription factor ChIP–seq peaks. Nucleic Acids Res. 47, W206–W211 (2019).
Google Scholar
Chablais, F. & Jazwinska, A. IGF signaling between blastema and wound epidermis is required for fin regeneration. Development 137, 871–879 (2010).
Google Scholar
Dhupkar, P., Zhao, H., Mujoo, K., An, Z. & Zhang, N. Crk II silencing down-regulates IGF-IR and inhibits migration and invasion of prostate cancer cells. Biochem. Biophys. Rep. 8, 382–388 (2016).
Google Scholar
Zhang, J. et al. CRKL mediates p110β-dependent PI3K signaling in PTEN-deficient cancer cells. Cell Rep. 20, 549–557 (2017).
Google Scholar
Tanna, C. E., Goss, L. B., Ludwig, C. G. & Chen, P. W. Arf GAPs as regulators of the actin cytoskeleton—an update. Int. J. Mol. Sci. 20, 442 (2019).
Google Scholar
Fritsch, R. et al. RAS and RHO families of GTPases directly regulate distinct phosphoinositide 3-kinase isoforms. Cell 153, 1050–1063 (2013).
Google Scholar
Ye, L., Robertson, M. A., Mastracci, T. L. & Anderson, R. M. An insulin signaling feedback loop regulates pancreas progenitor cell differentiation during islet development and regeneration. Dev. Biol. 409, 354–369 (2016).
Google Scholar
Zhang, Y. M. et al. Distant insulin signaling regulates vertebrate pigmentation through the sheddase Bace2. Dev. Cell 45, 580–594.e587 (2018).
Google Scholar
Baggiolini, A. et al. Developmental chromatin programs determine oncogenic competence in melanoma. Science 373, eabc1048 (2021).
Google Scholar
Farshidfar, F. et al. Integrative molecular and clinical profiling of acral melanoma links focal amplification of 22q11.21 to metastasis. Nat Commun 13, 898 (2022). https://doi.org/10.1038/s41467-022-28566-4
Kim, K. et al. Clinicopathologic characteristics of early gastric cancer according to specific intragastric location. BMC Gastroenterol. 19, 24 (2019).
Google Scholar
Razumilava, N. & Gores, G. J. Cholangiocarcinoma. Lancet 383, 2168–2179 (2014).
Google Scholar
Tang, Q. et al. Anatomic mapping of molecular subtypes in diffuse glioma. BMC Neurol. 17, 183 (2017).
Google Scholar
White, R. M. et al. Transparent adult zebrafish as a tool for in vivo transplantation analysis. Cell Stem Cell 2, 183–189 (2008).
Google Scholar
White, R. M. et al. DHODH modulates transcriptional elongation in the neural crest and melanoma. Nature 471, 518–522 (2011).
Google Scholar
Kaufman, C. K. et al. A zebrafish melanoma model reveals emergence of neural crest identity during melanoma initiation. Science 351, aad2197 (2016).
Google Scholar
The Cancer Genome Atlas Research Network. Genomic classification of cutaneous melanoma. Cell 161, 1681–1696 (2015).
Dankort, D. et al. BrafV600E cooperates with Pten loss to induce metastatic melanoma. Nat. Genet. 41, 544–552 (2009).
Google Scholar
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
Google Scholar
Li, H. & Durbin, R. Fast and accurate long-read alignment with Burrows–Wheeler transform. Bioinformatics 26, 589–595 (2010).
Google Scholar
Cibulskis, K. et al. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat. Biotechnol. 31, 213–219 (2013).
Google Scholar
Shen, R. & Seshan, V. E. FACETS: allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing. Nucleic Acids Res. 44, e131 (2016).
Google Scholar
Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).
Google Scholar
Li, B. & Dewey, C. N. RSEM- accurate transcript quantification from RNA-seq data with or without a reference genome. BMC. Bioinformatics 12, 1471–2105 (2011).
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).
Google Scholar
Korotkevich, G., Sukhov, V. & Sergushichev, A. Fast gene set enrichment analysis. Preprint at https://doi.org/10.1101/060012 (2019).
Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576–589 (2010).
Google Scholar
Khan, A. et al. JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework. Nucleic Acids Res. 46, D260–D266 (2018).
Google Scholar
Grossman, R. L. et al. Toward a shared vision for cancer genomic data. N. Engl. J. Med. 375, 1109–1112 (2016).
Google Scholar
Hoadley, K. A. et al. Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin. Cell 158, 929–944 (2014).
Google Scholar
The Cancer Genome Atlas Research Network. Comprehensive and integrated genomic characterization of adult soft tissue sarcomas. Cell 171, 950–965.e928 (2017).
Google Scholar
The Cancer Genome Atlas Research Network. Comprehensive and integrative genomic characterization of hepatocellular carcinoma. Cell 169, 1327–1341.e1323 (2017).
Google Scholar
Robertson, A. G. et al. Comprehensive molecular characterization of muscle-invasive bladder cancer. Cell 171, 540–556.e525 (2017).
Google Scholar
Fishbein, L. et al. Comprehensive molecular characterization of pheochromocytoma and paraganglioma. Cancer Cell 31, 181–193 (2017).
Google Scholar
The Cancer Genome Atlas Research Network. Comprehensive molecular profiling of lung adenocarcinoma. Nature 511, 543–550 (2014).
Google Scholar
The Cancer Genome Atlas Research Network. Comprehensive molecular characterization of gastric adenocarcinoma. Nature 513, 202–209 (2014).
Google Scholar
The Cancer Genome Atlas Research Network. Comprehensive molecular characterization of urothelial bladder carcinoma. Nature 507, 315–322 (2014).
