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PubMed2005

Developing a sustainable process to provide quality control materials for genetic testing.

PURPOSE: To provide a summary of the outcomes of two working conferences organized by the Centers for Disease Control and Prevention (CDC), to develop recommendations for practical, sustainable mechanisms to make quality control (QC) materials available to the genetic testing community. METHODS: Participants were selected to include experts in genetic testing and molecular diagnostics from professional organizations, government agencies, industry, laboratories, academic institutions, cell repositories, and proficiency testing (PT)/external Quality Assessment (EQA) programs. Current efforts to develop QC materials for genetic tests were reviewed; key issues and areas of need were identified; and workgroups were formed to address each area of need and to formulate recommendations and next steps. RESULTS: Recommendations were developed toward establishing a sustainable process to improve the availability of appropriate QC materials for genetic testing, with an emphasis on molecular genetic testing as an initial step. CONCLUSIONS: Improving the availability of appropriate QC materials is of critical importance for assuring the quality of genetic testing, enhancing performance evaluation and PT/EQA programs, and facilitating new test development. To meet the needs of the rapidly expanding capacity of genetic testing in clinical and public health settings, a comprehensive, coordinated program should be developed. A Genetic Testing Quality Control Materials Program has therefore been established by CDC in March 2005 to serve these needs.

Centers for Disease Control and Prevention, U.S.↗

PubMed2026

Prospective clinical validation of targeted long-read sequencing for preimplantation genetic testing of α-thalassaemia.

BACKGROUND: Preimplantation genetic testing for monogenic disorders (PGT-M) can prevent transmission of severe α-thalassaemia, but conventional workflows remain limited by family-specific assay design for direct variant detection, dependence on additional family samples for haplotype construction, and labour-intensive multi-step procedures across several platforms. Targeted long-read sequencing-based PGT-M for α-thalassaemia (tlrPGT-α-thal) integrates direct variant detection and haplotype linkage analysis within a single assay, but prospective clinical validation is lacking. METHODS: This prospective clinical study enrolled 103 families at high risk of transmitting α-thalassaemia at a reproductive medicine centre between August 2024 and March 2025. All families underwent blinded parallel analysis using both conventional NGS-based PGT-M (comparator) and tlrPGT-α-thal. RESULTS: In the primary concordance analysis, tlrPGT-α-thal was fully concordant with conventional NGS-based PGT-M (507/507, 100.0%; exact 95% CI, 99.3-100.0). Direct variant detection was successful in 501/507 embryos (98.82%; 95% CI, 97.4-99.6), haplotype linkage was established in 505/507 embryos (99.61%; 95% CI, 98.6-100.0), and one meiotic recombination event was identified. Among 93 families proceeding to embryo transfer, 57 pregnancies underwent invasive prenatal diagnosis, and all were concordant with the corresponding tlrPGT-α-thal results. Of the 26 comparator-inconclusive embryos, tlrPGT-α-thal resolved 6 complex cases, including cases with incomplete pedigrees or insufficient informative SNPs. Among the remaining 20 embryos with HBA-region aneuploidies, genotype and parental origin could be determined in 12. CONCLUSIONS: The findings show that tlrPGT-α-thal enables direct detection of diverse α-thalassaemia-causing variants together with efficient haplotype linkage analysis within a single workflow, without requiring family-specific assay design or additional family samples. The method demonstrated high diagnostic accuracy while providing added value in complex scenarios. Taken together, tlrPGT-α-thal represents a simplified and broadly applicable strategy for α-thalassaemia PGT-M.

Humans↗

PubMed1993

Relative accuracy of the halothane challenge test and a molecular genetic test in detecting the gene for porcine stress syndrome.

Pietrain swine homozygous for the hal gene (n) associated with porcine stress syndrome (PSS) and a Pietrain-derivative breed, Near Pietrain (NP), with a frequency of .31 for n, were mated to produce reciprocal F1, F2, and purebred NP litters. The halothane challenge test was performed on all 40 parents and 240 progeny to predict their hal genotype and PSS susceptibility. The DNA-based assay for a C to T mutation at base pair 1,843 of the skeletal muscle ryanodine receptor (ryr1) cDNA, which is very highly correlated with PSS, was also determined for these animals. The predicted hal genotypes observed in the progeny differed significantly from the expected Mendelian ratios, and the halothane challenge test consistently overestimated the n/n hal genotype. However, the ryr1 genotypes observed in the progeny did not differ significantly from the expected Mendelian ratios, and this DNA-based assay apparently misidentified only one of the 40 parents. The results of this study indicate that the assay for the ryr1 mutation more accurately predicts both the homozygous and heterozygous forms of the PSS gene than does the halothane challenge test.

