1
|
Jacobs MF, Stoffel EM. Genetic and other risk factors for pancreatic ductal adenocarcinoma (PDAC). Fam Cancer 2024:10.1007/s10689-024-00372-5. [PMID: 38573398 DOI: 10.1007/s10689-024-00372-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 03/07/2024] [Indexed: 04/05/2024]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is often diagnosed at an advanced stage, resulting in poor prognosis and low 5-year survival rates. While early evidence suggests increased long-term survival in those with screen-detected resectable cancers, surveillance imaging is currently only recommended for individuals with a lifetime risk of PDAC ≥ 5%. Identification of risk factors for PDAC provides opportunities for early detection, risk reducing interventions, and targeted therapies, thus potentially improving patient outcomes. Here, we summarize modifiable and non-modifiable risk factors for PDAC. We review hereditary cancer syndromes associated with risk for PDAC and their implications for patients and their relatives. In addition, other biologically relevant pathways and environmental and lifestyle risk factors are discussed. Future work may focus on elucidating additional genetic, environmental, and lifestyle risk factors that may modify PDAC risk to continue to identify individuals at increased risk for PDAC who may benefit from surveillance and risk reducing interventions.
Collapse
Affiliation(s)
- Michelle F Jacobs
- Division of Genetic Medicine, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Elena M Stoffel
- Division of Gastroenterology, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA.
| |
Collapse
|
2
|
Jacobs MF, Goldman JW, Austin S, Koeppe ES, Murad AM, Koschmann CJ, Chinnaiyan AM, Mody RJ. Family Recall of and Response to Germline Pathologic Variants Found on Paired Tumor-Germline Sequencing in Pediatric Oncology. JCO Precis Oncol 2024; 8:e2300539. [PMID: 38484211 PMCID: PMC10954074 DOI: 10.1200/po.23.00539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 12/19/2023] [Accepted: 01/09/2024] [Indexed: 03/19/2024] Open
Abstract
PURPOSE Paired tumor-germline sequencing can identify somatic variants for targeted therapy and germline pathogenic variants (GPVs) causative of hereditary cancer/tumor predisposition syndromes. It is unknown how patients/families in pediatric oncology use information about an identified GPV. We assessed recall of germline results and actions taken on the basis of findings. METHODS We completed phone surveys with patients (and/or their parent) with GPVs identified via a single academic medical center's paired tumor-germline sequencing study. Seven hundred forty pediatric (aged 0-25 years) oncology patients were enrolled in this sequencing study between May 2012 and August 2021. Ninety-six participants (13.0%) had at least one GPV identified and were therefore eligible for this survey. The parent/guardian (for patients younger than 18 years or deceased patients) or patients themselves (if 18 years or older) were contacted. Survey topics included germline result recall, experience with genetic counseling, changes to patient's cancer treatment/screening, sharing of results with family members, and lifestyle changes. RESULTS Fifty-three surveys (response rate, 55.2%) were completed between October 2021 and June 2022. Thirty-seven (69.8%) respondents correctly recalled the identified GPV. Discussing results with a genetic counselor (P = .0001), having a GPV related to the cancer/tumor diagnosis (P = .002), and non-Hispanic White race/ethnicity (P = .02) were associated with accurate recall. Twenty-five respondents (47.2%) reported a change in the child's cancer treatment and/or screening recommendations, 17 respondents (32.1%) made a lifestyle change on the basis of the results, and 44 respondents (83.0%) shared results with at least one family member. CONCLUSION While most respondents remembered that a GPV was identified in the patient, some did not recall having a GPV found, and others recalled germline findings incorrectly. Future work may determine patient/family preferences for timing/method of result return to optimize patient recall and use of germline results.
Collapse
Affiliation(s)
- Michelle F. Jacobs
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI
| | | | - Sarah Austin
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI
| | - Erika S. Koeppe
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI
| | | | | | - Arul M. Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI
| | - Rajen J. Mody
- Department of Pediatrics, University of Michigan, Ann Arbor, MI
| |
Collapse
|
3
|
Jacobs MF, Koeppe ES, Chase CL, Martinez J, Henry ML, Osborne JM, Stoffel EM, Quinonez SC. Implementation of a dedicated cascade testing clinic for patients at risk for hereditary cancer syndromes. J Genet Couns 2023. [PMID: 37877326 DOI: 10.1002/jgc4.1814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 09/18/2023] [Accepted: 09/30/2023] [Indexed: 10/26/2023]
Abstract
Cascade testing, the site-specific genetic testing of relatives within families with an inherited condition, is underutilized. Long wait times for appointments in specialty genetics clinics are a known barrier to genetic testing access. In our cancer genetics, New Patient Clinic (NPC), the long wait time for an appointment (on average 5 months for routine referrals), was identified by both providers and patients as a barrier to uptake of cascade testing. Timely testing of at-risk relatives is essential to maximize the benefits of cascade testing and reduce cancer morbidity and mortality. Our objective was to improve access via implementation of a different clinical model that designated appointments for patients seeking cascade testing. A secondary goal was to improve use of genetic counselor time. We implemented a dedicated Cascade Testing Clinic (CTC) with an expedited triaging and unique scheduling model to decrease patient wait time to appointment and optimize clinician time. We report on the process and outcomes here. Between October 2016 and February 2020, the average wait time between referral date and first scheduled appointment date was 46 days for the CTC compared to 144 days for the NPC (p < 0.0001). No-show/cancelation/rescheduling rate was 11.7% in the CTC compared to 29.7% in the NPC (p < 0.0001). Genetic counselors saw approximately twice as many patients per half-day clinic in the CTC compared to the NPC (p < 0.00001). Modifications to clinic staffing and appointment times were made based on provider feedback. Implementation of a dedicated clinic specifically for patients seeking cascade testing significantly shortened wait times for this population, reduced patient drop-off, and improved clinician efficiency. The relatively straightforward indications and generally uncomplicated medical histories made this an ideal population for expedited appointments.
