Canadian experience with predictive testing for Huntington disease: lessons for genetic testing centers and policy makers.
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Canada↗
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Results for “Genetic Testing”
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Parent experiences with genetic testing for pediatric hearing loss.
The purpose of the current study was to assess parent perceptions and experiences of genetic testing, as well as barriers for not undergoing testing in a sample of families of children with hearing loss. A 44-item questionnaire, The Parent Perception of Genetic Testing Questionnaire developed by the research study team was administered. Participants were recruited from a pediatric otolaryngology/audiology practice and social media. A total of 146 parents of children with hearing loss participated. Approximately 47.6% of the children in our sample underwent genetic testing, 44.8% did not, and 7.6% of parents were unsure. For those that did not undergo testing, reasons included: unaware (6.2%), not interested (8.9%), cost (8.9%), time (3.4%), fearful of results (2.7%), and never offered (15.1%). For those that did undergo testing, over half of the parents reported that they did not receive counseling before (55.1%) and 41.7% reported they received counseling after the testing. Furthermore, parents were confused about the results with 18.3% reporting they were Very Confused, 28.3% Somewhat Confused, 20% A Little Confused, and 33.3% Not Confused at All about the variant of uncertain or unknown significance. Notably, less than half of parents (43.4%) remembered what they were told about the mode of inheritance. Overall, our study highlighted the low adoption rate of genetic testing and lack of integration into standard of care for otology/audiology practices. Collaboration between hearing healthcare professionals and geneticists is warranted to determine how to reduce barriers to access while improving pre- and post-counseling.
Humans↗
Genetic testing in the workplace: a view from the USA.
Progress in human genetics, accelerated by the Human Genome Project, is leading to a rapid proliferation in the number of genetic tests. Although they have their benefits, genetic tests have in the past been used by various societal institutions, including employers, to discriminate against and stigmatize individuals. In the light of the increase in the number of tests and some current reports of discrimination in employment, a variety of legal and regulatory measures have been proposed to prevent genetic discrimination in the workplace.
Genetic Diseases, Inborn↗
Genetic testing for Huntington's disease.
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Child↗
X-ray-induced specific-locus mutations in the ad-3 region of two-component heterokaryons of Neurospora crassa. II. More extensive genetic tests reveal an unexpectedly high frequency of multiple-locus mutations.
More extensive genetic tests have been performed on a series of 832 X-ray-induced specific-locus mutations in the ad-3 region of a 2-component heterokaryon (H-12) of Neurospora crassa, reported earlier (Webber and de Serres 1965). Using new tester strains and techniques for performing large-scale genetic tests (heterokaryon, dikaryon and trikaryon) to characterize ad-3 mutants induced in 2-component heterokaryons, new data have been obtained on this sample of X-ray-induced ad-3 mutants. These new data show that unexpectedly high frequencies of both single-locus (gene/point) mutations and multilocus deletions in the ad-3 region have additional, but separate, sites of recessive lethal (RLCL) damage in the immediately adjacent genetic regions. The frequencies of these X-ray-induced multiple-locus mutants in the ad-3 region are orders of magnitude higher than expected on the basis of target theory and classical models of chromosome structure during interphase. Current models of interphase chromosome structure in higher eukaryotes as revealed by chromosome "painting" offer a possible explanation of the Neurospora data.
Adenine↗
Use of nucleic acid probes in genetic tests.
Advances in molecular genetics have led to the development of clinical assays for several genetic diseases. Two general testing approaches are available: direct detection of the genetic mutation or indirect detection using DNA markers close to, or within, the defective gene. Direct testing at the nucleic acid level is available for diseases in which the basic defect is well characterized, such as sickle cell anemia. Several methods are available for detection of the point mutation that causes sickle cell anemia including: routine Southern blot analysis, allele specific oligonucleotides, and polymerase chain reaction gene amplification. For diseases such as cystic fibrosis, in which the basic genetic defect has not yet been characterized, an indirect approach is used. This approach relies on linkage analysis using DNA markers close to the genetic defect. Inheritance of the DNA marker is followed through the family. Unlike direct testing, the DNA marker does not detect the actual genetic defect. Therefore, a prediction of inheritance of the linked disease is given based on the risk of recombination between the disease locus and the DNA marker. An appreciation of the differences between the direct and indirect approaches is necessary to understand their attributes and their limitations.
