Diamond-Blackfan Anemia and Bone Marrow Failure via the RPS7 Gene

Diamond-Blackfan anemia (DBA) is a rare, inherited bone marrow failure syndrome characterized by macrocytic anemia, normal leukocyte and platelet numbers, and normocellular bone marrow (Freedman. 2000. PubMed ID: 11030041; Gazda and Sieff. 2006. PubMed ID: 16942586). Physical anomalies such as craniofacial dysmorphism, thumb and neck anomalies, congenital heart defects, and genitourinary tract defects are found in ~40% of patients. Growth retardation is observed in ~30% of patients (Clinton and Gazda. 2016. PubMed ID: 20301769). Onset of hematologic complications typically occurs in the first year of life. The severity of disease varies from mild anemia with no physical anomalies to severe anemia and severe physical anomalies. DBA is also associated with bone marrow failure and increased risk for myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML).

DBA is an autosomal dominant or X-linked disorder caused by inactivating variants within ribosomal protein genes RPS19 (Gazda and Sieff. 2006. PubMed ID: 16942586), RPL5 (Gazda et al. 2008. PubMed ID: 19061985), RPL11 (Gazda et al. 2008. PubMed ID: 19061985), RPL35a (Farrar et al. 2008. PubMed ID: 18535205), RPS26 (Doherty et al. 2010. PubMed ID: 20116044), RPS24 (Gazda et al. 2006. PubMed ID: 17186470), RPS17 (Gazda et al. 2008. PubMed ID: 19061985), RPS7 (Gazda et al. 2008. PubMed ID: 19061985), RPS10 (Doherty et al. 2010. PubMed ID: 20116044), RPL26 (Gazda et al. 2012. PubMed ID: 22431104), RPS27 (Wang et al. 2015. PubMed ID: 25424902), RPS29 (Mirabello et al. 2014. PubMed ID: 24829207), RPL31 (Farrar et al. 2014. PubMed ID: 25042156), RPS28 (Gripp et al. 2014. PubMed ID: 24942156), RPL15 (Landowski et al. 2013. PubMed ID: 23812780), RPL27 (Wang et al. 2015. PubMed ID: 25424902), or by variants in the GATA1 (Sankaran et al. 2012. PubMed ID: 22706301) or TSR2 (Gripp et al. 2014. PubMed ID: 24942156) genes. Variants in the RPS19 gene are found in up to 25% of patients (Gazda and Sieff. 2006. PubMed ID: 16942586). Variants in the RPL5 (6.6%), RPS26 (6.4%), RPL11 (4.8%), RPL35A (3%), RPS10 (2.6%), RPS24 (2%), and RPS17 (1%) genes are the next most frequent causes of DBA with variants in all other associated genes accounting for a very small fraction of disease (Clinton and Gazda. 2016. PubMed ID: 20301769). Approximately 65% of DBA cases are found to have a pathogenic variant in one of the DBA genes (Clinton and Gazda. 2016. PubMed ID: 20301769). 55-60% of DBA cases result from de novo pathogenic variants (Clinton and Gazda. 2016. PubMed ID: 20301769) with the remainder of cases resulting from inheritance of a pathogenic variant from an affected parent.

DBA results from loss of protein function and haploinsufficiency. Pathogenic variants consist primarily of missense variants and nonsense or other protein truncating variants including frameshift deletions and insertions. Large, multi-exon or full gene deletions of several ribosomal protein genes, in particular RPS19, RPL5, RPL11, RPL35A, RPS26, RPS24, RPS17, and RPL15, have been reported in patients with DBA. Dysfunctional ribosomal proteins are likely to alter the stability and/or function of the ribosomal complex causing destruction of blood-forming cells in the bone marrow and consequent anemia.

Similar to RPS24 gene variants, variants in RPS7 were shown to result in higher levels of 45S and 30S pre-rRNAs in patients (Gazda et al. 2008. PubMed ID: 19061985). Experiments in HeLa cells also indicated a defect in 5’ external transcribed spacer (ETS) processing (Gazda et al. 2008. PubMed ID: 19061985). Also similar to RPS24, splicing variants or small insertions/deletions affecting splice sites are the most frequent types of pathogenic variants reported for the RPS7 gene.

Other bone marrow failure syndromes such as Fanconi anemia, severe congenital neutropenia, dyskeratosis congenital, and Shwachman-Diamond syndrome should be considered in addition to DBA during diagnosis.

Approximately 65% of Diamond-Blackfan anemia (DBA) cases are found to have a pathogenic variant in one of the DBA genes (Clinton and Gazda. 2016. PubMed ID: 20301769). Variants in the RPS19 gene are found in up to 25% of patients (Gazda and Sieff. 2006. PubMed ID: 16942586). Variants in the RPL5 (6.6%), RPS26 (6.4%), RPL11 (4.8%), RPL35A (3%), RPS10 (2.6%), RPS24 (2%), and RPS17 (1%) genes are the next most frequent causes of DBA, with variants in all other associated genes accounting for a very small fraction of disease (Clinton and Gazda. 2016. PubMed ID: 20301769).

This test provides full coverage of all coding exons of the RPS7 gene plus 10 bases of flanking noncoding DNA in all available transcripts along with other non-coding regions in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere. We define full coverage as >20X NGS reads or Sanger sequencing. PGnome panels typically provide slightly increased coverage over the PGxome equivalent. PGnome sequencing panels have the added benefit of additional analysis and reporting of deep intronic regions (where applicable).

Dependent on the sequencing backbone selected for this testing, discounted reflex testing to any other similar backbone-based test is available (i.e., PGxome panel to whole PGxome; PGnome panel to whole PGnome).