Animals↗

PubMed2001

RB1 genetic testing as a clinical service: a follow-up study.

BACKGROUND: Genetic testing for inherited predisposition to diverse cancers has recently become available as a clinical service. We conducted a follow-up study of the initial series of US families who underwent RB1 genetic testing to evaluate long-term effects of the service. PROCEDURE: We enrolled 52 of 71 eligible families who responded to a follow-up study questionnaire administered 3-10 years after receipt of their RB1 results. Each family had one proband with unilateral, non-familial retinoblastoma, which is associated with a 12% pre-test probability of hereditary retinoblastoma. RB1 testing identified germline RB1 mutations in five patients, lowered the carrier probability to 2% in 21 patients, and did not substantially modify the carrier probability in the remaining 26. RESULTS: Diverse medical specialists offered and arranged for RB1 testing, and their recommendation was the most influential factor in the decision to be tested. Pre-test counseling was provided by ophthalmologists (30), oncologists (11), and geneticists and genetic counselors (11). Most respondents, regardless of test result, were satisfied and perceived gains from their genetic testing. Based on small numbers, families with reduced likelihood of hereditary retinoblastoma reported more positive outcomes. Parents of RB1 carriers were more likely to seek medical services, worry, and decide against having more children. CONCLUSIONS: This study demonstrates the feasibility of follow-up studies of families who had genetic testing. Results from our small series suggest that genetic information and counseling are important components of RB1 clinical genetic testing, and long-term adverse effects of testing are uncommon.

Adult↗

PubMed2002

BRCA1 and BRCA2 genetic testing for ovarian cancer: is it all good news?

In England and Wales, ovarian cancer is responsible for about 15 deaths per 100,000 women annually (NHS Executive 1999). It is estimated that only 5-10% of ovarian cancer cases have a hereditary basis (Watson et al. 1996, Hallowell 1999, Eeles & Powles 2000), although recent media excitement may have led some people to believe the odds are higher. The majority of these hereditary cases are thought to be caused by germline mutations in BRCA1 and BRCA2 cancer susceptibility genes (Antoniou et al. 2000, Berchuk et al. 1999). This article will examine current knowledge about BRCA1 and BRCA2 genetic testing for ovarian cancer and follow the journey taken by women who are considering such testing. Genetic counselling and genetic testing will be critically evaluated and the implications for clinical practice, the individual and society as a whole will be discussed.

Journal Article↗

PubMed2025

Characterizing trends in clinical genetic testing: A single-center analysis of EHR data from 1.8 million patients over two decades.

A lack of structural data in electronic health records (EHRs) makes assessing the impact of genetic testing on clinical practice challenging. We extracted clinical genetic tests from the EHRs of more than 1.8 million patients seen at Vanderbilt University Medical Center from 2002 to 2022. With these data, we quantified the use of clinical genetic testing in healthcare and described how testing patterns and results changed over time. We assessed trends in types of genetic tests, tracked usage across medical specialties, and introduced a new measure, the genetically attributable fraction (GAF), to quantify the proportion of observed phenotypes attributable to a genetic diagnosis over time. We identified 104,392 tests and 19,032 molecularly confirmed diagnoses. The proportion of patients with genetic testing in their EHRs increased from 1.0% in 2002 to 6.1% in 2022, and testing became more comprehensive with the growing use of multi-gene panels. The number of unique diseases diagnosed with genetic testing increased from 51 in 2002 to 509 in 2022, and there was a rise in the number of variants of uncertain significance. The phenome-wide GAF for 6,505,620 diagnoses made in 2022 was 0.46%, and the GAF was greater than 5% for 74 phenotypes, including pancreatic insufficiency (67%), chorea (64%), atrial septal defect (24%), microcephaly (17%), paraganglioma (17%), and ovarian cancer (6.8%). Our study provides a comprehensive quantification of the increasing role of genetic testing at a major academic medical institution and demonstrates its growing utility in explaining the observed medical phenome.