Google Scholar
The Cancer Genome Atlas Research Network. Comprehensive molecular characterization of human colon and rectal cancer. Nature 487, 330–337 (2012).
Google Scholar
The Cancer Genome Atlas Research Network. Comprehensive molecular portraits of human breast tumours. Nature 490, 61–70 (2012).
Google Scholar
The Cancer Genome Atlas Research Network. Comprehensive genomic characterization of squamous cell lung cancers. Nature 489, 519–525 (2012).
Google Scholar
Ciriello, G. et al. Comprehensive molecular portraits of invasive lobular breast cancer. Cell 163, 506–519 (2015).
Google Scholar
The Cancer Genome Atlas Research Network. The molecular taxonomy of primary prostate cancer. Cell 163, 1011–1025 (2015).
Google Scholar
The Cancer Genome Atlas Research Network. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature 455, 1061–1068 (2008).
The Cancer Genome Atlas Research Network. Comprehensive genomic characterization of head and neck squamous cell carcinomas. Nature 517, 576–582 (2015).
Google Scholar
The Cancer Genome Atlas Research Network. Integrated genomic characterization of endometrial carcinoma. Nature 497, 67–73 (2013).
Google Scholar
The Cancer Genome Atlas Research Network. Comprehensive molecular characterization of clear cell renal cell carcinoma. Nature 499, 43–49 (2013).
Google Scholar
Davis, C. F. et al. The somatic genomic landscape of chromophobe renal cell carcinoma. Cancer Cell 26, 319–330 (2014).
Google Scholar
The Cancer Genome Atlas Research Network. Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. N. Engl. J. Med. 368, 2059–2074 (2013).
Google Scholar
The Cancer Genome Atlas Research Network. Integrated genomic analyses of ovarian carcinoma. Nature 474, 609–615 (2011).
Google Scholar
Brennan, C. W. et al. The somatic genomic landscape of glioblastoma. Cell 155, 462–477 (2013).
Google Scholar
The Cancer Genome Atlas Research Network. Integrated genomic characterization of papillary thyroid carcinoma. Cell 159, 676–690 (2014).
Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).
Google Scholar
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
Google Scholar
Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
Google Scholar
Ramirez, F. et al. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res. 44, W160–W165 (2016).
Google Scholar
Zhang, Y. et al. Model-based analysis of ChIP–seq (MACS). Genome Biol. 9, R137 (2008).
Google Scholar
Skene, P. J., Henikoff, J. G. & Henikoff, S. Targeted in situ genome-wide profiling with high efficiency for low cell numbers. Nat. Protoc. 13, 1006–1019 (2018).
Google Scholar
Kall, L., Canterbury, J. D., Weston, J., Noble, W. S. & MacCoss, M. J. Semi-supervised learning for peptide identification from shotgun proteomics datasets. Nat. Methods 4, 923–925 (2007).
Google Scholar
The, M., MacCoss, M. J., Noble, W. S. & Kall, L. Fast and accurate protein false discovery rates on large-scale proteomics data sets with Percolator 3.0. J. Am. Soc. Mass. Spectrom. 27, 1719–1727 (2016).
Google Scholar
Sparks, A. B. et al. Distinct ligand preferences of Src homology 3 domains from Src, Yes, Abl, Cortactin, p53bp2, PLCy, Crk, and Grb2. Proc. Natl Acad. Sci. USA 93, 1540–1544 (1996).
Google Scholar
Birge, R. B., Kalodimos, C., Inagaki, F. & Tanaka, S. Crk and CrkL adaptor proteins: networks for physiological and pathological signaling. Cell Commun. Signal. 7, 13 (2009).
Google Scholar
Tothova, Z. et al. Multiplex CRISPR/Cas9-based genome editing in human hematopoietic stem cells models clonal hematopoiesis and myeloid neoplasia. Cell Stem Cell 21, 547–555.e548 (2017).
Google Scholar
Lindsay, H. et al. CrispRVariants charts the mutation spectrum of genome engineering experiments. Nat. Biotechnol. 34, 701–702 (2016).
Google Scholar
DeLuca, D. S. et al. RNA-SeQC: RNA-seq metrics for quality control and process optimization. Bioinformatics 28, 1530–1532 (2012).
Google Scholar
Hu, Y. et al. An integrative approach to ortholog prediction for disease-focused and other functional studies. BMC Bioinf. 12, 1471–2105 (2011).
Hao, Y. et al. Integrated analysis of multimodal single-cell data. Cell 184, 3573–3587.e3529 (2021).
Google Scholar
Hafemeister, C. & Satija, R. Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression. Genome Biol. 20, 296 (2019).
Google Scholar
Jolliffe, I. T. Principal Component Analysis and Factor Analysis (Springer, 1986).
McInnes, L., Healy, J. & Melville, J. UMAP: uniform manifold approximation and projection for dimension reduction. Preprint at https://doi.org/10.48550/arXiv.1802.03426 (2018).
Baron, M. et al. The stress-like cancer cell state is a consistent component of tumorigenesis. Cell Syst. 11, 536–546.e537 (2020).
Google Scholar
Hunter, M. V., Moncada, R., Weiss, J. M., Yanai, I. & White, R. M. Spatially resolved transcriptomics reveals the architecture of the tumor-microenvironment interface. Nat. Commun. 12, 6278 (2021).
Google Scholar
Freese, N. H., Norris, D. C. & Loraine, A. E. Integrated genome browser: visual analytics platform for genomics. Bioinformatics 32, 2089–2095 (2016).
Google Scholar