Challenges Of Genetic Testing Research Articles

VAV1 Gene Mutation in a Patient with NMOSD: Practical Challenges of Genetic Testing in an Autoimmune Neurology Clinic

VAV1 Gene Mutation in a Patient with NMOSD: Practical Challenges of Genetic Testing in an Autoimmune Neurology Clinic

Retinal Proteome Profiling of Inherited Retinal Degeneration Across Three Different Mouse Models Suggests Common Drug Targets in Retinitis Pigmentosa

Inherited retinal degenerations (IRDs) are a leading cause of blindness among the population of young people in the developed world. Approximately half of IRDs initially manifest as gradual loss of night vision and visual fields, characteristic of retinitis pigmentosa (RP). Due to challenges in genetic testing, and the large heterogeneity of mutations underlying RP, targeted gene therapies are an impractical largescale solution in the foreseeable future. For this reason, identifying key pathophysiological pathways in IRDs that could be targets for mutation-agnostic and disease-modifying therapies (DMTs) is warranted. In this study, we investigated the retinal proteome of three distinct IRD mouse models, in comparison to sex- and age-matched wild-type mice. Specifically, we used the Pde6βRd10 (rd10) and RhoP23H/WT (P23H) mouse models of autosomal recessive and autosomal dominant RP, respectively, as well as the Rpe65-/- mouse model of Leber´s congenital amaurosis type 2 (LCA2). The mice were housed at two distinct institutions and analyzed using LC-MS in three separate facilities/instruments following data-dependent and data-independent acquisition modes. This cross-institutional and multi-methodological approach signifies the reliability and reproducibility of the results. The largescale profiling of the retinal proteome, coupled with in vivo electroretinography recordings, provided us with a reliable basis for comparing the disease phenotypes and severity. Despite evident inflammation, cellular stress, and downscaled phototransduction observed consistently across all three models, the underlying pathologies of RP and LCA2 displayed many differences, sharing only four general KEGG pathways. The opposite is true for the two RP models in which we identify remarkable convergence in proteomic phenotype even though the mechanism of primary rod death in rd10 and P23H mice is different. Our data highlights the cAMP and cGMP second-messenger signaling pathways as potential targets for therapeutic intervention. The proteomic data is curated and made publicly available, facilitating the discovery of universal therapeutic targets for RP.

Perspectives on sperm donor anonymity: insights from donor-conceived adults in Belgium.

Are donor-conceived adults in Belgium interested in obtaining donor information, and do these interests vary based on their family backgrounds? Donor-conceived adults express a significant interest in obtaining donor-related information, with the highest interest reported by offspring from heterosexual couples compared to those from lesbian couple-parented or single-parent families. In Belgium, sperm donation is mainly anonymous, but the rise of direct-to-consumer genetic testing challenges this anonymity. This was a cross-sectional study involving an online nationwide survey conducted from July 2022 to October 2023. Participants, aged 18years and older and being aware of their anonymous sperm donor-conceived status, were recruited through various channels. A total of 203 participants were included: 62.6% grew up in heterosexual families with infertile fathers, 26.1% with lesbian couples, 8.4% with single parents, and 3.0% in various or diverse family structures. The survey was available in both French and Dutch and consisted of 43 questions, including a mix of yes/no questions and multiple-choice items. The average age of disclosure was 16.5 years, with notably later disclosure in heterosexual couple-parented households. A substantial 82.8% of donor-conceived individuals expressed a keen interest in obtaining non-personally identifiable donor information, while 69% were curious about personally identifiable donor data. Furthermore, 61.6% conveyed a desire for personal contact with their donors, and 26.6% advocated for the inclusion of the donor's name on their birth certificates. Participants raised in lesbian two-parent families exhibited the lowest level of interest in donor-related information compared with those raised in other family structures. An overwhelming 90.1% wondered about the possibility of having half-siblings from the same sperm donor. Analysis of survey responses on DNA database registration revealed that 55.2% of donor-conceived offspring were already registered, with 68.8% discovering the same donor offspring and 30.4% successfully locating their donors. Compared to individuals from other family structures, those raised in heterosexual couple-parented households exhibit a less positive attitude toward their conception through anonymous sperm donation. About 61.6% of donor-conceived individuals reported experiencing distinct emotions compared to their peers, while 44.1% encountered psychological difficulties related to anonymous sperm donation, primarily attributed to late disclosure. The majority supported the idea of informing the donor about the number of children he facilitated to conceive. Lastly, the study highlighted that 21.2% of donor-conceived adults considered becoming donors themselves, and 31.3% expressed willingness to use an anonymous donor whenever faced with fertility challenges. Our sample size may not fully represent all adults conceived through anonymous sperm donation in Belgium. Participation bias may have influenced the results, especially due to the overrepresentation of participants from heterosexual couples. Additionally, an association exists between individuals raised by heterosexual couples and late disclosure, complicating the analysis by introducing a confounding factor. The findings of this study contribute to a better understanding of the needs and preferences of donor-conceived adults, with significant potential impact on patient education and healthcare policy. Study funding was not obtained for this research. There are no conflicts of interest to disclose. N/A.