Humans↗

PubMed2005

Psychological impact of genetic testing for cancer susceptibility: an update of the literature.

This article presents an overview of the rapidly evolving body of literature on the psychological impact of genetic testing for hereditary breast/ovarian cancer susceptibility, hereditary non-polyposis colorectal cancer (HNPCC) and familial adenomatous polyposis (FAP). Uptake of genetic testing for BRCA1/2 and HNPCC-related mutations is more consistently related to psychological factors, rather than sociodemographic variables. Most studies on the psychological impact of genetic testing amongst individuals who have never been affected by cancer demonstrate that non-carriers derive significant psychological benefits from genetic testing, while no adverse effects have been observed amongst carriers. These benefits are more clear-cut for HNPCC, compared to hereditary breast/ovarian cancer, reflecting differences in risk management options. The few studies available on individuals affected with cancer indicate that the impact of genetic testing is mediated and amplified by their former experience of cancer. Future directions and challenges of research in this area are reviewed. In particular, more empirical data are needed on the broader impact of genetic testing on those with inconclusive results or results of uncertain significance. As genetic testing is becoming available for other types of familial cancer, additional investigations will be needed as there is evidence to suggest that the impact of genetic testing may be unique to each type of familial cancer.

Adenomatous Polyposis Coli↗

PubMed1999

Frequency of problems during clinical molecular-genetic testing.

Concerns have been raised about the quality of DNA-based genetic testing, but few data are available on the problems that occur during clinical genetic testing. We sought to determine the frequency and severity of such problems in US laboratories. Problems were defined as events that could or did impair patient care significantly. Data on the frequency and severity of adverse events during genetic testing were collected from laboratories by anonymous mail questionnaire and detailed on-site inspection. The surveyed laboratories (n = 42) reported significant problems in 0.33% of tests performed; the corresponding value in the inspected laboratories (n = 2) was 0.38%. Sixty percent of problems occurred in the pretest phase, 32% in the laboratory phase, and 8% in the posttest phase or multiple phases. The average level of actual harm resulting from these problems was low. Moderate or high levels of harm occurred in only 0.008% of total cases. No lawsuits, judgments, or disciplinary actions were taken against the laboratories in 277,000 tests performed. The overall frequency of problems in a given laboratory did not correlate with laboratory age, test volume, accreditation status, proficiency testing performance, or institution type (academic, private nonprofit, private for profit). In conclusion, significant problems during genetic testing occur infrequently (< 0.5% in most laboratories), and problems resulting in moderate or high levels of harm to patients are rare (0.008%).

Adult↗

PubMed2004

Regulatory approaches to reproductive genetic testing.

This report analyses the ethical and legal aspects of reproductive genetic testing in 11 countries (Australia, Austria, Canada, France, Germany, India, Israel, Japan, The Netherlands, Switzerland and the UK). The legal status of reproductive genetic testing in the countries under analysis is difficult to generalize due to the different regulatory systems adopted. These approaches are a reflection of the legal traditions and cultural and socio-religious beliefs which inform and shape public policy on assisted reproductive technologies and genetic testing. We divide approaches into two groups: public ordering (legislative, top-down approach) and private ordering (non-legislative, bottom-up approach). Even limiting our analysis to a number of countries that span the range from restrictive to pragmatic approaches, there is remarkable symmetry in both the (i) substantive requirements (i.e. gravity, health indications generally) and (ii) procedural safeguards (i.e. informed consent, counselling, confidentiality, civil status, oversight and accreditation) surrounding reproductive genetic testing. Indeed, irrespective of whether a country adopts a prohibitive or a permissive approach through legislation or self-regulation or a mix of both, the ultimate decision is--and should continue to be--a medical one. Nowhere is this more evident than in the substantive requirements.

Confidentiality↗

PubMed2004

An exploration of the legal and socio-ethical implications of predictive genetic testing of children.

