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Chrysafi P, Jani CT, Lotz M, Al Omari O, Singh H, Stafford K, Agarwal L, Rupal A, Dar AQ, Dangelo A, Lam P. Prevalence of Variants of Uncertain Significance in Patients Undergoing Genetic Testing for Hereditary Breast and Ovarian Cancer and Lynch Syndrome. Cancers (Basel) 2023; 15:5762. [PMID: 38136308 PMCID: PMC10742236 DOI: 10.3390/cancers15245762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 11/27/2023] [Accepted: 12/04/2023] [Indexed: 12/24/2023] Open
Abstract
Hereditary Breast and Ovarian Cancer (HBOC) and Lynch Syndrome (LS) are the most common inherited cancer syndromes identified with genetic testing. Testing, though, commonly reveals variants of uncertain significance (VUSs). This is a retrospective observational study designed to determine the prevalence of pathogenic mutations and VUSs in patients tested for HBOC and/or LS and to explore the characteristics of the VUS population. Patients 18-80 years old that met NCCN criteria for HBOC and/or LS genetic screening were tested between 2006 and 2020 at Mount Auburn Hospital in Cambridge, Massachusetts. A total of 663 patients were included in the study, with a mean age of 50 years old and 90% being females. Pathogenic mutations were identified in 12.5% and VUSs in 28.3%. VUS prevalence was associated with race (p-value = 0.019), being particularly higher in Asian populations. Patients with a personal history of breast cancer or family history of breast or ovarian cancer were more likely to have a VUS (personal breast: OR: 1.55; CI: 1.08-2.25; family breast: OR: 1.68; CI: 1.08-2.60, family ovarian OR: 2.29; CI: 1.04-5.45). In conclusion, VUSs appear to be detected in almost one third patients tested for cancer genetic syndromes, and thus future work is warranted to determine their significance in cancer development.
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Affiliation(s)
- Pavlina Chrysafi
- Department of Medicine, Mount Auburn Hospital, Cambridge, MA 02138, USA; (P.C.); (M.L.); (K.S.); (A.D.); (P.L.)
- Department of Medicine, Harvard Medical School, Boston, MA 02129, USA
| | - Chinmay T. Jani
- Department of Medicine, Mount Auburn Hospital, Cambridge, MA 02138, USA; (P.C.); (M.L.); (K.S.); (A.D.); (P.L.)
- Department of Medicine, Harvard Medical School, Boston, MA 02129, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33146, USA
| | - Margaret Lotz
- Department of Medicine, Mount Auburn Hospital, Cambridge, MA 02138, USA; (P.C.); (M.L.); (K.S.); (A.D.); (P.L.)
- Division of Hematology and Oncology, Mount Auburn Hospital, Cambridge, MA 02138, USA
| | - Omar Al Omari
- Department of Pulmonary and Critical Care, Temple University, Philadelphia, PA 19122, USA;
| | - Harpreet Singh
- Department of Pulmonary and Critical Care, Medical College of Wisconsin, Milwaukee, WI 53226, USA;
| | - Katherine Stafford
- Department of Medicine, Mount Auburn Hospital, Cambridge, MA 02138, USA; (P.C.); (M.L.); (K.S.); (A.D.); (P.L.)
- Department of Medicine, Harvard Medical School, Boston, MA 02129, USA
| | - Lipisha Agarwal
- Department of Pulmonary and Critical Care, University of Vermont, Burlington, VT 05405, USA;
| | - Arashdeep Rupal
- Department of Pulmonary and Critical Care, University of South Florida, Tampa, FL 33620, USA;
| | - Abdul Qadir Dar
- Department of Medicine, Lahey Medical Center, Burlington, MA 01805, USA;
| | - Abby Dangelo
- Department of Medicine, Mount Auburn Hospital, Cambridge, MA 02138, USA; (P.C.); (M.L.); (K.S.); (A.D.); (P.L.)
- Division of Hematology and Oncology, Mount Auburn Hospital, Cambridge, MA 02138, USA
| | - Prudence Lam
- Department of Medicine, Mount Auburn Hospital, Cambridge, MA 02138, USA; (P.C.); (M.L.); (K.S.); (A.D.); (P.L.)
