Molecular characterisation of sickle cell disease and classification of major haplotypes associated with the β-globin cluster (HBB gene) by means of SNP marker sequencing in a group of samples from Bolívar, Colombia

References

• Abdalla Elsayed MEA, Mura M, Al Dhibi H, Schellini S, Malik R, Kozak I, Schatz P. 2019. Sickle cell retinopathy. A focused review. Graefes Arch Clin Exp Ophthalmol. 257(7):1–13. doi: 10.1007/s00417-019-04294-2.
   PubMed Web of Science ®Google Scholar
• Adekile A, Akbulut-Jeradi N, Al Khaldi R, Fernandez MJ, Sukumaran J. 2021. Diagnosis of SCD and HBB haplotyping in the era of personalized medicine: role of next generation sequencing. J Pers Med. 11(6):454. doi: 10.3390/jpm11060454.
   PubMed Web of Science ®Google Scholar
• Aghajani F, Mahdavi MR, Kosaryan M, Mahdavi M, Hamidi M, Jalali H. 2016. Identification of β-globin haplotypes linked to sickle haemoglobin (Hb S) alleles in Mazandaran province, Iran. Genes Genet Syst. 91(6):311–313. doi: 10.1266/ggs.16-00005.
   PubMed Web of Science ®Google Scholar
• Aguilera-Díaz MM. 2006. El Canal del Dique y su subregión: una economía basada en la riqueza hídrica (PDF). Documentos de trabajo sobre economía regional. Banco de la República, CEER, Cartagena, p. 1692-3715. https://web.archive.org/web/20111105200007/http://www.banrep.gov.co/documentos/publicaciones/regional/documentos/DTSER-72%20%28VE%29.pdf.
   Google Scholar
• Alvarado-Ortega M, editor. 2001. Canal del Dique. Plan de restauración ambiental (1a etapa). Barranquilla: Uninorte, p. 12.
   Google Scholar
• Alvear C, Barboza M, Alayón AN, Viola M, Araque LM. 2012. Pilot study of haemoglobinopathies in newborns of the Rafael Calvo maternity clinic of Cartagena, Colombia. Colomb Med. 43:197–198.
   Web of Science ®Google Scholar
• Ansari-Pour N, Moñino Y, Duque C, Gallego N, Bedoya G, Thomas MG, Bradman N. 2016. Palenque de San Basilio in Colombia: genetic data support an oral history of a paternal ancestry in Congo. Proc Biol Sci. 283(1827):20152980. doi: 10.1098/rspb.2015.2980.
   PubMed Web of Science ®Google Scholar
• Bender MA. 2019. Sickle cell disease. Department of Pediatrics, University of Washington, Fred Hutchinson Cancer Research Center, Seattle, Washington (USA). National Organization for Rare Disorders (NORD), Inc. https://rarediseases.org/rarediseases/sickle-cell-disease.
   Google Scholar
• Bernal M, Collazos A, Bonilla RD, Tascón EP. 2010. Determination of the prevalence of haemoglobin S, C, D, and G in neonates from Buenaventura. Colomb Med. 41:141–147.
   Web of Science ®Google Scholar
• Bernal MDP, Giraldo A, Bermudez AJ, Moreno E. 1995. Estudio de la frecuencia de hemoglobinopatías en las islas de San Andrés y Providencia. Biomedica. 15(1):5–9. doi: 10.7705/biomedica.v15i1.850.
   Google Scholar
• Centers for Disease Control and Prevention (CDC). 2015. Hemoglobinopathies: current practices for screening, confirmation and follow-up. Association of Public Health Laboratories, US Dept of Health, and Human Services. 57. p.
   Google Scholar
• Coneo-Mendoza Y, López-Pineda LF, Barraza-Pava ME, Sáenz-Zapata JA. 2014. La Subregión del Canal del Dique: un mar de Necesidades en un océano de riqueza. Colombia: CEDEC. Primera edición. ©Cámara de Comercio de Cartagena; p. 328.
