Skip to main content
SpringerLink
Log in

The Concept of Immunogenetics

  • Chapter
  • First Online:
The Immunogenetics of Dermatologic Diseases

Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 1367))

  • 1179 Accesses

Abstract

Genetics plays a major role in shaping the immune responses in both physiological and pathological states such as psoriasis, alopecia areata, and other immune-mediated dermatological conditions. The genes encoding the elements of the immune system and its regulators are among the most polymorphous loci in the genome. Subtle variations in these genes can thus alter the balanced defensive responses of the immune system and make an individual liable to diseases and environmental triggers. Immunogenetics deals with finding the precise set of liability genes involved in the pathogenesis of specific complex diseases. In this chapter, we will briefly discuss the basic principles of genetic polymorphisms, the methods used in scanning these polymorphisms, and the strategies employed to find the role of these polymorphisms in complex diseases.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  • Alasoo K, Rodrigues J, Mukhopadhyay S, Knights AJ, Mann AL, Kundu K, Hale C, Dougan G, Gaffney DJ (2018) Shared genetic effects on chromatin and gene expression indicate a role for enhancer priming in immune response. Nat Genet 50:424–431

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Albers CA, Lunter G, MacArthur DG, McVean G, Ouwehand WH, Durbin R (2011) Dindel: accurate indel calls from short-read data. Genome Res 21:961–973

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Alkuraya FS (2010) Homozygosity mapping: one more tool in the clinical geneticist’s toolbox. Genet Med 12:236–239

    Article  PubMed  Google Scholar 

  • Altshuler D, Donnelly P, Consortium IH (2005) A haplotype map of the human genome. Nature 437:nature04226

    Google Scholar 

  • Asghari V, Sanyal S, Buchwaldt S, Paterson A, Jovanovic V, Van Tol HH (1995) Modulation of intracellular cyclic AMP levels by different human dopamine D4 receptor variants. J Neurochem 65:1157–1165

    Article  CAS  PubMed  Google Scholar 

  • Bakhtiari M, Park J, Ding Y-C, Shleizer-Burko S, Neuhausen SL, Halldórsson BV, Stefánsson K, Gymrek M, Bafna V (2021) Variable Number Tandem Repeats mediate the expression of proximal genes. Nat Commun 12:1–12

    Article  Google Scholar 

  • Bakhtiari M, Shleizer-Burko S, Gymrek M, Bansal V, Bafna V (2018) Targeted genotyping of variable number tandem repeats with adVNTR. Genome Res 28:1709–1719

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bannister AJ, Kouzarides T (2011) Regulation of chromatin by histone modifications. Cell Res 21:381–395

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bansal V, Libiger O (2011) A probabilistic method for the detection and genotyping of small indels from population-scale sequence data. Bioinf 27:2047–2053

    Article  CAS  Google Scholar 

  • Barrett JC, Cardon LR (2006) Evaluating coverage of genome-wide association studies. Nat Genet 38:659–662

    Article  CAS  PubMed  Google Scholar 

  • Behjati S, Tarpey PS (2013) What is next generation sequencing? Arch Dis Child-Educ Pract 98:236–238

    Article  Google Scholar 

  • Blumenberg M (2012) SKINOMICS: transcriptional profiling in dermatology and skin biology. Curr Genom 13:363–368

    Article  CAS  Google Scholar 

  • Bossini-Castillo L, Glinos DA, Kunowska N, Golda G, Lamikanra A, Spitzer M, Soskic B, Cano-Gamez E, Smyth DJ, Cattermole C (2019) Immune disease variants modulate gene expression in regulatory CD4+ T cells and inform drug targets. BioRxiv:654632

    Google Scholar 

  • Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32:314

    CAS  PubMed  PubMed Central  Google Scholar 

  • Boyle AP, Davis S, Shulha HP, Meltzer P, Margulies EH, Weng Z, Furey TS, Crawford GE (2008) High-resolution mapping and characterization of open chromatin across the genome. Cell 132:311–322

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Brookes K (2013) The VNTR in complex disorders: the forgotten polymorphisms? A functional way forward? Genomics 101:273–281