Misclassification of a frequent variant from PMS2CL pseudogene as a PMS2 loss of function variant in Brazilian patients.

PMS2, a Lynch Syndrome gene, presents challenges in genetic testing due to the existence of multiple pseudogenes. This study aims to describe a series of cases harboring a variant in the PMS2CL pseudogene that has been incorrectly assigned to PMS2 with different nomenclatures. We reviewed data from 647 Brazilian patients who underwent multigene genetic testing at a single center to identify those harboring the PMS2 V1:c.2186_2187delTC or V2:c.2182_2184delACTinsG variants, allegedly located at PMS2 exon 13. Gene-specific PCR and transcript sequencing was performed. Among the 647 individuals, 1.8% (12) carried the investigated variants, with variant allele frequencies ranging from 15 to 34%. By visually inspecting the alignments, we confirmed that both V1 and V2 represented the same variant and through gene-specific PCR and PMS2 transcript analysis, we demonstrated that V1/V2 is actually located in the PMS2CL pseudogene. Genomic databases (ExAC and gnomAD) report an incidence of 2.5 - 5.3% of this variant in the African population. Currently, V1 is classified as "uncertain significance" and V2 as "conflicting" in ClinVar, with several laboratories classifying them as "pathogenic". We identified a frequent African PMS2CL variant in the Brazilian population that is misclassified as a PMS2 variant. It is likely that V1/V2 have been erroneously assigned to PMS2 in several manuscripts and by clinical laboratories, underscoring a disparity-induced matter. Considering the limitations of short-read NGS differentiating between certain regions of PMS2 and PMS2CL, using complementary methodologies is imperative to provide an accurate diagnosis.

Current practices and challenges in genetic testing and counseling for women with breast and ovarian cancer in Asia.

This study assesses current practices and challenges in genetic testing and counseling (GT and C) for breast cancer gene (BRCA)1/2 mutations in Asia, considering the increased risk of ovarian cancer (OC) and breast cancer (BC) in women carrying these mutations. Insights were gathered through a questionnaire from breast surgeons, gynecologists, oncologists, and genetic clinicians in 10 Asian countries: Thailand, Hong Kong, South Korea, India, Vietnam, Malaysia, the Philippines, Taiwan, Singapore, and Indonesia. The questionnaire covered their knowledge, attitudes, and practices in GT and C for BRCA1/2 mutations, along with information on perceived gaps and unmet needs in the region. A total of 61 specialists participated in the survey. GT and C for BRCA1/2 mutations were less frequently offered in Asia compared to Western countries. Among the guidelines used, the National Comprehensive Cancer Network (NCCN) guidelines alone or in combination with other guidelines (American Society of Clinical Oncology [ASCO], National Institute for Health and Clinical Excellence [NICE], and European Society for Medical Oncology [ESMO]) were preferred for both BC and OC. Limited access to genetic counselors posed a significant challenge, resulting in delayed or no GT. Pretest genetic counseling was provided by the respondents themselves. Germline testing was preferred for BC, whereas both germline and somatic testing were preferred for OC, with the most preferred option being a multipanel germline test. Disparities exist in GT and C practices between Asian and Western countries. To address this, steps, such as patient and doctor education, increased accessibility and affordability of GT and C services, and improved infrastructure for identifying gene mutations, should be taken.