   Google Scholar
• Cruz PRS, Ananina G, Gil-da-Silva-Lopes VL, Simioni M, Menaa F, Bezerra MAC, Domingos IF, Araújo AS, Pellegrino R, Hakonarson H, et al. 2019. Genetic comparison of sickle cell anaemia cohorts from Brazil and the United States reveals high levels of divergence. Sci Rep. 9(1):10896. doi: 10.1038/s41598-019-47313-2.
   PubMedGoogle Scholar
• Cuéllar-Ambrosi F, Mondragón MC, Figueroa M, Préhu C, Galactéros F, Ruiz-Linares A. 2000. Sickle cell anaemia and beta-globin gene cluster haplotypes in Colombia. Haemoglobin. 24(3):221–225. doi: 10.3109/03630260008997529.
   PubMed Web of Science ®Google Scholar
• dbSNP Short Genetic Variations. 2022. National Center of Biotechnology Information (NCBI), U.S. National Library of Medicine. Available from: https://www.ncbi.nlm.nih.gov/SNP
   Google Scholar
• Díaz-Matallana M, Gómez Gutiérrez A, Briceño I, Rodríguez Cuenca JV. 2016. Genetic analysis of Paleo-Colombians from Nemocón, Cundinamarca provides insights on the early peopling of northwestern South America. Rev Acad Colomb Cienc Ex Fis Nat. 40(156):461–483. doi: 10.18257/raccefyn.328.
   Google Scholar
• Díaz-Matallana M, Márquez-Benítez Y, Martínez-Lozano JC, Briceño I, Benavides-Benítez E, Bernal JE. 2021. Anemia falciforme: una revisión sobre el genotipo de la enfermedad, haplotipos, diagnóstico y estudios asociados. Rev Méd Chile. 149(9):1322–1329. doi: 10.4067/S0034-98872021000901322.
   PubMedGoogle Scholar
• Díaz-Matallana M, Martínez-Cruzado JC. 2010. Estudios sobre ADN mitocondrial sugieren un linaje predominante en la Cordillera Oriental de Colombia y un vínculo suramericano para los arcaicos de Puerto Rico. Univ Med. 51(3):241–272. doi: 10.11144/Javeriana.umed51-3.esam.
   Google Scholar
• Díaz-Matallana M. 2015. Caracterización Genética de un grupo Paleoamericano Checua proveniente de Nemocón-Cundinamarca, Colombia: implicaciones para el Poblamiento Temprano de Suramérica [Tesis Ph.D]. Bogotá (DC): Ciencias Biológicas, Pontificia Universidad Javeriana.
   Google Scholar
• Durán CL, Morales OL, Echeverri SJ, Isaza M. 2012. Haplotipos del gen de la globina beta en portadores de hemoglobina S en Colombia. Biomédica. 32:103–111.
   PubMedGoogle Scholar
• El-Hazmi MAF, Warsy AS, Bashir N, Beshlawi A, Hussain IR, Temtamy S, Qubaili F. 1999. Haplotypes of the β-globin gene as prognostic factors in SCD. East Mediterr Health J. 5(6):1254–1258. doi: 10.26719/1999.5.6.1154.
   Google Scholar
• EMA – European Medicines Agency. 2023. First gene editing therapy to treat beta thalassemia and severe sickle cell disease [cited 2023 Dec 15]. www.ema.europa.eu.
   Google Scholar
• Fatima SS, Mussaed EM. 2015. Gene sequencing and SNP analysis of rs334 of beta haemoglobin involved in sickle cell anemia. Helix. 2:645–647.
   Google Scholar
• FDA – U.S. Food and Drug Administration. 2023. FDA approves first gene therapies to treat patients with sickle cell disease [cited 2023 Dec 8]. https://www.fda.gov/news-events/press-announcements/fda-approves-first-gene-therapies-treat-patients-sickle-cell-disease.
   Google Scholar
• Figueiredo MS, Silva MCBO, Guerreiro JF, Souza GP, Pires ACR, Zago MA. 1994. The heterogeneity of the βS cluster haplotypes in Brazil. Gene Geogr. 8:7–12.
   PubMedGoogle Scholar
• Fong C, Lizarralde-Iragorri MA, Rojas-Gallardo D, Barreto G. 2013. Frequency and origin of haplotypes associated with the beta-globin gene cluster in individuals with trait and sickle cell anemia in the Atlantic and Pacific coastal regions of Colombia. Genet Mol Biol. 36(4):494–497. doi: 10.1590/S1415-47572013000400005.
