Screening for Tay‐Sachs disease carriers by full‐exon sequencing with novel variant interpretation outperforms enzyme testing in a pan‐ethnic cohort

Background Pathogenic variants in HEXA that impair β‐hexosaminidase A (Hex A) enzyme activity cause Tay‐Sachs Disease (TSD), a severe autosomal‐recessive neurodegenerative disorder. Hex A enzyme analysis demonstrates near‐zero activity in patients affected with TSD and can also identify carriers, wh...

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Published in:	Molecular genetics & genomic medicine Vol. 7; no. 8; pp. 1 - 12
Main Authors:	Cecchi, Alana C., Vengoechea, Elizabeth S., Kaseniit, Kristjan E., Hardy, Melanie W., Kiger, Laura A., Mehta, Nikita, Haque, Imran S., Moyer, Krista, Page, Patricia Z., Muzzey, Dale, Grinzaid, Karen A.
Format:	Journal Article
Language:	English
Published:	United States John Wiley & Sons, Inc 01-08-2019 John Wiley and Sons Inc Wiley
Subjects:	beta-Hexosaminidase alpha Chain - genetics Biological evolution carrier screening Cohort Studies Deoxyribonucleic acid Disease DNA Enzymatic activity Enzyme activity Enzyme Assays - standards Enzymes Ethnic Groups - genetics Ethnicity False Negative Reactions False Positive Reactions Genetic Carrier Screening - methods Genetic Carrier Screening - standards Genetic Counseling - methods Genetic Counseling - standards Genetic screening Hereditary diseases Heterozygote HEXA enzyme testing High-Throughput Nucleotide Sequencing - standards Humans Minority & ethnic groups Mutation Neurodegenerative diseases Original Polymorphism, Single Nucleotide Population Population genetics Practice Guidelines as Topic Reclassification Retrospective Studies Screening Sensitivity Sensitivity and Specificity Tay-Sachs Disease - diagnosis Tay-Sachs Disease - genetics Tay‐Sachs disease variant interpretation VUS reclassification Womens health United States > US HEXA enzyme testing Tay-Sachs disease carrier screening VUS reclassification variant interpretation
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Summary:	Background Pathogenic variants in HEXA that impair β‐hexosaminidase A (Hex A) enzyme activity cause Tay‐Sachs Disease (TSD), a severe autosomal‐recessive neurodegenerative disorder. Hex A enzyme analysis demonstrates near‐zero activity in patients affected with TSD and can also identify carriers, whose single functional copy of HEXA results in reduced enzyme activity relative to noncarriers. Although enzyme testing has been optimized and widely used for carrier screening in Ashkenazi Jewish (AJ) individuals, it has unproven sensitivity and specificity in a pan‐ethnic population. The ability to detect HEXA variants via DNA analysis has evolved from limited targeting of a few ethnicity‐specific variants to next‐generation sequencing (NGS) of the entire coding region coupled with interpretation of any discovered novel variants. Methods We combined results of enzyme testing, retrospective computational analysis, and variant reclassification to estimate the respective clinical performance of TSD screening via enzyme analysis and NGS. We maximized NGS accuracy by reclassifying variants of uncertain significance and compared to the maximum performance of enzyme analysis estimated by calculating ethnicity‐specific frequencies of variants known to yield false‐positive or false‐negative enzyme results (e.g., pseudodeficiency and B1 alleles). Results In both AJ and non‐AJ populations, the estimated clinical sensitivity, specificity, and positive predictive value were higher by NGS than by enzyme testing. The differences were significant for all comparisons except for AJ clinical sensitivity, where NGS exceeded enzyme testing, but not significantly. Conclusions Our results suggest that performance of an NGS‐based TSD carrier screen that interrogates the entire coding region and employs novel variant interpretation exceeds that of Hex A enzyme testing, warranting a reconsideration of existing guidelines. Clinical test performance of sequencing‐based HEXA carrier screening matches or exceeds that of enzyme‐based HexA screening. The top panel indicates the population‐specific HEXA carrier rate estimated from NGS data. The bottom panel shows the clinical sensitivity, specificity, and positive predictive values of sequencing‐ and enzyme‐based HEXA carrier screening. The sensitivity and specificity of sequencing‐based carrier screening are reduced by potentially incorrect variant classifications, while enzyme‐based carrier screening has false negatives due to the B1 allele and false positives due to pseudodeficiency alleles.
Bibliography:	ObjectType-Article-2 SourceType-Scholarly Journals-1 ObjectType-Undefined-1 ObjectType-Feature-3 content type line 23 Alana C. Cecchi, Elizabeth S. Vengoechea, and Kristjan E. Kaseniit contributed equally. Melanie W. Hardy, Laura A. Kiger, and Nikita Mehta contributed equally. Dale Muzzey and Karen A. Grinzaid contributed equally.
ISSN:	2324-9269 2324-9269
DOI:	10.1002/mgg3.836