Understanding Challenges of Genetic Testing on Neuromuscular Disorders from the Parental Lens.

Neuromuscular disorders, characterized by progressive muscle degeneration and weakness, present substantial challenges to both affected individuals and their families. Genetic testing assumes a pivotal role in facilitating early diagnosis, intervention, treatment, and informed family planning for these conditions. The objective of this qualitative study is to delve into the knowledge, awareness, and perceptions surrounding genetic testing within the cohort of parents caring for individuals with neuromuscular disorders in Malaysia. A semi-structured interview approach was employed to elicit data from parents of individuals diagnosed with neuromuscular disorders, encompassing those with clinical diagnoses and those diagnosed through genetic testing. Examination of the interview responses yielded nine overarching themes, which furnish invaluable insights into the perspectives of Malaysian parents concerning genetic testing. The study discerned several challenges associated with genetic testing, notably encompassing the limited awareness among parents, the financial constraints associated with genetic testing, and the perceived significance of genetic testing in the context of neuromuscular disorders. The findings suggest that the level of knowledge and awareness pertaining to genetic testing for neuromuscular disorders among parents in Malaysia varies, with initial levels of awareness ranging from relatively low to reasonably sufficient prior to and following the birth of an affected child. However, the investigation revealed that parents tended to cultivate more favorable perceptions regarding genetic testing subsequent to their experience with genetic counseling. This underscores the potential for heightened awareness and comprehension as a consequence of the personal experience of parenting an affected child confirmed through genetic testing and genetic counseling, ultimately influencing parental awareness.

Genetic Testing Enhances the Precision Diagnosis and Treatment of Breast Cancer.

The contemporary comprehension of breast cancer has progressed to the molecular level. As a heterogeneous malignancy, conventional pathological diagnosis and histological classification could no longer meet the needs of precisely managing breast cancer. Genetic testing based on gene expression profiles and gene mutations has emerged and substantially contributed to the precise diagnosis and treatment of breast cancer. Multigene assays (MGAs) are explored for early-stage breast cancer patients, aiding the selection of adjuvant therapy and predicting prognosis. For metastatic breast cancer patients, testing specific genes indicates potentially effective antitumor agents. In this review, genetic testing in early-stage and metastatic breast cancer is summarized, as well as the advantages and challenges of genetic testing in breast cancer.

The Merits and Challenges of Genetic Testing.

The Merits and Challenges of Genetic Testing.

Evidence-based consensus guidelines for ALS genetic testing and counseling.

Advances in amyotrophic lateral sclerosis (ALS) gene discovery, ongoing gene therapy trials, and patient demand have driven increased use of ALS genetic testing. Despite this progress, the offer of genetic testing to persons with ALS is not yet "standard of care." Our primary goal is to develop clinical ALS genetic counseling and testing guidelines to improve and standardize genetic counseling and testing practice among neurologists, genetic counselors or any provider caring for persons with ALS. Core clinical questions were identified and a rapid review performed according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA-P) 2015 method. Guideline recommendations were drafted and the strength of evidence for each recommendation was assessed by combining two systems: the Grading of Recommendations, Assessment, Development and Evaluation (GRADE) System and the Evaluation of Genomic Applications in Practice and Prevention (EGAPP). A modified Delphi approach was used to reach consensus among a group of content experts for each guideline statement. A total of 35 guideline statements were developed. In summary, all persons with ALS should be offered single-step genetic testing, consisting of a C9orf72 assay, along with sequencing of SOD1, FUS, and TARDBP, at a minimum. The key education and genetic risk assessments that should be provided before and after testing are delineated. Specific guidance regarding testing methods and reporting for C9orf72 and other genes is provided for commercial laboratories. These evidence-based, consensus guidelines will support all stakeholders in the ALS community in navigating benefits and challenges of genetic testing.

Molecular basis and genetic testing strategies for diagnosing 21-hydroxylase deficiency, including CAH-X syndrome.

