Variant classification is negatively impacted by the absence of biochemical data in published patient reports
Clinical Genetics and Therapeutics
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Primary Categories:
- Clinical Genetics
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Secondary Categories:
- Clinical Genetics
Introduction:
Phenylketonuria (PKU) is a rare genetic disorder causing a deficiency in the enzyme phenylalanine hydroxylase (PAH). If untreated, PKU patients experience an excess of phenylalanine in the blood, resulting in intellectual disability and other neurological consequences. Criteria for diagnosing PKU include plasma phenylalanine concentration consistently greater than 120 µmol/L and genetic confirmation of disease-causing variants in the PAH gene.
Methods:
Evidence from citing literature references was automatically extracted using the Mastermind Genomic Intelligence Platform for the PAH gene and subject to semi-automated curation followed by manual expert review to catalog genetic variants and biochemical values for classification according to the ACMG/AMP criteria. To identify and stratify PKU cases from the literature, 66 different terms were used to capture all possible diagnoses, which were subsequently stratified by disease severity.
Results:
A total of 13,800 PKU patients were collected from 490 literature sources, 53 study locations, and 115 ethnicities. Among these patients, a total of 1611 unique PAH variants including 575 P/LP variants and 706 VUS were identified. The most recurrently encountered variants were p.Arg408Trp (3,142 patients), c.1066-11G>A (1,446), p.Arg261Gln (1,156), and p.Arg243Gln (1,122) and were all designated as pathogenic. Whereas every one of these patients had PAH variants, values for plasma phenylalanine concentration levels were reported for only 5053 (37%) among whom 99% had levels above the diagnostic threshold of 120 µmol/L demonstrating a consistency in application of biochemical diagnostic criteria. However for the majority of these patients, functional studies are absent. Because of this lack of functional evidence, the ability to make likely pathogenic or pathogenic designations for the associated variants is delimited. Specifically, only 723 (54%) PAH variants in this dataset had phenylalanine values reported in the literature. However, 100% of variants with a biochemical threshold reported in the literature had at least one value that met the threshold strongly suggesting that patient-associated variants are likely to have functional studies demonstrating the deleterious effects on protein function if tested. Excluding the cohort of patients without biochemical data from the variant assessment results in 46% of the PAH variants likely being downgraded with VUS variants and their classification particularly impacted by the lack of biochemical information accompanying clinical reports in the literature (53% VUS downgrades) as compared to 32% pathogenic variant downgrades.
Conclusion:
Classification of PAH variants is significantly impacted by the extent of reported biochemical values. Only 37% of PKU patients in literature had a reported value for plasma phenylalanine concentration levels and only 46% of PAH variants had associated functional studies. PAH variants without biochemical data that might undergo classification downgrades could have a large impact on carrier screening for individuals with biochemical results that are near the threshold.
Phenylketonuria (PKU) is a rare genetic disorder causing a deficiency in the enzyme phenylalanine hydroxylase (PAH). If untreated, PKU patients experience an excess of phenylalanine in the blood, resulting in intellectual disability and other neurological consequences. Criteria for diagnosing PKU include plasma phenylalanine concentration consistently greater than 120 µmol/L and genetic confirmation of disease-causing variants in the PAH gene.
Methods:
Evidence from citing literature references was automatically extracted using the Mastermind Genomic Intelligence Platform for the PAH gene and subject to semi-automated curation followed by manual expert review to catalog genetic variants and biochemical values for classification according to the ACMG/AMP criteria. To identify and stratify PKU cases from the literature, 66 different terms were used to capture all possible diagnoses, which were subsequently stratified by disease severity.
Results:
A total of 13,800 PKU patients were collected from 490 literature sources, 53 study locations, and 115 ethnicities. Among these patients, a total of 1611 unique PAH variants including 575 P/LP variants and 706 VUS were identified. The most recurrently encountered variants were p.Arg408Trp (3,142 patients), c.1066-11G>A (1,446), p.Arg261Gln (1,156), and p.Arg243Gln (1,122) and were all designated as pathogenic. Whereas every one of these patients had PAH variants, values for plasma phenylalanine concentration levels were reported for only 5053 (37%) among whom 99% had levels above the diagnostic threshold of 120 µmol/L demonstrating a consistency in application of biochemical diagnostic criteria. However for the majority of these patients, functional studies are absent. Because of this lack of functional evidence, the ability to make likely pathogenic or pathogenic designations for the associated variants is delimited. Specifically, only 723 (54%) PAH variants in this dataset had phenylalanine values reported in the literature. However, 100% of variants with a biochemical threshold reported in the literature had at least one value that met the threshold strongly suggesting that patient-associated variants are likely to have functional studies demonstrating the deleterious effects on protein function if tested. Excluding the cohort of patients without biochemical data from the variant assessment results in 46% of the PAH variants likely being downgraded with VUS variants and their classification particularly impacted by the lack of biochemical information accompanying clinical reports in the literature (53% VUS downgrades) as compared to 32% pathogenic variant downgrades.
Conclusion:
Classification of PAH variants is significantly impacted by the extent of reported biochemical values. Only 37% of PKU patients in literature had a reported value for plasma phenylalanine concentration levels and only 46% of PAH variants had associated functional studies. PAH variants without biochemical data that might undergo classification downgrades could have a large impact on carrier screening for individuals with biochemical results that are near the threshold.