    Article  CAS  PubMed  Google Scholar 

  • Cai CQ, Zhang T, Breslin MB, Giraud M, Lan MS (2011) Both polymorphic variable number of tandem repeats and autoimmune regulator modulate differential expression of insulin in human thymic epithelial cells. Diabetes 60:336–344

    Article  CAS  PubMed  Google Scholar 

  • Cano-Gamez E, Trynka G (2020) From GWAS to function: using functional genomics to identify the mechanisms underlying complex diseases. Front Genet 11

    Google Scholar 

  • Cao MD, Tasker E, Willadsen K, Imelfort M, Vishwanathan S, Sureshkumar S, Balasubramanian S, Boden M (2014) Inferring short tandem repeat variation from paired-end short reads. Nucleic Acids Res 42:e16–e16

    Article  CAS  PubMed  Google Scholar 

  • Carter NP (2007) Methods and strategies for analyzing copy number variation using DNA microarrays. Nat Genet 39:S16–S21

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mingorance Gámez CG, Martínez Chamorro A, Moreno Casares AM, Tercedor Sánchez J, Arias‐Santiago S, García‐Lora E, López‐Nevot MA(2020) Joint study of the associations of HLA-B and the transmembrane STR polymorphism of MICA with alopecia areata shows independent associations of both of them with the disease. Clin Exp Dermatol

    Google Scholar 

  • Chen L, Ge B, Casale FP, Vasquez L, Kwan T, Garrido-Martín D, Watt S, Yan Y, Kundu K, Ecker S (2016) Genetic drivers of epigenetic and transcriptional variation in human immune cells. Cell 167:1398–1414. e1324

    Google Scholar 

  • Chiang C, Scott AJ, Davis JR, Tsang EK, Li X, Kim Y, Hadzic T, Damani FN, Ganel L, Montgomery SB (2017) The impact of structural variation on human gene expression. Nat Genet 49:692–699

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Clark TG, Andrew T, Cooper GM, Margulies EH, Mullikin JC, Balding DJ (2007) Functional constraint and small insertions and deletions in the ENCODE regions of the human genome. Genome Biol 8:1–14

    Article  Google Scholar 

  • Collins FS, Drumm ML, Cole JL, Lockwood WK, Woude GV, Iannuzzi MC (1987) Construction of a general human chromosome jumping library, with application to cystic fibrosis. Science 235:1046–1049

    Article  CAS  PubMed  Google Scholar 

  • Conde L, Vaquerizas JM, Santoyo J, Al-Shahrour F, Ruiz-Llorente S, Robledo M, Dopazo J (2004) PupaSNP Finder: a web tool for finding SNPs with putative effect at transcriptional level. Nucleic Acids Res 32:W242–W248

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Conrad DF, Keebler JE, DePristo MA, Lindsay SJ, Zhang Y, Casals F, Idaghdour Y, Hartl CL, Torroja C, Garimella KV (2011) Variation in genome-wide mutation rates within and between human families. Nat Genet 43:712

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Consortium EP (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489:57

    Article  Google Scholar 

  • Consortium WTCC (2007) Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 447:661

    Article  Google Scholar 

  • Crux NB, Elahi S (2017) Human leukocyte antigen (HLA) and immune regulation: how do classical and non-classical HLA alleles modulate immune response to human immunodeficiency virus and hepatitis C virus infections? Front Immunol 8:832

    Article  PubMed  PubMed Central  Google Scholar 

  • Dashnow H, Lek M, Phipson B, Halman A, Sadedin S, Lonsdale A, Davis M, Lamont P, Clayton JS, Laing NG (2018) STRetch: detecting and discovering pathogenic short tandem repeat expansions. Genome Biol 19:1–13

    Article  Google Scholar 

  • DeWan A, Liu M, Hartman S, Zhang SS-M, Liu DT, Zhao C, Tam PO, Chan WM, Lam DS, Snyder M (2006) HTRA1 promoter polymorphism in wet age-related macular degeneration. Science 314:989–992

