Clinical Cancer Genomics Program

临床癌症遗传学服务（CCGS）是部分工作人员，有1名兼职和2名全职癌症遗传顾问（GC）。我们的临床癌症遗传学家Chimene Kesserwan博士决定从2022年7月1日开始攻读血液病理学奖学金。202年6月30日，她过渡到NIH研究合作者的职位，继续提供临床遗传专业知识，咨询，并为临床和T/N WES种系变异策展做出贡献。一旦豁免获得批准，她将进行克隆造血研究。CCGS每周与同事、学生和其他人员举行病例会议，以进行测试决策、结果解释和讨论复杂的患者。Sheila Rajagopal医生参加了我们的病例会议，并提供医疗支持，Meltzer医生认为她有所需的专业知识。CCGS取得了以下成就：1)遗传咨询师培训计划：与国家人类基因组研究所（NHGRI）就NIH遗传咨询培训计划（GCTP）重新谈判签署了谅解备忘录，于2022年4月签署。在这次更新中，NHGRI拒绝在CCR资助的2名学生之外扩大年度学生人数。第四批学员将于2022年8月开始，第二批扩展学员将于2022年12月毕业。NCI资助的GCTP助理主任继续作为希望之城癌症遗传实践社区的积极成员。今年，与dr。Biesecker和Meltzer她开发并实施了精确肿瘤学GC课程，并向约翰霍普金斯大学健康、行为与社会系申请获得信贷批准。她创建了癌症遗传标准化患者（SP）轮转，其中包括编写患者病例、演员培训、结果评估和确定额外的训导。她正在与GCTP领导层合作，编写一份关于SP最佳实践的手稿。她还设计并教授了一门配套课程，旨在提高遗传咨询学生在癌症案例准备方面的技能。她参加了外部顾问课程审查，并继续面试和排名申请人。CCGS GCs接受学生的临床经验，指导和论文建议。2) CCGS提供方案开发支持和临床服务，以管理基因组结果，并提供遗传咨询/测试。我们在2019年成为正式咨询服务的请求没有被批准。CCGS为咨询请求保留了一个中央电子邮件和电话线路，并与NHGRI合作，因此提交给NHGRI咨询服务的癌症咨询会被转回给我们。Drs。Gulley和Levine正在探索解决这个问题的方法。从2021年7月10日至2022年7月9日，CCGS收到了216次咨询（不包括t /N WES[以下数据]），另外还有125次图表和/或基因检测报告审查请求。大多数生殖系检测是由外部实验室进行的，即Invitae。外部实验室的测试请求表格由见过病人的气相色谱完成。我们组进入所有的POTS，我的CAN支付测试费用，然后每季度与PI CAN核对。Invitae已经解雇了1000名员工，这是重组的一部分，未来可能会改变我们的合同基因检测成本。Gulley博士正在与LP一起探索各种选择，以扩大他们的测试平台，包括临床级生殖细胞测试。CCGS继续看到大多数患者使用远程医疗，而不影响咨询的可用性或质量。当有临床指征时，应亲自对患者进行检查，并提取血样供实验室运送。大多数种系样本是用唾液或口腔拭子收集的。根据咨询号码和/或需要生殖系检测的协议，GCs嵌入四种服务：前列腺；肺;间皮瘤;和遗传性胃癌。从2021年7月10日至2022年7月9日，T/N WES有49个CCR。Dr. Calzone和GC Yi Liu参加了每周一次由LP组织的配对T/N WES签到会。我们的团队是QCI中所有种系变异的主要审稿人，提供最初的变异分类，并在种系报告中制作最初的变异解释部分。CCGS GC助理是所有NIH的T/N WES同意请求和患者安排的中心联系人。另有47宗不属于CCGS的T/N WES个案，其中大部分（44宗）将交由CCR POB/NOB GC处理。当患者不在临床中心时，唾液或口腔拭子试剂盒会邮寄给患者，并附有联邦快递的返回标签。CCGS目前支付所有套件购买和邮寄费用。2022年6月15日，Calzone博士会见了CCR淋巴瘤团队，包括dr。Roschewski和Staudt。他们已获得Ken aldap医生的批准，对该团队所见的所有患者进行T/N WES。所提供的估计是来自淋巴瘤小组的大约250 T/N WES病例/年。CCGS于2022年4月1日至2022年4月29日进行了工作量研究。这些数据被用于确定当前工作量，开始确定遗传咨询师用于诸如T/N WES同意/结果披露等活动的时间，以及基于病例复杂性的一般咨询的平均咨询时间。然而，这项评估是在Kesserwan博士宣布离职之前进行的。因此，正在进行第二次评估，由GC在Kesserwan博士审核确认后，对与变体管理相关的时间/工作量进行评估。这些数据将有助于了解我们是否能够适应T/N WES病例的显著增加，包括现有工作人员的变体管理。继续教育工作包括与泌尿外科肿瘤科合作的一个项目，该项目于2020年9月至2022年6月运行。每周一小时的课程向校内和校外提供者开放，授予1个CE，并录制以备将来使用。主题包括基本的癌症基因组学，遗传咨询基础，泌尿系统癌症遗传学包括治疗，期刊文章和临床病例的回顾。CCGS正在NHGRI的资助下创建一个全球遗传学和基因组学社区在线展开案例https://www.genomicscases.net/en。该案件已被拍摄下来，正处于上传到网上的最后阶段。这个网站今年将转移到genome.gov。CCGS还支持对遗传咨询职业感兴趣的学生的教育和指导。GC Grace-Ann Fasaye共同创立了遗传学机会、学习、发展、赋权和网络（GOLDEN）项目，为有兴趣从事遗传学职业的传统黑人学院和大学的学生提供服务。GOLDEN旨在增加专业多样性，并改善医疗服务不足社区的基因组服务。CCR支持了2022年3月1日开始的GOLDEN后bacc Elise Travis。她完成了一项遗传性胃癌级联测试研究，并已被录取进入2022年8月开始的博士/GC项目。3)基因组变异管理：解释基因组变异是一个挑战。ClinGen建立了一个中心资源来定义基因组变异的临床相关性，并召集了CCGS积极参与的几个工作组（WG）、工作组（TF）、基因管理专家小组和变异管理专家小组（VCEP）。随着Kesserwan博士的离职，CCGS在这些小组中的代表人数有限。Grace Fasaye继续担任CDH1 VCEP的成员。

The Clinical Cancer Genetics Service (CCGS) is partially staffed, with 1-parttime and 2 full-time cancer genetic counselors (GC). Our clinical cancer geneticist Dr. Chimene Kesserwan, decided to pursue a hematopathology fellowship starting 7/1/2022. On 6/30/202 she transitioned to an NIH Research Collaborator position continues to provide clinical genetic expertise, consultation and contributes to clinical and T/N WES germline variant curation. She will be conducting a Clonal Hematopoiesis study once the exemption is approved. The CCGS conducts weekly case conferences with fellows, students, and others for testing decisions, result interpretations and to discuss complex patients. Dr. Sheila