SELAdb: A database of exonic variants in a Brazilian population referred to a quaternary medical center in Sao Paulo

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dc.contributorSistema FMUSP-HC: Faculdade de Medicina da Universidade de São Paulo (FMUSP) e Hospital das Clínicas da FMUSP
dc.contributor.authorLERARIO, Antonio Marcondes
dc.contributor.authorMOHAN, Dipika R.
dc.contributor.authorMONTENEGRO, Luciana Ribeiro
dc.contributor.authorFUNARI, Mariana Ferreira de Assis
dc.contributor.authorNISHI, Mirian Yumie
dc.contributor.authorNARCIZO, Amanda de Moraes
dc.contributor.authorBENEDETTI, Anna Flavia Figueredo
dc.contributor.authorOBA-SHINJO, Sueli Mieko
dc.contributor.authorVITORINO, Aurelio Jose
dc.contributor.authorSANTOS, Rogerio Alexandre Scripnic Xavier dos
dc.contributor.authorJORGE, Alexander Augusto de Lima
dc.contributor.authorONUCHIC, Luiz Fernando
dc.contributor.authorMARIE, Suely Kazue Nagahashi
dc.contributor.authorMENDONCA, Berenice Bilharinho
dc.date.accessioned2020-10-15T14:30:52Z
dc.date.available2020-10-15T14:30:52Z
dc.date.issued2020
dc.description.abstractOBJECTIVES: High-throughput sequencing of genomes, exomes, and disease-focused gene panels is becoming increasingly common for molecular diagnostics. However, identifying a single clinically relevant pathogenic variant among thousands of genetic polymorphisms is a challenging task. Publicly available genomic databases are useful resources to filter out common genetic variants present in the population and enable the identification of each disease-causing variant. Based on our experience applying these technologies at Hospital das Clinicas da Faculdade de Medicina da Universidade de Sao Paulo (HCFMUSP), Sao Paulo, Brazil, we recognized that the Brazilian population is not adequately represented in widely available genomic databases. METHODS: Here, we took advantage of our 5-year experience as a high-throughput sequencing core facility focused on individuals with putative genetic disorders to build a genomic database that may serve as a more accurate reference for our patient population: SELAdb. RESULTS/CONCLUSIONS: Currently, our database comprises a final cohort of 523 unrelated individuals, including patients or family members managed by different clinics of HCFMUSP. We compared SELAdb with other publicly available genomic databases and demonstrated that this population is very heterogeneous, largely resembling Latin American individuals of mixed origin, rather than individuals of pure European ancestry. Interestingly, exclusively through SELAdb, we identified a spectrum of known and potentially novel pathogenic variants in genes associated with highly penetrant Mendelian disorders, illustrating that pathogenic variants circulating in the Brazilian population that is treated in our clinics are underrepresented in other population databases. SELAdb is freely available for public consultation at: http://intranet.fm.usp.br/selaeng
dc.description.indexMEDLINEeng
dc.description.sponsorshipFundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP)Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP) [2013/02162-8, 2014/50137-5]
dc.identifier.citationCLINICS, v.75, article ID e1913, 9p, 2020
dc.identifier.doi10.6061/clinics/2020/e1913
dc.identifier.eissn1980-5322
dc.identifier.issn1807-5932
dc.identifier.urihttps://observatorio.fm.usp.br/handle/OPI/37667
dc.language.isoeng
dc.publisherHOSPITAL CLINICAS, UNIV SAO PAULOeng
dc.relation.ispartofClinics
dc.rightsopenAccesseng
dc.rights.holderCopyright HOSPITAL CLINICAS, UNIV SAO PAULOeng
dc.subjectNext Generation Sequencingeng
dc.subjectDatabaseeng
dc.subjectMendelian Disorderseng
dc.subjectBrazileng
dc.subjectPopulation Geneticseng
dc.subject.otherhomozygous 1-bp deletioneng
dc.subject.othermutationeng
dc.subject.otherassociationeng
dc.subject.otherprogrameng
dc.subject.othergenomeeng
dc.subject.othergeneeng
dc.subject.wosMedicine, General & Internaleng
dc.titleSELAdb: A database of exonic variants in a Brazilian population referred to a quaternary medical center in Sao Pauloeng
dc.typearticleeng
dc.type.categoryoriginal articleeng
dc.type.versionpublishedVersioneng
dspace.entity.typePublication
hcfmusp.affiliation.countryEstados Unidos
hcfmusp.affiliation.countryisous
hcfmusp.author.externalMOHAN, Dipika R.:Univ Michigan, Med Scientist Training Program, Ann Arbor, MI 48109 USA; Univ Michigan, Doctoral Program Canc Biol, Ann Arbor, MI 48109 USA
hcfmusp.citation.scopus15
hcfmusp.contributor.author-fmusphcANTONIO MARCONDES LERARIO
hcfmusp.contributor.author-fmusphcLUCIANA RIBEIRO MONTENEGRO
hcfmusp.contributor.author-fmusphcMARIANA FERREIRA DE ASSIS FUNARI
hcfmusp.contributor.author-fmusphcMIRIAN YUMIE NISHI
hcfmusp.contributor.author-fmusphcAMANDA DE MORAES NARCIZO
hcfmusp.contributor.author-fmusphcANNA FLAVIA FIGUEREDO BENEDETTI
hcfmusp.contributor.author-fmusphcSUELI MIEKO OBA SHINJO
hcfmusp.contributor.author-fmusphcAURELIO JOSE VITORINO
hcfmusp.contributor.author-fmusphcROGERIO ALEXANDRE SCRIPNIC XAVIER DOS SANTOS
hcfmusp.contributor.author-fmusphcALEXANDER AUGUSTO DE LIMA JORGE
hcfmusp.contributor.author-fmusphcLUIZ FERNANDO ONUCHIC
hcfmusp.contributor.author-fmusphcSUELY KAZUE NAGAHASHI MARIE
hcfmusp.contributor.author-fmusphcBERENICE BILHARINHO DE MENDONCA
hcfmusp.description.articlenumbere1913
hcfmusp.description.volume75
hcfmusp.origemWOS
hcfmusp.origem.pubmed32785571
hcfmusp.origem.scieloSCIELO:S1807-59322020000100260
hcfmusp.origem.scopus2-s2.0-85089408282
hcfmusp.origem.wosWOS:000562144000001
hcfmusp.publisher.citySAO PAULOeng
hcfmusp.publisher.countryBRAZILeng
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