The development of the Clinician-reported Genetic testing Utility InDEx (C-GUIDE): a novel strategy for measuring the clinical utility of genetic testing.

PURPOSE: Clinical utility describes a genetic test's value to patients, families, health-care providers, systems, or society. This study aims to define clinical utility from the perspective of clinicians and develop a novel outcome measure that operationalizes this concept. METHODS: Item selection for the Clinician-reported Genetic testing Utility InDEx (C-GUIDE) was informed by a scoping review of the literature. Item reduction was guided by qualitative and quantitative feedback from semistructured interviews and a cross-sectional survey of genetics and nongenetics specialists. Final item selection, index scoring, and structure were guided by feedback from an expert panel of genetics professionals. RESULTS: A review of 194 publications informed the selection of a preliminary set of 25 items. Feedback from 35 semistructured interviews, 113 surveys, and 11 expert panelists informed the content and wording of C-GUIDE's final set of 18 items that reflect on the utility of testing related to diagnosis, management, and familial/psychosocial impact. C-GUIDE achieves content and face validity for use in a range of diagnostic genetic testing settings. CONCLUSION: Work to establish reliability and construct validity is underway. C-GUIDE will be useful in comparative studies to generate policy-relevant evidence pertaining to the clinical utility of genetic testing across a range of settings.

Parents perspectives on whole genome sequencing for their children: qualified enthusiasm?

OBJECTIVE: To better understand the consequences of returning whole genome sequencing (WGS) results in paediatrics and facilitate its evidence-based clinical implementation, we studied parents' experiences with WGS and their preferences for the return of adult-onset secondary variants (SVs)-medically actionable genomic variants unrelated to their child's current medical condition that predict adult-onset disease. METHODS: We conducted qualitative interviews with parents whose children were undergoing WGS as part of the SickKids Genome Clinic, a research project that studies the impact of clinical WGS on patients, families, and the healthcare system. Interviews probed parents' experience with and motivation for WGS as well as their preferences related to SVs. Interviews were analysed thematically. RESULTS: Of 83 invited, 23 parents from 18 families participated. These parents supported WGS as a diagnostic test, perceiving clear intrinsic and instrumental value. However, many parents were ambivalent about receiving SVs, conveying a sense of self-imposed obligation to take on the 'weight' of knowing their child's SVs, however unpleasant. Some parents chose to learn about adult-onset SVs for their child but not for themselves. CONCLUSIONS: Despite general enthusiasm for WGS as a diagnostic test, many parents felt a duty to learn adult-onset SVs. Analogous to 'inflicted insight', we call this phenomenon 'inflicted ought'. Importantly, not all parents of children undergoing WGS view the best interests of their child in relational terms, thereby challenging an underlying justification for current ACMG guidelines for reporting incidental secondary findings from whole exome and WGS.

The SickKids Genome Clinic: developing and evaluating a pediatric model for individualized genomic medicine.

Our increasing knowledge of how genomic variants affect human health and the falling costs of whole-genome sequencing are driving the development of individualized genomic medicine. This new clinical paradigm uses knowledge of an individual's genomic variants to anticipate, diagnose and manage disease. While individualized genetic medicine offers the promise of transformative change in health care, it forces us to reconsider existing ethical, scientific and clinical paradigms. The potential benefits of pre-symptomatic identification of at-risk individuals, improved diagnostics, individualized therapy, accurate prognosis and avoidance of adverse drug reactions coexist with the potential risks of uninterpretable results, psychological harm, outmoded counseling models and increased health care costs. Here we review the challenges, opportunities and limits of integrating genomic analysis into pediatric clinical practice and describe a model for implementing individualized genomic medicine. Our multidisciplinary team of bioinformaticians, health economists, health services and policy researchers, ethicists, geneticists, genetic counselors and clinicians has designed a 'Genome Clinic' research project that addresses multiple challenges in pediatric genomic medicine--ranging from development of bioinformatics tools for the clinical assessment of genomic variants and the discovery of disease genes to health policy inquiries, assessment of clinical care models, patient preference and the ethics of consent.

Predictive genetic testing for adult-onset disorders in minors: a critical analysis of the arguments for and against the 2013 ACMG guidelines.