Collapse
Affiliation(s)
- Michelle F Jacobs
- Division of Genetic Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Rogel Cancer Center, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Erika S Koeppe
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Colby L Chase
- Division of Genetic Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Rogel Cancer Center, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Julia Martinez
- Rogel Cancer Center, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Marie-Louise Henry
- Division of Genetic Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Rogel Cancer Center, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Jenae M Osborne
- Rogel Cancer Center, Michigan Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Elena M Stoffel
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Shane C Quinonez
- Division of Genetic Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Department of Pediatric Genetics, Metabolism and Genomic Medicine, University of Michigan, Ann Arbor, Michigan, USA
| |
Collapse
|
4
|
Abusamra SM, Solorzano MA, Luke M, Quarles J, Jacobs MF, Das S, Kasputis A, Okoth LA, Patel M, Seymore M, Caram MEV, Dunn RL, Merajver SD, Stoffel EM, Reichert ZR, Morgan TM. Satisfaction With Clinician-Led Germline Genetic Counseling in Patients With Prostate Cancer. J Urol 2022; 208:1007-1017. [PMID: 35930793 PMCID: PMC10544847 DOI: 10.1097/ju.0000000000002865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 06/28/2022] [Indexed: 11/26/2022]
Abstract
PURPOSE Indications for germline testing in prostate cancer patients have expanded substantially over the past decade. With a near-universal shortage of genetic counselors and increasing demand, increased access to genetic counseling is crucial. We sought to prospectively implement and assess a clinician-led approach to genetic counseling and testing. MATERIALS AND METHODS Patients with metastatic or localized prostate cancer meeting National Comprehensive Cancer Network® criteria for consideration of genetic testing were offered pre-test genetic counseling by their urologist or medical oncologist as part of their routine clinical care and concurrently approached for enrollment in the Germline Genetics in Prostate Cancer Study. Consented patients filled out a post-counseling survey using validated instruments to assess the quality of counseling. For patients who elected to undergo genetic testing, an additional validated questionnaire was completed following disclosure of results. The primary outcome was the proportion of patients undergoing testing, with a target >60% of patients. The secondary outcome was overall satisfaction with counseling, with a target >85% of patients. RESULTS A total of 275 patients enrolled, and 203 patients elected to undergo genetic testing. Post-counseling surveys were obtained from 265 patients, and post-genetic testing surveys were obtained from 132 patients. Patient satisfaction was high, with 98% of patients reporting being satisfied with the overall quality of pre-test counseling, and 74% of patients elected to undergo genetic testing. CONCLUSIONS These results support the effectiveness of clinician-led genetic counseling in prostate cancer. With clinician training, this approach can be utilized to expand access to appropriate germline genetic testing.
Collapse
Affiliation(s)
| | - Marissa A Solorzano
- Department of Urology, University of Michigan, Ann Arbor, Michigan
- College of Human Medicine, Michigan State University, East Lansing, Michigan
| | - Mallory Luke
- Department of Urology, University of Michigan, Ann Arbor, Michigan
- School of Dentistry, University of Michigan, Ann Arbor, Michigan
| | | | - Michelle F Jacobs
- Department of Internal Medicine, Division of Genetic Medicine, University of Michigan, Ann Arbor, Michigan
| | - Sanjay Das
- Department of Urology, University of Michigan, Ann Arbor, Michigan
| | - Amy Kasputis
- Department of Urology, University of Michigan, Ann Arbor, Michigan
| | - Linda A Okoth
- Department of Urology, University of Michigan, Ann Arbor, Michigan
| | - Milan Patel
- Department of Urology, University of Michigan, Ann Arbor, Michigan
| | - Mariana Seymore
- Department of Urology, University of Michigan, Ann Arbor, Michigan
| | - Megan E V Caram
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan
| | - Rodney L Dunn
- Department of Urology, Dow Division of Health Services Research, University of Michigan, Ann Arbor, Michigan
| | - Sofia D Merajver
- Department of Internal Medicine, Division of Genetic Medicine, University of Michigan, Ann Arbor, Michigan
| | - Elena M Stoffel
- Department of Internal Medicine, Division of Genetic Medicine, University of Michigan, Ann Arbor, Michigan
| | - Zachery R Reichert
- Department of Internal Medicine, Hematology/Oncology Division, University of Michigan Medical School, Ann Arbor, Michigan
| | - Todd M Morgan
- Department of Urology, Division of Urologic Oncology, University of Michigan, Ann Arbor, Michigan
| |
Collapse
|
5
|
Sedig LK, Jacobs MF, Mody RJ, Le LQ, Bartnik NJ, Gornick MC, Anderson B, Chinnaiyan AM, Roberts JS. Adolescent and parent perspectives on genomic sequencing to inform cancer care. Pediatr Blood Cancer 2022; 69:e29791. [PMID: 35735208 DOI: 10.1002/pbc.29791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 04/28/2022] [Accepted: 05/05/2022] [Indexed: 11/11/2022]
Abstract
Next-generation sequencing offers opportunities for targeted cancer therapies and may identify pathogenic germline variants. Adolescents' perception of testing is not well understood. We surveyed 16 adolescents and 59 parents regarding motivations, attitudes, and knowledge related to paired tumor/germline sequencing. Participants generally had a good objective understanding of germline genetics and cancer risk, with parents scoring higher than adolescents. Nearly all participants were motivated by a desire to help other patients and to treat their child/themselves. Most adolescents reported involvement in the decision to enroll in the study. Study findings suggest important similarities and differences between parent and adolescent views.
Collapse
Affiliation(s)
- Laura K Sedig
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Michelle F Jacobs
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Rajen J Mody
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Lan Q Le
- Department of Health Behavior & Health Education, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Natalie J Bartnik
- Department of Health Behavior & Health Education, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Michele C Gornick
- Center for Bioethics & Social Sciences in Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Bailey Anderson
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - Arul M Chinnaiyan
- Department of Pathology, University of Michigan Medical School, Ann Arbor, Michigan, USA
| | - J Scott Roberts
- Department of Health Behavior & Health Education, University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| |
Collapse
|
6
|
Jacobs MF, Robinson D, Wu YM, Opipari VP, Mody R. Homozygous ATM mutation due to germline uniparental isodisomy in patient with T acute lymphoblastic leukemia and hepatosplenic T-cell lymphoma. Cancer Genet 2022; 266-267:15-18. [DOI: 10.1016/j.cancergen.2022.05.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 03/05/2022] [Accepted: 05/16/2022] [Indexed: 11/16/2022]
|
7
|
Maurer LM, Daley JD, Mukherjee E, Venier RE, Julian CM, Bailey NG, Jacobs MF, Kumar-Sinha C, Raphael H, Periyapatna N, Weiss K, Janeway KA, Mody R, Lucas PC, McAllister-Lucas LM, Bailey KM. BRCA1-associated RING domain-1 (BARD1) loss and GBP1 expression enhance sensitivity to DNA damage in Ewing sarcoma. Cancer Res Commun 2022; 2:220-232. [PMID: 36187937 PMCID: PMC9524505 DOI: 10.1158/2767-9764.crc-21-0047] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Ewing sarcoma is a fusion oncoprotein-driven primary bone tumor. A subset of patients (~10%) with Ewing sarcoma are known to harbor germline variants in a growing number of genes involved in DNA damage repair. We recently reported our discovery of a germline mutation in the DNA damage repair protein BARD1 (BRCA1-associated RING domain-1) in a patient with Ewing sarcoma. BARD1 is recruited to the site of DNA double stranded breaks via the poly(ADP-ribose) polymerase (PARP) protein and plays a critical role in DNA damage response pathways including homologous recombination. We thus questioned the impact of BARD1 loss on Ewing cell sensitivity to DNA damage and the Ewing sarcoma transcriptome. We demonstrate that PSaRC318 cells, a novel patient-derived cell line harboring a pathogenic BARD1 variant, are sensitive to PARP inhibition and by testing the effect of BARD1 depletion in additional Ewing sarcoma cell lines, we confirm that BARD1 loss enhances cell sensitivity to PARP inhibition plus radiation. Additionally, RNA-seq analysis revealed that loss of BARD1 results in the upregulation of GBP1 (guanylate-binding protein 1), a protein whose expression is associated with variable response to therapy depending on the adult carcinoma subtype examined. Here, we demonstrate that GBP1 contributes to the enhanced sensitivity of BARD1 deficient Ewing cells to DNA damage. Together, our findings demonstrate the impact of loss-of function mutations in DNA damage repair genes, such as BARD1, on Ewing sarcoma treatment response.
