Investigating the Validity of the Fitzpatrick Scale to Infer Quantitative Pigmentation Phenotype and Melanoma Risk Allele Status in Diverse Populations A thesis submitted to the Graduate School of the University of Cincinnati in partial fulfillment of the requirements for the degree of Master of Arts in the Department of Anthropology of the College of Arts and Sciences by Lindsay A. Fist B.A. University of Cincinnati, 2016 Committee Chair: Heather L. Norton, Ph.D. Committee Member: C. Jeffrey Jacobson, Ph.D. Abstract Approximately 60-80% of all skin cancer deaths are attributed to melanoma, making it the deadliest form of skin cancer. Melanoma is most prevalent in white populations, but African American and Hispanic patients have much lower 5-year survival rates, partly due to the fact that melanoma is often diagnosed at more advanced stages in people of color (Cormier et al., 2006). While exposure to UV radiation is the primary environmental factor for the development of melanoma, a genetic predisposition is an important factor as well. The Fitzpatrick Skin Type scale, which measures skin phototype, is the most widespread method of determining skin’s sensitivity to UV radiation and susceptibility to skin cancers. However, studies have noted that the scale may not be an accurate indicator of melanoma risk in people of color. The goal of this study was to investigate how well the Fitzpatrick Skin Type scale correlated with another known melanoma risk factor (skin pigmentation) and genotype at melanoma risk alleles. Saliva samples and phenotypic data, including melanin index (MI) and Fitzpatrick skin type, were available for 189 self-identified African Americans, 81 self-identified Hispanics, and 213 self-identified European-Americans. Nineteen SNPs (single nucleotide polymorphisms) that had previously been associated with melanoma risk were genotyped in all participants. African Americans in this study exhibited a very wide range in skin pigmentation (33.4 – 104.7), and MI values overlapped between all populations. The MI values of the Hispanic individuals sampled in this study are more similar to those observed in the European-American sample. Associations were found between FST and MI in the African American and Hispanic groups, but not in the European-American group, suggesting that FST is not an accurate indicator of skin pigmentation in some populations. Twelve out of nineteen SNPs are common (occurring ii at frequency of 10% or greater) in all three populations, with many occurring at frequencies greater than 50%. Among African Americans, the IRF4 SNP rs12203592 was significantly associated with lower MI (P = 0.0021, β = - 15.7). Among Hispanics, rs16953002 in intron 8 of FTO was significantly associated with FST I (p=0.00022). In the European-American sample, rs1805008 (p=0.000082) and rs1805009 (p=0.000082), both in MC1R, were significantly associated with FST I. Increased awareness of melanoma risk for people of all backgrounds is needed in order to reduce the prevalence of melanoma in the United States. iii © Copyright 2019 by Lindsay A. Fist All Rights Reserved iv Acknowledgements Financial support for this thesis was provided by the University of Cincinnati Charles Phelps Taft Research Center Graduate Enrichment Award. It is with great pleasure that I acknowledge the individuals who provided support and assistance to me while completing this thesis. I am eternally grateful to my thesis advisor, Dr. Heather Norton, for her guidance, patience, and enthusiasm throughout this entire journey. She has awarded me so many opportunities that I appreciate immensely. I have learned so much from her, and I could not have imagined having a better advisor and mentor. I would also like to thank my thesis committee member, Dr. Jeff Jacobson, for his insightful comments and encouragement. I owe great thanks to my parents, Sandy and Alan, who have always pushed me to achieve my goals and have never failed to acknowledge my hard work, which I owe to them. Thank you for always believing in me even when I didn’t believe in myself. I truly could not have done this without you both and I cannot thank you enough. Thank you to Jeremy for your endless patience through the many late nights spent writing. The support and love you have given me while writing this thesis, and in life in general, has meant everything to me. And lastly, thank you to my daughter, Alexa, whose laughter has rescued me from peril more times than I can recall. Thank you for being my biggest inspiration and for making this all worth it. v Table of Contents 1. Introduction .......................................................................................................................... 1 1.1 Overview ........................................................................................................................... 1 1.2 Research Goals and Hypotheses .................................................................................... 3 2. Background ........................................................................................................................... 5 2.1 Fitzpatrick Scale ............................................................................................................... 5 2.2 Variation in Skin Pigmentation ...................................................................................... 7 2.3 African American Skin Pigmentation and Melanoma Risk ....................................... 9 2.4 Hispanic Skin Pigmentation and Melanoma Risk ..................................................... 12 2.5 Biology and Genetics of Melanoma ............................................................................. 15 3. Methods ............................................................................................................................... 21 3.1 Phenotype Data Collection ........................................................................................... 21 3.2 Genetic Data Collection and Analyses ........................................................................ 22 3.3 Statistical Analyses ........................................................................................................ 26 4. Results .................................................................................................................................. 27 4.1 Phenotype Data .............................................................................................................. 27 4.2 Genotype Data ................................................................................................................ 31 5. Discussion ........................................................................................................................... 46 6. Conclusion .......................................................................................................................... 52 References .................................................................................................................................. 56 Appendix A ............................................................................................................................... 66 vi List of Tables Table 2.1. Fitzpatrick Skin Types ................................................................................................ 7 Table 3.1 SNPs genotyped in this study .................................................................................. 25 Table 3.2. Restriction digest enzyme PCR conditions of rs6059655 ..................................... 25 Table 4.1. Raw mean (and SD) Melanin Index values and range in each population .................................................................................................................................... 27 Table 4.2. Risk allele frequencies, genotypes, and HWE in African American, Hispanic, and European-American study populations ......................................................... 32 Table 4.3. Genotype Association with Melanin Index ........................................................... 34 Table 4.4. Genotype Association with FST I ............................................................................ 36 Table 4.5. Genotype Association with FST II .......................................................................... 37 Table 4.6. Genotype Association with FST III ......................................................................... 39 Table 4.7. Genotype Association with FST IV ......................................................................... 41 Table 4.8. Genotype Association with FST V .......................................................................... 42 Table 4.9. Genotype Association with FST VI ......................................................................... 44 vii List of Figures Figure 3.1. DNA Extraction Protocol ........................................................................................ 23 Figure 4.1. Skin Melanin Index values of European-American, Hispanic, and African Americans for Fitzpatrick Skin Types I through VI ............................................................... 28 Figure 4.2. FST distribution in Hispanics ................................................................................ 30 Figure 4.3. FST distribution in African Americans ................................................................. 30 Figure 4.4. FST distribution in European-Americans ............................................................ 31 viii 1. Introduction 1.1 Overview Melanoma is