- Department of Medicine, Harvard Medical School, Boston, MA 02129, USA
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Lin PH, Tien YW, Cheng WF, Chiang YC, Wu CH, Yang K, Huang CS. Diverse genetic spectrum among patients who met the criteria of hereditary breast, ovarian and pancreatic cancer syndrome. J Gynecol Oncol 2023; 34:e66. [PMID: 37170728 PMCID: PMC10482589 DOI: 10.3802/jgo.2023.34.e66] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 03/06/2023] [Accepted: 04/16/2023] [Indexed: 05/13/2023] Open
Abstract
OBJECTIVE Genetic high-risk assessment combines hereditary breast, ovarian and pancreatic cancer into one syndrome. However, there is a lack of data for comparing the germline mutational spectrum of the cancer predisposing genes between these three cancers. METHODS Patients who met the criteria of the hereditary breast, ovarian and pancreatic cancer were enrolled and received multi-gene sequencing. RESULTS We enrolled 730 probands: 418 developed breast cancer, 185 had ovarian cancer, and 145 had pancreatic cancer. Out of the 18 patients who had two types of cancer, 16 had breast and ovarian cancer and 2 had breast and pancreatic cancer. A total of 167 (22.9%) patients had 170 mutations. Mutation frequency in breast, ovarian and pancreatic cancer was 22.3%, 33.5% and 17.2%, respectively. The mutation rate was significantly higher in patients with double cancers than those with a single cancer (p<0.001). BRCA1 and BRCA2 were the most dominant genes associated with hereditary breast and ovarian cancer, whereas ATM was the most prevalent gene related to hereditary pancreatic cancer. Genes of hereditary colon cancer such as lynch syndrome were presented in a part of patients with pancreatic or ovarian cancer but seldom in those with breast cancer. Families with a history of both ovarian and breast cancer were associated with a higher mutation rate than those with other histories. CONCLUSION The mutation spectrum varies across the three cancer types and family histories. Our analysis provides guidance for physicians, counsellors, and counselees on the offer and uptake of genetic counseling.
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Affiliation(s)
- Po-Han Lin
- Department of Medical Genetics, National Taiwan University Hospital, Taipei, Taiwan
- Institute of Medical Genomics and Proteomics, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yun-Wen Tien
- Department of Surgery, National Taiwan University Hospital and Medical College of the National Taiwan University, Taipei, Taiwan
| | - Wen-Fang Cheng
- Department of Gynecology and Obstetrics, National Taiwan University Hospital, Taipei, Taiwan
| | - Ying-Cheng Chiang
- Department of Gynecology and Obstetrics, National Taiwan University Hospital, Taipei, Taiwan
| | - Chien-Huei Wu
- Department of Surgery, National Taiwan University Hospital and Medical College of the National Taiwan University, Taipei, Taiwan
| | - Karen Yang
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Chiun-Sheng Huang
- Department of Surgery, National Taiwan University Hospital and Medical College of the National Taiwan University, Taipei, Taiwan.
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Ferrer‐Avargues R, Castillejo MI, Dámaso E, Díez‐Obrero V, Garrigos N, Molina T, Codoñer‐Alejos A, Segura Á, Sánchez‐Heras AB, Castillejo A, Soto JL. Co-occurrence of germline pathogenic variants for different hereditary cancer syndromes in patients with Lynch syndrome. Cancer Commun (Lond) 2021; 41:218-228. [PMID: 33630411 PMCID: PMC7968885 DOI: 10.1002/cac2.12134] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 01/05/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Lynch syndrome (LS) is a hereditary condition characterized by a high risk of colorectal cancer, endometrial cancer, and other neoplasia associated with germline alterations in DNA mismatch repair genes. The classical genetic diagnostic strategy for LS consists of the Sanger sequencing of genes associated with the suspected syndrome. Next-generation sequencing (NGS) enables the simultaneous sequencing of a large number of hereditary cancer genes. Here, we aimed to study whether other germline pathogenic variants of hereditary cancer genes are present in patients with LS. METHODS A cohort of 84 probands with a previous genetic diagnosis of LS by Sanger sequencing was reanalyzed using NGS via a commercial panel of 94 hereditary cancer genes by hybrid capture. The American College of Medical Genetics and Genomics criteria were used to classify the clinical significance of the variants. The findings of NGS were confirmed by Sanger sequencing. When possible, genetic analyses of the new findings in the proband's relatives were also performed by Sanger sequencing. RESULTS We identified five families (6%), out of 84, with at least two germline pathogenic variants conferring to high or moderate risk in different dominant cancer-predisposing genes: [MLH1-BRCA2-NBN], [MLH1-BRCA1], [MSH2-ATM], [MSH6-NF1], and [MLH1-FANCA]. Interestingly, only one out of these five families exhibited a clinical phenotype associated with the new pathogenic variants. The family with three pathogenic variants of the [MLH1-BRCA2-NBN] genes showed a high aggregation of tumors associated with LS and breast and ovarian cancer syndrome. CONCLUSIONS Our results showed that the co-occurrence of more than one pathogenic variant in cancer-predisposing genes was remarkable among cases of LS. In most cases, no clinicial manifestations were associated with the secondary pathogenic variants. Further studies are needed to confirm these findings and elucidate their clinical impact. Reanalysis of LS families should be considered only in families with mixed clinical phenotypes.
