genome sequencing of human cancer tissues

Conditions: Cancer

Summary: the goal of this study is to develop a new, local system that will use special tests based on patients' genetic makeup to better tailor cancer care at the university of new mexico cancer center. the food and drug administration has already approved over forty (40) drugs to treat cancer patients based on specific genetic makeup, and more agents are in development that will support this new approach to treatment, often referred to as "personalized medicine." the goal of performing specific tests on patients' genetic material is to discover tumor-specific, single nucleotide variations (snvs) and other forms of genetic changes (called epigenetic changes) that can be detected when comparing normal tissue and tumor tissue. this can help guide cancer care decisions that may be more effective for patients. these will be called clinically actionable findings, or caf. additional health related findings may be made, not related to cancer but to other conditions, diseases or syndromes. these are called secondary findings (sf). in this study the investigators will also measure how often they find sf and will discuss their possible impact on other aspects of patients' health. if patients want to know about these findings, they will be discussed with a panel of experts including genetic counselors. finally, the investigators will compare how often caf and sf differ from those identified in nationwide samples.

for brevity, the investigators include the approaches of whole genome sequencing, whole exome sequencing of just the protein-coding exons, enrichment and sequencing of methylated dna and rna or transcriptome-sequencing under the broad category term, whole genome sequencing (wgs). the development of rapid and low cost next-generation genome sequencing technologies brings the promise of a new era of precision therapeutics to clinical practice, but it is associated with significant challenges, including reproducible generation of high-quality sequence data and the need for comprehensive data analysis and interpretation that is translatable to clinical action. equally critical are the ethical, legal, and social issues surrounding the introduction of wgs testing and its clinical application in multiethnic, multicultural populations, particularly those who have historically experienced discrimination or even unethical research practices. of particular concern are issues surrounding the privacy, ownership, storage, and use of wgs data.

Eligibility criteria:
inclusion criteria: * any patient with a malignant diagnosis at the time of diagnosis or relapse * any age (minimum 0 days old) * male or female * pregnant women are eligible for this study * patients may have existing, non-oncological genetic disorders * patients may have received any amount of prior treatment * participants (or their parent/legal guardian in the case of minors) must have the ability to understand and the willingness to sign a written informed consent or assent form exclusion criteria: * subjects for whom sufficient cancer tissues are not available to meet the objectives of the study. * cognitively impaired adults are excluded from participation * adults not able to consent for themselves are excluded from participation * prisoners may not participate in this study

Keywords: cancer oncology malignant malignancy genetics genomics exome dna rna sequencing epigenetic clinically actionable findings caf secondary findings sf single nucleotide variants snv bioinformatics genotype the american college of medical genetics and genomics acmg