Sara Huston Katsanis

Molecular genetic testing and the future of clinical genomics

Genomic technologies are reaching the point of being able to detect genetic variation in patients at high accuracy and reduced cost, offering the promise of fundamentally altering medicine. Still, although scientists and policy advisers grapple with how to interpret and how to handle the onslaught and ambiguity of genome-wide data, established and well-validated molecular technologies continue to have an important role, especially in regions of the world that have more limited access to next-generation sequencing capabilities. Here we review the range of methods currently available in a clinical setting as well as emerging approaches in clinical molecular diagnostics. In parallel, we outline implementation challenges that will be necessary to address to ensure the future of genetic medicine.

A Case Study of Personalized Medicine

Inhibitor of Apoptosis (IAP) proteins block programmed cell death and are expressed at high levels in various human cancers, thus making them attractive targets for cancer drug development. Second mitochondrial activator of caspases (Smac) mimetics are small-molecule inhibitors that mimic Smac, an endogenous antagonist of IAP proteins. Preclinical studies have shown that Smac mimetics can directly trigger cancer cell death or, even more importantly, sensitize tumor cells for various cytotoxic therapies, including conventional chemotherapy, radiotherapy, or novel agents. Currently, several Smac mimetics are under evaluation in early clinical trials as monotherapy or in rational combinations (i.e., GDC-0917/CUDC-427, LCL161, AT-406/Debio1143, HGS1029, and TL32711/birinapant). This review discusses the promise as well as some challenges at the translational interface of exploiting Smac mimetics as cancer therapeutics. Clin Cancer Res; 21(22); 5030–6. ©2015 AACR. See all articles in this CCR Focus section, “Cell Death and Cancer Therapy.”

Oversight of US genetic testing laboratories

Despite the boom in genetic tests available in US laboratories, oversight remains patchy. A survey of laboratory directors suggests that mandatory proficiency testing would result in fewer errors.

A synonymous mutation in TCOF1 causes Treacher Collins syndrome due to mis-splicing of a constitutive exon.

Interpretation of the pathogenicity of sequence alterations in disease‐associated genes is challenging. This is especially true for novel alterations that lack obvious functional consequences. We report here on a patient with Treacher Collins syndrome (TCS) found to carry a previously reported mutation, c.122C > T, which predicts p.A41V, and a novel synonymous mutation, c.3612A > C. Pedigree analysis showed that the c.122C > T mutation segregated with normal phenotypes in multiple family members while the c.3612A  >  C was de novo in the patient. Analysis of TCOF1 RNA in lymphocytes showed a transcript missing exon 22. These results show that TCS in the patient is due to haploinsufficiency of TCOF1 caused by the synonymous de novo c.3612A > C mutation. This study highlights the importance of clinical and pedigree evaluation in the interpretation of known and novel sequence alterations.

Developing the Blueprint for a Genetic Testing Registry

While the number of genetic tests continues to grow, publicly accessible information about the analytic and clinical validity of such tests is lagging. Information gaps impede informed decision making by health care providers and patients. Enhancing the transparency of information about what tests are being offered, for which indications tests are being offered, and the analytic and clinical validity of tests is a key prerequisite to ensuring test quality. A recent government recommendation for a mandatory genetic test registry has received wide stakeholder support but leaves many practical questions unanswered. We propose a ‘blueprint’ for the creation of a genetic test registry in order to expedite its implementation. We describe the goals of a registry, propose criteria for the inclusion of registrants and tests in the registry, and define the categories of information that should be included for such tests. We discuss the sources of legal authority that empower the government to mandate that a registry be established and identify the federal agencies with the relevant expertise and resources to do so. We conclude that establishing a registry is a critical first step in the development of a more transparent, quality-centered system of oversight that will better inform and protect the public.

Characterization of the Standard and Recommended CODIS Markers

As U.S. courts grapple with constitutional challenges to DNA identification applications, judges are resting legal decisions on the fingerprint analogy, questioning whether the information from a DNA profile could, in light of scientific advances, reveal biomedically relevant information. While CODIS loci were selected largely because they lack phenotypic associations, how this criterion was assessed is unclear. To clarify their phenotypic relevance, we describe the standard and recommended CODIS markers within the context of what is known currently about the genome. We characterize the genomic regions and phenotypic associations of the 24 standard and suggested CODIS markers. None of the markers are within exons, although 12 are intragenic. No CODIS genotypes are associated with known phenotypes. This study provides clarification of the genomic significance of the key identification markers and supports—independent of the forensic scientific community—that the CODIS profiles provide identification but not sensitive or biomedically relevant information.

Policy implications for familial searching.