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Affiliation(s)
- Rosario Ferrer‐Avargues
- Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO)FISABIO‐ Elche Health DepartmentElche032303Spain
| | - María Isabel Castillejo
- Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO)FISABIO‐ Elche Health DepartmentElche032303Spain
- Molecular Genetics Unit. Elche University HospitalElche032303Spain
| | - Estela Dámaso
- Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO)FISABIO‐ Elche Health DepartmentElche032303Spain
- Molecular Genetics Unit. Elche University HospitalElche032303Spain
| | - Virginia Díez‐Obrero
- Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO)FISABIO‐ Elche Health DepartmentElche032303Spain
| | - Noemí Garrigos
- Department of Molecular BiopathologyImmunological Center of AlicanteSan Juan‐Alicante03550Spain
| | - Tatiana Molina
- Department of Molecular BiopathologyImmunological Center of AlicanteSan Juan‐Alicante03550Spain
| | - Alan Codoñer‐Alejos
- Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO)FISABIO‐ Elche Health DepartmentElche032303Spain
- Molecular Genetics Unit. Elche University HospitalElche032303Spain
| | - Ángel Segura
- Medical Oncology DepartmentCancer Genetic Counseling Unit. La Fe University HospitalValencia46026Spain
| | - Ana Beatriz Sánchez‐Heras
- Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO)FISABIO‐ Elche Health DepartmentElche032303Spain
- Medical Oncology DepartmentCancer Genetic Counseling Unit. Elche University HospitalElche03203Spain
| | - Adela Castillejo
- Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO)FISABIO‐ Elche Health DepartmentElche032303Spain
- Molecular Genetics Unit. Elche University HospitalElche032303Spain
| | - José Luis Soto
- Foundation for the Promotion of Health and Biomedical Research of Valencia Region (FISABIO)FISABIO‐ Elche Health DepartmentElche032303Spain
- Molecular Genetics Unit. Elche University HospitalElche032303Spain
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Mannucci A, Furniss CS, Ukaegbu C, Horiguchi M, Fehlmann T, Uno H, Yurgelun MB, Syngal S. Comparison of Colorectal and Endometrial Microsatellite Instability Tumor Analysis and Premm 5 Risk Assessment for Predicting Pathogenic Germline Variants on Multigene Panel Testing. J Clin Oncol 2020; 38:4086-4094. [PMID: 32997573 PMCID: PMC7768341 DOI: 10.1200/jco.20.01470] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/17/2020] [Indexed: 12/30/2022] Open
Abstract
PURPOSE Tumor testing for microsatellite instability and/or mismatch repair-deficiency (MSI/IHC) and clinical prediction models effectively screen for Lynch syndrome (LS)-associated colorectal cancer (CRC) and endometrial cancer (EC), but they have not been assessed for their ability to identify non-LS forms of inherited risk. The aim of this study was to compare MSI/IHC and the PREMM5 prediction model to identify carriers of LS and non-LS pathogenic variants (PVs) among patients with CRC and EC. PATIENTS AND METHODS Data were retrospectively analyzed from two single-institution cohorts: 706 patients with CRC and/or EC referred for genetic evaluation/testing (high-risk cohort) and 1,058 consecutively ascertained patients with CRC (oncology clinic cohort), unselected for familial risk. All participants underwent germline multigene panel testing. PREMM5 scores were calculated from personal/family cancer history. The primary outcome was the proportion of individuals with germline PVs (LS PVs, high-penetrance PVs, and any PVs) who had abnormal MSI/IHC testing and/or PREMM5 score ≥ 2.5%. RESULTS MSI/IHC and PREMM5 had comparable sensitivity for identifying LS carriers in high-risk (89.3% v 85.7%; P = .712) and oncology clinic patients (96.6% v 96.6%; P = 1.000), although MSI/IHC had significantly