   PubMed Web of Science ®Google Scholar
• Fong C, Menzel S, Lizarralde MA, Barreto G. 2015. Genetic variants associated with fetal hemoglobin levels show the diverse ethnic origin in Colombian patients with sickle cell anemia. Biomedica. 35(3):437–443. doi: 10.7705/biomedica.v35i3.2573.
   PubMed Web of Science ®Google Scholar
• GE Healthcare. 2010. Whatman Application Note-28-9822-22AA.
   Google Scholar
• Gómez-Gutérrez A, Casas-Gómez C. 2014. Interpretación Clínica del Laboratorio. Bogotá: Editorial Médica Panamericana. p. 846.
   Google Scholar
• Gomez A, Kurf B. 2018. Chapter 5. Genetic testing techniques – Sanger sequencing. In: Robin NH, Farmer MB, editors. Pediatric cancer genetics. Canada: Elsevier; p. 47–64. https://www.sciencedirect.com/science/article/abs/pii/B9780323485555000053.
   Google Scholar
• Hanchard N, Elzein A, Trafford C, Rockett K, Pinder M, Jallow M, Harding R, Kwiatkowski D, McKenzie C. 2007. Classical sickle beta-globin haplotypes exhibit a high degree of long-range haplotype similarity in African and Afro-Caribbean populations. BMC Genet. 8(1):52. doi: 10.1186/1471-2156-8-52.
   PubMedGoogle Scholar
• Ibarra-Cortés B, Guzmán LF, Perea-Díaz FJ. 2019. Anexo IV. Anemia drepanocítica. In: del Castillo-Ruiz V, Uranga-Hernández RD, Zafra de la Rosa G. Genética Clínica. 2nd ed. México (DF): Manual Moderno; p. 651.
   Google Scholar
• Jiménez-Cobo C, Sebastián- Pérez E, Sevilla-Navarro J. 2021. Hemoglobinopatías: talasemia y drepanocitosis. Pediatría Integral. 25 (5):241.e1–241.e13.
   Google Scholar
• Joutovsky A, Hadzi-Nesic J, Nardi MA. 2004. HPLC retention time as a diagnostic tool for hemoglobin variants and hemoglobinopathies: a study of 60,000 samples in a clinical diagnostic laboratory. Clin Chem. 50(10):1736–1747. doi: 10.1373/clinchem.2004.034991.
   PubMed Web of Science ®Google Scholar
• Lettre G. 2012. The search for genetic modifiers of disease severity in the β-hemoglobinopathies. Cold Spring Harb Perspect Med. 2(10):a015032. doi: 10.1101/cshperspect.a015032.
   PubMed Web of Science ®Google Scholar
• Lucena-Giraldo M. 2017. “Una obra digna de romanos”: El Canal del Dique, desde su apertura hasta la independencia. Expediente sobre el Canal del Dique (1647-63). Archivo General de Indias, AGI, Santa Fe, 199. https://www.banrepcultural.org/biblioteca-virtual/credencial-historia/numero-287/una-obra-digna-de-romanos-el-canal-del-dique-apertura-independencia.
   Google Scholar
• Lyra IM, Gonçalves MS, Pellegriinei JA, Gesteira M, Carvalho MH, Olalla ST, Figueiredo MS, Costa FF. 2005. Clinical, haematological, and molecular characterization of sickle cell anemia pediatric patients from two different cities in Brazil. Cad Saúde Pública. 21:1287–1290.
   Google Scholar
• MaxStat. 2015. MaxStat Lite v.3.60 program (Jever-OT Cleverns, Germany). Available from: https://maxstatlite.en.softonic.com/
   Google Scholar
• Medline Plus. 2023. Glucose-6-Phosphate dehydrogenase deficiency. Bethesda (MD): National Library of Medicine – NIH. Last Updated April 12, 2023. https://medlineplus.gov/genetics/condition/glucose-6-phosphate-dehydrogenase-deficiency/.