    Article  CAS  PubMed  Google Scholar 

  • Dolzhenko E, van Vugt JJ, Shaw RJ, Bekritsky MA, van Blitterswijk M, Narzisi G, Ajay SS, Rajan V, Lajoie BR, Johnson NH (2017) Detection of long repeat expansions from PCR-free whole-genome sequence data. Genome Res 27:1895–1903

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dubois PC, Trynka G, Franke L, Hunt KA, Romanos J, Curtotti A, Zhernakova A, Heap GA, Ádány R, Aromaa A (2010) Multiple common variants for celiac disease influencing immune gene expression. Nat Genet 42:295–302

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dunne MR, Byrne G, Chirdo FG, Feighery C (2020) Coeliac disease pathogenesis: the uncertainties of a well-known immune mediated disorder. Front Immunol 11:1374

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ewald H, Kruse TA, Mors O (2003) Genome wide scan using homozygosity mapping and linkage analyses of a single pedigree with affective disorder suggests oligogenic inheritance. Am J Med Genet B Neuropsychiatr Genet 120:63–71

    Article  Google Scholar 

  • Fischer J, Degenhardt F, Hofmann A, Redler S, Basmanav FB, Heilmann-Heimbach S, Hanneken S, Giehl KA, Wolff H, Moebus S (2017) Genomewide analysis of copy number variants in alopecia areata in a Central European cohort reveals association with MCHR 2. Exp Dermatol 26:536–541

    Article  CAS  PubMed  Google Scholar 

  • Fortune MD, Guo H, Burren O, Schofield E, Walker NM, Ban M, Sawcer SJ, Bowes J, Worthington J, Barton A (2015) Statistical colocalization of genetic risk variants for related autoimmune diseases in the context of common controls. Nat Genet 47:839–846

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Frommer M, McDonald LE, Millar DS, Collis CM, Watt F, Grigg GW, Molloy PL, Paul CL (1992) A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc Natl Acad Sci 89:1827–1831

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gamazon ER, Stranger BE (2015) The impact of human copy number variation on gene expression. Brief Funct Genom 14:352–357

    Article  CAS  Google Scholar 

  • Gelfand Y, Hernandez Y, Loving J, Benson G (2014) VNTRseek—a computational tool to detect tandem repeat variants in high-throughput sequencing data. Nucleic Acids Res 42:8884–8894

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gerrits A, Li Y, Tesson BM, Bystrykh LV, Weersing E, Ausema A, Dontje B, Wang X, Breitling R, Jansen RC (2009) Expression quantitative trait loci are highly sensitive to cellular differentiation state. PLoS Genet 5:e1000692

    Google Scholar 

  • Gheldof N, Witwicki RM, Migliavacca E, Leleu M, Didelot G, Harewood L, Rougemont J, Reymond A (2013) Structural variation-associated expression changes are paralleled by chromatin architecture modifications. PloS One 8:e79973

    Google Scholar 

  • Ghodke Y, Joshi K, Chopra A, Patwardhan B (2005) HLA and disease. Eur J Epidemiol 20:475–488

    Article  PubMed  Google Scholar 

  • Giambartolomei C, Vukcevic D, Schadt EE, Franke L, Hingorani AD, Wallace C, Plagnol V (2014) Bayesian test for colocalisation between pairs of genetic association studies using summary statistics. PLoS Genet 10:e1004383

    Google Scholar 

  • Glavač D, Ravnik-Glavač M (2015) Essential role of microRNA in skin physiology and disease. In: microRNA: medical evidence. Springer, pp 307–330

    Google Scholar 

  • Goltsov AA, Eisensmith RC, Konecki D, Lichter-Konecki U, Woo S (1992) Associations between mutations and a VNTR in the human phenylalanine hydroxylase gene. Am J Hum Genet 51:627

    CAS  PubMed  PubMed Central  Google Scholar 

  • Gong J, Tong Y, Zhang HM, Wang K, Hu T, Shan G, Sun J, Guo AY (2012) Genome-wide identification of SNPs in microRNA genes and the SNP effects on microRNA target binding and biogenesis. Hum Mutat 33:254–263

    Article  CAS  PubMed  Google Scholar 

  • Gymrek M, Golan D, Rosset S, Erlich Y (2012) lobSTR: a short tandem repeat profiler for personal genomes. Genome Res 22:1154–1162