superior specificity for LS (81.3% v 20.1%; P < .001; 92.3% v 24.3%; P < .001). In both cohorts, PREMM5 had superior sensitivity to MSI/IHC at identifying patients with any high-penetrance PVs and any low-, moderate-, and high-penetrance PVs. Among patients with normal MSI/IHC, PREMM5 identified 84.2% and 83.3% of high-risk patients with CRC/EC and oncology clinic CRC patients with high-penetrance PVs, respectively. CONCLUSION MSI/IHC and PREMM5 effectively identify patients with CRC and/or EC with LS, although MSI/IHC has better specificity for LS. Because PREMM5 identifies non-LS, high-penetrance germline PVs, patients with CRC and/or EC with PREMM5 score ≥ 2.5%, including those with normal MSI/IHC, should be offered multigene panel testing.
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Affiliation(s)
- Alessandro Mannucci
- IRCCS Ospedale San Raffaele Scientific Institute, Milan, Italy
- Dana-Farber Cancer Institute, Boston, MA
| | - C. Sloane Furniss
- Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
| | | | - Miki Horiguchi
- Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
| | | | - Hajime Uno
- Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
| | - Matthew B. Yurgelun
- Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
- Brigham and Women’s Hospital, Boston, MA
| | - Sapna Syngal
- Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
- Brigham and Women’s Hospital, Boston, MA
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Identification of germline pathogenic variants in DNA damage repair genes by a next-generation sequencing multigene panel in BRCAX patients. Clin Biochem 2019; 76:17-23. [PMID: 31786208 DOI: 10.1016/j.clinbiochem.2019.11.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 11/06/2019] [Accepted: 11/26/2019] [Indexed: 12/24/2022]
Abstract
BACKGROUND Approximately 5-10% of breast carcinomas have been related to hereditary conditions and are attributable to pathogenic variants in the BRCA1 and BRCA2 genes, which is referred to as hereditary breast and ovarian cancer (HBOC) syndrome. The inclusion of additional genes that can be related to HBOC syndrome is under intense evaluation due to the high proportion of patients with HBOC criteria who do not present pathogenic mutations in BRCA genes, named BRCAX, despite having high clinical suspicion of hereditary cancer. The main aim is to identify new potentially pathogenic gene variants that may contribute to HBOC to improve the efficiency of routine diagnostic tests in this hereditary condition. METHODS A retrospective cohort of 77 HBOC BRCAX patients was analyzed by next-generation sequencing using a targeted multigene panel composed of 25 genes related to hereditary cancer and deficiencies in DNA repair pathways. RESULTS We found 9 variants in 7 different genes, which were confirmed by automated sequencing. Six variants were classified as pathogenic or likely pathogenic. Three of them were located in the PALB2 gene, one in the BRIP1 gene, one in the BARD1 gene and 1 in the RAD50 gene. In addition, three variants of uncertain significance (VUS) were detected in the TP53, CHEK2, and CDH1 genes. CONCLUSIONS We identified that 8% of BRCAX patients were carriers of pathogenic variants in genes other than BRCA1 and BRCA2. Therefore, wide gene panels, including clinically actionable genes, should be routinely used in the screening of HBOC in our population. We observed differences from other studies in the prevalence of mutated genes, most likely due to differences in the selection criteria of the probands and in the population analyzed. The high incidence of deleterious variant detection in PALB2 supports its significant role in breast cancer susceptibility and reinforces its inclusion in the HBOC genetic diagnostic process.