Base Sequence↗
The diffusion of new genetic tests for predicting disease.
This paper examines the pathways by which new genetic tests will become available to the public. In view of the scarcity of genetic specialists, the pathway is likely to involve primary care physicians. Other pathways entail state-mandated testing, community-based programs, or testing by laboratories without much involvement of primary care physicians. When testing does become available the "destination" will be either family-centered testing or population-oriented screening. The deterrent to screening will not be the inability to detect disease-causing mutations but the costs and attitudes of providers and the public. When tests are provided primarily to provide information about risks to future children, some people will oppose screening on religious or moral grounds. When there are no inexpensive treatments, some will fear that insurance companies and employers will use tests to deny them health care coverage. Some may not want to know their risks for disorders about which little can be done. For common, multifactorial disorders, genetic tests will have low predictive value. Because of these problems, the decision to be tested, regardless of the destination, requires that "testees" be fully informed and consent to testing. When acceptance rates are low, screening is less likely to be cost-effective; family-centered testing becomes the default destination.
Genetic Diseases, Inborn↗
Genetic testing for neurologic diseases. A rose with thorns.
Genetic testing for neurologic conditions, including HD, requires that the primary concerns of informed consent, counseling and support, and confidentiality be recognized and addressed. A safe, reliable test should be available to those who want the information and understand the limitations of the testing procedure. However, testing should be in the context of multifaceted counseling, which combines a variety of components. Safeguards for confidentiality should be assured. Predictive testing for hereditary disease emphasizes the need to focus on capabilities rather than disability. This is an extension of the larger reality that continuing advances in health care can extend the length of an individual's life and stave off death without restoring health. Certainly, new developments in molecular biology may provide new tools, but the basic ethical problems are fundamental issues independent of technology. Just as change is not necessarily progress, the application of scientific advances to health care does not automatically benefit humanity. Sensitivity to human needs is the art of applying medical technology.
Ethics, Medical↗
Role and relevance of genetic testing in patients with kidney stones: a review from EAU Section of Endourology.
PURPOSE OF REVIEW: Kidney stones have a high heritability. More than 40 genes have been identified causing monogenic forms of kidney stone disease (KSD). Kidney stone formers with genetic variants implicated in monogenic forms of KSD often suffer from early onset, high recurrence rates, and chronic kidney disease. Some patients may also exhibit extrarenal disease requiring attention. RECENT FINDINGS: Recent analysis of KSD patients identified a likely monogenic cause in pediatric populations in 17-30% of participants while in adult unselected populations 2.7-8% had a positive finding. More patients carry single genetic variants in monogenic forms that are classically considered as autosomal recessive but may cause an intermediate genetic risk for the development of KSD possibly in interaction with environmental or lifestyle factors. Genome-wide association studies have identified additional risk loci associating with KSD. Their clinical relevance are currently investigated. Patients with recurrent kidney stone episodes may be at elevated risk of progressive chronic kidney disease. SUMMARY: Monogenic causes of KSD are prevalent in patients less than 25 years of age and in some patients with high-risk metabolic profiles. These patients should undergo genetic testing to enable a precise molecular genetic diagnosis and personalized therapy as well as family counseling and screening.
Humans↗
IVF patient subgroups benefit from preimplantation genetic testing for aneuploidy: a prospective multicentre cohort study.
