Genetic Testing Approaches Research Articles

Determining the Optimal Approach for Government-Regulated Genetic Testing

With recent activity by both the US Food and Drug Administration (FDA)2 and the US Government Accountability Office (GAO), a new era of government-regulated genetic testing is upon us. In the past 10 years, the scope and volume of genetic tests [most falling into the category of laboratory-developed tests (LDTs)] being offered has increased dramatically. Traditionally, genetic tests have been for single-gene disorders, such as cystic fibrosis and Marfan syndrome. In recent years, the scope and complexity of genetic testing has increased, and there has been a shift in emphasis toward predicting disease, especially complex disease. This shift has been mainly due to the arrival of direct-to-consumer (DTC) testing to the genetic-testing market. DTC genetic tests, which have not been under the review of the FDA, are traditionally offered via the Internet and are performed in the manufacturers' accredited laboratories as LDTs. The FDA's first public foray into oversight of DTC genetic testing was in May 2010, after Pathway Genomics, a DTC genetic-testing company based in San Diego, announced the upcoming availability of their personal genetic-testing kits at Walgreens drugstores nationwide. After Pathway's announcement, the FDA promptly sent an enforcement letter to Pathway, in which they declared Pathway's testing kit a medical device, and asked them to respond within 15 days to explain why their test should not require premarket review (1). The FDA followed suit by sending similar letters to 19 additional genetic-testing companies in the following months. In July, the FDA held its 2-day “Public Meeting on Oversight of Laboratory Developed Tests,” at which many genetic-testing companies and genetics organizations participated (2). During this …

Shortcuts to genetic characterization of polyposis patients in a high-risk registry

Background Mutations in the APC gene lead to Familial adenomatous polyposis (FAP) and an attenuated form of this condition (AFAP). Mutation detection fails using DNAbased technology in 20% of FAP and 50% of AFAP patients due to testing limitations, inability to determine significance of change, or other responsible genes. A testing protocol in our Hereditary Gastrointestinal Cancer Registry has been developed as a research tool in uncharacterized cases to rule out the obvious APC mutations, using a multi-step approach. This approach offers a significant cost savings which could be applied to clinical genetic testing approaches. Methods

Hereditary nephrotic syndrome: a systematic approach for genetic testing and a review of associated podocyte gene mutations

Several genes have been implicated in genetic forms of nephrotic syndrome occurring in children. It is now known that the phenotypes associated with mutations in these genes display significant variability, rendering genetic testing and counselling a more complex task. This review will focus on the recent clinical findings associated with those genes known to be involved in isolated steroid-resistant nephrotic syndrome in children and, thereby, propose an approach for appropriate mutational screening. The recurrence of proteinuria after transplantation in patients with hereditary forms of nephrotic syndrome will also be discussed.

Screening and Surveillance Recommendations for Pediatric Gastrointestinal Polyposis Syndromes

Inherited polyposis syndromes are relatively rare disorders in pediatric gastroenterology practice, even in busy academic settings. It is important, however, for pediatric gastroenterologists to be aware of the serious health risks for children and their families affected by these disorders. The diagnosis of a polyp syndrome is often made in the first or second decade of life, long before the risk of gastrointestinal neoplasia. Pediatric gastroenterologists must be prepared then to offer families predictive genetic screening as well as endoscopic surveillance when appropriately indicated. The current overview is designed to provide general guidelines and, whenever possible, evidence-based recommendations for genetic testing, endoscopic surveillance and other screening approaches for children with inherited gastrointestinal polyposis syndromes. In this presentation, the focus is on screening for neoplastic change and complications in the gastrointestinal tract. It is important to understand that extraintestinal cancers are frequent in some of these disorders and the reader is referred to other authoritative sources for additional information about comprehensive health screening outside the gastrointestinal system.

Cascade genetic testing for mismatch repair gene mutations

Mismatch repair gene mutation carriers have a high risk of developing colorectal cancer, and can benefit from appropriate surveillance. A combined population based ascertainment cascade genetic testing approach provides a systematic and potentially effective strategy for identifying such carriers. We have developed a Markov Chain computer model system which simulates various factors influencing cascade genetic testing; including demographics, uptake, genetic epidemiology and family size. This was used to evaluate cascade genetic testing for mismatch repair gene mutations in theory and practice. Simulations focussed on the population of Scotland by way of illustration, and were based on a 20-year programme in which index cases were ascertained from colorectal cancer cases aged<55 years at onset. Results indicated that without practical barriers to cascade genetic testing, 545 (95% CI=522, 568) carriers could be identified; 42% of the population total. This comprised approximately 140 index cases, 302 asymptomatic relatives and 104 previously affected relatives. However, when realistic ascertainment and acceptance rates were used to inform simulations, only 257 (95% CI=246, 268) carriers, about 20% of the carrier population, were identifiable. Of these approximately 112 were index cases, 108 were asymptomatic relatives, and 37 were previously affected relatives. This contrast emphasises the importance of ascertainment and acceptance rates. Likewise the low number of index cases shows that case identification is a limiting factor. In the absence of robust data from epidemiological studies, these findings can inform decisions about the use of cascade genetic testing for mismatch repair gene mutations.