The publication of the ACMG recommendations has reignited the debate over predictive testing for adult-onset disorders in minors. Response has been polarized. With this in mind, we review and critically analyze this debate. First, we identify long-standing inconsistencies between consensus guidelines and clinical practice regarding risk assessment for adult-onset genetic disorders in children using family history and molecular analysis. Second, we discuss the disparate assumptions regarding the nature of whole genome and exome sequencing underlying arguments of both supporters and critics, and the role these assumptions play in the arguments for and against reporting. Third, we suggest that implicit differences regarding the definition of best interests of the child underlie disparate conclusions as to the best interests of children in this context. We conclude by calling for clarity and consensus concerning the central foci of this debate.

High spontaneous intrachromosomal recombination rates in ataxia-telangiectasia.

Ataxia-telangiectasia (A-T) is an inherited human disease associated with neurologic degeneration, immune dysfunction, and high cancer risk. It has been proposed that the underlying abnormality in A-T is a defect in genetic recombination that interferes with immune gene rearrangements and the repair of DNA damage. Recombination was studied in A-T and control human fibroblast lines by means of two recombination vectors. Unexpectedly, spontaneous intrachromosomal recombination rates were 30 to 200 times higher in A-T fibroblast lines than in normal cells, whereas extrachromosomal recombination frequencies were near normal. Increased recombination is thus a component of genetic instability in A-T and may contribute to the cancer risk seen in A-T patients.

Views from the clinic: Healthcare provider perspectives on whole genome sequencing in paediatrics.

Whole genome sequencing (WGS) is a transformative technology which promises improved diagnostic rates compared to conventional genetic testing strategies and tailored approaches to patient care. Due to the practical and ethical complexities associated with using WGS, particularly in the paediatric context, input from a broad spectrum of healthcare providers can guide implementation strategies. We recruited healthcare providers from the largest paediatric academic health science centre in Canada and conducted semi-structured qualitative interviews, exploring experiences with and perceptions of the opportunities and challenges associated with WGS. Interview transcripts were coded and analyzed thematically. Interviews were completed with 14 genetics professionals (geneticists and genetic counsellors) and 15 non-genetics professionals (physician sub-specialists and nurses). Genetics professionals ordered genetic tests more often and reported greater confidence on pre- and post-test genetic counselling compared to non-genetics professionals. Most healthcare providers endorsed WGS when a more specific test was either not available or not likely to yield a diagnosis. While genetics professionals raised concerns regarding the time demands associated with reviewing WGS variants, non-genetics professionals reflected concerns about knowledge and training. Providers' position on reporting secondary variants to parents drew upon but was not limited to the concept of best interests. Taken together, understanding practical and principled matters of WGS from healthcare providers' perspectives can guide ongoing efforts to implement WGS in paediatrics.

The yeast TEL1 gene partially substitutes for human ATM in suppressing hyperrecombination, radiation-induced apoptosis and telomere shortening in A-T cells.

Homozygous mutations in the human ATM gene lead to a pleiotropic clinical phenotype of ataxia-telangiectasia (A-T) patients and correlating cellular deficiencies in cells derived from A-T donors. Saccharomyces cerevisiae tel1 mutants lacking Tel1p, which is the closest sequence homologue to the ATM protein, share some of the cellular defects with A-T. Through genetic complementation of A-T cells with the yeast TEL1 gene, we provide evidence that Tel1p can partially compensate for ATM in suppressing hyperrecombination, radiation-induced apoptosis, and telomere shortening. Complementation appears to be independent of p53 activation. The data provided suggest that TEL1 is a functional homologue of human ATM in yeast, and they help to elucidate different cellular and biochemical pathways in human cells regulated by the ATM protein.

Ataxia-telangiectasia and cellular responses to DNA damage.