RESEARCH QUESTION: Can preimplantation genetic testing for aneuploidy (PGT-A) improve the ongoing pregnancy rate per transfer and reduce miscarriage rate in patients with advanced maternal age (AMA), recurrent implantation failure (RIF), recurrent pregnancy loss (RPL), or both, without affecting cumulative pregnancy rate? DESIGN: Prospective cohort study of 260 patients undergoing PGT-A aged 36 years or over (AMA group), with a history of three or more blastocyst transfers without birth (RIF group), two or more early pregnancy losses (RPL group), or all. Trophectoderm biopsy was conducted day 5 or 6, and comprehensive chromosome screening was used for PGT-A before single frozen embryo transfer (PGT-A-FET). A total of 3060 patients undergoing single conventional frozen embryo transfer (FET) served as a historical reference group. RESULTS: Patients had increased odds of positive serum beta-HCG after PGT-A-FET compared with FET in the AMA (OR 1.53, 95% CI 1.06 to 2.21) and RIF (OR 2.11, 95% CI 1.41 to 3.14) groups. The PGT-A-FET group significantly improved the odds of ongoing pregnancy in the AMA (OR 2.20, 95% CI 1.52 to 3.18), RIF (OR 3.96, 95% CI 2.60 to 6.04) and RPL (OR 2.81, 95% CI 1.52 to 5.21) groups. The odds of pregnancy loss were significantly reduced with PGT-A-FET in the AMA (OR 0.36, 95% CI 0.21 to 0.64), RIF (OR 0.10, 95% CI 0.04 to 0.26) and RPL (OR 0.14, 95% CI 0.04 to 0.53) groups. Cumulative pregnancy rate did not differ between PGT-A and conventional cycles (RR 0.94, 95% CI 0.80 to 1.10). CONCLUSIONS: PGT-A improved the odds of ongoing pregnancy and reduced the odds of pregnancy loss in all groups. The cumulative pregnancy rate did not differ between PGT-A and conventional cycles. Findings should be interpreted in the context of the observational design.
Adult↗
SOD1 Variants in Patients With Amyotrophic Lateral Sclerosis in Central Eastern Europe: From Genetic Testing to SOD1 Targeted Therapy.
BACKGROUND: Amyotrophic lateral sclerosis (ALS) is one of the most devastating fatal motor neuron diseases, characterized by progressive degeneration of motor neurons in the brain and spinal cord. A significant advance in ALS therapy was achieved with the recent European Medicines Agency approval of Tofersen, the first antisense oligonucleotide (ASO) specifically targeting SOD1 mRNA, a key genetic determinant of the disease. Yet, despite its clinical relevance, data on SOD1-ALS in Central Eastern Europe remain scarce. METHODS: Here, we present a multicentric study across six countries-Austria, Czechia, Poland, Hungary, Slovakia, and Slovenia-representing approximately 16% of the European Union's population. We report all pathogenic, likely pathogenic, and uncertain SOD1 variants, along with the phenotypic features, including heritability, age, site of onset, and survival. We also assessed the availability of genetic testing, counseling, and access to Tofersen therapy across the region. RESULTS: Out of 1200 patients with confirmed ALS, we identified 24 distinct pathogenic SOD1 variants in a total of 67 patients (median age at onset 47 [40-55] years), of whom 65.7% had familial ALS (fALS) and 34.3% had sporadic ALS (sALS). We characterized the associated phenotypes and reported that 42 patients are currently receiving Tofersen therapy. CONCLUSION: This study provides the first comprehensive overview of SOD1-ALS in Central Eastern Europe. Our findings underscore the importance of genetic testing and counseling, as well as equitable access to targeted therapies such as Tofersen to advance patient-specific care in this region.
Humans↗
Impact of BRCA1/2 status on young women's sexual function, relationships, and reproduction after predictive genetic testing.
The experiences and outcomes for women identified with a BRCA1/2 pathogenic variant during young adulthood are qualitatively described but not well quantified. This study investigated the impact of BRCA1/2 status on women's reproduction, intimate partner relationships, and sexual functioning. Australian women aged 18-40 years who had predictive BRCA1/2 testing, received either a positive or negative result, and had no personal cancer history, completed an online survey that used a case-control design. Outcome measures included childbearing, use of reproductive technologies, relationship status, and sexual functioning. 579 women participated (62.0% with a BRCA1/2 PV; 38.0% without a BRCA1/2 PV). More women with a BRCA1/2 PV had children compared to those who did not (49.0% c.f., 40.5%; p = 0.045). BRCA1/2 status did not predict whether women were partnered at survey completion (Odds Ratio 1.20; 95% CI 0.80, 1.78) or their sexual functioning over the previous month (β-coefficient -0.08; 95% CI -1.15, 0.98). Women with a BRCA1/2 PV were more likely to have children after genetic testing (OR 1.83: 95% CI 1.05, 3.21) and were more likely to have a greater number of children after genetic testing (β-coefficient 0.41; 95% CI 0.10, 0.73) compared to women without a BRCA1/2 PV, after adjustment for confounders. Receiving a positive predictive BRCA1/2 result is associated with an increased likelihood of childbearing and having a greater number of children compared to receiving a negative predictive BRCA1/2 result. These findings contribute to the evidence base to inform long-term follow-up for women after predictive BRCA1/2 testing.