Congenital adrenal hyperplasia (CAH) is a group of autosomally recessive disorders that result from impaired synthesis of glucocorticoid and mineralocorticoid. Most cases (~95%) are caused by mutations in the CYP21A2 gene, which encodes steroid 21-hydroxylase. CAH patients manifest a wide phenotypic spectrum according to their degree of residual enzyme activity. CYP21A2 and its pseudogene (CYP21A1P) are located 30 kb apart in the 6q21.3 region and share approximately 98% of their sequences in the coding region. Both genes are aligned in tandem with the C4, SKT19, and TNX genes, forming 2 segments of the RCCX modules that are arranged as STK19-C4A-CYP21A1P-TNXA-STK19B-C4B-CYP21A2-TNXB. The high sequence homology between the active gene and pseudogene leads to frequent microconversions and large rearrangements through intergenic recombination. The TNXB gene encodes an extracellular matrix glycoprotein, tenascin-X (TNX), and defects in TNXB cause Ehlers-Danlos syndrome. Deletions affecting both CYP21A2 and TNXB result in a contiguous gene deletion syndrome known as CAH-X syndrome. Because of the high homology between CYP21A2 and CYP21A1P, genetic testing for CAH should include an evaluation of copy number variations, as well as Sanger sequencing. Although it poses challenges for genetic testing, a large number of mutations and their associated phenotypes have been identified, which has helped to establish genotype-phenotype correlations. The genotype is helpful for guiding early treatment, predicting the clinical phenotype and prognosis, and providing genetic counseling. In particular, it can help ensure proper management of the potential complications of CAH-X syndrome, such as musculoskeletal and cardiac defects. This review focuses on the molecular pathophysiology and genetic diagnosis of 21-hydroxylase deficiency and highlights genetic testing strategies for CAH-X syndrome.

Germline BRCA-Mutated HER2-Negative Advanced Breast Cancer: Overcoming Challenges in Genetic Testing and Clinical Considerations When Using Talazoparib

Genetic testing is essential to the diagnosis and management of patients with breast cancer. For example, women who carry mutations in BRCA1/2 genes have an increased lifetime risk of breast cancer and the presence of these mutations may sensitize the patient to treatment with poly(ADP-ribose) polymerase (PARP) inhibitors. Two PARP inhibitors are approved by the US Food and Drug Administration for patients with germline BRCA-mutated advanced breast cancer (olaparib and talazoparib). The NCCN Clinical Practice Guidelines in Oncology (NCCN Guidelines) for Breast Cancer (Version 2.2023) recommend that all patients with recurrent or metastatic breast cancer (mBC) be assessed for the presence of germline BRCA1/2 mutations. However, many women eligible for genetic testing do not receive it. Here, we provide our perspectives on both the importance of genetic testing and the challenges patients and community clinicians may face when trying to access genetic testing. We also present a hypothetical case study involving a female patient with germline BRCA-mutated human epidermal growth factor receptor 2 (HER2)-negative mBC to highlight potential clinical considerations on the use of talazoparib, including the decision to initiate therapy, dosing considerations, potential drug-drug interactions, and managing side effects. This case illustrates the benefits of a multidisciplinary approach to managing patients with mBC and involving the patient in the decision-making process. This patient case is fictional and does not represent events or a response from an actual patient; this fictional case is for educational purposes only.

An approach to genetic testing in patients with metastatic castration-resistant prostate cancer in Singapore.

There has been a rapid evolution in the treatment strategies for metastatic castration-resistant prostate cancer (mCRPC) following the identification of targetable mutations, making genetic testing essential for patient selection. Although several international guidelines recommend genetic testing for patients with mCRPC, there is a lack of locally endorsed clinical practice guidelines in Singapore. A multidisciplinary specialist panel with representation from medical and radiation oncology, urology, pathology, interventional radiology, and medical genetics discussed the challenges associated with patient selection, genetic counselling and sample processing in mCRPC. A clinical model for incorporating genetic testing into routine clinical practice in Singapore was formulated. Tumour testing with an assay that is able to detect both somatic and germline mutations should be utilised. The panel also recommended the "mainstreaming" approach for genetic counselling in which pre-test counselling is conducted by the managing clinician and post-test discussion with a genetic counsellor, to alleviate the bottlenecks at genetic counselling stage in Singapore. The need for training of clinicians to provide pre-test genetic counselling and educating the laboratory personnel for appropriate sample processing that facilitates downstream genetic testing was recognised. Molecular tumour boards and multidisciplinary discussions are recommended to guide therapeutic decisions in mCRPC. The panel also highlighted the issue of reimbursement for genetic testing to reduce patient-borne costs and increase the reach of genetic testing among this patient population. This article aims to provide strategic and implementable recommendations to overcome the challenges in genetic testing for patients with mCRPC in Singapore.