Ataxia-telangiectasia (A-T) is a human disease characterized by high cancer risk, immune defects, radiation sensitivity, and genetic instability. Although A-T homozygotes are rare, the A-T gene may play a role in sporadic breast cancer and other common cancers. Abnormalities of DNA repair, genetic recombination, chromatin structure, and cell cycle checkpoint control have been proposed as the underlying defect in A-T; however, previous models cannot satisfactorily explain the pleiotropic A-T phenotype. Two recent observations help clarify the molecular pathology of A-T: (a) inappropriate p53-mediated apoptosis is the major cause of death in A-T cells irradiated in culture; and (b) ATM, the putative gene for A-T, has extensive homology to several cell cycle checkpoint genes from other organisms. Building on these new observations, a comprehensive model is presented in which the ATM gene plays a crucial role in a signal transduction network that activates multiple cellular functions in response to DNA damage. In this Damage Surveillance Network model, there is no intrinsic defect in the machinery of DNA repair in A-T homozygotes, but their lack of a functional ATM gene results in an inability to: (a) halt at multiple cell cycle checkpoints in response to DNA damage; (b) activate damage-inducible DNA repair; and (c) prevent the triggering of programmed cell death by spontaneous and induced DNA damage. Absence of damage-sensitive cell cycle checkpoints and damage-induced repair disrupts immune gene rearrangements and leads to genetic instability and cancer. Triggering of apoptosis by otherwise nonlethal DNA damage is primarily responsible for the radiation sensitivity of A-T homozygotes and results in an ongoing loss of cells, leading to cerebellar ataxia and neurological deterioration, as well as thymic atrophy, lymphocytopenia, and a paucity of germ cells. Experimental evidence supporting the Damage Surveillance Network model is summarized, followed by a discussion of how defects in the ATM-dependent signal transduction network might account for the A-T phenotype and what insights this new understanding of A-T can offer regarding DNA damage response networks, genomic instability, and cancer.

WRN or telomerase constructs reverse 4-nitroquinoline 1-oxide sensitivity in transformed Werner syndrome fibroblasts.

WRN encodes a RecQ helicase, which is mutated in Werner syndrome. Werner syndrome is a genetic condition of young adults characterized by premature aging, limited replicative capacity of cells in vitro, and increased cancer risk. Telomerase is a reverse transcriptase that extends the G-rich strand of telomeric DNA. Primary cells in vitro typically lack telomerase activity and undergo senescence, whereas telomerase is reactivated in many, but not all, tumors. The roles of the two genes are not known to be related. Here we report the development of an effective colony-forming assay in which a SV40-transformed Werner fibroblast cell line is 6-18-fold more sensitive to 4-nitroquinoline 1-oxide than SV40-transformed normal cell lines. The sensitivity can be partially reversed by transfecting a normal WRN gene but not a mutated WRN gene into the cells. Curiously, the sensitivity can be reversed equally well by transfecting a telomerase gene (TERT) into the cells. These data indicate the possibility of an interdependent function of these two genes.

Novel lacZ-based recombination vectors for mammalian cells.

We have constructed two sets of Escherichia coli lacZ-based vectors for use in studies of general mitotic recombination, both in somatic mammalian cells grown in culture and in transgenic animals. The vectors use two mutant copies of the E. coli lacZ gene as their recombination substrates and contain a neo gene for selection of stable transformants. In one vector, pLrec, an SV40 promoter drives lacZ, while the other vector, pArec, utilizes a human non-muscle beta-actin promoter for lacZ expression. Gene conversions, unequal sister chromatid exchanges and reciprocal exchanges between the two lacZ genes result in expression of beta-galactosidase, which can be detected in situ by histochemical staining. These vectors yield rates and frequencies of mitotic intrachromosomal recombination in human and rodent cell lines which are similar to rates reported using conventional recombination vectors. Molecular analysis of recombinational events involving the lacZ-based vectors can be carried out on genomic DNA isolated from clonally expanded populations and individual LacZ+ cells and cell clusters can be analyzed using PCR amplification. These reporter gene-based vectors may facilitate the study of recombination in cells with limited proliferative capacities, allow for analysis of both products of an unequal sister chromatid exchange, and permit in situ detection of recombination in the tissues of transgenic animals.

Effects of arsenite on DNA repair in Escherichia coli.

Since environmental exposure to arsenicals has been correlated with a high skin cancer risk among populations exposed to sunlight, it is possible that arsenicals might interfere with the repair of damage to DNA (mostly thymine dimers) resulting from the ultraviolet rays in sunlight. To test this hypothesis, strains of E. coli, differing from each other only in one or more repair functions, were exposed to UV light and then plated in the presence or absence of sodium arsenite. Survival after irradiation of wild type E. coli (WP(2)) was significantly decreased by 0.5mM arsenite. This effect was also seen in strains which are unable to carry out excision repair, suggesting that arsenite inhibits one or more steps in the post-replication repair pathways. This is confirmed by the finding that arsenite has no effect on the post-irradiation survival of a recA mutant, which does not carry out post-replication repair. Mutagenesis after ultraviolet irradiation depends on the rec(+) and lex(+) genes. Arsenite decreases mutagenesis in strains containing these genes. In order to determine its mechanism of action, dose-response relationships of arsenite on a number of cellular functions were carried out. The most sensitive cellular functions found were the induction of beta-galactosidase and the synthesis of RNA. Since error-prone repair in E. coli is an inducible process, the inhibition of mutagenesis after UV irradiation may be the result of inhibition of messenger RNA synthesis.

