Genetics and Genomics in Clinical Practice

*Methods in Molecular Medicine*

Landmark. 2018;**23**:1360-1369

[173] Wang-Johanning F et al. Immunotherapeutic potential of anti-human endogenous retrovirus-K envelope protein antibodies in targeting breast tumors. Journal of the National Cancer Institute. 2012;**104**(3):189-210

cancer therapy. Frontiers in Bioscience-

[174] Hodges-Vazquez M et al. The yellow fever 17D vaccine and risk of malignant melanoma in the United States military. Vaccine. 2012;**30**(30):4476-4479

[175] Mastrangelo G et al. Does yellow fever 17D vaccine protect against melanoma? Vaccine. 2009;**27**(4):588-591

[177] Kong Y et al. Transposable element expression in tumors is associated with immune infiltration and increased antigenicity. Nature Communications.

[178] Grandi N, Tramontano E. Human endogenous retroviruses are ancient acquired elements still shaping innate immune responses. Frontiers in Immunology. 2018;**9**:2039

demethylating agents target colorectal cancer cells by inducing viral mimicry by endogenous transcripts. Cell.

[179] Roulois D et al. DNA-

2015;**162**(5):961-973

[176] Mullins CS, Linnebacher M. Endogenous retrovirus sequences as a novel class of tumor-specific antigens: An example of HERV-H env encoding strong CTL epitopes. Cancer Immunology, Immunotherapy.

2012;**61**(7):1093-1100

2019;**10**:5228

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**Chapter 6**

**Abstract**

**1. Introduction**

Landscape Genetics: From Classic

Landscape genetics combines population genetics and landscape ecology to understand processes that shape the distribution and organization of human, animal, or plant populations. This field of genetics emerged from the availability of several studies with classical molecular markers, such as isozymes, RAPD, AFLP, and microsatellites. Population genetic studies enabled the detection of population structure with those markers, but a more comprehensive analysis of natural populations was only possible with the development of statistical methods that combined both molecular data and environmental variables. Ultimately, the rapid development of sequencing technologies allowed studies at the genomic level, augmenting the resolution of association with environment factors. This chapter outlines basic concepts in landscape genetics, the main statistical methods used so far, and the perspectives of this field of knowledge into strategies for conservation of natural populations of plant and animal species. Moreover, we briefly describe the application of the field to understand historical human migration processes as well as how

**Keywords:** molecular studies, environmental variables, population structure,

spatial genetic structure, paternity, linkage, and association mapping.

Population genetic studies deal with allele frequencies and processes that shape their variation within and among populations. Multiple studies have addressed genetic variation and their structure based on the screening of molecular markers such as allozymes (began with Lewontin and Hubby [1]), random amplified polymorphic DNA (RAPD) [2], amplified fragment length polymorphism (AFLP) [3], microsatellites or simple sequence repeats (SSR) [4], intersimple sequence repeats (ISSR) [5] and single nucleotide polymorphisms (SNP). The use of allozyme markers started up a series of population genetic studies, allowing relatively precise estimation of heterozygosity levels due to their codominance nature. Those markers were largely employed until the end of the 1990s. The development of techniques for screening directly at the level of DNA has accelerated the discovery of numberless markers in humans, animals, plants, fungi, and other organisms. RAPD, ISSR, and AFLP, in general, are more limited in describing genetic variation due to their dominance. In contrast, several SSR markers have been developed for studying a diverse set of species, enabling precise estimates of genetic diversity, gene flow,

Molecular Markers to Genomics

*Enéas Ricardo Konzen and Maria Imaculada Zucchi*

some diseases are spread throughout the world.

genetic diversity, single nucleotide polymorphisms