This article explores the current position in relation to predictive genetic testing of children, highlighting some of the legal and socio-ethical issues and complexities that such testing presents. It evaluates the existing regulatory framework for predictive genetic testing of children in Australia, including the possible role of the Family Court in protecting children from inappropriate testing, and suggests that introducing a more interventionist approach would create its own difficulties. The article also considers a particular issue arising in the context of predictive genetic testing of children which the ALRC/AHEC inquiry canvassed concerning disclosure obligations to insurers. The article argues that creating an exception to established principles of disclosure would mitigate the impact of predictive genetic testing of children and would be consistent with international instruments which seek to protect against unfair genetic discrimination.

Australia↗

PubMed2005

Compendium of cardiac channel mutations in 541 consecutive unrelated patients referred for long QT syndrome genetic testing.

OBJECTIVES: The purpose of this study was to determine the spectrum and prevalence of cardiac channel mutations among a large cohort of consecutive, unrelated patients referred for long QT syndrome (LQTS) genetic testing. BACKGROUND: Congenital LQTS is a primary cardiac channelopathy. More than 300 mutations have been identified in five genes encoding key ion channel subunits. Until the recent release of the commercial clinical genetic test, LQTS genetic testing had been performed in research laboratories during the past decade. METHODS: A cardiac channel gene screen for LQTS-causing mutations in KCNQ1 (LQT1), KCNH2 (LQT2), SCN5A (LQT3), KCNE1 (LQT5), and KCNE2 (LQT6) was performed for 541 consecutive, unrelated patients (358 females, average age at diagnosis 24 +/- 16 years, average QTc 482 +/- 57 ms) referred to Mayo Clinic's Sudden Death Genomics Laboratory for LQTS genetic testing between August 1997 and July 2004. A comprehensive open reading frame and splice site analysis of the 60 protein-encoding exons was conducted using polymerase chain reaction, denaturing high-performance liquid chromatography, and DNA sequencing. RESULTS: Overall, 211 putative pathogenic mutations in KCNQ1 (88), KCNH2 (89), SCN5A (32), KCNE1 (1), and KCNE2 (1) were found in 272 unrelated patients (50%). Among the genotype positive patients (N = 272), 243 had single pathogenic mutations (LQT1: n = 120 patients; LQT2: n = 93; LQT3: n = 26; LQT5: n = 3; LQT6: n = 1), and 29 patients (10% of genotype-positive patients and 5% overall) had two LQTS-causing mutations. The majority of mutations were missense mutations (154/210 [73%]), singletons (identified in only a single unrelated patient: 165/210 [79%]), and novel (125/211 [59%]). None of the mutations identified were seen in more than 1,500 reference alleles. Those patients harboring multiple mutations were younger at diagnosis (15 +/- 11 years vs 24 +/- 16 years, P = .003). CONCLUSIONS: In this comprehensive cardiac channel gene screen of the largest cohort of consecutive, unrelated patients referred for LQTS genetic testing, half of the patients had an identifiable mutation. The majority of mutations continue to represent novel singletons that expand the published compendium of LQTS-causing mutations by 35%. These observations should facilitate diagnostic interpretation of the clinical genetic test for LQTS.

Adolescent↗

PubMed2002

Genetic testing and risk assessment for spinal muscular atrophy (SMA).

Spinal muscular atrophy (SMA) is one of the most common autosomal recessive diseases, affecting approximately 1 in 10,000 live births, and with a carrier frequency of approximately 1 in 50. Because of gene deletion or conversion, SMN1 exon 7 is homozygously absent in approximately 94% of patients with clinically typical SMA. Approximately 30 small intragenic SMN1 mutations have also been described. These mutations are present in many of the approximately 6% of SMA patients who do not lack both copies of SMN1, whereas SMA of other patients without a homozygous absence of SMN1 is unrelated to SMN1. A commonly used polymerase chain reaction/restriction fragment length polymorphism (PCR-RFLP) assay can be used to detect a homozygous absence of SMN1 exon 7. SMN gene dosage analyses, which can determine the copy numbers of SMN1 and SMN2 (an SMN1 homolog and a modifier for SMA), have been developed for SMA carrier testing and to confirm that SMN1 is heterozygously absent in symptomatic individuals who do not lack both copies of SMN1. In conjunction with SMN gene dosage analysis, linkage analysis remains an important component of SMA genetic testing in certain circumstances. Genetic risk assessment is an essential and integral component of SMA genetic testing and impacts genetic counseling both before and after genetic testing is performed. Comprehensive SMA genetic testing, comprising PCR-RFLP assay, SMN gene dosage analysis, and linkage analysis, combined with appropriate genetic risk assessment and genetic counseling, offers the most complete evaluation of SMA patients and their families at this time. New technologies, such as haploid analysis techniques, may be widely available in the future.