Aberrant splicing is a common mutational mechanism inMKS1, a key player in Meckel-Gruber syndrome

Meckel-Gruber syndrome (MKS) is an autosomal recessive, usually lethal multisystemic disorder characterized by early developmental anomalies of the central nervous system, cystic kidney dysplasia, hepatobiliary ductal plate malformation, and postaxial polydactyly. Three MKS loci have been mapped and recently, two genes were identified: MKS1 on 17q22 in Caucasian kindreds and MKS3 on 8q22 in Omani and Pakistani families, putting MKS on the growing list of ciliary disorders ("ciliopathies"). We performed linkage analysis for MKS1-3 in 14 consanguineous and/or multiplex families of different ethnic origins with histologic diagnosis and at least three classic MKS manifestations in each kindred. Unexpectedly, only five families were linked to any of the known MKS loci, clearly indicating further locus heterogeneity. All five families showed homozygosity for MKS1 and, intriguingly, were of non-Caucasian origin. MKS1 sequencing revealed no mutation in two of these pedigrees, whereas different, novel splicing defects were identified in the three other families and an additional sporadic German patient. Given that all of our mutations and two of the in total four known MKS1 changes cause aberrant splicing (while the other two known mutations were frameshift mutations), we hypothesize that splicing defects are a crucial mutational mechanism in MKS1 which apparently is one of the main loci and key players in MKS. Our results indicate that MKS1 mutations are not restricted to the Caucasian gene pool and suggest further genetic heterogeneity for MKS. Overall, our data have immediate implications for genetic counselling and testing approaches in MKS.

Using the TBX5 transcription factor to grow and sculpt the heart

TBX5 mutations cause the cardiac and limb defects of the autosomal dominant Holt-Oram syndrome (HOS). We have explored the role of the TBX5 transcription factor during cardiogenesis and have elucidated some of its functions in regulating myocardial cell proliferation and proepicardial cell migration. Our identification of TBX5 mutations has enabled us to offer genetic testing for diagnosis of HOS in patients and also to perform preimplantation genetic diagnosis on blastocysts for couples desiring to have a child unaffected by HOS. We hope that our genetic testing approach will serve as a paradigm for mutation screening in other inherited syndromes.

PedGenie: an analysis approach for genetic association testing in extended pedigrees and genealogies of arbitrary size.

BackgroundWe present a general approach to perform association analyses in pedigrees of arbitrary size and structure, which also allows for a mixture of pedigree members and independent individuals to be analyzed together, to test genetic markers and qualitative or quantitative traits. Our software, PedGenie, uses Monte Carlo significance testing to provide a valid test for related individuals that can be applied to any test statistic, including transmission disequilibrium statistics. Single locus at a time, composite genotype tests, and haplotype analyses may all be performed. We illustrate the validity and functionality of PedGenie using simulated and real data sets. For the real data set, we evaluated the role of two tagging-single nucleotide polymorphisms (tSNPs) in the DNA repair gene, NBS1, and their association with female breast cancer in 462 cases and 572 controls selected to be BRCA1/2 mutation negative from 139 high-risk Utah breast cancer families.ResultsThe results from PedGenie were shown to be valid both for accurate p-value calculations and consideration of pedigree structure in the simulated data set. A nominally significant association with breast cancer was observed with the NBS1 tSNP rs709816 for carriage of the rare allele (OR = 1.61, 95% CI = 1.10–2.35, p = 0.019).ConclusionPedGenie is a flexible and valid statistical tool that is intuitively simple to understand, makes efficient use of all the data available from pedigrees without requiring trimming, and is flexible to the types of tests to which it can be applied. Further, our analyses of real data indicate NBS1 may play a role in the genetic etiology of heritable breast cancer.

