Projects

The CSER consortium represents a diverse collection of projects investigating the application of genome-scale sequencing in different clinical settings including pediatric and adult sub-specialties, germline diagnostic testing and tumor sequencing, and specialty and primary care. Projects also examine the ethical, legal, and social implications of moving genomic sequencing into the clinic.

U-awards

BASIC3

Baylor Advancing Sequencing into Childhood Cancer Care

The Baylor College of Medicine Baylor Advancing Sequencing into Childhood Cancer Care (BASIC3) project aims to incorporate and evaluate the integration of CLIA-certified tumor and whole exome sequencing (WES) into the care of children with newly diagnosed solid tumors and brain tumors

CanSeq

The Use of Whole-Exome Sequencing to Guide the Care of Cancer Patients

CanSeq is a collaborative project between the Dana-Farber Cancer Institute and Broad Institute (DFCI/Broad) geared towards adult patients with advanced cancer. CanSeq aims to integrate and evaluate the integration of using whole exome sequencing (WES) in the care of cancer patients by identifying biologically consequential somatic (tumor) alterations that can be targeted by existing or emerging anticancer agents to improve patient outcomes.

CLINSEQ

A Large-Scale Medical Sequencing Clinical Research Pilot Study

ClinSeq is a pilot project that investigates the use of whole genome sequencing (WGS) for clinical research. The project aims to develop hypothesis-generating approaches for research in genomic medicine through acquiring large amounts of DNA sequence data. In the process, issues such as informed consent, disclosure of genetic information and the ethics of returning results to participants are explored.

Genomic Diagnoses for Children with Developmental Delay

The HudsonAlpha Genomic Diagnoses for Children with Developmental Delay aims to integrate whole exome sequencing (WES) to meet the diagnostic needs of children with developmental delay, intellectual disability and related health problems ("DD/ID"). This project also aims to evaluate the impact of returning genomic information to patients and parents on clinical care, family planning and other aspects.

MedSeq

Integration of Whole Genome Sequencing into Clinical Medicine

The Brigham and Women’s Hospital/Harvard Medical School (BWH/HMS) MedSeq project is focused on comparing whole genome sequencing (WGS) and current standards of care in two clinical contexts: disease-specific genomic medicine in a cardiomyopathy clinic and generic genomic medicine in primary care. This project seeks to develop a process to integrate genome sequencing into clinical medicine and explore the impact of doing so.

MI-ONCOSEQ

Exploring Precision Cancer Medicine for Sarcoma and Rare Cancers

The Michigan Oncology Sequencing Center (MI-ONCOSEQ) focuses on clinical sequencing efforts for patients with sarcoma and rare cancers. This project combines clinical oncology, cancer genetics, genomic science/bioinformatics, clinical pathology, social and behavioral sciences, and bioethics in order to implement a clinical cancer sequencing project.

NCGENES

North Carolina clinical Genomic Evaluation by Next-generation Exome Sequencing

The North Carolina clinical Genomic Evaluation by Next-generation Exome Sequencing (NCGENES) project investigates the use of whole exome sequencing (WES) as a diagnostic tool in the care of a broad range of patients, including traditionally underrepresented populations. This project also aims to evaluate the performance of WES in these clinical settings.

NEXT Medicine

Clinical sequencing in cancer: Clinical, ethical, and technological studies

The New EXome Technology in Medicine (NEXT Medicine) project at the University of Washington (UW) is a randomized controlled trial of whole exome sequencing (WES) in patients with colorectal cancer or polyposis (CRC/P) for whom a genetic test is ordered in the course of usual clinical care.

NextGen

Clinical Implementation of Carrier Testing Using Next Generation Sequencing (NGS)

NextGen aims to investigate the integration of whole genome sequencing (WGS) for women and their partners seeking pre-conception carrier status testing. A randomized clinical trial is conducted to compare couples who receive WGS to couples who receive usual care to test the clinical implications of WGS and its integration into pre-conception care.