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gymrek M, Willems T, Guilmatre A, Zeng H, Markus B, Georgiev S, Daly MJ, Price AL, Pritchard JK, Sharp AJ (2016) Abundant contribution of short tandem repeats to gene expression variation in humans. Nat Genet 48:22–29

    Article  CAS  PubMed  Google Scholar 

  • Hasan MS, Wu X, Zhang L (2015) Performance evaluation of indel calling tools using real short-read data. Hum Genom 9:1–14

    Article  Google Scholar 

  • He X, Fuller CK, Song Y, Meng Q, Zhang B, Yang X, Li H (2013) Sherlock: detecting gene-disease associations by matching patterns of expression QTL and GWAS. Am J Hum Genet 92:667–680

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hersberger M, Thun G-A, Imboden M, Brandstätter A, Waechter V, Summerer M, Schmid-Grendelmeier P, Bircher A, Rohrer L, Berger W (2010) Association of STR polymorphisms in CMA1 and IL-4 with asthma and atopy: the SAPALDIA cohort. Hum Immunol 71:1154–1160

    Article  CAS  PubMed  Google Scholar 

  • Hollox EJ, Huffmeier U, Zeeuwen PL, Palla R, Lascorz J, Rodijk-Olthuis D, Van De Kerkhof PC, Traupe H, De Jongh G, Den Heijer M (2008) Psoriasis is associated with increased β-defensin genomic copy number. Nat Genet 40:23–25

    Article  CAS  PubMed  Google Scholar 

  • Hormozdiari F, Van De Bunt M, Segre AV, Li X, Joo JWJ, Bilow M, Sul JH, Sankararaman S, Pasaniuc B, Eskin E (2016) Colocalization of GWAS and eQTL signals detects target genes. Am J Hum Genet 99:1245–1260

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Howell W (2014) HLA and disease: guilt by association. Int J Immunogenet 41:1–12

    Article  CAS  PubMed  Google Scholar 

  • Hsieh FH (2014) Primer to the immune response. Ann Allergy Asthma Immunol 113:333

    Article  Google Scholar 

  • Hu X, Kim H, Stahl E, Plenge R, Daly M, Raychaudhuri S (2011) Integrating autoimmune risk loci with gene-expression data identifies specific pathogenic immune cell subsets. Am J Hum Genet 89:496–506

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Huang J, Chen J, Esparza J, Ding J, Elder JT, Abecasis GR, Lee Y-A, Lathrop GM, Moffatt MF, Cookson WO (2015) eQTL mapping identifies insertion-and deletion-specific eQTLs in multiple tissues. Nat Commun 6:1–8

    Article  Google Scholar 

  • Jin Y, Wang J, Bachtiar M, Chong SS, Lee CG (2018) Architecture of polymorphisms in the human genome reveals functionally important and positively selected variants in immune response and drug transporter genes. Hum Genom 12:1–13

    Article  CAS  Google Scholar 

  • Jinnin M (2014) Various applications of microRNAs in skin diseases. J Dermatol Sci 74:3–8

    Article  CAS  PubMed  Google Scholar 

  • Kalkan G, Karakus N, Baş Y, Takçı Z, Özuğuz P, Ateş Ö, Yigit S (2013) The association between Interleukin (IL)-4 gene intron 3 VNTR polymorphism and alopecia areata (AA) in Turkish population. Gene 527:565–569

    Article  CAS  PubMed  Google Scholar 

  • Kim B-C, Kim W-Y, Park D, Chung W-H, Shin K-s, Bhak J (2008) SNP@ Promoter: a database of human SNPs (single nucleotide polymorphisms) within the putative promoter regions. In: BMC bioinformatics. Springer, pp 1–5

    Google Scholar 

  • Ku CS, Loy EY, Salim A, Pawitan Y, Chia KS (2010) The discovery of human genetic variations and their use as disease markers: past, present and future. J Hum Genet 55:403–415

    Article  PubMed  Google Scholar 

  • Ku CS, Naidoo N, Teo SM, Pawitan Y (2011) Regions of homozygosity and their impact on complex diseases and traits. Hum Genet 129:1–15