   Google Scholar
• Middleton D, Williams F, Meenagh A, Daar AS, Gorodezky C, Hammond M, Nascimento E, Briceno I, Perez MP. 2000. Analysis of the distribution of HLA-A alleles in populations from five continents. Hum Immunol. 61(10):1048–1052. doi: 10.1016/s0198-8859(00)00178-6.
   PubMed Web of Science ®Google Scholar
• Moreno N, Martínez JA, Blanco Z, Osorio L, Hackshaw P. 2002. Beta-globin gene cluster haplotypes in Venezuelan sickle cell patients from the state of Aragua. Genet Mol Biol. 25(1):21–34. doi: 10.1590/S1415-47572002000100005.
   Web of Science ®Google Scholar
• Muniz A, Corral L, Alaez C, Svarch E, Espinosa E, Carbonell N, di Leo R, Felicetti L, Nagel RL, Martinez G. 1995. Sickle cell anemia and beta-gene cluster haplotypes in Cuba. Am J Hematol. 49(2):163–164. doi: 10.1002/ajh.2830490212.
   PubMed Web of Science ®Google Scholar
• Muñiz A, Puig A, Cabrera M, Fernández J, Martínez G. 2000. Marcadores genéticos en pacientes con anemia drepanocítica de la provincia de Cienfuegos: haplotipos del bloque α y β - talasemia. Rev Cubana Hematol Inmunol Hemoter. 16:142–144.
   Google Scholar
• National Center of Biotechnology Information (NCBI). 2022. dbSNP SHORT GENETIC VARIATIONS. U.S. National Library of Medicine. https://www.ncbi.nlm.nih.gov/SNP.
   Google Scholar
• Navarrete MC. 2005. Génesis y Desarrollo de la Esclavitud en Colombia: siglo XVI y XVII. Cali: Programa Editorial Universidad del Valle; p. 377.
   Google Scholar
• Noguera MC, Schwegler A, Gomes V, Briceño I, Alvarez L, Uricoechea D, Amorim A, Benavides E, Silvera C, Charris M, et al. 2014. Colombia’s racial crucible: Y chromosome evidence from six admixed communities in the Department of Bolivar. Ann Hum Biol. 41(5):453–459. doi: 10.3109/03014460.2013.852244.
   PubMed Web of Science ®Google Scholar
• Old JM. 2003. Screening and genetic diagnosis of haemoglobin disorders. Blood Rev. 17(1):43–53. doi: 10.1016/s0268-960x(02)00061-9.
   PubMed Web of Science ®Google Scholar
• OMIM Database. 2022. Sickle cell anemia. Johns Hopkins University. https://www.omim.org/entry/603903?search=sickle%20cell%20anemia&highlight=cell%20anemia%20anaemia%20sickle
   Google Scholar
• OpenSNP. 2023. https://opensnp.org/.
   Google Scholar
• Orphanet. 2021. The portal for rare diseases and orphan drugs. Sickle cell anemia. https://www.orpha.net/consor/cgi-bin/index.php?lng=EN.
   Google Scholar
• Ortega DC, Fong C, Cárdenas H, Barreto G. 2015. Evidence of over-dominance for sickle cell trait in a population sample from Buenaventura, Colombia. Int J Genet Mol Biol. 7(1):1–7. doi: 10.5897/IJGMB2014.0106.
   Google Scholar
• Powars DR, Chan L, Schroeder WA. 1990. Beta S-gene-cluster haplotypes in sickle cell anemia: clinical implications. Am J Pediatr Hematol Oncol. 12(3):367–374. doi: 10.1097/00043426-199023000-00022.
   PubMedGoogle Scholar
• Rihet P, Flori L, Tall F, Traore AS, Fumoux F. 2004. Haemoglobin C is associated with reduced Plasmodium falciparum parasitemia and low risk of mild malaria attack. Hum Mol Genet. 13(1):1–6. doi: 10.1093/hmg/ddh002.
   PubMed Web of Science ®Google Scholar
• Romero-Sánchez C, Gómez Gutiérrez A, Duarte Y, Amazo C, Manosalva C, Chila M L, Casas-Gómez MC, Briceño Balcázar I. 2015. Variantes de hemoglobina en una población con impresión diagnóstica positiva para hemoglobinopatías en Colombia. Rev Med Chil. 143(10):1260–1268. doi: 10.4067/S0034-98872015001000004.