Genetic Testing for Inherited Colon Cancer

The genes associated with each of the inherited syndromes of colon cancer have now been identified, and genetic testing is available for diagnosis. These syndromes include familial adenomatous polyposis, hereditary nonpolyposis colorectal cancer, Peutz-Jeghers syndrome, juvenile polyposis syndrome, and, possibly, Cowden's syndrome. Clinical genetic testing approaches have been developed for each of these syndromes and are now a part of accepted clinical care. Disease-causing mutations can be found in the majority of families affected with one of the inherited syndromes, and, most importantly, once a mutation is found in an index case of the family, relatives can be tested for the presence or absence of that mutation with near 100% accuracy. Cancer screening and management in syndrome families is then based on the results of genetic testing. For the physician to order and properly interpret genetic tests, a basic understanding of the types of mutations that lead to inherited disease and the methods for detecting them is vital. These issues will be presented. Additional clinical issues somewhat unique to genetic testing include genetic counseling and informed consent for genetic testing, both of which will also be reviewed. Often the most difficult aspect of genetic testing is deciding which patients and families should undergo the testing. Furthermore, this issue is quite specific for each of the syndromes. Thus, following presentation of general principles of selection for genetic testing, a detailed approach for identifying persons who should undergo testing for each of the individual syndromes will be given, together with relevant descriptions of the syndromes. Finally, the ongoing work to discover new and possibly more common but less penetrant colon cancer susceptibility genes that cause common familial colon cancer will be presented.

Análise da pureza genética e discriminação de cultivares de vinca (Catharanthus roseus (L.) G.Don) usando "random amplified polymorphic DNA" em DNA extraído de sementes e folhas

A técnica "Random Amplified Polymorphic DNA" (RAPD) surgiu como uma ferramenta útil para testar a pureza genética e a discriminação de cultivares em muitas espécies. É uma técnica simples, rápida, relativamente de baixo custo e permite o uso de DNA extraído de sementes secas, o que é muito importante em um programa de análise de sementes. O uso desta tecnologia no teste da pureza genética pode ser muito interessante para algumas espécies, como a vinca (Catharanthus roseus (L.) G.Don), pois pouco se conhece a respeito da seqüência de seu DNA. É interessante, também, pelo fato de existir grande número de "primers" comercialmente disponíveis, que podem ser prontamente utilizados para gerar dados. Essa técnica pode ser mais facilmente utilizada para gerar padrões de bandas polimórficas suficientes para discriminar genótipos diferentes. Todavia, no presente estudo, os padrões RAPD de bandas obtidas de amostras de DNA extraído de sementes de vinca em "bulk" foram não-consistentes, o mesmo ocorrendo com o uso de DNA extraído de sementes individuais de um mesmo cultivar, o que evidencia que a técnica não é aplicável para testar a pureza genética e a discriminação de cultivares de vinca. Entretanto, os padrões de bandas RAPD gerados a partir de DNA extraído de tecido foliar de plântulas foram mais reproduzíveis e poderiam ser considerados na caracterização de cultivares.

Familial occurrence of pigment dispersion syndrome

Background: Pigment dispersion syndrome affects up to 4% of the white population. It is characterized by the presence of transillumination defects, Krukenberg's spindle and dense trabecular meshwork pigmentation. Open-angle glaucoma will develop in as many as 50% of affected patients. In this study we describe the familial occurrence of pigment dispersion syndrome in six North American pedigrees and the phenotypic characteristics with respect to pigment dispersion syndrome and glaucoma.Methods: Probands with pigment dispersion syndrome were identified in glaucoma clinics at university eye centres in Ottawa and Durham, NC. Families with two or more affected members were evaluated. All willing members in each family underwent a thorough clinical examination and were classified as affected with pigment dispersion syndrome, suspect or unaffected. The previous medical records were reviewed to obtain the past medical and ocular history, including risk factors for glaucoma.Results: All six families are white. Three families show at least two generations of affected members. Of the 43 subjects examined 58% were women. All 14 affected members showed moderate to heavy trabecular meshwork pigmentation and either Krukenberg's spindle or transillumination defects. The affected members were also considerably more myopic (mean spherical equivalent for the right eye -4.72 dioptres) than the suspect group or the unaffected group (mean spherical equivalent -0.79 D and + I . 19 D respectively) (p ≤ 0.001), and the intraocular pressure was higher for the affected than the unaffected group (mean for the right eye 20 mm Hg vs. 16 mm Hg) (p = 0.004). Half of those affected also had open-angle glaucoma.Interpretation: We have identified and phenotypically characterized six North American families with autosomal dominant pigment dispersion syndrome. Our ultimate goal is to identify the gene(s) that causes this disorder in order to clarify its molecular etiology and pathophysiology. This may give rise to a molecular classification of the disease as well as provide the foundation for genetic testing and new treatment approaches.

Cost comparison of predictive genetic testing versus conventional clinical screening for familial adenomatous polyposis

BACKGROUNDMutations of theAPC gene cause familial adenomatous polyposis (FAP), a hereditary colorectal cancer predisposition syndrome.AIMSTo conduct a cost comparison analysis of predictive genetic testing versus conventional clinical screening for individuals...