Collapse
Affiliation(s)
- Lisa M Maurer
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Jessica D Daley
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Elina Mukherjee
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Rosemarie E Venier
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA.,Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA
| | - Claire M Julian
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Nathanael G Bailey
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Michelle F Jacobs
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI
| | | | - Haley Raphael
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Nivitha Periyapatna
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Kurt Weiss
- Department of Orthopedic Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Katherine A Janeway
- Pediatric Oncology, Dana-Farber / Boston Children's Cancer and Blood Disorders Center, Boston, MA
| | - Rajen Mody
- Department of Pediatrics, University of Michigan Medical School, Ann Arbor, MI
| | - Peter C Lucas
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | | | - Kelly M Bailey
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA
| |
Collapse
|
8
|
Abstract
A new software package provides more accurate cancer risk prediction profiles and has the ability to integrate more genes and cancer types in the future.
Collapse
|
9
|
Dettwyler SA, Koeppe ES, Jacobs MF, Stoffel EM. Outcomes of retesting in patients with previously uninformative cancer genetics evaluations. Fam Cancer 2021; 21:375-385. [PMID: 34545504 DOI: 10.1007/s10689-021-00276-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 09/12/2021] [Indexed: 11/24/2022]
Abstract
Advances in cancer genetics have increased germline pathogenic/likely pathogenic variant (PV/LPV) detection rates. More data is needed to inform which patients with previously uninformative results could benefit most from retesting, especially beyond breast/ovarian cancer populations. Here, we describe retesting outcomes and predictors of PV/LPVs in a cohort of patients unselected by cancer diagnosis. Retrospective chart reviews were conducted for patients at a cancer genetics clinic between 1998 and 2019 who underwent genetic testing (GT) on ≥ 2 dates with ≥ 1 year between tests, with no PV/LPVs on first-line GT. Demographics, retesting indications, and GT details were reviewed to evaluate predictive factors of PV/LPV identification. 139 patients underwent retesting, of whom 24 (17.3%) had a PV/LPV, encompassing 15 genes. 14 PV/LPV carriers (58.3%) only returned for retesting after personal or familial history changes (typically new cancer diagnoses), while 10 (41.7%) retested due to updated GT availability. No specific GT method was most likely to identify PV/LPVs and no specific clinical factors were predictive of a PV/LPV. The identified PV/LPVs were consistent with patients' personal or family histories, but were discordant with the initial referral indication for GT. For 16 (66.7%) PV/LPV carriers, the genetic diagnosis changed clinical management. This study adds to the limited body of literature on retesting outcomes beyond first-line BRCA analysis alone and confirms the utility of multigene panel testing. Retesting certain affected individuals when updated GT is available could result in earlier PV/LPV identification, significantly impacting screening recommendations and potentially reducing cancer-related morbidity and mortality.
Collapse
Affiliation(s)
| | - Erika S Koeppe
- Michigan Medicine Cancer Genetics Clinic, Ann Arbor, MI, USA
| | | | - Elena M Stoffel
- Michigan Medicine Cancer Genetics Clinic, Ann Arbor, MI, USA
| |
Collapse
|
10
|
Quinonez SC, O’Connor BC, Jacobs MF, Mekonnen Tekleab A, Marye A, Bekele D, Yashar BM, Hanson E, Yeshidinber A, Wedaje G. The introduction of genetic counseling in Ethiopia: Results of a training workshop and lessons learned. PLoS One 2021; 16:e0255278. [PMID: 34297771 PMCID: PMC8301664 DOI: 10.1371/journal.pone.0255278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 07/14/2021] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Over the past two decades non-communicable diseases (NCDs) have steadily increased as a cause of worldwide disability and mortality with a concomitant decrease in disease burden from communicable, maternal, neonatal and nutritional conditions. Congenital anomalies, the most common NCD affecting children, have recently become the fifth leading cause of under-five mortality worldwide, ahead of other conditions such as malaria, neonatal sepsis and malnutrition. Genetic counseling has been shown to be an effective method to decrease the impact of congenital anomalies and genetic conditions but is absent in almost all sub-Saharan Africa countries. To address this need for counseling services we designed and implemented the first broad-based genetic counseling curriculum in Ethiopia, launching it at St. Paul's Millennium Medical College (SPHMMC) in Addis Ababa, Ethiopia. METHODS The curriculum, created by Michigan Medicine and SPHMMC specialists, consisted of medical knowledge and genetic counseling content and was delivered to two cohorts of nurses. Curriculum evaluation consisted of satisfaction surveys and pre- and post-assessments covering medical knowledge and genetic counseling content. Following Cohort 1 training, the curriculum was modified to increase the medical knowledge material and decrease Western genetic counseling principles material. RESULTS Both cohorts reported high levels of satisfaction but felt the workshop was too short. No significant improvements in assessment scores were seen for Cohort 1 in terms of total scores and medical knowledge and genetic counseling-specific questions. Following curriculum modification, improvements were seen in Cohort 2 with an increase in total assessment scores from 63% to 73% (p = 0.043), with medical knowledge-specific questions increasing from 57% to 79% (p = 0.01) with no significant change in genetic counseling-specific scores. Multiple logistic, financial, cultural and systems-specific barriers were identified with recommendations for their consideration presented. CONCLUSION Genetics medical knowledge of Ethiopian nurses increased significantly following curriculum delivery though difficulty was encountered with Western genetic counseling material.