In the United States, several states have made policy decisions regarding whether and how to use familial searching of the Combined DNA Index System (CODIS) database in criminal investigations. Familial searching pushes DNA typing beyond merely identifying individuals to detecting genetic relatedness, an application previously reserved for missing persons identifications and custody battles. The intentional search of CODIS for partial matches to an item of evidence offers law enforcement agencies a powerful tool for developing investigative leads, apprehending criminals, revitalizing cold cases and exonerating wrongfully convicted individuals. As familial searching involves a range of logistical, social, ethical and legal considerations, states are now grappling with policy options for implementing familial searching to balance crime fighting with its potential impact on society. When developing policies for familial searching, legislators should take into account the impact of familial searching on select populations and the need to minimize personal intrusion on relatives of individuals in the DNA database. This review describes the approaches used to narrow a suspect pool from a partial match search of CODIS and summarizes the economic, ethical, logistical and political challenges of implementing familial searching. We examine particular US state policies and the policy options adopted to address these issues. The aim of this review is to provide objective background information on the controversial approach of familial searching to inform policy decisions in this area. Herein we highlight key policy options and recommendations regarding effective utilization of familial searching that minimize harm to and afford maximum protection of US citizens.

Biochemical analysis of cultured chorionic villi for the prenatal diagnosis of peroxisomal disorders: biochemical thresholds and molecular sensitivity for maternal cell contamination detection

Objectives: The prenatal diagnosis of peroxisomal disorders is most often performed by biochemical analysis of cultured chorionic villus sample (CVS) or amniocytes. We aimed to (a) highlight the risk of maternal cell contamination (MCC) in biochemical prenatal diagnosis, (b) establish the threshold of these biochemical assays to MCC, and (c) document the sensitivity of PCR based genotyping of microsatellites for the detection of MCC in prenatal diagnosis of inborn errors by biochemical analysis. Methods: The threshold of each biochemical assay was assessed by co-cultivating fibroblasts from known affected and normal individuals. Genotypes for three polymorphic loci were determined by PCR and GeneScan analysis. The sensitivity of the molecular test was determined by DNA mixing experiments and isolation of DNA from co-cultivated fibroblasts. Results: MCC was detected in 2.5% of at risk CVS cultures (n = 79). Co-cultivation of defective and normal fibroblasts demonstrated that the peroxisomal biochemical assays were accurate at 25% contamination. Very low level DNA or cell contamination (1–5%) was detectable by genotyping, but an allele did not yield a definitive peak based on morphology until ∼10% contamination. Furthermore, we demonstrated that other inborn errors of metabolism might be more susceptible to diagnostic error by low level MCC. Conclusion: The sensitivity of the microsatellite analysis (⩾10%) is well within the threshold of peroxisomal biochemical assays. Although peroxisomal biochemical assays would not be predicted to introduce a false positive or negative result if MCC <10% were present but not recognised by molecular analysis, the same may not be true for other inborn errors of metabolism.

Perspectives on Genetic and Genomic Technologies in an Academic Medical Center: The Duke Experience

In this age of personalized medicine, genetic and genomic testing is expected to become instrumental in health care delivery, but little is known about its actual implementation in clinical practice. Methods. We surveyed Duke faculty and healthcare providers to examine the extent of genetic and genomic testing adoption. We assessed providers’ use of genetic and genomic testing options and indications in clinical practice, providers’ awareness of pharmacogenetic applications, and providers’ opinions on returning research-generated genetic test results to participants. Most clinician respondents currently use family history routinely in their clinical practice, but only 18 percent of clinicians use pharmacogenetics. Only two respondents correctly identified the number of drug package inserts with pharmacogenetic indications. We also found strong support for the return of genetic research results to participants. Our results demonstrate that while Duke healthcare providers are enthusiastic about genomic technologies, use of genomic tools outside of research has been limited. Respondents favor return of research-based genetic results to participants, but clinicians lack knowledge about pharmacogenetic applications. We identified challenges faced by this institution when implementing genetic and genomic testing into patient care that should inform a policy and education agenda to improve provider support and clinician-researcher partnerships.

Carrier screening for cystic fibrosis in US genetic testing laboratories : a survey of laboratory directors

Initial guidelines for cystic fibrosis (CF) carrier screening were issued in 2001 by the American College of Medical Genetics and the American College of Obstetricians and Gynecologists and updated in 2004. It is unknown how these guidelines have influenced laboratory practice. This study examined the uptake of two components of these guidelines for CF screening in genetic testing laboratories. A survey of directors of US genetic testing laboratories was conducted. Of 190 respondents, 178 answered questions about CF testing. Nearly half (49%) performed some type of DNA testing for CF; most of these (92%) performed CF carrier screening. Ten percent used a 23‐mutation panel for CF screening. The results of 5T tests were reported as a reflex test by 79% of laboratories, while 8% always returned 5T results and 7% never returned them. Seven percent of laboratories adopted both guidelines, 80% adopted one of the two guidelines, and 13% had not adopted either recommendation, suggesting that factors other than clinical guidelines may influence laboratories’ CF screening practices. Further studies are needed to determine whether the adoption of CF screening guidelines has significant clinical or economic effects on population‐based CF screening programs.