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Multigene panel testing in unselected Israeli breast cancer cases: mutational spectrum and use of BRCA1/2 mutation prediction algorithms. Breast Cancer Res Treat 2019; 176:165-170. [DOI: 10.1007/s10549-019-05228-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 04/08/2019] [Indexed: 12/29/2022]
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Abstract
Next-generation sequencing (NGS) technology has led to the ability to test for multiple cancer susceptibility genes simultaneously without significantly increasing cost or turnaround time. With growing usage of multigene testing for inherited cancer, ongoing education for nurses and other health-care providers about hereditary cancer screening is imperative to ensure appropriate testing candidate identification, test selection, and posttest management. The purpose of this review article is to (1) provide an overview of how NGS works to detect germline mutations, (2) summarize the benefits and limitations of multigene panel testing, (3) describe risk categories of cancer susceptibility genes, and (4) highlight the counseling considerations for patients pursuing multigene testing.
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Corso G, Feroce I, Intra M, Veronesi P, Sacchini V, Bonanni B, Galimberti V. Prognostic impact of germline mutations in inherited cancer syndromes. Future Oncol 2017; 13:2125-2127. [PMID: 28984488 DOI: 10.2217/fon-2017-0296] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Giovanni Corso
- European Institute of Oncology, Division of Breast Cancer Surgery, Via G. Ripamonti 435, Milan 20141, Italy
| | - Irene Feroce
- European Institute of Oncology, Division of Cancer Prevention & Genetics, Via G. Ripamonti 435, Milan 20141, Italy
| | - Mattia Intra
- European Institute of Oncology, Division of Breast Cancer Surgery, Via G. Ripamonti 435, Milan 20141, Italy
| | - Paolo Veronesi
- European Institute of Oncology, Division of Breast Cancer Surgery, Via G. Ripamonti 435, Milan 20141, Italy
| | - Virgilio Sacchini
- European Institute of Oncology, Division of Breast Cancer Surgery, Via G. Ripamonti 435, Milan 20141, Italy
| | - Bernardo Bonanni
- European Institute of Oncology, Division of Cancer Prevention & Genetics, Via G. Ripamonti 435, Milan 20141, Italy
| | - Viviana Galimberti
- European Institute of Oncology, Division of Breast Cancer Surgery, Via G. Ripamonti 435, Milan 20141, Italy
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Coffee B, Cox HC, Kidd J, Sizemore S, Brown K, Manley S, Mancini-DiNardo D. Detection of somatic variants in peripheral blood lymphocytes using a next generation sequencing multigene pan cancer panel. Cancer Genet 2017; 211:5-8. [PMID: 28279308 DOI: 10.1016/j.cancergen.2017.01.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 12/21/2016] [Accepted: 01/06/2017] [Indexed: 12/13/2022]
Abstract
Next Generation Sequencing (NGS) multigene panels, which are routinely used to assess hereditary cancer risk, can detect both inherited germline variants and somatic variants in cancer-risk genes. We evaluated the frequency and distribution of likely somatic Pathogenic and Likely Pathogenic variants (PVs) detected in >220,000 individuals who underwent clinical testing with a 25-gene panel between September 2013 and March 2016. Likely somatic PVs are defined as variants with NGS read frequencies from 10% to 30%. Overall, 137 (0.06%) individuals were identified as carrying likely somatic PVs, most commonly in TP53 (73), CHEK2 (27), and ATM (20). Among this group, a second PV with a NGS read frequency consistent with a germline variant within the same gene or a different gene on the panel was detected in 21 individuals (15.3%), which is similar to the detection rate in our general testing population. Likely somatic PVs accounted for 38.8% of all PVs in TP53. In comparison, likely somatic PVs accounted for <1% of PVs in most other genes. Likely somatic PVs were more frequently identified in older individuals (p < 0.001). Additional studies are ongoing to further investigate the incidence and clinical implications of somatic variants, enabling the appropriate medical management for these patients.
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Affiliation(s)
- Bradford Coffee
- Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT, USA.
| | - Hannah C Cox
- Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT, USA
| | - John Kidd
- Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT, USA
| | - Scott Sizemore
- Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT, USA
| | - Krystal Brown
- Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT, USA
| | - Susan Manley
- Myriad Genetic Laboratories, Inc., 320 Wakara Way, Salt Lake City, UT, USA
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