Patient-controlled encrypted genomic data: an approach to advance clinical genomics

The Ethical Implications of the Reclassification of Noninvasive Follicular Variant Papillary Thyroid Carcinoma

BACKGROUND

Several studies have highlighted the lack of consensus in the diagnosis of follicular variant of papillary thyroid carcinoma (FVPTC). An international multidisciplinary panel to address the controversy was assembled at the annual meeting of the Endocrine Pathology Society in March of 2015, leading to the recent publication reclassifying encapsulated (or noninvasive) FVPTC (EFVPTC) as a benign neoplasm. Does this change in histologic taxonomy warrant a change in clinical practice, and how should it affect those who have been given this diagnosis in the past? We consider the financial and psychological impact of this reclassification and discuss the ethical, legal, and practical issues involved with sharing this information with the patients who are affected.

SUMMARY

The total direct and indirect cost of thyroid cancer surveillance in patients is significant. High levels of clinically relevant distress affect up to 43% of patients with papillary thyroid carcinoma, as estimated by the Distress Thermometer developed by the National Comprehensive Cancer Network for detecting distress in cancer patients. Although there are currently no legal opinions that establish a precedent for recontacting patients whose clinical status is altered by a change in nomenclature, the prudent course would be to attend to the requirements of medical ethics.

CONCLUSION

Informing patients with a previous diagnosis of EFVPTC that the disease has been reclassified as benign is expected to have a dramatic effect on their surveillance needs and to alleviate the psychological impact of living with a diagnosis of cancer. It is important to re-evaluate the pathologic slides of those patients at risk to ensure that the invasive nature of the tumor is comprehensively evaluated before notifying a patient of a change in diagnosis. The availability of the entire tumor for evaluation of the capsule may prove to be a challenge for a portion of the population at risk. We believe that it is the clinician's professional duty to make a sincere and reasonable effort to convey the information to the affected patients. We also believe that the cost savings with respect to the need for additional surgery, radioactive iodine, and rigorous surveillance associated with a misinterpretation of the biology of the diagnosis of EFVPTC in less experienced hands will likely more than offset the cost incurred in histologic review and patient notification.

Is there a duty to recontact in light of new genetic technologies? A systematic review of the literature

PURPOSE

With rapid advances in genetic technologies, new genetic information becomes available much faster today than just a few years ago. This has raised questions about whether clinicians have a duty to recontact eligible patients when new genetic information becomes available and, if such duties exist, how they might be implemented in practice.

METHODS

We report the results of a systematic literature search on the ethical, legal, social (including psychological), and practical issues involved in recontacting former patients who received genetic services. We identified 1,428 articles, of which 61 are covered in this review.

RESULTS

The empirical evidence available indicates that most but not all patients value being recontacted. A minority of (older) articles conclude that recontacting should be a legal duty. Most authors consider recontacting to be ethically desirable but practically unfeasible. Various solutions to overcome these practical barriers have been proposed, involving efforts of laboratories, clinicians, and patients.

CONCLUSION

To advance the discussion on implementing recontacting in clinical genetics, we suggest focusing on the question of in what situations recontacting might be regarded as good standard of care. To this end, reaching a professional consensus, obtaining more extensive empirical evidence, and developing professional guidelines are important.

PhenoVar: a phenotype-driven approach in clinical genomics for the diagnosis of polymalformative syndromes

BACKGROUND

We propose a phenotype-driven analysis of encrypted exome data to facilitate the widespread implementation of exome sequencing as a clinical genetic screening test.Twenty test-patients with varied syndromes were selected from the literature. For each patient, the mutation, phenotypic data, and genetic diagnosis were available. Next, control exome-files, each modified to include one of these twenty mutations, were assigned to the corresponding test-patients. These data were used by a geneticist blinded to the diagnoses to test the efficiency of our software, PhenoVar. The score assigned by PhenoVar to any genetic diagnosis listed in OMIM (Online Mendelian Inheritance in Man) took into consideration both the patient's phenotype and all variations present in the corresponding exome. The physician did not have access to the individual mutations. PhenoVar filtered the search using a cut-off phenotypic match threshold to prevent undesired discovery of incidental findings and ranked the OMIM entries according to diagnostic score.

RESULTS

When assigning the same weight to all variants in the exome, PhenoVar predicted the correct diagnosis in 10/20 patients, while in 15/20 the correct diagnosis was among the 4 highest ranked diagnoses. When assigning a higher weight to variants known, or bioinformatically predicted, to cause disease, PhenoVar's yield increased to 14/20 (18/20 in top 4). No incidental findings were identified using our cut-off phenotypic threshold.

CONCLUSION

The phenotype-driven approach described could render widespread use of ES more practical, ethical and clinically useful. The implications about novel disease identification, advancement of complex diseases and personalized medicine are discussed.

Expanded genetic codes in next generation sequencing enable decontamination and mitochondrial enrichment

We have developed a PCR method, coined Déjà vu PCR, that utilizes six nucleotides in PCR with two methyl specific restriction enzymes that respectively digest these additional nucleotides. Use of this enzyme-and-nucleotide combination enables what we term a “DNA diode”, where DNA can advance in a laboratory in only one direction and cannot feedback into upstream assays. Here we describe aspects of this method that enable consecutive amplification with the introduction of a 5^th and 6^th base while simultaneously providing methylation dependent mitochondrial DNA enrichment. These additional nucleotides enable a novel DNA decontamination technique that generates ephemeral and easy to decontaminate DNA.

Research participants' attitudes towards the confidentiality of genomic sequence information

Respecting the confidentiality of personal data contributed to genomic studies is an important issue for researchers using genomic sequencing in humans. Although most studies adhere to rules of confidentiality, there are different conceptions of confidentiality and why it is important. The resulting ambiguity obscures what is at stake when making tradeoffs between data protection and other goals in research, such as transparency, reciprocity, and public benefit. Few studies have examined why participants in genomic research care about how their information is used. To explore this topic, we conducted semi-structured phone interviews with 30 participants in two National Institutes of Health research protocols using genomic sequencing. Our results show that research participants value confidentiality as a form of control over information about themselves. To the individuals we interviewed, control was valued as a safeguard against discrimination in a climate of uncertainty about future uses of individual genome data. Attitudes towards data sharing were related to the goals of research and details of participants' personal lives. Expectations of confidentiality, trust in researchers, and a desire to advance science were common reasons for willingness to share identifiable data with investigators. Nearly, all participants were comfortable sharing personal data that had been de-identified. These findings suggest that views about confidentiality and data sharing are highly nuanced and are related to the perceived benefits of joining a research study.

Self-guided management of exome and whole-genome sequencing results: changing the results return model

Researchers and clinicians face the practical and ethical challenge of if and how to offer for return the wide and varied scope of results available from individual exome sequencing and whole-genome sequencing. We argue that rather than viewing individual exome sequencing and whole-genome sequencing as a test for which results need to be "returned," that the technology should instead be framed as a dynamic resource of information from which results should be "managed" over the lifetime of an individual. We further suggest that individual exome sequencing and whole-genome sequencing results management is optimized using a self-guided approach that enables individuals to self-select among results offered for return in a convenient, confidential, personalized context that is responsive to their value system. This approach respects autonomy, allows individuals to maximize potential benefits of genomic information (beneficence) and minimize potential harms (nonmaleficence), and also preserves their right to an open future to the extent they desire or think is appropriate. We describe key challenges and advantages of such a self-guided management system and offer guidance on implementation using an information systems approach.