Mapping the genetic landscape of treatable inherited metabolic disorders in a large Middle Eastern biobank.

BACKGROUND: To date, approximately 1,400 inherited metabolic disorders (IMDs) have been described, some of which are treatable. It is estimated that 2-3% of live births worldwide are affected by treatable IMDs. Roughly 80% of IMDs are autosomal recessive, leading to a potentially higher incidence in regions with high consanguinity. METHODOLOGY: The study utilized genome sequencing (GS) data from 14,060 adult Qatari participants who were recruited by the Qatar Biobank (QBB) and sequenced by the Qatar Genome Program (QGP). The GS data was analysed for 125 nuclear genes known to be associated with 115 treatable IMDs. RESULTS: Our study identified 253 pathogenic/likely pathogenic SNVs associated with 69 treatable IMDs, including 211 known and 42 novel predicted loss-of-function variants. We estimated that approximately 1 in 13 unrelated individuals (8%) carry a heterozygous pathogenic variant for at least one of 46 treatable IMDs. Notably, phenylketonuria/hyperphenylalaninemia and homocystinuria had among the highest carrier frequencies (1 in 68 and 1 in 85, respectively). CONCLUSION: Population-based studies of treatable IMDs, particularly in globally under-studied populations, can identify high-frequency alleles segregating in the community and inform public health policies, including carrier and newborn screening.

Release of reclassified VUS results of now deceased patients to family members: Practices and opinions.

Variants of uncertain significance (VUS) are commonly identified in genetic testing. The rate at which a VUS is reclassified depends on multiple factors. However, as the amount of time it might take for a VUS to be reclassified varies, some patients with a VUS genetic testing result might have passed away before the VUS is reclassified. A VUS that is reclassified after the patient's death has clinical implications for the deceased patient's family members. The disclosure of reclassified VUS results for a deceased patient has complex legal and ethical implications. There are no established guidelines on how the reclassified VUS result for a deceased patient should be disclosed to at-risk relatives. An online survey was sent to members of the National Society of Genetic Counselors (NSGCs) to elicit practices and opinions regarding this issue. A total of 153 (4%) NSGC members completed the survey. Thirty-seven (24.2%) respondents reported having received a reclassified VUS for a deceased patient. Respondents were more likely to attempt disclosure if the variant was reclassified as pathogenic (93.5%) versus benign (76.5%), although the difference did not reach statistical significance (p = 0.06). Respondents more often reported the impact on family members (85.5%) than the decedent's right to privacy (15.0%) as extremely important when considering disclosure to family members. A legal mechanism to allow disclosure to relatives was supported by 70.6% of respondents and 97.4% felt the issue was important enough to pursue if such a process was in place. Only 9.8% of respondents supported a legal requirement of consent before disclosing to family members when a VUS is reclassified after the patient has passed away. Our results indicate that there is no consensus for how these results should be handled and a mechanism for disclosure of reclassified results to family members is supported.

Identification of Spliceogenic Variants beyond Canonical GT-AG Splice Sites in Hereditary Cancer Genes.

Pathogenic/likely pathogenic variants in susceptibility genes that interrupt RNA splicing are a well-documented mechanism of hereditary cancer syndromes development. However, if RNA studies are not performed, most of the variants beyond the canonical GT-AG splice site are characterized as variants of uncertain significance (VUS). To decrease the VUS burden, we have bioinformatically evaluated all novel VUS detected in 732 consecutive patients tested in the routine genetic counseling process. Twelve VUS that were predicted to cause splicing defects were selected for mRNA analysis. Here, we report a functional characterization of 12 variants located beyond the first two intronic nucleotides using RNAseq in APC, ATM, FH, LZTR1, MSH6, PALB2, RAD51C, and TP53 genes. Based on the analysis of mRNA, we have successfully reclassified 50% of investigated variants. 25% of variants were downgraded to likely benign, whereas 25% were upgraded to likely pathogenic leading to improved clinical management of the patient and the family members.

Genetic counselors' practices and confidence regarding variant of uncertain significance results and reclassification from BRCA testing.

Studies indicate variant of uncertain significance (VUS) results are challenging for genetic counselors and patients, often resulting in negative patient outcomes. Genetic counselors' current practices regarding VUS are unknown. This study utilized a national survey of genetic counselors (n = 932) to examine current practices and confidence related to disclosing BRCA VUS results and reclassification information. For participants (n = 398), descriptive statistics were calculated regarding patient demographic characteristics, practices and confidence, and cross tabulation was used to identify participant's actions when receiving a reclassified VUS. Upon receiving a BRCA VUS report, the majority reported providing patients with information about the frequency with which their VUS was seen and patient ancestry, but a minority discussed DNA banking. Most were confident in their understanding of, and ability to explain, VUS results to patients, but felt less confident about achieving high levels of patient understanding. Upon reclassification, the majority reported calling the patient and mailing the results, but when the reclassification was deleterious, the majority also met with the patient face-to-face. Given the lack of standard professional guidelines about informing patients of initial and reclassified VUS results, this overview provides important insight into genetic counselors' current practices and confidence.

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 ß-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.

From the laboratory to the clinic: sharing BRCA VUS reclassification tools with practicing genetics professionals.

Despite ongoing research efforts to reclassify BRCA variant of uncertain significance (VUS), results for strategies to disseminate findings to genetic counselors are lacking. We disseminated results from a study on reclassification of BRCA VUS using a mailed reclassification packet including a reclassification guide, patient education aid, and patient letter template for patients/families with BRCA VUS. This study reports on genetic counselors' responses to the dissemination materials. Eligible participants (n = 1015) were identified using mailing lists from professional genetics organizations. Participants were mailed a BRCA VUS reclassification packet and a return postcard to assess responses to the materials. Closed-ended responses were analyzed using descriptive statistics, and thematic analysis was conducted on open-ended responses. In response to the mailing, 128 (13.0%) genetic counselors completed and returned postcards. The majority of respondents (n = 117; 91.4%) requested the patient letter template and patient education guides as PDFs (n = 122; 95.3%). The majority (n = 123; 96.9%) wanted an updated reclassification guide upon availability. Open-ended responses demonstrate the material was well-received; some specified they would tailor the patient letter to fit their practice and patients' needs. Participants requested additional patient and provider educational materials for use in practice. Materials communicating BRCA VUS reclassification updates were liked and were likely to be used in practice. To achieve the benefits of VUS reclassification in clinical practice, ongoing efforts are needed to continuously and effectively disseminate findings to providers and patients.