Arthrogryposis↗

PubMed1994

Attitudes about genetic testing for breast-ovarian cancer susceptibility.

PURPOSE: In anticipation of the availability of genetic testing for a breast-ovarian cancer susceptibility gene (BRCA1), this study examined interest in and expectations about the impact of a potential genetic test. PATIENTS AND METHODS: The subjects were 121 first-degree relatives (FDRs) of ovarian cancer patients. The design was cross-sectional. Subjects completed a structured telephone interview of attitudes about cancer and genetic testing, and self-report psychologic questionnaires to assess coping style and mood disturbance. RESULTS: Overall, 75% of FDRs said that they would definitely want to be tested for BRCA1 and 20% said they probably would. In bivariate analyses, interest was associated positively with education, perceived likelihood of being a gene carrier, perceived risk of ovarian cancer, ovarian cancer worries, and mood disturbance. In logistic regression analysis, perceived likelihood of being a gene carrier was associated strongly with interest (odds ratio, 3.7; P = .006). Results of stepwise linear regression modeling indicated that an anticipated negative impact of genetic testing was associated with being younger (beta = -.66, P = .009), having more mood disturbance (beta = .015, P = .01), and having an information-seeking coping style (beta = .19, P = .002). CONCLUSION: These results suggest that the demand for genetic testing for BRCA1 among FDRs of cancer patients may be great. Moreover, those who elect to participate may represent a more psychologically vulnerable subgroup of high-risk women.

Adolescent↗

PubMed1999

Commercialization of BRCA1/2 testing: practitioner awareness and use of a new genetic test.

It was our purpose to determine the characteristics of practitioners in the United States who were among the first to inquire about and use the BRCA1 and BRCA2 (BRCA1/2) genetic tests outside of a research protocol. Questionnaires were mailed to all practitioners who requested information on or ordered a BRCA1/2 test from the University of Pennsylvania (UPenn) Genetic Diagnostics Laboratory (GDL) between October 1, 1995 and January 1, 1997 (the first 15 months the test was available for clinical use). The response rate was 67% of practitioners; 54% (121/225) were genetic counselors, 39% (87/225) were physicians or lab directors. Most physicians were oncologists, pathologists, or obstetrician/gynecologists, but 20% practiced surgery or internal or general medicine. Fifty-six percent (125/225) had ordered a BRCA1/2 test for a patient; most of the rest had offered or were willing to offer testing. Of those who had offered testing, 70% had a patient decline BRCA1/2 testing when offered. Practitioners perceived that patients' fear of loss of confidentiality was a major reason for declining. Nearly 60% of practitioners reported that their patients had access to a genetic counselor, but 28% of physicians who ordered a BRCA1/2 test reported having no such access, despite the GDL's counseling requirement. The proportion of physicians reporting no access to genetic counselors for their patients increased from 22.4% in the first half of the study to 50% in the last half. Many practitioners have an interest in BRCA1/2 testing, despite policy statements that discourage its use outside of research protocols. Practitioner responses suggest that patient interest in testing seems to be tempered by knowledge of potential risks. An apparent increase in patient concern about confidentiality and inability to pay for testing could indicate growing barriers to testing. Although most practitioners reported having access to counseling facilities, perceived lack of such access among an increasing proportion of practitioners indicates that lab requirements for counseling are difficult to enforce and suggests that an increasing proportion of patients may not be getting access to counseling.

Awareness↗

PubMed2006

Institutionalized paternalism? Stakeholders' views on public access to genetic testing.