Rajagopal attends our case conference and provides medical support which Dr. Meltzer agreed she had the expertise needed. The CCGS has achieved the following: 1) Genetic Counselor Training Program: The MOU with the National Human Genome Research Institute (NHGRI) for the NIH Genetic Counseling Training Program (GCTP) was renegotiated signed April 2022. In this renewal, NHGRI declined to expand the cohort of annual student beyond the 2 funded by CCR. The 4th cohort begins 8/2022 and the 2nd expanded cohort will graduate 12/2022. The NCI funded GCTP Assistant Director continues as an active member of the City of Hope cancer genetic Community of Practice. This year, working with Drs. Biesecker and Meltzer she developed and conducted a Precision Oncology GC course and applied to Johns Hopkins Department of Health, Behavior and Society to obtain credit approval. She created a cancer genetic standardized patient (SP) rotation that included scripting 7 patient cases, actor training, outcome assessments, and identifying additional preceptors. She is working with GCTP leadership to develop a manuscript about SP best practices. She also designed and taught a companion course aimed at improving genetic counseling students' case preparation skills in the cancer. She participated in an outside consultant curriculum review and continues to interview and rank applicants. CCGS GCs accepts students for clinical experiences, mentoring and thesis advising. Dr. Jamal continues 50% effort with the NIH Department of Bioethics. 2) CCGS provides protocol development support and clinical services to manage genomic results and provides genetic counseling/testing. Our request to be a formal consult service in 2019 was not approved. CCGS maintains a central email and phone line for consult requests and worked with NHGRI so cancer consults submitted to the NHGRI consult service are referred back to us. Drs. Gulley and Levine are exploring ways to address this. From 7/10/2021-7/9/2022 CCGS saw 216 consults (not includingT/N WES [data below]) with an additional 125 requests for chart and/or genetic test report reviews. Most germline tests are conducted by outside laboratories i.e. Invitae. Test request forms for outside labs are completed by the GC that saw the patient. Our group enters all POTS, my CAN pays for the test, then quarterly reconciles with the PI CAN. Invitae has laid off 1000 staff as part of restructuring which in the future may change our contract genetic test cost. Dr. Gulley is exploring options with LP to expand their testing platform to include clinical grade germline testing. CCGS continues to see patients mostly using telemedicine without compromising consult availability or quality. Patients are seen in person when clinically indicated and to retrieve blood samples for laboratory shipment. Most germline samples are collected using saliva or buccal swabs. GCs are embedded in four services based on consult numbers and/or protocols requiring germline testing: Prostate; Lung; Mesothelioma; and Inherited Gastric Cancer. From 7/10/2021-7/9/2022 there were 49 CCR for T/N WES. Dr. Calzone and GC Yi Liu participate in the weekly paired T/N WES signout meeting conducted by LP. Our team is the primary reviewer of all germline variants in QCI, provides