    Article  PubMed  Google Scholar 

  • Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ (2015) Integrative analysis of 111 reference human epigenomes. Nature 518:317–330

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Küster W, Happle R (1984) The inheritance of common baldness: two B or not two B? J Am Acad Dermatol 11:921–926

    Article  PubMed  Google Scholar 

  • Lee-Kirsch MA, Gong M, Schulz H, Rüschendorf F, Stein A, Pfeiffer C, Ballarini A, Gahr M, Hubner N, Linné M (2006) Familial chilblain lupus, a monogenic form of cutaneous lupus erythematosus, maps to chromosome 3p. Am J Hum Genet 79:731–737

    Article  CAS  Google Scholar 

  • Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25:2078–2079

    Article  PubMed  PubMed Central  Google Scholar 

  • Liao WW, Arthur JW (2011) Predicting peptide binding to major histocompatibility complex molecules. Autoimmun Rev 10:469–473

    Article  CAS  PubMed  Google Scholar 

  • Lieben L (2016) Repeat, repeat, repeat—gene expression variability explained. Nat Rev Genet 17:69

    CAS  PubMed  Google Scholar 

  • Lin M, Whitmire S, Chen J, Farrel A, Shi X, Guo J-t (2017) Effects of short indels on protein structure and function in human genomes. Sci Rep 7:1–9

    Google Scholar 

  • Lonsdale J, Thomas J, Salvatore M, Phillips R, Lo E, Shad S, Hasz R, Walters G, Garcia F, Young N (2013) The genotype-tissue expression (GTEx) project. Nat Genet 45:580–585

    Article  CAS  Google Scholar 

  • Lu D, Chen L, Shi X, Zhang X, Ling X, Chen X, Xie L, Jiang L, Ding L, He Y (2013) A functional polymorphism in interleukin-1α (IL1A) gene is associated with risk of alopecia areata in Chinese populations. Gene 521:282–286

    Article  CAS  PubMed  Google Scholar 

  • Mack SJ, Cano P, Hollenbach JA, He J, Hurley CK, Middleton D, Moraes ME, Pereira SE, Kempenich JH, Reed EF (2013) Common and well-documented HLA alleles: 2012 update to the CWD catalogue. Tissue Antigens 81:194–203

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Marsh SG, Albert E, Bodmer W, Bontrop R, Dupont B, Erlich H, Fernández-Viña M, Geraghty D, Holdsworth R, Hurley C (2010) Nomenclature for factors of the HLA system, 2010. Tissue Antigens 75:291

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Maurano MT, Humbert R, Rynes E, Thurman RE, Haugen E, Wang H, Reynolds AP, Sandstrom R, Qu H, Brody J (2012) Systematic localization of common disease-associated variation in regulatory DNA. Science 337:1190–1195

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • McCarroll SA, Altshuler DM (2007) Copy-number variation and association studies of human disease. Nat Genet 39:S37–S42

    Article  CAS  PubMed  Google Scholar 

  • McDonald-McGinn DM, Sullivan KE, Marino B, Philip N, Swillen A, Vorstman JA, Zackai EH, Emanuel BS, Vermeesch JR, Morrow BE (2015) 22q11. 2 deletion syndrome. Nat Rev Dis Primers 1:1–19

    Article  Google Scholar 

  • Mignone F, Gissi C, Liuni S, Pesole G (2002) Untranslated regions of mRNAs. Genome Biol 3:1–10

    Article  Google Scholar 

  • Mills RE, Luttig CT, Larkins CE, Beauchamp A, Tsui C, Pittard WS, Devine SE (2006) An initial map of insertion and deletion (INDEL) variation in the human genome. Genome Res 16:1182–1190

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mirkin SM (2007) Expandable DNA repeats and human disease. Nature 447:932–940

    Article  CAS  PubMed  Google Scholar 

  • Mirza SP, Olivier M (2008) Methods and approaches for the comprehensive characterization and quantification of cellular proteomes using mass spectrometry. Physiol Genomics 33:3–11