Collapse
Affiliation(s)
- Shane C. Quinonez
- Division of Pediatric Genetics, Metabolism and Genomic Medicine, Department of Pediatrics, Michigan Medicine, Ann Arbor, Michigan, United States of America
- Division of Genetic Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Bridget C. O’Connor
- Division of Pediatric Genetics, Metabolism and Genomic Medicine, Department of Pediatrics, Michigan Medicine, Ann Arbor, Michigan, United States of America
| | - Michelle F. Jacobs
- Division of Genetic Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Atnafu Mekonnen Tekleab
- Department of Pediatrics, St. Paul’s Hospital Millennium Medical College, Addis Ababa, Ethiopia
| | - Ayalew Marye
- Department of Obstetrics and Gynecology, Saint Paul’s Hospital Millennium Medical College, Addis Ababa, Ethiopia
| | - Delayehu Bekele
- Department of Obstetrics and Gynecology, Saint Paul’s Hospital Millennium Medical College, Addis Ababa, Ethiopia
| | - Beverly M. Yashar
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Erika Hanson
- Division of Genetic Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Abate Yeshidinber
- Department of Pediatrics, St. Paul’s Hospital Millennium Medical College, Addis Ababa, Ethiopia
| | - Getahun Wedaje
- Department of Pediatrics, St. Paul’s Hospital Millennium Medical College, Addis Ababa, Ethiopia
| |
Collapse
|
11
|
Sessine MS, Das S, Park B, Salami SS, Kaffenberger SD, Kasputis A, Solorzano M, Luke M, Vince RA, Kaye DR, Borza T, Stoffel EM, Cobain E, Merajver SD, Jacobs MF, Milliron KJ, Caba L, van Neste L, Mondul AM, Morgan TM. Initial Findings from a High Genetic Risk Prostate Cancer Clinic. Urology 2021; 156:96-103. [PMID: 34280438 DOI: 10.1016/j.urology.2021.05.078] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 05/06/2021] [Accepted: 05/11/2021] [Indexed: 01/23/2023]
Abstract
OBJECTIVE To improve prostate cancer screening for high-risk men, we developed an early detection clinic for patients at high genetic risk of developing prostate cancer. Despite the rapidly growing understanding of germline variants in driving aggressive prostate cancer and the increased availability of genetic testing, there is little evidence surrounding how best to screen these men. METHODS We are reporting on the first 45 patients enrolled, men between the ages of 35-75, primarily with known pathogenic germline variants in prostate cancer susceptibility genes. Screening consists of an intake lifestyle survey, PSA, DRE, and SelectMDx urine assay. A biopsy was recommended for any of the following indications: 1) abnormal DRE, 2) PSA above threshold, or 3) SelectMDx above threshold. The primary outcomes were number needed to screen, and number needed to biopsy to diagnose a patient with prostate cancer. RESULTS Patients enrolled in the clinic included those with BRCA1 (n=7), BRCA2 (n=16), Lynch Syndrome (n=6), and CHEK2 (n = 4) known pathogenic germline variants. The median age and PSA were 58 (range 35-71) and 1.4 ng/ml (range 0.1-11.4 ng/ml), respectively. 12 patients underwent a prostate needle biopsy and there were 4positive biopsies for prostate cancer. CONCLUSION These early data support the feasibility of opening a dedicated clinic for men at high genetic risk of prostate cancer. This early report on the initial enrollment of our long-term study will help optimize early detection protocols and provide evidence for personalized prostate cancer screening in men with key pathogenic germline variants.
Collapse
Affiliation(s)
| | - Sanjay Das
- Department of Urology, Michigan Medicine
| | - Bumsoo Park
- Department of Urology, Michigan Medicine; Department of Family Medicine, Michigan Medicine
| | | | | | | | | | | | | | | | - Tudor Borza
- Department of Urology, University of Wisconsin School of Medicine and Public Health; Division of Urology, William S Middleton Memorial Veterans Hospital
| | | | - Erin Cobain
- Medical Genetics, Rogel Cancer Center, Michigan Medicine
| | | | | | | | | | | | | | | |
Collapse
|
12
|
Grogan NM, Wu YM, Robinson DR, Rae JM, Henry NL, Hayes DF, Jacobs MF, Milliron KJ, Hulswit B, Hipp LE, Merajver S, Stoffel EM, Chinnaiyan A, Cobain EF. Use of comprehensive next-generation sequencing to identify pathogenic germline variants with therapeutic relevance in metastatic breast cancer. J Clin Oncol 2021. [DOI: 10.1200/jco.2021.39.15_suppl.10527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
10527 Background: Among patients with early-stage breast cancer, approximately 6-10% have a pathogenic germline variant (PGV) conferring inherited cancer predisposition. In contrast, few studies have explored the frequency and types of PGVs identified in patients with metastatic breast cancer (MBC); therefore, additional data is needed. Methods: From 2011-2020, 278 patients with MBC underwent fresh tumor biopsy and blood sample collection for paired tumor/normal DNA (targeted exome capture with analysis of 1700 genes) and RNA (tumor transcriptome) sequencing through the Michigan Oncology Sequencing (Mi-ONCOSEQ) program. Somatic and germline alterations were annotated and classified according to degree of clinical actionability with results returned to treating oncologists. Retrospective chart review was performed to determine if: 1) a PGV was identified prior to Mi-ONCOSEQ testing, 2) patients met National Comprehensive Cancer Network (NCCN) guideline criteria for genetic testing on the basis of personal or family cancer history and 3) patients received subsequent therapy informed by a PGV. Results: Forty-eight of the 278 patients (17.3%) had at least one PGV identified, with a total of 50 PGVs identified in this cohort. Only twelve of these PGVs (24%) had been identified prior to Mi-ONCOSEQ testing. The most frequent PGVs identified were in CHEK 2 (n = 9, 18%), MUTYH (n = 6, 12%), BRCA 1 (n = 5, 10%), BRCA2 (n = 5, 10%), ATM (n = 4, 8%) and PALB2 (n = 4, 8%). Somatic loss of heterozygosity events (LOH) occurred in 30 of the 50 cases with PGVs identified (60%). LOH events were observed in 83.3% of BRCA1, BRCA2, ATM and PALB2 PGVs, but were less frequently observed with CHEK2 (33.3%) and MUTYH (66.7%). Two hundred sixteen out of 278 patients (77.7%) in this cohort met NCCN criteria for genetic testing, although six patients with a PGV identified (CHEK2: n = 5; MUTYH: n = 1) did not meet NCCN criteria. Twenty-nine PGVs identified (58%) had potential therapeutic relevance and 11 patients (22.9%) received targeted therapy based on the PGV. Conclusions: The frequency of PGVs identified in this cohort is nearly double the frequency reported for patients with early-stage disease, suggesting that certain PGVs may confer worse prognosis. CHEK2, the most frequently identified PGV, was less likely to have an identifiable LOH event. The direct role of CHEK2 PGVs in tumor pathogenesis is uncertain, but other mechanisms of silencing the wild type allele must be considered. Despite the majority of patients meeting NCCN criteria for genetic testing, those with PGVs in CHEK2 were less reliably identified by this mechanism. The majority of PGVs identified were of potential therapeutic relevance, supporting the recommendation for genetic testing in all patients with MBC.