OBJECTIVES: To explore the views of UK stakeholder group representatives about genetic tests for complex disease risks, and in particular the regulation of public access to genetic testing in order to assess the capacity of public consultations to represent the views of the public and representative groups accurately. METHODS: A purposive sample of 16 people was selected who had responded to a previous consultation by the Human Genetics Commission (a UK government body), or who were known to have relevant interests. Interviews were undertaken in June and July 2003, and recorded, transcribed and analysed thematically. RESULTS: Interviewees believed that genetic information is not inherently different from other health risk information, such as family histories or body mass indices. However, they tended to think that members of the public are unable to take a similarly informed view and that special regulation is therefore required. Individuals acting as representatives of organizations tended to express opinions more in favour of protective regulation and professionally controlled access to genetic testing for complex disease risks than those they held as individuals. CONCLUSIONS: Stakeholder representatives' perceptions of public vulnerability may give rise to precautionary regulatory policies on genetic testing that limit public access to potentially valuable information. This could undermine other public health policies aimed at encouraging individuals to act independently to reduce risks to their health. 'Stakeholder consultations' may generate biased findings. Further rigorous research is needed to validate and explain the opinions and assumptions of individuals asked to contribute to such consultations.

Genetic Testing↗

PubMed1995

Removing the shadow of the law from the debate about genetic testing of children.

When physicians view efforts to obtain genetic testing for children as unwise or contrary to the children's interests, they face difficult problems both of ethics and of communicating with the parents. Contrary to the suggestions of some, the law has little to say about how physicians resolve these dilemmas. Parents do not have a constitutionally protected right to demand that unwilling physicians perform these tests. In addition, there is little risk of liability for damages unless the child suffers physical harm as a result of the physician's refusal to do the test. The debate about genetic testing of children needs to take place with a clear understanding of the law's limited impact.

Child↗

PubMed2005

A literature review of the psychological impact of genetic testing on breast cancer patients.

OBJECTIVE: Easier access and increased awareness results in more referral for genetic testing for hereditary breast cancer in healthy at-risk women and breast cancer patients. To investigate the psychological impact of genetic testing on breast cancer patients, literature pertaining to this group was reviewed. METHOD: Medline and PsychInfo databases were searched over the period 1995-2004 for studies aimed at breast cancer patients referred for genetic testing. Qualitative and quantitative psychological outcome measures were identified. RESULTS: Eight papers were identified focusing on women affected by breast cancer and undergoing genetic counseling and DNA testing. CONCLUSION: Genetic testing does not lead to an increase in psychological distress in breast cancer patients. However, a recent breast cancer diagnosis adds to general and cancer-specific distress prior to genetic counseling and after DNA test disclosure. PRACTICE IMPLICATIONS: Clinicians need to be aware of possible high psychological distress and additional counseling needs of recently diagnosed breast cancer patients taking part in genetic testing. Further research should focus on patients who decline genetic counseling or receive an inconclusive test result, including age upon and time since diagnosis.

Adaptation, Psychological↗

PubMed2006

Comparing knowledge and attitudes towards genetic testing in Parkinson's disease in an American and Asian population.

INTRODUCTION: Recent discoveries of disease-causing genes in Parkinson's disease (PD) have generated considerable interest regarding genetic testing in PD. The attitudes toward genetic testing are largely influenced by knowledge and preconceived notions. OBJECTIVE: We investigated the relationship between knowledge of and attitude towards predictive genetic testing of PD in two independent centers in America and Asia involving PD patients and caregivers. METHODS: In a prospective study involving 515 subjects comprising of PD patients and their caregivers in two independent centers in America and Asia, the level of knowledge about genetic testing and patients' attitudes towards such testing were evaluated using a standardized questionnaire. RESULTS: American PD patients had a higher level of knowledge of PD genetics than Asian PD (31.1% vs. 12.3%, p=0.0002). A greater number of American PD patients and caregivers reported a positive attitude towards the potential medical benefits of genetic testing compared to their Asian counterparts (85.4% vs. 42.2%, 92.2% vs. 32.1%, p<0.00005), but a more negative attitude towards potential compromise in getting health and life insurance (43.7% vs. 25.8%, p=0.0002). However, in the Asian cohort, multivariate analysis revealed that a high level of genetics knowledge was associated with a positive attitude response regarding the potential medical benefits of testing (p<0.0005), but a negative attitude towards compromises in healthcare and life insurance, getting a job and starting a family (p<0.0005). These associations were not observed amongst American subjects. CONCLUSIONS: The relationship between level of genetic knowledge and attitude towards potential risks and benefits of predictive genetic testing in PD was distinctly different in two independent, racially and culturally different PD populations and caregivers. These observations have clinical implications in the development of PD genetic counseling programs.

Adult↗