ClinSeq: A Large-Scale Medical Sequencing Clinical Research Pilot Study

This study will examine genome sequencing in clinical research. Genome sequencing is a process in which researchers analyze (or sequence) part or all of the genome from a single person. The human genome is the material in cells that includes thousands of genes. Gene changes that cause or contribute to disease can be passed on from one generation to the next. This study first focuses on heart disease. Later, researchers hope to study other conditions and genes, with the eventual goal of sequencing most or all of participants genes.

Participants ages 45 to 65 years of age and who do not smoke, may be eligible for this study. Patients will come to the NIH Clinical Research Center for an initial study to last about half a day. They will donate a blood sample and complete a short survey. Then they will meet the genetic counselor to learn more about genome sequencing. Those who join the study will undergo the following procedures and evaluations:

• Family history and medical history.
• Measurement of height and blood pressure.
• Noninvasive heart tests, including electrocardiogram and echocardiogram.
• Drawing of about 3 ounces of blood (5 to 6 tablespoons); part of the blood sample will be used for research and another part for clinical testing.
• Multidetector computed tomography (CT), a test to measure coronary artery calcification, that is, condition of inflexibility.

Each patient will receive a letter with results of the clinical laboratory values and evaluations. There will be recommendations for follow-up with the patient s doctors. Risks in this study include exposure to radiation from the CT test. The radiation amount used is about the same that a person normally receives from natural sources, such as from the sun, outer space, and radioactive materials found naturally in the earth s air and soil. Another slight risk involves reactions to a contrast agent that may be used in the echocardiogram. Side effects can be headache, nausea or vomiting, a warm sensation, and dizziness.

With the samples that patients provide, researchers will start by sequencing about 400 genes related to heart disease. Analysis will take months to complete. Genome sequencing is difficult to do, and researchers have much to learn about the genes they sequence and the gene changes they find. If the researchers find gene changes that are important to the health of a participant, they will contact that participant and give him/her the choice of learning such results.

This study may or may not have a direct benefit for participants. Patients would get free clinical testing for cholesterol, diabetes, and other conditions, as well as information about gene changes. Knowledge gained will benefit people in the future as researchers learn about the relationship between gene changes and health.

The purpose of ClinSeq is to pilot large-scale medical sequencing (LSMS) in a clinical

research setting. By sequencing a person s exome or genome and returning relevant and

individual results to that person, we will begin investigating some of the technical, medical,

and genetic counseling issues that accompany the implementation of LSMS in the clinical

setting. Specifically, we seek to develop technologic and procedural infrastructures to

facilitate this type of research and demonstrate that it is feasible to sequence and interpret

large amounts of genomic sequence data and return individual results to subjects.

A cohort of ~1,500 individuals selected from the surrounding general population will be

evaluated at the NIH Clinical Center for a common set of cardiovascular phenotypic

features, including, but not limited to, coronary artery calcification, lipid profiles, and blood

pressure. Participants will be selected to fall within a spectrum of coronary artery

calcification from normal to disease phenotype based on Framingham scores. During their

initial visit, participants will undergo a clinical evaluation, targeted clinical tests, and blood

sample collection for genomic analysis. Additionally, they will be asked to provide baseline

information about pertinent health behavior and a family history. During their initial visit

and as the study progresses, participants may be asked to complete surveys related to

various socio-behavioral aspects of their participation, such as their attitudes toward

learning individual results or health behaviors related to receipt of results.

Most participants will have exome sequencing (ES), and selected participants will have

genome sequencing (GS). ClinSeq will further our understanding of the relative

contributions of rare versus common variants to the architecture of common disease.

Currently, only direct sequencing can address the question of the frequency of rare variants,

which is of particular interest to us. We will test for associations of genomic variants, some

of which will be rare, with the cardiovascular phenotype in question, as well as other

phenotypes. We have developed analytic algorithms to distinguish potentially pathogenic

genetic alterations from normal variation (Johnston et al., 2012; Ng et al., 2013; Gonsalves

et al., 2013). Sequence variants deemed clinically relevant will be validated in a CLIAcertified

laboratory and the results offered to that subject. ClinSeq is designed to provide

the long-term potential for pursuing many different clinical projects.

Relatives of ClinSeq participants may be invited to enroll in the project for more limited

studies if their participation aids our understanding of the gene variants detected in the

probands. For example, these relatives may undergo genetic testing for co-segregation of

known or suspected disease-causing variants, and/or phenotyping relevant to the disease in

question.

