Utilizing Whole-Exome Sequencing to Characterize the Phenotypic Variability of Sickle Cell Disease.
PMID 30183354 | DOI 10.1089/gtmb.2018.0058 · Genetic testing and molecular biomarkers · 2018
BACKGROUND: Sickle cell disease (SCD) is a monogenic disease that has wide variety of phenotypes with both and environmental factors contributing to its severity. METHODS: We performed whole-exome sequencing (WES) in 22 Saudi SCD patients to identify variants that could explain differences in disease phenotypes. All variants, except those that were benign and likely benign, described in the ClinVar database, were considered in our analysis. Gene-based association testing using sequence kernel association optimal unified test (SKAT-O) with small sample adjustment was performed to evaluate the effect of multiple variants in genes on SCD phenotypes. RESULTS: The mean age of participants was 28 (range, 10-48 years). All patients were homozygous for the sickle cell mutation. The Benin haplotype was present in 15 patients and the Arab-Indian haplotype in 7 patients. One patient who had both SCD and CHARGE association was heterozygous for pathogenic mutation p.Arg987Ter in the CHD7 gene. One SCD individual who had a stroke was a carrier of the pathogenic variant p.Asp36Tyr in the VKORC1 gene which is, associated with warfarin resistance. Two patients with steady hemoglobin levels of 7.5 and 7.1 g/dL were carriers of the pathogenic mutation p.Gly140Ser in the RPL5 gene that is associated with Diamond-Blackfan anemia. None of the patients were transfusion dependent. A heterozygous pathogenic mutation in the LDLR gene associated with autosomal dominant familial hypercholesterolemia was present in one patient with deep venous thrombosis, although their cholesterol level was normal. One individual with stroke was a carrier for the p.Arg284Ter variant in the NLRP12 gene, which is associated with familial cold autoinflammatory syndrome 2. Another patient with stroke and a pulmonary embolism was heterozygous for the p.Pro106Leu variant of the MPL gene, which has been associated with thrombocytosis. Coding variants in the GOLGB1, ENPP1, and PON1 genes showed no association with stroke in our study. SKAT-O analysis did not explain SCD heterogeneity. CONCLUSION: WES provided limited information to explain the severity of SCD. Whole genome sequencing, epigenetic studies, and assessment of environmental factors might expand our knowledge of SCD heterogeneity.
Validated evidence
| Type | Entity | Source evidence | Confidence | Extractor |
|---|---|---|---|---|
| gene | CHD7 | “One patient who had both SCD and CHARGE association was heterozygous for pathogenic mutation p.Arg987Ter in the CHD7 gene.” | 0.98 | hgnc_dict_v1 |
| gene | VKORC1 | “One SCD individual who had a stroke was a carrier of the pathogenic variant p.Asp36Tyr in the VKORC1 gene which is, associated with warfarin resistance.” | 0.98 | hgnc_dict_v1 |
| gene | RPL5 | “Two patients with steady hemoglobin levels of 7.5 and 7.1 g/dL were carriers of the pathogenic mutation p.Gly140Ser in the RPL5 gene that is associated with Diamond-Blackfan anemia.” | 0.98 | hgnc_dict_v1 |
| gene | LDLR | “A heterozygous pathogenic mutation in the LDLR gene associated with autosomal dominant familial hypercholesterolemia was present in one patient with deep venous thrombosis, although their cholesterol level was normal.” | 0.98 | hgnc_dict_v1 |
| gene | NLRP12 | “One individual with stroke was a carrier for the p.Arg284Ter variant in the NLRP12 gene, which is associated with familial cold autoinflammatory syndrome 2.” | 0.98 | hgnc_dict_v1 |
| gene | MPL | “Another patient with stroke and a pulmonary embolism was heterozygous for the p.Pro106Leu variant of the MPL gene, which has been associated with thrombocytosis.” | 0.98 | hgnc_dict_v1 |
| gene | GOLGB1 | “Coding variants in the GOLGB1, ENPP1, and PON1 genes showed no association with stroke in our study.” | 0.98 | hgnc_dict_v1 |
| gene | ENPP1 | “Coding variants in the GOLGB1, ENPP1, and PON1 genes showed no association with stroke in our study.” | 0.98 | hgnc_dict_v1 |
| gene | PON1 | “Coding variants in the GOLGB1, ENPP1, and PON1 genes showed no association with stroke in our study.” | 0.98 | hgnc_dict_v1 |
| phenotype | sickle cell disease | “Utilizing Whole-Exome Sequencing to Characterize the Phenotypic Variability of Sickle Cell Disease.” | 0.98 | phenotype_alias_lexicon_v2 |
| phenotype | stroke | “One SCD individual who had a stroke was a carrier of the pathogenic variant p.Asp36Tyr in the VKORC1 gene which is, associated with warfarin resistance.” | 0.98 | phenotype_alias_lexicon_v2 |
| phenotype | familial hypercholesterolemia | “A heterozygous pathogenic mutation in the LDLR gene associated with autosomal dominant familial hypercholesterolemia was present in one patient with deep venous thrombosis, although their cholesterol level was normal.” | 0.98 | phenotype_alias_lexicon_v2 |
| population | Saudi Arabia | “METHODS: We performed whole-exome sequencing (WES) in 22 Saudi SCD patients to identify variants that could explain differences in disease phenotypes.” | 0.95 | saudi_context_rules_v1 |
| variant | p.Arg987Ter | “One patient who had both SCD and CHARGE association was heterozygous for pathogenic mutation p.Arg987Ter in the CHD7 gene.” | 0.95 | hgvs_regex_v1 |
| variant | p.Asp36Tyr | “One SCD individual who had a stroke was a carrier of the pathogenic variant p.Asp36Tyr in the VKORC1 gene which is, associated with warfarin resistance.” | 0.95 | hgvs_regex_v1 |
| variant | p.Gly140Ser | “Two patients with steady hemoglobin levels of 7.5 and 7.1 g/dL were carriers of the pathogenic mutation p.Gly140Ser in the RPL5 gene that is associated with Diamond-Blackfan anemia.” | 0.95 | hgvs_regex_v1 |
| variant | p.Arg284Ter | “One individual with stroke was a carrier for the p.Arg284Ter variant in the NLRP12 gene, which is associated with familial cold autoinflammatory syndrome 2.” | 0.95 | hgvs_regex_v1 |
| variant | p.Pro106Leu | “Another patient with stroke and a pulmonary embolism was heterozygous for the p.Pro106Leu variant of the MPL gene, which has been associated with thrombocytosis.” | 0.95 | hgvs_regex_v1 |