Aarskog syndrome: report of a family with review and discussion of nosology.

Five individuals in one family, including dizygotic male twins, a half brother and their mother, had Aarskog syndrome (AS). Phenotypic variability is wide not only between mother and sons but also between sibs. Collectively, the affected relatives have the full spectrum of findings seen in AS. Based on analysis of this family and others from the literature, we derive primary and secondary diagnostic criteria for AS. Primary criteria include: short stature, hypertelorism, short nose with anteverted nares, maxillary hypoplasia, a crease below the lower lip, mild interdigital webbing with short and broad hands, short fifth finger with clinodactyly, and shawl scrotum. Secondary criteria include: abnormal auricles with fleshy lobules, posteriorly angulated ears, widow's peak, ptosis, downward slant of palpebral fissures, joint hyperextensibility, broad feet with bulbous toes, cryptorchidism, inguinal hernia, and prominent umbilicus. Literature pertaining to the clinical manifestations and genetics of AS is reviewed and nosology of similar syndromes is discussed.

Pseudo-trisomy 13 syndrome with upper limb shortness and radial hypoplasia.

We report on a fetus with holoprosencephaly, postaxial polydactyly, multiple visceral anomalies, upper limb shortness, and radial hypoplasia with normal chromosomes. We provide a brief review of the newly delineated "pseudo-trisomy 13 syndrome." Severe limb shortness of radial hypoplasia has not been described previously in this syndrome. The present case may expand the spectrum of the pseudo-trisomy 13 syndrome, or may represent a distinct entity.

Velo-facio-skeletal syndrome in a mother and daughter.

We present a woman and her daughter with an apparently new short stature syndrome associated with facial and skeletal anomalies and hypernasality. Manifestations included hypertelorism with broad and high nasal bridge, epicanthal folds, narrow and high arched palate, mild mesomelic brachymelia, short broad hands, prominent finger pads, hyperextensibility of hand joints, small feet, nasal voice, and normal intelligence. The mother had short stubby thumbs and the daughter had posteriorly angulated ears and delayed bone age. The morphology of the nose and the hypernasality are reminiscent to those in the velo-cardio-facial syndrome. High resolution banding and fluorescent in situ hybridization studies showed no evidence of 22q11 deletions. Differentiation from Aarskog syndrome and Robinow syndrome is discussed.

Gene for topoisomerase III maps within the Smith-Magenis syndrome critical region: analysis of cell-cycle distribution and radiation sensitivity.

Smith-Magenis syndrome (SMS) is caused by an interstitial deletion of chromosome band 17p11.2 averaging 4-5 Mb. This deletion is likely to contain a large number of genes, each of which could potentially contribute toward the clinical phenotype. We report that the gene for topoisomerase III (hTOP3) is commonly deleted in SMS patients and maps between D17S447 and D17S258 on the short arm of chromosome 17. Cellular studies of SMS patient lymphoblasts and their respective parental cell lines were undertaken to determine the consequences of haploinsufficiency of hTOP3. Our studies indicate that hemizygosity for hTOP3 does not appreciably affect cell-cycle kinetics or activation of ionizing radiation-sensitive cell-cycle checkpoints. Furthermore, the induction of apoptosis in response to ionizing radiation in SMS and parental cells was similar. Our studies suggest that haploinsufficiency of hTOP3 does not have a major impact on the behavior of cells from SMS patients and may not play a significant role in the SMS phenotype.

Molecular and cytogenetic characterization of 9p- abnormalities.

We report on 2 girls with terminal deletion of the short arm of chromosome 9 with concurrent duplication unrecognizable by routine chromosome studies. The phenotype of the patients was not specifically suggestive of the 9p-syndrome in the absence of trigonocephaly and long philtrum as cardinal manifestations. In addition to psychomotor retardation, their manifestations were mild and include upward slant of palpebral fissures and dolichomesophalangy which are characteristic of del(9p). Chromosome abnormalities were de novo in both cases. The two rearranged chromosomes 9 exhibit similar G-banding patterns and suggested the possible duplication of distal 7p. Fluorescence in situ hybridization (FISH) with a chromosome-7 specific library probe indeed identified that one derivative chromosome 9 was the result of a translocation between chromosomes 7 and 9 [der(9)t(7;9)(p15.3;p24] but failed to detect a signal on the other derivative 9. In the second case, the concurrent abnormality was an inverted duplication of proximal 9p and deletion of distal 9p [inv dup(9)(p13-->p22::p22-->qter)] confirmed by FISH using a chromosome 9 specific library probe. FISH clearly identified the origin of these 2 abnormal chromosomes 9 and provided crucial information for clinical evaluation. We emphasize the importance of utilizing updated cytogenetic and molecular techniques in the precise delineation of subtle or complex abnormalities where there are no useful phenotypic clues.