    Article  CAS  PubMed  Google Scholar 

  • Neel JV (1978) Rare variants, private polymorphisms, and locus heterozygosity in Amerindian populations. Am J Hum Genet 30:465

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ng PC, Henikoff S (2002) Accounting for human polymorphisms predicted to affect protein function. Genome Res 12:436–446

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nica AC, Montgomery SB, Dimas AS, Stranger BE, Beazley C, Barroso I, Dermitzakis ET (2010) Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations. PLoS Genet 6:e1000895

    Google Scholar 

  • O’Brien J, Hayder H, Zayed Y, Peng C (2018) Overview of microRNA biogenesis, mechanisms of actions, and circulation. Front Endocrinol 9:402

    Article  Google Scholar 

  • Ok Yang J, Kim WY, Bhak J (2009) ssSNPTarget: genome-wide splice-site single nucleotide polymorphism database. Hum Mutat 30:E1010–E1020

    Article  Google Scholar 

  • Oldenburg J, Schröder J, Schmitt C, Brackmann H, Schwaab R (1998) Small deletion/insertion mutations within poly-A runs of the factor VIII gene mitigate the severe haemophilia A phenotype. Thromb Haemost 79:452–453

    Article  CAS  PubMed  Google Scholar 

  • Onengut-Gumuscu S, Chen W-M, Burren O, Cooper NJ, Quinlan AR, Mychaleckyj JC, Farber E, Bonnie JK, Szpak M, Schofield E (2015) Fine mapping of type 1 diabetes susceptibility loci and evidence for colocalization of causal variants with lymphoid gene enhancers. Nat Genet 47:381–386

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ostertag EM, Kazazian HH Jr (2001) Biology of mammalian L1 retrotransposons. Annu Rev Genet 35:501–538

    Article  CAS  PubMed  Google Scholar 

  • Ott J, Wang J, Leal SM (2015) Genetic linkage analysis in the age of whole-genome sequencing. Nat Rev Genet 16:275–284

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Patwardhan M, Pradhan V, Taylor L, Thakkar V, Kharkar V, Khopkar U, Ghosh K, Gawkrodger D, Teare M, Weetman A (2013) The angiotensin-converting enzyme gene insertion/deletion polymorphism in Indian patients with vitiligo: a case–control study and meta-analysis. Br J Dermatol 168:1195–1204

    Article  CAS  PubMed  Google Scholar 

  • Pearson TA, Manolio TA (2008) How to interpret a genome-wide association study. JAMA 299:1335–1344

    Article  CAS  PubMed  Google Scholar 

  • Pehlivan S, Ozkinay F, Alper S, Onay H, Yuksel E, Pehlivan M, Ozkinay C (2009) Association between IL4 (–590), ACE (I)/(D), CCR5 (Δ32), CTLA4 (+ 49) and IL1-RN (VNTR in intron 2) gene polymorphisms and vitiligo. Eur J Dermatol 19:126–128

    Article  CAS  PubMed  Google Scholar 

  • Pulst SM (1999) Genetic linkage analysis. Arch Neurol 56:667–672

    Article  CAS  PubMed  Google Scholar 

  • Ratan A, Olson TL, Loughran TP, Miller W (2015) Identification of indels in next-generation sequencing data. BMC Bioinf 16:1–8

    Article  Google Scholar 

  • Redon R, Ishikawa S, Fitch KR, Feuk L, Perry GH, Andrews TD, Fiegler H, Shapero MH, Carson AR, Chen W (2006) Global variation in copy number in the human genome. Nature 444:444–454

    Google Scholar 

  • Rimmer A, Phan H, Mathieson I, Iqbal Z, Twigg SR, Wilkie AO, McVean G, Lunter G (2014) Integrating mapping-, assembly-and haplotype-based approaches for calling variants in clinical sequencing applications. Nat Genet 46:912–918

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rizzo AE, Maibach HI (2012) Personalizing dermatology: the future of genomic expression profiling to individualize dermatologic therapy. J Dermatol Treat 23:161–167

    Article  CAS  Google Scholar 

  • Robinson J, Halliwell JA, Hayhurst JD, Flicek P, Parham P, Marsh SG (2015) The IPD and IMGT/HLA database: allele variant databases. Nucleic Acids Res 43:D423–D431