Humans↗
The role of pathology laboratories in integrating genetic testing into Australian primary care: an implementation science perspective.
As genomic testing moves into mainstream healthcare, non-genetic healthcare professionals, including general practitioners (GPs), play a critical role as gatekeepers to genetic services. Laboratories are essential in supporting this transition by providing not only high-quality genetic tests but also point-of-care tools, educational materials and clinical guidance to support their use. This study aimed to explore how these tools and supports are conceptualized, developed, implemented and evaluated and how laboratories integrate them into their relationships with GPs, an essential process for paving the way toward better use of genomics in primary care. A qualitative study design was employed using semi-structured, in-depth interviews with representatives from genetic laboratories across Australia. The Consolidated Framework for Implementation Research (CFIR) guided deductive content analysis of data. Findings spanned the four CFIR domains (Intervention Characteristics, Outer Setting, Inner Setting and Implementation Process) across 34 constructs. Participants reported that laboratories viewed point-of-care tools and resources as essential responses to persistent genomic knowledge gaps among GPs. Development of evidence-based, practice-driven and adaptable resources was supported and rewarded within laboratory organisations. A strong culture of clinical responsibility and implementation readiness, combined with robust networks and communications, enabled timely support for GPs. Gaps identified included lack of implementation planning, misalignments between laboratory-developed resources and GPs' real-world needs and inadequate mechanisms for obtaining GPs' feedback, which made evaluation problematic. By applying an implementation science framework, these findings provide insights for future efforts to build and sustain the provision of point-of-care tools and support, ultimately improving the integration of genomics in primary care.
Journal Article↗
Prenatal genetic testing and screening: constructing needs and reinforcing inequities.
This Article considers the influence and implications of the application of genetic technologies to definitions of disease and to the treatment of illness. The concept of "geneticization" is introduced to emphasize the dominant discourse in today's stories of health and disease and the social construction of biological phenomenon is described. The reassurance, choice and control supposedly provided by prenatal genetic testing and screening are critically examined, and their role in constructing the need for such technology is addressed. Using the stories told about prenatal diagnosis as a focus, the consequences of a genetic perspective for and on women and their health care needs are explored.
Abortion, Induced↗
The "genetic test request": A genomic stewardship intervention for inpatient exome and genome orders at a tertiary pediatric hospital.
PURPOSE: Exome sequencing (ES) and genome sequencing (GS) are useful tests to diagnose rare diseases in pediatric patients in critical care settings. Genomic test stewardship can increase the appropriate use of these tests leading to improved diagnostics and cost savings. METHODS: A mandatory review of ES and GS orders for admitted patients was implemented in March 2023. Outcomes of the reviews, cost analysis, and subsequent test results through February 2024 were analyzed with descriptive statistics. RESULTS: There were 444 genetic test request orders placed for 412 unique patients. Of these, 81 (18.2%) were redirected and 57 (12.8%) required modification after approval, leading to an overall cost savings of $345,821.00 or $778.88 per order. The combined diagnostic rate was 28.2% in this patient population. CONCLUSION: Stewardship of ES/GS orders for pediatric inpatients is an effective tool to improve the appropriate usage of these genomic tests. Additional collaboration with stakeholders and expansion of genomic stewardship initiatives may shorten the diagnostic odyssey for critically ill pediatric patients and result in cost savings.
Humans↗
The importance of integrating genetic testing into reproductive medicine: a retrospective observational study investigating the monogenic causes of human infertility in couples considering ICSI.