Collapse
Affiliation(s)
| | - Yi-Mi Wu
- University of Michigan, Ann Arbor, MI
| | | | - James M. Rae
- University of Michigain Health System, Ann Arbor, MI
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
13
|
Cobain EF, Wu YM, Vats P, Chugh R, Worden F, Smith DC, Schuetze SM, Zalupski MM, Sahai V, Alva A, Schott AF, Caram MEV, Hayes DF, Stoffel EM, Jacobs MF, Kumar-Sinha C, Cao X, Wang R, Lucas D, Ning Y, Rabban E, Bell J, Camelo-Piragua S, Udager AM, Cieslik M, Lonigro RJ, Kunju LP, Robinson DR, Talpaz M, Chinnaiyan AM. Assessment of Clinical Benefit of Integrative Genomic Profiling in Advanced Solid Tumors. JAMA Oncol 2021; 7:525-533. [PMID: 33630025 PMCID: PMC7907987 DOI: 10.1001/jamaoncol.2020.7987] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Question What is the clinical utility of genomic profiling for patients with advanced solid tumors? Findings In this cohort study of 1015 patients who underwent integrative genomic profiling, a high rate of pathogenic germline variants and a subset of patients who derive substantial clinical benefit from sequencing information were identified. Meaning These findings support (1) directed germline testing for inherited cancer predisposition in all patients with advanced cancer and (2) use of integrative genomic profiling as a component of standard of care for patients with cancer of unknown origin and other rare malignant neoplasms. Importance Use of next-generation sequencing (NGS) to identify clinically actionable genomic targets has been incorporated into routine clinical practice in the management of advanced solid tumors; however, the clinical utility of this testing remains uncertain. Objective To determine which patients derived the greatest degree of clinical benefit from NGS profiling. Design, Setting, and Participants Patients in this cohort study underwent fresh tumor biopsy and blood sample collection for genomic profiling of paired tumor and normal DNA (whole-exome or targeted-exome capture with analysis of 1700 genes) and tumor transcriptome (RNA) sequencing. Somatic and germline genomic alterations were annotated and classified according to degree of clinical actionability. Results were returned to treating oncologists. Data were collected from May 1, 2011, to February 28, 2018, and analyzed from May 1, 2011, to April 30, 2020. Main Outcomes and Measures Patients’ subsequent therapy and treatment response were extracted from the medical record to determine clinical benefit rate from NGS-directed therapy at 6 months and exceptional responses lasting 12 months or longer. Results During the study period, NGS was attempted on tumors from 1138 patients and was successful in 1015 (89.2%) (MET1000 cohort) (538 men [53.0%]; mean [SD] age, 57.7 [13.3] years). Potentially clinically actionable genomic alterations were discovered in 817 patients (80.5%). Of these, 132 patients (16.2%) received sequencing-directed therapy, and 49 had clinical benefit (37.1%). Exceptional responses were observed in 26 patients (19.7% of treated patients). Pathogenic germline variants (PGVs) were identified in 160 patients (15.8% of cohort), including 49 PGVs (4.8% of cohort) with therapeutic relevance. For 55 patients with carcinoma of unknown primary origin, NGS identified the primary site in 28 (50.9%), and sequencing-directed therapy in 13 patients resulted in clinical benefit in 7 instances (53.8%), including 5 exceptional responses. Conclusions and Relevance The high rate of therapeutically relevant PGVs identified across diverse cancer types supports a recommendation for directed germline testing in all patients with advanced cancer. The high frequency of therapeutically relevant somatic and germline findings in patients with carcinoma of unknown primary origin and other rare cancers supports the use of comprehensive NGS profiling as a component of standard of care for these disease entities.
Collapse
Affiliation(s)
- Erin F Cobain
- Department of Internal Medicine, University of Michigan, Ann Arbor
| | - Yi-Mi Wu
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor.,Department of Pathology, University of Michigan, Ann Arbor
| | - Pankaj Vats
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor
| | - Rashmi Chugh
- Department of Internal Medicine, University of Michigan, Ann Arbor
| | - Francis Worden
- Department of Internal Medicine, University of Michigan, Ann Arbor
| | - David C Smith
- Department of Internal Medicine, University of Michigan, Ann Arbor
| | - Scott M Schuetze
- Department of Internal Medicine, University of Michigan, Ann Arbor
| | - Mark M Zalupski
- Department of Internal Medicine, University of Michigan, Ann Arbor
| | - Vaibhav Sahai
- Department of Internal Medicine, University of Michigan, Ann Arbor
| | - Ajjai Alva
- Department of Internal Medicine, University of Michigan, Ann Arbor.,Michigan Center for Translational Pathology, University of Michigan, Ann Arbor
| | - Anne F Schott
- Department of Internal Medicine, University of Michigan, Ann Arbor
| | - Megan E V Caram
- Department of Internal Medicine, University of Michigan, Ann Arbor
| | - Daniel F Hayes
- Department of Internal Medicine, University of Michigan, Ann Arbor
| | - Elena M Stoffel
- Department of Internal Medicine, University of Michigan, Ann Arbor
| | | | - Chandan Kumar-Sinha
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor.,Department of Pathology, University of Michigan, Ann Arbor
| | - Xuhong Cao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor
| | - Rui Wang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor
| | - David Lucas
- Department of Pathology, University of Michigan, Ann Arbor
| | - Yu Ning
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor
| | - Erica Rabban
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor
| | - Janice Bell
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor
| | | | - Aaron M Udager
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor.,Department of Pathology, University of Michigan, Ann Arbor
| | - Marcin Cieslik
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor.,Department of Pathology, University of Michigan, Ann Arbor
| | - Robert J Lonigro
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor
| | - Lakshmi P Kunju
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor.,Department of Pathology, University of Michigan, Ann Arbor
| | - Dan R Robinson
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor.,Department of Pathology, University of Michigan, Ann Arbor
| | - Moshe Talpaz
- Department of Internal Medicine, University of Michigan, Ann Arbor.,Rogel Cancer Center, University of Michigan, Ann Arbor
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor.,Department of Pathology, University of Michigan, Ann Arbor.,Rogel Cancer Center, University of Michigan, Ann Arbor.,Department of Urology, University of Michigan, Ann Arbor.,Howard Hughes Medical Institute, University of Michigan, Ann Arbor
| |
Collapse
|
14
|
Jacobs MF, O'Connor BC, Weldetsadik AY, Tekleab AM, Bekele D, Hanson E, Quinonez SC. Knowledge and attitudes about genetic counseling in patients at a major hospital in Addis Ababa, Ethiopia. J Genet Couns 2020; 30:544-552. [PMID: 33118289 DOI: 10.1002/jgc4.1340] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 09/03/2020] [Accepted: 09/08/2020] [Indexed: 11/11/2022]
Abstract
Previous work at St. Paul's Hospital Millennium Medical College (SPHMMC) in Addis Ababa, Ethiopia, demonstrated a need for genetic counseling (GC) services, with 4% of pediatric, neonatal intensive care, and prenatal patients identified as having indications for genetic evaluation (Quinonez et al, 2019). The aim of this study was to investigate SPHMMC patients' familiarity with, knowledge of, and attitudes toward GC services. Surveys were adapted from previous work in North America populations (Riesgraf et al, 2015 and Gemmell et al, 2017) and administered to 102 patients, and results were compared to North American populations using Student's t test. 30% of respondents reported at least some familiarity with GC, primarily via the media or healthcare providers. Patients had generally positive attitudes toward GC, reporting they would trust information provided by a genetic counselor and that GC is in line with their values. Knowledge of GC showed similar trends overall when compared to results from North American populations. Our work indicates limited exposure to GC in this population, but generally positive feelings toward GC. Patients' attitudes toward GC were comparable to rural North American populations surveyed using the same tool on most items; however, cultural differences including views on abortions and directiveness of healthcare providers could account for discrepancies and are important considerations when implementing genetic services globally.