   PubMedGoogle Scholar
• Rosero MJ, Bermúdez AJ. 2012. Análisis de hemoglobinopatías en regiones afrocolombianas usando muestras de sangre seca de cordón umbilical. Acta Médica Colombiana. 37(3):118–124.
   Google Scholar
• Ruiz-Morales AJ, Gómez-Restrepo C. 2015. Epidemiología Clínica, Investigación Clínica Aplicada. 2nd ed. Bogotá (DC): Editorial Médica Panamericana. p. 625.
   Google Scholar
• Rusanova I, Cossio G, Moreno B, Javier Perea F, De Borace RG, Perea M, Escames G, Acuña-Castroviejo D. 2011. β-globin gene cluster haplotypes in sickle cell patients from Panamá. Am J Hum Biol. 23(3):377–380. doi: 10.1002/ajhb.21148.
   PubMed Web of Science ®Google Scholar
• Sambrook J, Russell DW. 2001. Molecular cloning A laboratory manual. Vol. 1. 3rd ed. New York: Cold Spring Harbor Laboratory Press.
   Google Scholar
• Schaefer GB, Thompson JN. 2016. Genética Médica, Un Enfoque Integrado. México (DF): McGraw-Hill Interamericana; p. 372.
   Google Scholar
• Schwegler A. 2012. Sobre el origen africano de la lengua criolla de Palenque (Colombia). Much augmented Spanish version of ‘‘Palenque(ro): the search for its African substrate’’, Schwegler 2011 above. In: Maglia G, Schwegler A, editors. Palenque (Colombia): oralidad, identidad y resistencia. Un enfoque interdisciplinario. Bogotá: Instituto Caro y Cuervo & Universidad Javeriana; p. 107–179.
   Google Scholar
• Shaikho EM, Farrell JJ, Alsultan A, Qutub H, Al-Ali AK, Figueiredo MS, Chui DHK, Farrer LA, Murphy GJ, Mostoslavsky G, et al. 2017. A phased SNP-based classification of sickle cell anemia HBB haplotypes. BMC Genomics. 18(1):608. doi: 10.1186/s12864-017-4013-y.
   PubMedGoogle Scholar
• Shriner D, Rotimi C. 2018. Whole-genome-sequence-based haplotypes reveal single origin of the sickle allele during the holocene wet phase. Am J Hum Genet. 102(4):547–556. doi: 10.1016/j.ajhg.2018.02.003.
   PubMed Web of Science ®Google Scholar
• SNPedia. 2022–2023. https://www.snpedia.com/
   Google Scholar
• Thein SL, Menzel S. 2009. Discovering the genetics underlying foetal haemoglobin production in adults. Br J Haematol. 145(4):455–467. doi: 10.1111/j.1365-2141.2009.07650.x.
   PubMed Web of Science ®Google Scholar
• Tripathi P. 2022. Genetics of thalassemia. In: Rajashekaraiah V. The ­erythrocyte – A unique cell. IntechOpen. doi: 10.5772/intechopen.106748.
   Google Scholar
• UNESCO. 1992–2023. Cultural Space of Palenque de San Basilio. https://ich.unesco.org/en/RL/cultural-space-of-palenque-de-san-basilio-00102.
   Google Scholar
• Varela I, Sequera A, Olivero R. 2013. Detección de hemoglobinopatías en recién nacidos del Hospital Materno Infantil “Dr. José María Vargas” de la ciudad de Valencia, Venezuela. Salud Online. 17(2):6–12.
   Google Scholar
• Wong C. 2023. UK is first nation to approve CRISPR therapy for diseases. Landmark decision could transform the treatment of sickle-cell disease and β-Thalassaemia. Nature. 623(7988):676–677. 23/11/2023). doi: 10.1038/d41586-023-03590-6.
   PubMedGoogle Scholar
• Yunis JJ, Yunis EJ. 2013. Mitochondrial (mtDNA) haplogroups in 1526 unrelated individuals from 11 Departments of Colombia. Genet Mol Biol. 36(3):329–335. doi: 10.1590/S1415-47572013000300005.
   PubMed Web of Science ®Google Scholar