The genetic landscape of human infertility is complex with diverse etiologies. Identifying the underlying etiology is crucial for guiding reproductive decisions and improving management for infertile couples. Here, we aim to report on the molecular spectrum of monogenic genetic causes of reproductive failure. Over a 3-year period, we recruited all infertile couples considering assisted reproductive technologies (ART) for whom the underlying genetic cause had been identified, in either partner, using exome sequencing (ES). Clinical data of all participants along with their hormonal profiles, sonographic findings and spermograms were recorded. The study included 50 couples with primary infertility. Clinically, male factor infertility was documented in 26 patients, female factor infertility in 10, while reproductive failure was unexplained in the remaining 14 couples. All participating couples had potentially disease-causing variants in infertility genes. ES identified variants related to male infertility in 26 men, while variants in female infertility-related genes were detected in the remaining couples (n = 24). According to ACMG classification criteria, 78% (39/50) of couples harbored pathogenic/likely pathogenic (P/LP) variants, whereas 22% (11/50) carried variants of uncertain significance (VUS). In view of the identified genetic etiologies, the cohort was stratified into two groups based on the predicted reproductive outcome: (1) couples with significantly impaired reproductive potential, and (2) couples who can have biological children using appropriate medical interventions. However, classifications involving VUS were interpreted cautiously and considered exploratory. This study provides further evidence for the molecular heterogeneity of human infertility and highlights the usefulness of genetic testing for infertile couples pursuing ARTs.
Humans↗
Accurate identification of abnormal ploidy using an artificial intelligence model in preimplantation genetic testing.
STUDY QUESTION: Can ultra-low-coverage whole-genome sequencing (ulc-WGS) accurately identify abnormal ploidy during preimplantation genetic testing (PGT)? SUMMARY ANSWER: The artificial intelligence (AI)-based PGT-Plus model demonstrates high accuracy in ploidy detection, offering a cost-effective solution that enhances clinical utility of PGT. WHAT IS KNOWN ALREADY: The predominant PGT for aneuploidy can identify chromosomal aneuploidies but cannot determine ploidy status. Transferring embryos with ploidy abnormalities can result in miscarriage and molar pregnancy. On the other hand, in ART, fertilization is assessed by morphological pronuclear assessment at the zygote stage. However, it has a low specificity in the prediction of abnormal ploidy status and embryos deemed abnormally fertilized can yield healthy pregnancies. Accurately identified abnormal ploidy in PGT-A can resolve current limitations and expand the utility range of PGT-A. Several studies have identified ploidy abnormalities; however, they were mainly based on single-nucleotide polymorphism (SNP) arrays or needed to combine additional targeted-next-generation sequencing (NGS) information. Studies based on ulc-WGS remain scarce. STUDY DESIGN SIZE DURATION: The study consisted of two stages: methodology establishment and validation. An AI model, named PGT-Plus, was developed using 653 samples with known ploidy status, which was further validated using 792 different ploidy status samples. In the clinical application stage, the approach was used to analyse the ploidy status of 19 103 normally fertilized PGT blastocysts and 140 single pronucleus (1PN)-derived blastocysts collected between May 2022 and December 2023. All blastocysts were tested using trophectoderm biopsy and NGS. PARTICIPANTS/MATERIALS SETTING METHODS: The methodology is based on the ulc-WGS data. First, based on samples with known ploidy status: the heterozygosity rate of high-frequency biallelic SNPs, the likelihood ratio (LLR) of alleles was calculated under different assumptions ('both parental homologs' [BPH] from a single parent, 'single parental homolog' [SPH] from each parent, disomy, and monosomy) by leveraging allele frequencies and linkage disequilibrium (LD) measured in the 1000 genomes project database. Twenty-three continuous candidate features derived from heterozygosity rates and LLRs of chromosomes or selected windows were included to establish the ploidy prediction AI model. Gini importance analysis and multicollinearity mitigation was performed for feature selection, then the performance of Random Forest (RF), Support Vector Machine (SVM), and Logistic Regression for modelling was compared. Subsequently, the parameter optimization was performed based on the RF model. Ploidy constitution concordance was evaluated in known ploidy status samples. The frequency of abnormal ploidy in normal fertilized PGT blastocysts and 1PN-derived blastocysts (including conventional IVF and ICSI) was