Collapse
Affiliation(s)
- Michelle F Jacobs
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA.,Rogel Cancer Center, Michigan Medicine, Ann Arbor, MI, USA
| | | | | | - Atnafu Mekonnen Tekleab
- Department of Pediatrics, St. Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia
| | - Delayehu Bekele
- Department of Gynecology/Obstetrics, St. Paul's Hospital Millennium Medical College, Addis Ababa, Ethiopia
| | - Erika Hanson
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Shane C Quinonez
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA.,Department of Pediatrics, University of Michigan, Ann Arbor, MI, USA
| |
Collapse
|
15
|
Khairi S, Osborne J, Jacobs MF, Clines GT, Miller BS, Hughes DT, Else T. Outcome of Clinical Genetic Testing in Patients with Features Suggestive for Hereditary Predisposition to PTH-Mediated Hypercalcemia. Discov Oncol 2020; 11:250-255. [PMID: 32761341 DOI: 10.1007/s12672-020-00394-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 07/27/2020] [Indexed: 12/16/2022] Open
Abstract
Primary hyperparathyroidism (pHPT) is associated with familial syndromes such as multiple endocrine neoplasia type 1 (MEN1), 2A (MEN2A), MEN-like syndromes (CDKN1B), and CDC73-related disorder (hyperparathyroidism - jaw tumor syndrome (HPJT)). Familial hypocalciuric hypercalcemia (FHH) caused by CASR variants is an important differential diagnosis for pHPT. In order to evaluate the contribution of hereditary causes to pHPT in patients encountered in a specialized clinic, we conducted a retrospective study on patients with pHPT that underwent germline genetic testing. We evaluated 46 patients referred to a Cancer Genetics Clinic. Reasons for referral were young age (age < 40) for 29 patients (63%), multi-gland disease for 23 patients (50%), and a positive family history of pHPT for 11 patients (24%). All 46 patients underwent genetic evaluation. A total of 11 rare variants were found (CASR (4), CDC73 (2), MEN1 (2) CDKN1B (1), and RET (2)). One MEN1 variant was classified as pathogenic, and all others were variants of uncertain significance (VUS). All patients with CASR variants had clinical features of FHH and were counselled against parathyroidectomy. Both patients with CDC73 variants were counselled about recurrence of pHPT and parathyroid cancer. Neither of the RET variants were MEN2-associated. The CDKN1B variant was regarded as a true VUS and no action was taken. In this study, genetic testing impacted clinical care in 7 (15%) patients. We suggest that all patients < 40 years of age, with multi-gland disease, single gland disease refractory to treatment, and a positive family history for pHPT or associated tumors should be considered for genetic evaluation.
Collapse
Affiliation(s)
- Shafaq Khairi
- Department of Internal Medicine, Division of Metabolism, Endocrinology and Diabetes, University of Michigan, 1150 West Medical Center Drive, Ann Arbor, MI, 48109, USA
| | - Jenae Osborne
- Department of Internal Medicine, Division of Genetic Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Michelle F Jacobs
- Department of Internal Medicine, Division of Genetic Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Gregory T Clines
- Department of Internal Medicine, Division of Metabolism, Endocrinology and Diabetes, University of Michigan, 1150 West Medical Center Drive, Ann Arbor, MI, 48109, USA
| | - Barbra S Miller
- Department of Surgery, Division of Endocrine Surgery, University of Michigan, Ann Arbor, MI, USA
| | - David T Hughes
- Department of Surgery, Division of Endocrine Surgery, University of Michigan, Ann Arbor, MI, USA
| | - Tobias Else
- Department of Internal Medicine, Division of Metabolism, Endocrinology and Diabetes, University of Michigan, 1150 West Medical Center Drive, Ann Arbor, MI, 48109, USA.
| |
Collapse
|
16
|
Scott AJ, Tokaz MC, Jacobs MF, Chinnaiyan AM, Phillips TJ, Wilcox RA. Germline variants discovered in lymphoma patients undergoing tumor profiling: a case series. Fam Cancer 2020; 20:61-65. [PMID: 32504211 DOI: 10.1007/s10689-020-00192-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 06/02/2020] [Indexed: 11/29/2022]
Abstract
Clinical tumor sequencing protocols often depend on obtaining germline DNA from patients to aid in the identification of de novo variants in the tumor, and therefore come with the possibility for the incidental discovery of germline variants. Ninety-one adult patients with lymphoma were consented and enrolled in MIONCOSEQ, an IRB-approved tumor profiling protocol that utilizes an exome sequencing platform. Charts were retrospectively reviewed for germline variants from sequencing results, personal and/or family history of cancer and genetic counseling referral. After review of the 91 lymphoma cases, seven (8%) cases revealed germline variants. Only one of these, CHEK2 p.I157T, has been previously recovered as a germline variant in lymphoma. Two of the seven patients received genetic counseling, two died before genetic counseling could be arranged and three did not follow-up with a genetics provider. None of the patients had a personal or family history that would have otherwise suggested an indication for cancer genetics referral, especially notable as lymphoma is not traditionally associated with inherited cancer syndromes. Importantly, as only two of seven patients had appropriate genetic counseling for their variant, timely genetic counseling should be a critical part of all tumor profiling platforms that use non-tumor DNA.