The Future of Genetic Testing in Taekwondo: Opportunities and Challenges

As far as we know, genetics in sports is a rapidly growing science field, due to new technologies and the cost decrease of such investigations. Onwards, genetic predispositions, besides the relations between the biological and chronological age play one of the main roles in talent identification processes. Utilization of such analyses in practice is unfortunately insignificant, perhaps because of the complexity of the genome and genotype-phenotype interrelations. Therefore, the aim of this investigation is to collect all relevant data about gene research in taekwondo. The authors tracked appropriate articles through three databases: Web of Science, PubMed and Google Scholar. A number of n=11 appropriate articles were found. Results suggest there is evidence that several genes may highly impact taekwondo performance, including ACE I/D, ACTN3, IGF-1, while the GABPb1, HSP90AA1 & HSP90AB1 and mtDNA haplogroups M, N9 and J have the moderate overall impact. Still, there are challenges in genetic testing of young athletes, of methodological and ethical nature, which should be avoided with a professional staff and correct approach towards such testings. Significant scores of listed genes shed a light towards the clarification of possible genetic impact on taekwondo success. Accordingly, the authors have established precise guidelines for future examination of genetics in taekwondo. This work presents the current knowledge about genetic examinations regarding taekwondo.

Challenges in genetic testing: clinician variant interpretation processes and the impact on clinical care

Efforts have been made to standardize laboratory variant interpretation, but clinicians are ultimately tasked with clinical correlation and application of genetic test results in patient care. This study aimed to explore processes clinicians utilize when reviewing and returning genetic test results, and how they impact patient care. Medical geneticists, genetic counselors, and nongenetics clinicians from two Midwestern states completed surveys (n = 98) and in-depth interviews (n = 29) on practices of reviewing and returning genetic test results. Retrospective chart review (n = 130) examined discordant interpretations and the impact on care. Participants reported variable behaviors in both reviewing and returning results based on factors such as confidence, view of role, practice setting, and relationship with the lab. Providers did not report requesting changes to variant classifications from laboratories, but indicated relaying conflicting classifications to patients in some cases. Chart reviews revealed medically impactful differences in interpretation between laboratories and clinicians in 18 (13.8%) records. Clinician practices for reviewing and integrating genetic test results into patient care vary within and between specialties and impact patient care. Strategies to better incorporate both laboratory and clinician expertise into interpretation of genetic results could result in improved care across providers and settings.

Genetic evaluation in children with short stature.

Short stature is a common clinical manifestation in children. Yet, a cause is often unidentifiable in the majority of children with short stature by a routine screening approach. The purpose of this review is to describe the optimal genetic approach for evaluating short stature, challenges of genetic testing, and recent advances in genetic testing for short stature. Genetic testing, such as karyotype, chromosomal microarray, targeted gene sequencing, or exome sequencing, has served to identify the underlying genetic causes of short stature. When determining which short stature patient would benefit from genetic evaluation, it is important to consider whether the patient would have a single identifiable genetic cause. Specific diagnoses permit clinicians to predict responses to growth hormone treatment, to understand the phenotypic spectrum, and to understand any associated co-morbidities. The continued progress in the field of genetics and enhanced capabilities provided by genetic testing methods expands the ability of physicians to evaluate children with short stature for underlying genetic defects. Continued effort is needed to elaborate new genetic causes of linear growth disorders, therefore, we expand the list of known genes for short stature, which will subsequently increase the rate of genetic diagnosis for children with short stature.