the initial variant classification and crafts the initial variant interpretation section on the germline report.. The CCGS GC Assistant is the central contact for T/N WES consent requests and patient scheduling for all NIH. An additional 47 T/N WES cases not for CCGS were scheduled with most (44) going to the CCR POB/NOB GC. For T/N WES encounter occurs when the patient is not at the Clinical Center, saliva or buccal swab kits are mailed to the patient with a return Fedex label. CCGS currently covers all kit purchases and mailing costs. On 6/15/2022 Dr. Calzone met with the CCR Lymphoma team including Drs. Roschewski and Staudt. They have obtained approval from Dr. Ken Aldape to perform T/N WES on all patients seen by this team. The estimate provided is approximately 250 T/N WES cases/year from the lymphoma team. CCGS conducted a workload study from 4/1/2022-4/29/2022. These data are being used to establish current workload begin to establish genetic counselor time for activities such as T/N WES consent/result disclosure and average counselor time based for general consults based on case complexity. However, this assessment was conducted prior to Dr. Kesserwan announcing her departure. Therefore, a second assessment of the time/workload associated with variant curation when done by the GC followed by confirmation by Dr. Kesserwan review is underway. These data will help inform whether we can accommodate this significant increase in T/N WES cases including variant curation with existing staff. Continuing education efforts included a program in collaboration with the Urologic Oncology Branch which ran 9/2020-6/2022. Weekly one-hours sessions open to intramural and extramural providers awarded 1 CE and were taped for future use. Topics included basic cancer genomics, genetic counseling fundamentals, urologic cancer genetics including therapeutics, review of journal articles and clinical cases. CCGS is creating a Global Genetics and Genomics Community online unfolding case https://www.genomicscases.net/en with NHGRI funding. The case has been filmed and is in the final phases of going up online. This webite will move to genome.gov this year. CCGS also supports education and mentoring of students interested in a genetic counseling career. GC Grace-Ann Fasaye co-founded the Genetics Opportunities, Learning, Development, Empowerment and Networking (GOLDEN) Program for students at Historically Black Colleges and Universities interested in pursuing a GC career. GOLDEN aims to increase the profession diversity and improve genomic service access in medically underserved communities. CCR supported a GOLDEN post-bacc Elise Travis who started 1/3/2022. She completed an inherited gastric cancer cascade testing study and has been accepted into a PhD/GC program which begins 8/2022. 3) Genomic Variant Curation: Interpreting genomic variants is a challenge. ClinGen has built a central resource to define the clinical relevance of genomic variants and convened several Working Groups (WG), Task Forces (TF), Gene Curation Expert Panels, and Variant Curation Expert Panels (VCEP) which CCGS actively participates. With Dr. Kesserwan's departure for the fellowship, the CCGS representation on these panels is limited. Grace Fasaye continues as a member on the CDH1 VCEP.