Collapse
Affiliation(s)
- Anthony J Scott
- Division of Genetics, Metabolism and Genomic Medicine, Department of Pediatrics, University of Michigan, 1500 East Medical Center Drive, Ann Arbor, MI, 48109, USA.
| | - Molly C Tokaz
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Michelle F Jacobs
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | | | - Tycel J Phillips
- Division of Hematology/Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Ryan A Wilcox
- Division of Hematology/Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| |
Collapse
|
17
|
Wolf KI, Jacobs MF, Mehra R, Begani P, Davenport MS, Marentette LJ, Basura GJ, Hughes DT, Else T. A Family With a Carotid Body Paraganglioma and Thyroid Neoplasias With a New SDHAF2 Germline Variant. J Endocr Soc 2019; 3:2151-2157. [PMID: 31687641 PMCID: PMC6821206 DOI: 10.1210/js.2018-00353] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2018] [Accepted: 08/29/2019] [Indexed: 01/17/2023] Open
Abstract
At least 30% of all pheochromocytomas (PCCs)/paragangliomas (PGLs) arise in patients with a germline predisposition syndrome. Variants in succinate dehydrogenase subunits A, B, C, and D (SDHA, SDHB, SDHC, and SDHD) are the most common pathogenic germline alterations. Few pathogenic variants have been reported in succinate dehydrogenase assembly factor 2 (SDHAF2). Here, we describe a 30-year-old female patient who presented with a left-sided neck mass, which was later characterized as a carotid body PGL. Genetic testing revealed a likely pathogenic SDHAF2 variant (c.347G>A;p.W116X). Two sisters carried the same pathologic variant, and screening protocols were recommended. Whole-body MRI revealed thyroid nodules; this testing was followed by fine-needle aspiration, which confirmed papillary thyroid carcinoma in one sister and a follicular adenoma in the other. The two sisters then underwent hemithyroidectomy and total thyroidectomy, respectively. Because evidence for pathogenic variants in SDHAF2 causing predisposition to PCC/PGL is limited, we discuss the challenges in mutational variant interpretation and decision making regarding screening for associated tumors.
Collapse
Affiliation(s)
- Katherine I Wolf
- Department of Internal Medicine, Division of Metabolism, Endocrinology and Diabetes, Michigan Medicine, Ann Arbor, Michigan
| | - Michelle F Jacobs
- Department of Internal Medicine, Division of Genetic Medicine, Michigan Medicine, Ann Arbor, Michigan
| | - Rohit Mehra
- Department of Pathology, Michigan Center for Translational Pathology, Michigan Medicine, Ann Arbor, Michigan
| | - Priya Begani
- Department of Internal Medicine, Division of Metabolism, Endocrinology and Diabetes, Michigan Medicine, Ann Arbor, Michigan
| | | | - Lawrence J Marentette
- Department of Otolaryngology-Head and Neck Surgery, Michigan Medicine, Ann Arbor, Michigan
| | - Gregory J Basura
- Department of Otolaryngology-Head and Neck Surgery, Kresge Hearing Research Institute, Michigan Medicine, Ann Arbor, Michigan
| | - David T Hughes
- Department of Surgery, Division of Endocrine Surgery, Michigan Medicine, Ann Arbor, Michigan
| | - Tobias Else
- Department of Internal Medicine, Division of Metabolism, Endocrinology and Diabetes, Michigan Medicine, Ann Arbor, Michigan
| |
Collapse
|
18
|
Jacobs MF, Dust H, Koeppe E, Wong S, Mulholland M, Choi EY, Appelman H, Stoffel EM. Outcomes of Endoscopic Surveillance in Individuals With Genetic Predisposition to Hereditary Diffuse Gastric Cancer. Gastroenterology 2019; 157:87-96. [PMID: 30935944 DOI: 10.1053/j.gastro.2019.03.047] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 03/18/2019] [Accepted: 03/25/2019] [Indexed: 12/18/2022]
Abstract
BACKGROUND & AIMS Pathogenic germline variants in CDH1 are associated with risk for diffuse gastric cancer (DGC) and lobular breast cancer. The reported high incidence of DGC and limited sensitivity of endoscopy in detection have prompted recommendation for total prophylactic gastrectomy for carriers of pathogenic or likely pathogenic (PLP) germline variants of CDH1. Multigene panel tests have identified increasing numbers of carriers of PLP variants in CDH1 who lack a family history of DGC. We evaluated outcomes of endoscopic surveillance for carriers of PLP variants of CDH1 with and without family history of DGC. METHODS Individuals from 13 families with germline PLP variants of CDH1 were evaluated at the Michigan Medicine Cancer Genetics Clinic from January 1998 through May 2018. Outcomes of esophagogastroduodenoscopy examinations, histopathology analyses, and surgery were compared between individuals with and without a family history of DGC. RESULTS We identified 20 carriers of germline CDH1 PLP variants; they underwent endoscopic examinations and/or gastrectomy. None had abnormal findings visible during endoscopy. Signet ring cell carcinoma (SRCC) was detected in 12 of 20 subjects. All but 1 of the carcinomas were tiny and confined to the lamina propria, and 1 was transmural. Seven of 12 subjects who had SRCC reported no diagnoses of DGC in first-degree relatives and did not meet established criteria for CDH1 analysis based on a 3-generation family pedigree. CONCLUSIONS More than half of individuals with germlines variants of CDH1 that are PLP had histopathologic evidence for DGC on endoscopy and/or gastrectomy. Family history of DGC and endoscopic findings therefore do not appear to be reliable determinants of risk of SRCC in individuals with genetic predisposition to DGC.
Collapse
Affiliation(s)
- Michelle F Jacobs
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Henry Dust
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Erika Koeppe
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan
| | - Sandra Wong
- Department of Surgery, Dartmouth Hitchcock Medical Center, Lebanon, New Hampshire
| | | | - Eun-Young Choi
- Department of Pathology, University of Michigan, Ann Arbor, Michigan
| | - Henry Appelman
- Department of Pathology, University of Michigan, Ann Arbor, Michigan
| | - Elena M Stoffel
- Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan.
