Comprehensive Genomic Analysis Identifies a Diverse Landscape of Sideroblastic and Nonsideroblastic Iron-Related Anemias with Novel and Pathogenic Variants in an Iron-Deficient Endemic Setting

Abstract

Inherited iron metabolism defects are possibly missed or underdiagnosed in iron-deficient endemic settings due to a lack of awareness or a methodical screening approach. Hence, we planned a systematic evaluation of anemia cases (2019-2021) based on clinical phenotype, normal screening tests (HPLC, alpha gene sequencing, ESR, CRP, tTG), and abnormal iron profile by targeted NGS (26 gene-panel) supplemented with whole exome, MLPA/mtDNA sequencing and CMA. Novel variants in ALAS2, STEAP3, and HSPA9 genes were functionally validated. 290 anemia cases were screened and 41 (14%) enrolled for genomic testing as per inclusion criteria. Comprehensive genomic testing revealed pathogenic variants in 23/41 (56%) cases. Congenital sideroblastic anemia (CSA) was the most common diagnosis (14/23;61%) with pathogenic variations in ALAS2 (6), SLC25A38 (3), HSPA9 (2) and HSCB, SLC19A2 and mtDNA deletion (1 each). Non-sideroblastic iron defects included STEAP3-related microcytic anemia (2/23;8.7%) and hypotransferrenemia (1/23;4.3%). 6/22 (27%) revealed a non-iron metabolism gene defect on whole exome sequencing. A total of 11 novel variants (including VUS) were noted in 13 cases. Genotype-phenotype correlation revealed a significant association of frameshift/nonsense/splice variants with lower presentation age (0.8 months vs. 9 years; p-<0.01) compared to missense variants. The systematic evaluation helped uncover an inherited iron defect in 41% (17/41) cases, suggesting the need for active screening and awareness for these rare diseases in an iron deficient endemic population.