Human fibroblasts transfected with an ATM antisense vector respond abnormally to ionizing radiation.

ATM, the gene mutated in ataxia-telangiectasia (A-T), mediates multiple cellular responses to DNA damage. A-T homozygotes have a high risk of cancer and exhibit spontaneous chromosomal instability, and cultured A-T cells react abnormally to ionizing radiation. We have developed an ATM antisense vector that confers an A-T phenotype on normal cells. An episomal antisense vector was created that contained a 1.3 kb segment of the ATM cDNA, and was transfected into normal human fibroblasts. Intracellular levels of ATM protein were typically reduced 10-fold in antisense-expressing (GM639-46alpha) clones. GM639-46alpha clones exhibited the low threshold for radiation-induced apoptosis, low clonogenic survival, and cell cycle defects normally seen in A-T cells. Transfection with the corresponding ATM sense strand vector had no effect on the behavior of normal cells, and neither vector affected the behavior of A-T cells. Our results demonstrate that interference with ATM gene expression recreates the A-T phenotype in normal cells, and provide functional evidence linking the ATM gene to cellular DNA damage responses. The ATM antisense vector should prove a useful tool for studying ATM function in a variety of normal, mutant, and malignant cell lines.

Testing the role of p53 in the expression of genetic instability and apoptosis in ataxia-telangiectasia.

We have obtained initial evidence supporting a new model for the human disease ataxia-telangiectasia (A-T), in which the A-T and p53 genes play crucial roles in a signal transduction network that activates multiple cellular functions in response to DNA damage. Three of the model's predictions were tested. (1) Disrupting cell cycle checkpoints should increase spontaneous rates in normal cells. In order to interfere with the G1/S checkpoint, we transfected a normal cell line with vectors expressing either a dominant-negative p53ala143 mutant or a human papilloma virus E6 gene. These transformants showed 10-80-fold elevations in spontaneous recombination rates when compared with their parent. (2) A-T cells should be sensitive to DNA damage-induced apoptosis. Widespread apoptosis was detectable in four A-T fibroblast lines, but not two control lines, beginning 24 h after exposure to X-rays or streptonigrin, but not UV. Streptonigrin also induced widespread apoptosis in A-T lymphoblasts but not in control lymphoblasts. (3) Disruption of p53 function in A-T cells should increase their mutagen resistance by interfering with apoptosis. Stable transfection of either the p53143ala or the HPV18 E6 construct was associated with acquisition of streptonigrin and radiation resistance, while transfection with the p53143ala construct did not affect the streptonigrin sensitivity of a control cell line.

Effects of sodium arsenite on the survival of UV-irradiated Escherichia coli: inhibition of a recA-dependent function.

Epidemiological studies and clinical observation suggesting potential hazards of arsenic compounds in increasing the incidence of cancer have been in complete contradiction with experimental findings in animals. Because of the predominance of skin cancers in the epidemiological reports, we decided to investigate the possibility that arsenic compounds might interfere with DNA repair. Using Escherichia coli as a test system, we show that this is indeed the case. Sodium arsenite, at concentrations of 0.1 mM and higher, decreases the survival of ultraviolet-irradiated E. coli WP2, a strain which possesses the full complement of repair genes. The effect of the arsenite increases with increasing ultraviolet dose. Similar results were obtained with the excision repair deficient strains WWP2 (uvrA) and WP6 (polA). Sodium arsenite had no effect on the survival of a recA mutant, WP10. Survival of ultraviolet-irradiated WP5 (exrA) was enhanced by sodium ardenite, the effect being greatest at low ultraviolet doses. It is postulated that arsenite inhibits a recA-dependent step in DNA repair. To account for the increased survival of the exrA mutant, we suggest that in the absence of the exr+ gene, the arsenite-sensitive recA-dependent function is deleterious. The ability of arsenite to inhibit DNA repair may account for the clinical and epidemiological reports linking arsenicals with an increased incidence of cancer.