evaluated. MAIN RESULTS AND THE ROLE OF CHANCE: Eleven features were collected for model architecture compared to SVM and Logistic Regression; RF achieved superior performance for ploidy detection. The AI model achieved an AUC of 1 for genome-wide-uniparental diploidy (GW-UPD), 1 for triploidy, and 0.99 for diploidy. For the 792 validation samples, 99.5% of samples were successfully detected using the AI model, and the model showed 100% accuracy for ploidy classification. In the clinical application stage, out of 19 103 PGT samples, 19 069 were successfully analysed using the model, with 110 (0.57%) identified as having abnormal ploidy embryos. Among these, 12.7% (14/110) were identified as GW-UPD, and 87.3% (96/110) were triploid. Among 5563 diploid blastocysts transferred, 3478 clinical pregnancies were achieved. Subsequent ploidy analysis was performed for 217 spontaneous abortion and 935 prenatal diagnostic samples, and no abnormal ploidy was identified. Furthermore, of the 140 1PN embryos tested, 40 (28.6%) exhibited GW-UPD, 3 (2.1%) exhibited triploidy, and 97 (69.3%) were determined to be biparental and normally fertilized. Among the 97 biparental embryos, 46 were diploid, 11 were mosaic, and 40 were aneuploid. In terms of the insemination pattern, the percentage of abnormal ploidy in ICSI was significantly higher than in conventional IVF (P < 0.01, 37.1% vs. 2.9%, respectively). With full informed consent, 20 patients without euploidy from normal fertilization chose 1PN-derived biparental and diploid blastocysts to transfer, resulting in 10 clinical pregnancies and 9 ongoing pregnancies. LARGE-SCALE DATA: N/A. LIMITATIONS REASONS FOR CAUTION: Some rare ploidy abnormalities, such as polyploidy with an equal number of identical sets of chromosomes and ploidy mosaicism cannot be accurately identified. Moreover, the origin of abnormal ploidy was not identified due to the unavailability of DNA from both parents. WIDER IMPLICATIONS OF THE FINDINGS: The PGT-Plus AI model provides a ploidy evaluation method based on the conventional PGT-A data and integrates directly into standard PGT-A workflows. Clinical utility results suggest that the model is a valuable tool for identifying embryos with abnormal ploidy in PGT-A and rescuing normal diploid embryos from abnormally fertilized embryos. These findings demonstrate that PGT-Plus significantly enhances the diagnostic accuracy of PGT. STUDY FUNDING/COMPETING INTERESTS: This study was supported by grants from Major Scientific Program of CITIC Group (No. 2023ZXKYB34100, to Ge.L.), Hunan Provincial Grant for Innovative Province Construction (2019SK4012), Hunan Xiangjiang New District (Changsha High-tech Zone) key core technology research project in 2023, and Science Foundation of Hunan Province (Grant 2023JJ30422). All authors declared no conflicts of interest..
artificial intelligence↗
Paired Exome-Based Comprehensive Genomic Profiling and Germline Genetic Testing for Unselected Patients With Colorectal Cancer in a Multicenter Prospective Study.
BACKGROUND AND AIMS: Comprehensive genomic profiling (CGP) for tumors and germline genetic testing (GGT) inform precision therapy and clinical management of patients with colorectal cancer (CRC), and evidence is growing in support of universal paired CGP-GGT patient testing. However, the utility of combining CGP and GGT for early-stage CRC (ESC) and early-onset CRC (EOC) is unclear. METHODS: We performed a prospective, multisite study featuring GGT using an 80+ gene next-generation sequencing platform and exome-based CGP among CRC patients (unselected for age, stage, family history) receiving care at Mayo Clinic Cancer Centers between April 1, 2018, and March 31, 2020. RESULTS: A total of 150 CRC patients had GGT and exome-based CGP performed. ESC patients had an enrichment of high microsatellite instability and high tumor mutation burden. High microsatellite instability was also enriched in those with smoking history, and in tumors with mutated BRAF, homologous recombination deficiency, or at least 1 variant in the rat sarcoma virus pathway. Moreover, patients with smoking history were enriched in BRAF and other Tier 1 or 2 variants overall. Sixteen percent of patients harbored a pathogenic germline variant, most frequent being in Lynch syndrome genes. Paired GGT and CGP testing had high rates of clinically significant findings (≈70%) with the most frequent being high tumor mutation burden status. Pathway and mutational signature analysis revealed frequent CGP mutations in DNA repair and cell cycle pathways. CONCLUSION: These data suggest that universal, combined GGT-CGP increases clinical utility for EOC and ESC patients. This is key for EOC patients who tend to experience poorer outcomes. CGP-GGT expedites germline resolution for tumor mutations in hereditary cancer genes, reducing delays and facilitating identification of relevant therapies, clinical trials, and management recommendations.
Colorectal Cancer↗