| |
Collapse
|
19
|
Bailey KM, Jacobs MF, Anderson B, Rabah R, Wu YM, Else T, Mody RJ. DICER1 Mutations in the Era of Expanding Integrative Clinical Sequencing in Pediatric Oncology. JCO Precis Oncol 2019; 3. [PMID: 32832834 DOI: 10.1200/po.18.00172] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE DICER1 syndrome is a recently described inherited cancer predisposition syndrome caused by pathogenic variants in DICER1. With the recent increase in integrative clinical sequencing for pediatric patients with cancer, our understanding of the DICER1 syndrome continues to evolve, as new and rare pathogenic variants are reported. As the frequency of integrative clinical sequencing increases, discussions regarding challenges encountered in the interpretation of sequencing results are essential to continue to advance the field of cancer predisposition. The purpose of this work was to identify patients with somatic and/or germline DICER1 variants in our patient population and to discuss sequencing interpretation and the clinical recommendations that result from the integrative clinical sequencing results. METHODS Patients were enrolled in the PEDS-MIONCOSEQ study. This integrative clinical sequencing study includes paired tumor/normal whole-exome sequencing and tumor transcriptome sequencing. Patients identified as having DICER1 variants were included. RESULTS We report a DICER1 variant of unknown clinical significance in a patient with a highly unusual response to therapy. Two patients had diagnoses clarified once the integrative clinical sequencing revealing a DICER1 variant was available. We also discovered a patient with low-level DICER1 mosaicism and the challenges encountered in the sequencing interpretation for this patient. In addition to the sequencing data and result interpretation, this work also highlights testing and screening recommendations made to patients with DICER1 variants and their families on the basis of these results. CONCLUSION This work serves to extend the DICER1 phenotype and advance the utility of clinical integrative sequencing in the fields of pediatric oncology and cancer genetic predisposition.
Collapse
Affiliation(s)
- Kelly M Bailey
- University of Pittsburgh School of Medicine, Pittsburgh, PA
| | | | | | | | - Yi-Mi Wu
- Michigan Medicine, Ann Arbor, MI
| | | | | |
Collapse
|
20
|
Jacobs MF, Reid PM, Kelly PD. General Medical Council registration. J Accid Emerg Med 1999; 16:461. [PMID: 10572833 PMCID: PMC1343426 DOI: 10.1136/emj.16.6.461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
|
21
|
Jacobs MF, Tynkkynen S, Sibakov M. Highly bioluminescent Streptococcus thermophilus strain for the detection of diary-relevant antibiotics in milk. Appl Microbiol Biotechnol 1995; 44:405-12. [PMID: 8597542 DOI: 10.1007/bf00169936] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Inefficient translational initiation is often the cause of poor foreign gene expression in gram-positive organisms. The expression of bacterial luciferase (lux) genes in Streptococcus thermophilus (bioluminescence) was improved by addressing this problem in two ways; by ribosome-binding site (RBS) replacement, and by enhancing lux RBS access by polymerase chain reaction modification either alone or combined with translational coupling to a truncated upstream open- reading frame (orf') having its own RBS. Lactococcal expression signals were employed for plasmid-based lux expression. The same constructs were used to monitor bioluminescence in Lactococcus lactis, as well as two non-lactic bacterial strains, for comparison. High lux expression was achieved in all four organisms with a heterodimeric thermostable enzyme. Surprisingly, where ready access to the lux RBS was predicted, translational coupling to the lactococcal orf remained a prerequisite for detectable lux expression in L. lactis. In contrast, high bioluminescence in S. thermophilus was independent of coupling. Consistent with these observations, inspection of published gene sequences suggests that RBS "strength" may be a more important factor in translation in S. thermophilus than in L. lactis. Using reduced light production in highly bioluminescent S. thermophilus as an indicator of biocide presence in milk, test times could be significantly shortened compared with a commercial test utilizing the related non-bioluminescent strain. lux genes appear to be sensitive, exponential-phase reporters of gene activity in S. thermophilus, an organism with molecular biology and genetics that remain largely unstudied.
Collapse
Affiliation(s)
- M F Jacobs
- Department of Microbiology, University of Maryland, College Park 20742, USA
| | | | | |
Collapse
|
22
|
Jacobs MF, Andersen JB, Borchert TV, Kontinen VP. Identification of a Bacillus subtilis secretion mutant using a beta-galactosidase screening procedure. Microbiology (Reading) 1995; 141 ( Pt 7):1771-9. [PMID: 7551041 DOI: 10.1099/13500872-141-7-1771] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
High-level synthesis of exportable beta-galactosidase (LacZ) fusion proteins in Bacillus subtilis results in a lethal phenotype, and has been suggested as a tool for the selection of secretion mutants. We tested a plasmid-based, inducible lacZ fusion gene system for this purpose, but frequent mutations in cis, which reduced expression of the fusion gene, forced abandonment of the induction-selection strategy. Instead, after modification of the indicator plasmid, a screening procedure for increased basal LacZ activity levels was adopted. This led to the identification of a conditional B. subtilis secretion mutant after nitrosoguanidine mutagenesis. At 42 degrees C, but not at 30 degrees C, this mutant displayed extreme growth retardation when the LacZ fusion protein was produced, and and was also defective in the secretion of subtilisin Carlsberg. The processing kinetics and secretion of a subtilisin Carlsberg-alkaline phosphatase fusion derivative were found to be defective specifically at the non-permissive temperature. The secretion defect was not linked to the secA/div locus.
Collapse
Affiliation(s)
- M F Jacobs
- Department of Microbiology, Technical University of Denmark, Lyngby
| | | | | | | |
Collapse
|
23
|
Abstract
The cloning and sequence of the 5' untranslated region (5'-UTR) of the Bacillus licheniformis (Bl) 6816 subtilisin Carlsberg gene (subC) are reported here. The 5' and 3' ends of subC transcripts were characterized, and the promoter identified. Expression was studied using a fused lacZ reporter gene integrated into the chromosome of heterologous host Bacillus subtilis (Bs). beta Gal activities of mutants deleted within the promoter region identified a region which is required for stimulation by the transcriptional activator proteins, DegU and DegQ. This region is close to the transcription start point (tsp), and is adjacent to a sequence homologous to that involved in DegU/Q stimulation of the Bs subtilisin gene, aprE. Expression of subC in Bs was optimized by the use of heterologous promoter and by the deletion of UTR sequences predicted to be involved in secondary structures in the native subC mRNA. Sequence comparison with other subtilisin Carlsberg-type-encoding genes revealed a high degree of conservation of the entire 5'-UTR, including regulatory sequences and promoter, as well as part of the structural gene.
Collapse
Affiliation(s)
- M F Jacobs
- Department of Microbiology, Technical University of Denmark, Lundtofte
| |
Collapse
|
24
|
Abstract
The integrity and stability of nucleosomes under transcription assay conditions has been found to depend on concentration and ionic environment. Rifamycin AF/013, a commonly used inhibitor of initiation, is particularly effective in destabilisation of nucleosomes. Intact nucleosomes are refractory to transcription by wheat RNA polymerase II, the histone core preventing initiation. Template titration suggests that the polymerase can, however, bind to nucleosomes, and a 15--16S complex has been observed on sucrose gradients. DNase I digestion of polymerase-nucleosome incubations indicates that whilst histone is still present in the complex, the nucleosome conformation is altered resulting in enhanced nucleolysis at sites near the DNA centre but reduced overall kinetics of digestion.
Collapse
|
25
|
|