PediSeq

Applying Genomic Sequencing in Pediatrics

The Children’s Hospital of Philadelphia (CHOP) PediSeq project is investigating the use of whole exome sequencing (WES) and whole genome sequencing (WGS) in four heterogeneous pediatric disease cohorts (bilateral sensorineural hearing impairment, intellectual disability, nuclear-encoded mitochondrial respiratory chain disorders, and sudden cardiac arrest/death).

R-awards

Challenges of informed consent in return of data from genomic research

Dr. Appelbaum will develop a menu of potential approaches for dealing with the challenges of informed consent that must be addressed before widespread efforts to return genomic research results are put into place. He will obtain the perspectives of genomic investigators and research participants, their suggestions for addressing them, and their thoughts about the various options. He will also analyze the normative issues involved and identify realistic options for future researchers.

Disclosing genomic incidental findings in a cancer biobank: An ELSI experiment

A goal of this project is to understand whether the family members of participants in cancer biobank research wish to be told about unanticipated genetic findings - a contested topic. Leaders in law, bioethics, and genetics, working with patient advocates, will consider the preferences of cancer patients and family members, asking: "what is the right thing to do?" In a first-of-its-kind study, they will next develop-and go on to test- procedures to offer information about unexpected findings to future research participants. The results of this study will have a direct impact on: (1) genetics and cancer researchers, and, (2) participants in biobanks and genetic research, including cancer patients and their families.

Impact of return of incidental genetic test results to research participants in the genomic era

Dr. Chung will investigate the preferences of participants who have enrolled in genomic research studies with respect to getting back incidental genetic results, as well as the potential psychosocial and behavioral consequences of receiving this information. Her findings will provide a more complete picture of the possible benefits and burdens of returning incidental research results to participants. Her findings will also identify the responsibilities of various users of genomic data depending on their degree of access to and connection with research participants. She will analyze a range of possible incidental findings that could be reported and explore researchers' varying responsibilities to report these results based upon their clinical and psychosocial implications.

Innovative approaches to returning results in exome and genome sequencing studies

Dr. Tabor will work with experts in clinical genetics, genomics, genetic counseling and biomedical informatics to compare the use of traditional approaches for returning research results (using face-to-face sessions with genetic counselors) to an innovative web-based tool. Based on the study findings, she will develop a framework, guidelines and proposed policies for returning genome sequencing results to research participants.

Presenting diagnostic results from large-scale clinical mutation testing

With recent advances in genotyping methods, specifically improvements in DNA microarrays and chip-scanning instrumentation, it is now technically possible and economically feasible to test large numbers of patients for several thousand known mutations associated with Mendelian disease phenotypes.

Return of research results from samples obtained for newborn screening

Dr. Lewis will conduct research to develop the normative and legal framework that will be necessary to consider if newborn screening programs are to be expanded and if efforts are to be made to offer to return results to parents for research conducted with dried blood samples. She will evaluate existing state policies on newborn screening and the development of biorepositories using dried blood samples, identify gaps in existing regulations, and develop recommendations for policymakers.

Returning research results in children: Parental preferences and expert oversight

Dr. Holm will explore the extent to which research participants' preferences can reliably guide the return of individual genomic research results and how participants' preferences regarding the return of results can be incorporated into a governance structure for a genetic research registry or biobank. At the end of this study, genetic research repositories should be better able to understand the importance of incorporating participant preferences into their governance practices around return of research results and the best approaches to do this.

Returning research results of pediatric genomic research to participants

Dr. Clayton will identify criteria to guide decisions about returning individual research results to children who participate in genomic research. She will examine U.S. law and international guidelines about decision making for and by minors as the foundation for her study. She will analyze what weight should be given to various benefits potentially associated with returning pediatric research results. These range from immediate benefit to the minor's health or for the minor's reproductive decision making later in life, to benefits to parents, the minor's siblings, or the family as a whole.

The presumptive case against returning individual results in biobanking research

Dr. Garrett will conduct philosophical research to analyze critically the claim that it is morally obligatory, or at least morally permissible, for genomic researchers who study samples in biorepositories to return individual research results participants. He will also identify and consider potential solutions for any significant practical challenges that may be encountered if a biorepository decides not to return individual research results.