    Article  CAS  PubMed  Google Scholar 

  • Rockman MV, Kruglyak L (2006) Genetics of global gene expression. Nat Rev Genet 7:862–872

    Article  CAS  PubMed  Google Scholar 

  • Sachidanandam R, Weissman D, Schmidt SC, Kakol JM, Stein LD, Marth G, Sherry S, Mullikin JC, Mortimore BJ, Willey DL (2001) A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409:928–934

    Article  CAS  PubMed  Google Scholar 

  • Saiki RK, Scharf S, Faloona F, Mullis KB, Horn GT, Erlich HA, Arnheim N (1985) Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science 230:1350–1354

    Article  CAS  PubMed  Google Scholar 

  • Sehn JK (2015) Insertions and deletions (indels). In: Clinical genomics. Elsevier, pp 129–150

    Google Scholar 

  • Shan N, Wang Z, Hou L (2019) Identification of trans-eQTLs using mediation analysis with multiple mediators. BMC Bioinformatics 20:87–97

    Article  Google Scholar 

  • Shao H, Bellos E, Yin H, Liu X, Zou J, Li Y, Wang J, Coin LJ (2013) A population model for genotyping indels from next-generation sequence data. Nucleic Acids Res 41:e46–e46

    Article  CAS  PubMed  Google Scholar 

  • Sheehan NJ (2004) The ramifications of HLA-B27. J R Soc Med 97:10–14

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sherry ST, Ward M-H, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K (2001) dbSNP: the NCBI database of genetic variation. Nucleic Acids Res 29:308–311

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shiina T, Hosomichi K, Inoko H, Kulski JK (2009) The HLA genomic loci map: expression, interaction, diversity and disease. J Hum Genet 54:15–39

    Article  CAS  PubMed  Google Scholar 

  • Slatkin M (2008) Linkage disequilibrium—understanding the evolutionary past and mapping the medical future. Nat Rev Genet 9:477–485

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Stankiewicz P, Lupski JR (2010) Structural variation in the human genome and its role in disease. Annu Rev Med 61:437–455

    Article  CAS  PubMed  Google Scholar 

  • Stein LD (2004) End of the beginning. Nature 431:915–916

    Article  CAS  PubMed  Google Scholar 

  • Subramanya RD, Coda AB, Sinha AA (2010) Transcriptional profiling in alopecia areata defines immune and cell cycle control related genes within disease-specific signatures. Genomics 96:146–153

    Article  CAS  PubMed  Google Scholar 

  • Tang H, Kirkness EF, Lippert C, Biggs WH, Fabani M, Guzman E, Ramakrishnan S, Lavrenko V, Kakaradov B, Hou C (2017) Profiling of short-tandem-repeat disease alleles in 12,632 human whole genomes. Am J Hum Genet 101:700–715

    Article  CAS  Google Scholar 

  • Ting JP-Y, Trowsdale J (2002) Genetic control of MHC class II expression. Cell 109:S21–S33

    Article  CAS  PubMed  Google Scholar 

  • Turnpenny PD, Ellard S, Emery AEH (2022) Emery’s elements of medical genetics and genomics

    Google Scholar 

  • Van der Linden S, Valkenburg H, De Jongh B, Cats A (1984) The risk of developing ankylosing spondylitis in HLA-B27 positive individuals. A comparison of relatives of spondylitis patients with the general population. Arthritis Rheum 27:241–249

    Article  PubMed  Google Scholar 

  • Veyrieras J-B, Kudaravalli S, Kim SY, Dermitzakis ET, Gilad Y, Stephens M, Pritchard JK (2008) High-resolution mapping of expression-QTLs yields insight into human gene regulation. PLoS Genet 4:e1000214.