Challenges in genetic testing

Challenges in genetic testing

Establishing Identity: How Direct‐to‐Consumer Genetic Testing Challenges the Assumption of Donor Anonymity

The rise of direct‐to‐consumer genetic testing is challenging the rules and expectations of the fertility industry concerning donor anonymity. While ethicists debate whose rights should prevail, many donor conceived people, recipient parents and donors are currently sharing their genetic information, along with methods to identify genetic links, in vast online communities, invalidating donor anonymity and providing a platform for those who advocate globally for legislative change to support donor‐linking practices. This article looks at why it is important to access this information in relation to identity and kinship formation and how the Family Court Community can apply this knowledge in order to achieve better outcomes for children and families.

Genetic Testing for Cancer Predisposition Syndromes in Adolescents and Young Adults (AYAs)

Adolescents and young adults (AYAs) represent a unique patient cohort, straddling the realms of paediatric and adult medicine. AYA cancers may include traditionally “paediatric” cancers occurring at older than expected ages, or conversely, adult-onset cancers occurring at unusually young ages. Cancer incidence in AYAs (aged 15–39) is increasing, and disappointingly, survival data are worse than those in paediatric or older adult settings. Early recognition of underlying cancer predisposition syndromes (CPS) in AYAs may facilitate individualised therapies, initiation of tumour surveillance strategies and cascade testing in at-risk relatives. Increasingly, physicians together with the wider AYA multidisciplinary team recognise AYAs as a unique group that merit special considerations, particularly regarding the psychosocial impact of cancer and genetic diagnoses on self-identity, fertility and family planning. AYA referral rates for genetic evaluation are suboptimal, but are improving with expanded access to testing, increasing clinician awareness and increasing public demand for genomic investigation. Herein, we outline recent developments in CPS testing in the AYA cohort. We highlight clinical tools useful in identifying patients that may warrant genetic counselling and/or genetic testing. We also discuss AYA-specific ethical and psychosocial challenges of genetic testing.

Clinical diagnostic exome sequencing in dystonia: Genetic testing challenges for complex conditions.

Patients with dystonia are particularly appropriate for diagnostic exome sequencing (DES), due to the complex, diverse features and genetic heterogeneity. Personal and family history data were collected from test requisition forms and medical records from 189 patients with reported dystonia and available family members received for clinical DES. Of them, 20.2% patients had a positive genetic finding associated with dystonia. Detection rates for cases with isolated and combined dystonia were 22.4% and 25.0%, respectively. 71.4% of the cohort had co-occurring non-movement-related findings and a detection rate of 24.4%. Patients with childhood-onset dystonia trended toward higher detection rates (31.8%) compared to infancy (23.6%), adolescence (12.5%), and early-adulthood onset (16%). Uncharacterized gene findings were found in 6.7% (8/119) of cases that underwent analysis for genes without an established disease relationship. Patients with intellectual disability/developmental delay, seizures/epilepsy and/or multifocal dystonia were more likely to have positive findings (P = .0093, .0397, .0006). Four (2.1%) patients had findings in two genes, and seven (3.7%) had reclassification after the original report due to new literature, new clinical information or reanalysis request. Pediatric patients were more likely to have positive findings (P = .0180). Our observations show utility of family-based DES in patients with dystonia and illustrate the complexity of testing.

Precision medicine in the era of CRISPR-Cas9: evidence from Bosnia and Herzegovina

This article explores the possibilities and challenges of genetic testing, genetic counseling, and genome editing (collectively referred to in this piece as precision medicine) in Bosnia and Herzegovina, in the era of CRISP-Cas9. It is informed by recent developments in the field which reached new heights in the radar of global awareness in the wake of the research scandal from China in November of 2018. The scandal generated intense debates, some of it still ongoing, regarding the appropriate boundaries for scientific research on human DNA. Bearing on independent developments within this country, complemented with global events, the article covers several grounds related to the topic, including: the nature and limits of emerging legislation; measures of genetic testing and genetic counseling; public engagement meant to increase awareness among stakeholders, beginning with the public, regarding these novel technologies; and corresponding bioethical and social implications. BH decision makers must work to ensure that socioeconomic factors do not pose obstacles to healthcare access, including matters bordering on precision medicine, and they must strive to realize standards for citizens, whether in healthcare delivery, research, or general educational services, that do not lag behind the rest of Europe. The route to reaching these governance goals will be through well-timed legislation, level-headed implementation, and diligent legislative oversight of the work of administrative agencies.