Identification of pathogenic variants in the Brazilian cohort with Familial hypercholesterolemia using exon-targeted gene sequencing

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Borges, Jessica Bassani ; Oliveira, Victor Fernandes ; Dagli-Hernandez, Carolina ; Ferreira, Glaucio Monteiro ; Barbosa, Thais Kristini Almendros Afonso ; Marcal, Elisangela da Silva Rodrigues ; Los, Bruna ; Malaquias, Vanessa Barbosa ; Bortolin, Raul Hernandes ; Freitas, Renata Caroline Costa ; Mori, Augusto Akira ; Bastos, Gisele Medeiros ; Goncalves, Rodrigo Marques ; Araujo, Daniel Branco ; Zatz, Henry ; Bertolami, Adriana ; Faludi, Andre Arpad ; Bertolami, Marcelo Chiara ; Souza, Amanda Guerra de Moraes Rego ; Franca, Joao Italo Dias ; Thurow, Helena Strelow ; Hirata, Thiago Dominguez Crespo ; Nakaya, Helder Takashi Imoto ; Jannes, Cinthia Elim ; Pereira, Alexandre da Costa ; Silbiger, Vivian Nogueira ; Luchessi, Andre Ducati ; Araujo, Jessica Nayara Goes ; Nakazone, Marcelo Arruda ; Carmo, Tayanne Silva ; Souza, Doroteia Rossi Silva ; Moriel, Patricia ; Wang, Jaqueline Yu Ting ; Naslavsky, Michel Satya ; Gorjao, Renata ; Pithon-Curi, Tania Cristina ; Curio, Rui ; Fajardo, Cristina Moreno ; Wang, Hui-Tzu Lin ; Garofalo, Adriana Regina ; Cerda, Alvaro ; Sampaio, Marcelo Ferraz ; Hirata, Rosario Dominguez Crespo ; Hirata, Mario Hiroyuki

• Document type: Journal article
• Source: Gene; v. 875, p. 10-pg., 2023-05-26.

Abstract

Familial hypercholesterolemia (FH) is a monogenic disease characterized by high plasma low-density lipoprotein cholesterol (LDL-c) levels and increased risk of premature atherosclerotic cardiovascular disease. Mutations in FH-related genes account for 40% of FH cases worldwide. In this study, we aimed to assess the pathogenic variants in FH-related genes in the Brazilian FH cohort FHBGEP using exon-targeted gene sequencing (ETGS) strategy. FH patients (n = 210) were enrolled at five clinical sites and peripheral blood samples were obtained for laboratory testing and genomic DNA extraction. ETGS was performed using MiSeq platform (Illumina). To identify deleterious variants in LDLR, APOB, PCSK9, and LDLRAP1, the long-reads were subjected to Burrows -Wheeler Aligner (BWA) for alignment and mapping, followed by variant calling using Genome Analysis Tool -kit (GATK) and ANNOVAR for variant annotation. The variants were further filtered using in-house custom scripts and classified according to the American College Medical Genetics and Genomics (ACMG) guidelines. A total of 174 variants were identified including 85 missense, 3 stop-gain, 9 splice-site, 6 InDel, and 71 in regu-latory regions (3 & PRIME;UTR and 5 & PRIME;UTR). Fifty-two patients (24.7%) had 30 known pathogenic or likely pathogenic variants in FH-related genes according to the American College Medical and Genetics and Genomics guidelines. Fifty-three known variants were classified as benign, or likely benign and 87 known variants have shown un-certain significance. Four novel variants were discovered and classified as such due to their absence in existing databases. In conclusion, ETGS and in silico prediction studies are useful tools for screening deleterious variants and identification of novel variants in FH-related genes, they also contribute to the molecular diagnosis in the FHBGEP cohort. (AU)

• FAPESP's process: 16/12899-6 - Genomics, epigenomics and pharmacogenomics characterization of familial hypercholesterolemia in the Brazilian population
• Grantee: Mario Hiroyuki Hirata
• Support Opportunities: Research Projects - Thematic Grants