    Google Scholar 

  • Visscher PM, Brown MA, McCarthy MI, Yang J (2012) Five years of GWAS discovery. Am J Hum Genet 90:7–24

    Article  CAS  Google Scholar 

  • Vogels A, Fryns J-P (2002) The Prader-Willi syndrome and the Angelman syndrome. Genet Couns (geneva, Switzerland) 13:385–396

    CAS  Google Scholar 

  • Wallace C, Rotival M, Cooper JD, Rice CM, Yang JH, McNeill M, Smyth DJ, Niblett D, Cambien F, Consortium C (2012) Statistical colocalization of monocyte gene expression and genetic risk variants for type 1 diabetes. Hum Mol Genet 21:2815–2824

    Google Scholar 

  • Wang E, Miller LD, Ohnmacht GA, Liu ET, Marincola FM (2000) High-fidelity mRNA amplification for gene profiling. Nat Biotechnol 18:457–459

    Article  CAS  PubMed  Google Scholar 

  • Wang J, Ronaghi M, Chong SS, Lee CG (2011) pfSNP: an integrated potentially functional SNP resource that facilitates hypotheses generation through knowledge syntheses. Hum Mutat 32:19–24

    Article  PubMed  Google Scholar 

  • Weissenbach J, Gyapay G, Dib C, Vignal A, Morissette J, Millasseau P, Vaysseix G, Lathrop M (1992) A second-generation linkage map of the human genome. Nature 359:794–801

    Article  CAS  PubMed  Google Scholar 

  • Wenzel J, Peters B, Zahn S, Birth M, Hofmann K, Kuesters D, Tomiuk S, Baron JM, Merk HF, Mauch C (2008) Gene expression profiling of lichen planus reflects CXCL9+-mediated inflammation and distinguishes this disease from atopic dermatitis and psoriasis. J Investig Dermatol 128:67–78

    Article  CAS  PubMed  Google Scholar 

  • Willems T, Zielinski D, Yuan J, Gordon A, Gymrek M, Erlich Y (2017) Genome-wide profiling of heritable and de novo STR variations. Nat Methods 14:590–592

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ye K, Schulz MH, Long Q, Apweiler R, Ning Z (2009) Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics 25:2865–2871

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yi C, Li Q, Xiao J (2020) Familial chilblain lupus due to a novel mutation in TREX1 associated with Aicardi–Goutie’res syndrome. Pediatr Rheumatol 18:1–7

    Article  Google Scholar 

  • Zhen Q, Yang Z, Wang W, Li B, Bai M, Wu J, Ge H, Dong Z, Shen J, Tang H (2019) Genetic study on small insertions and deletions in psoriasis reveals a role in complex human diseases. J Investig Dermatol 139:2302–2312. e2314

    Google Scholar 

  • Zondervan KT, Cardon LR (2004) The complex interplay among factors that influence allelic association. Nat Rev Genet 5:89–100

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Network of Dermatology Research (NDR), Universal Scientific Education and Research Network (USERN), Tehran, Iran

    Fateme Rajabi & Navid Jabalameli

  2. Center for Research & Training in Skin Diseases & Leprosy, Tehran University of Medical Sciences, Tehran, Iran

    Fateme Rajabi

  3. Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Sheffield, UK

    Nima Rezaei

  4. Research Center for Immunodeficiencies, Children’s Medical Center, Tehran University of Medical Sciences, Tehran, Iran

    Nima Rezaei

  5. Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran

    Nima Rezaei

Authors
  1. Fateme Rajabi
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Navid Jabalameli
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Nima Rezaei
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Nima Rezaei .

Editor information

Editors and Affiliations

  1. Research Center for Immunodeficiencies, Children’s Medical Center, Tehran University of Medical Sciences, Tehran, Iran

    Nima Rezaei

  2. Center for Research and Training in Skin Diseases and Leprosy, Tehran University of Medical Sciences, Tehran, Iran

    Fateme Rajabi

Rights and permissions

Reprints and permissions

Copyright information

© 2022 Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Rajabi, F., Jabalameli, N., Rezaei, N. (2022). The Concept of Immunogenetics. In: Rezaei, N., Rajabi, F. (eds) The Immunogenetics of Dermatologic Diseases. Advances in Experimental Medicine and Biology, vol 1367. Springer, Cham. https://doi.org/10.1007/978-3-030-92616-8_1

Download citation

Publish with us

Policies and ethics

Search

Navigation