We aim to pilot procedures for generating data, address some of the analytical hurdles of

interpreting these data, and develop approaches for the medical and counseling challenges

of utilizing the relevant data for clinical research.

• Cardiovascular Disease
• Coronary Artery Calcification

• Antoniou A, Pharoah PD, Narod S, Risch HA, Eyfjord JE, Hopper JL, Loman N, Olsson H, Johannsson O, Borg A, Pasini B, Radice P, Manoukian S, Eccles DM, Tang N, Olah E, Anton-Culver H, Warner E, Lubinski J, Gronwald J, Gorski B, Tulinius H, Thorlacius S, Eerola H, Nevanlinna H, Syrjäkoski K, Kallioniemi OP, Thompson D, Evans C, Peto J, Lalloo F, Evans DG, Easton DF. Average risks of breast and ovarian cancer associated with BRCA1 or BRCA2 mutations detected in case Series unselected for family history: a combined analysis of 22 studies. Am J Hum Genet. 2003 May;72(5):1117-30. Epub 2003 Apr 3. Erratum in: Am J Hum Genet. 2003 Sep;73(3):709.
• Austin MA, Harding S, McElroy C. Genebanks: a comparison of eight proposed international genetic databases. Community Genet. 2003;6(1):37-45.
• Bell J. Predicting disease using genomics. Nature. 2004 May 27;429(6990):453-6. Review.

• INCLUSION CRITERIA:

Group A

We plan to recruit a cohort whose risk to develop coronary artery disease will range from less than 5 percent, based on the 10-year-risk provided by the Framingham risk score, to greater than 10 percent, and including those with known coronary artery disease. The 10-year-risk will be measured by the Framingham risk score based on LDL cholesterol levels.

Individuals eligible for Bins 1-3 of this study will be 45 to 65 years of age, and individuals eligible for Bin 4 must be 35-65 years of age. We selected this cutoff as we are interested in recruiting a cohort whose coronary artery calcification (CAC) measurements range from normal to diseased, and it has been shown that abnormal CAC is infrequent below this age. Also, individuals eligible for this study will be required to have a primary care physician or equivalent with whom we can communicate in the event we uncover a condition that merits follow-up. The exception to this includes individuals in Group A2 who are recruited through the community outreach being done by Ms. Sandra Epps. These individuals will not be required to have a primary care physician, although we will strongly recommend that they attend a community health clinic for follow-up on clinical recommendations from the study. Additionally, individuals eligible for this study will be required to be non-smokers at the time of enrollment, for our purposes defined as someone who has not smoked regularly during the previous 12 months.

Due to the large number of individuals to be recruited and the intention to follow this cohort longitudinally, we will focus our efforts on the metropolitan DC and Baltimore areas (in order to minimize reluctance to participate because of travel limitations). If recruitment is below anticipated levels, we may seek additional subjects from the Richmond, VA metropolitan area. Individuals who are not local to these areas may be considered for participation if they are part of other protocols within NHLBI, and travel to the NIH Clinical Research Center on a regular basis for follow-up, or if they are willing to travel to the NIH as needed for protocol participation (at their own expense). Bin 4 participants will be eligible to have the cost of their transportation, meals and lodging covered if they must travel >500 miles for their clinical visits.

An eligibility screen will be performed by telephone to ascertain age, basic demographics, smoking history, and presence or absence of known cardiovascular disease. We intend to recruit persons of both sexes, of diverse ethnic and racial categories, and from various socio-economic backgrounds.

Group B

The eligibility for Group B is distinct from Group A. Group B eligibility requires:

1. relative enrolled in Group A
2. age over 18 years, unless the phenotype under study affects children

EXCLUSION CRITERIA:

Individual excluded from participating in the study include: (1) first-degree relatives of enrolled ClinSeq participants (unless they fall into Group B); and (2) individuals who are directly involved with gathering data and analyzing the clinical and genotyping data, including the Principal Investigator, the Associate Investigators, the ClinSeq staff involved with the subjects at the clinical level (such as the Nurse Practitioner, Genetic counselor, etc.), and the staff at NISC involved with generating and analyzing the sequence data ; and (3) individuals who request access to their raw sequence data for analysis outside of ClinSeq ; and (4) individuals who are already enrolled in another study that provides genome or exome sequencing, such as the GENE-FORECAST Study (14-HG-0048).