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Abduljaleel Z. Molecular insights into TP53 mutation (p. Arg267Trp) and its connection to Choroid Plexus Carcinomas and Li-Fraumeni Syndrome. Genes Genomics 2024; 46:941-953. [PMID: 38896352 DOI: 10.1007/s13258-024-01531-9] [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: 04/22/2024] [Accepted: 06/07/2024] [Indexed: 06/21/2024]
Abstract
BACKGROUND Choroid plexus carcinomas (CPCs) are rare malignant tumors primarily affecting pediatric patients and often co-occur with Li-Fraumeni Syndrome (LFS), an inherited predisposition to early-onset malignancies in multiple organ systems. LFS is closely linked to TP53 mutations, with germline TP53 gene mutations present in approximately 75% of Li-Fraumeni syndrome families and 25% of Li-Fraumeni-like syndrome families. Individuals with TP53 mutations also have an elevated probability of carrying mutations in BRCA1 and BRCA2 genes. OBJECTIVE To investigate the structural and functional implications of the TP53: 799C > T, p. (Arg267Trp) missense mutation, initially identified in a Saudi family, and understand its impact on TP53 functionality and related intermolecular interactions. METHODS Computational analyses were conducted to examine the structural modifications resulting from the TP53: 799C > T, p. (Arg267Trp) mutation. These analyses focused on the mutation's impact on hydrogen bonding, ionic interactions, and the specific interaction with Cell Cycle and Apoptosis Regulator 2 (CCAR2), as annotated in UniProt. RESULTS The study revealed that the native Arg267 residue is critical for a salt bridge interaction with glutamic acid at position 258. The mutation-induced charge alteration has the potential to disrupt this ionic bonding. Additionally, the mutation is located within an amino acid region crucial for interaction with CCAR2. The altered properties of the amino acid within this domain may affect its functionality and disrupt this interaction, thereby impacting the regulation of catalytic enzyme activity. CONCLUSIONS Our findings highlight the intricate intermolecular interactions governing TP53 functionality. The TP53: 799C > T, p. (Arg267Trp) mutation causes structural modifications that potentially disrupt critical ionic bonds and protein interactions, offering valuable insights for the development of targeted mutants with distinct functional attributes. These insights could inform therapeutic strategies for conditions associated with TP53 mutations.
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Affiliation(s)
- Zainularifeen Abduljaleel
- Science and Technology Unit, Umm Al Qura University, P.O. Box 715, 21955, Makkah, Saudi Arabia.
- Faculty of Medicine, Department of Medical Genetics, Umm Al-Qura University, P.O. Box 715, 21955, Makkah, Saudi Arabia.
- Molecular Diagnostics Unit, Department of Molecular Biology, The Regional Laboratory, Ministry of Health (MOH), P.O. Box 6251, Makkah, Kingdom of Saudi Arabia.
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Gao J, Wu Y, Yu J, Qiu Y, Yi T, Luo C, Zhang J, Lu G, Li X, Xiong F, Wu X, Pan X. Impact of genomic and epigenomic alterations of multigene on a multicancer pedigree. Cancer Med 2024; 13:e7394. [PMID: 38970307 PMCID: PMC11226725 DOI: 10.1002/cam4.7394] [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: 01/24/2024] [Revised: 05/14/2024] [Accepted: 06/05/2024] [Indexed: 07/08/2024] Open
Abstract
BACKGROUND Germline mutations have been identified in a small number of hereditary cancers, but the genetic predisposition for many familial cancers remains to be elucidated. METHODS This study identified a Chinese pedigree that presented different cancers (breast cancer, BRCA; adenocarcinoma of the esophagogastric junction, AEG; and B-cell acute lymphoblastic leukemia, B-ALL) in each of the three generations. Whole-genome sequencing and whole-exome sequencing were performed on peripheral blood or bone marrow and cancer biopsy samples. Whole-genome bisulfite sequencing was conducted on the monozygotic twin brothers, one of whom developed B-ALL. RESULTS According to the ACMG guidelines, bioinformatic analysis of the genome sequencing revealed 20 germline mutations, particularly mutations in the DNAH11 (c.9463G > A) and CFH (c.2314G > A) genes that were documented in the COSMIC database and validated by Sanger sequencing. Forty-one common somatic mutated genes were identified in the cancer samples, displaying the same type of single nucleotide substitution Signature 5. Meanwhile, hypomethylation of PLEK2, MRAS, and RXRA as well as hypermethylation of CpG island associated with WT1 was shown in the twin with B-ALL. CONCLUSIONS These findings reveal genomic alterations in a pedigree with multiple cancers. Mutations found in the DNAH11, CFH genes, and other genes predispose to malignancies in this family. Dysregulated methylation of WT1, PLEK2, MRAS, and RXRA in the twin with B-ALL increases cancer susceptibility. The similarity of the somatic genetic changes among the three cancers indicates a hereditary impact on the pedigree. These familial cancers with germline and somatic mutations, as well as epigenomic alterations, represent a common molecular basis for many multiple cancer pedigrees.
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Affiliation(s)
- Jinyu Gao
- Department of PediatricsNanfang Hospital, Southern Medical UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Single Cell Technology and ApplicationSouthern Medical UniversityGuangzhouChina
| | - Yongzhang Wu
- Guangdong Provincial Key Laboratory of Single Cell Technology and ApplicationSouthern Medical UniversityGuangzhouChina
- Department of Biochemistry and Molecular BiologySchool of Basic Medical Sciences, Southern Medical UniversityGuangzhouChina
| | - Jieming Yu
- Guangdong Provincial Key Laboratory of Single Cell Technology and ApplicationSouthern Medical UniversityGuangzhouChina
- Affiliated Shenzhen Maternity and Child Healthcare Hospital, Southern Medical UniversityShenzhenChina
| | - Yinbin Qiu
- Guangdong Provincial Key Laboratory of Single Cell Technology and ApplicationSouthern Medical UniversityGuangzhouChina
| | - Tiantian Yi
- Department of PediatricsNanfang Hospital, Southern Medical UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Single Cell Technology and ApplicationSouthern Medical UniversityGuangzhouChina
| | - Chaochao Luo
- Guangdong Provincial Key Laboratory of Single Cell Technology and ApplicationSouthern Medical UniversityGuangzhouChina
| | - Junxiao Zhang
- SequMed Institute of Biomedical SciencesGuangzhouChina
| | - Gary Lu
- Department of Fetal Medicine and Prenatal DiagnosisZhujiang Hospital, Southern Medical UniversityGuangzhouChina
| | - Xu Li
- Kaiser Permanente Regional Genetics Laboratory, San Jose Medical CenterSan JoseCaliforniaUSA
| | - Fu Xiong
- Department of Medical GeneticsSchool of Basic Medical Sciences, Southern Medical UniversityGuangzhouChina
| | - Xuedong Wu
- Department of PediatricsNanfang Hospital, Southern Medical UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Single Cell Technology and ApplicationSouthern Medical UniversityGuangzhouChina
| | - Xinghua Pan
- Department of PediatricsNanfang Hospital, Southern Medical UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Single Cell Technology and ApplicationSouthern Medical UniversityGuangzhouChina
- Department of Biochemistry and Molecular BiologySchool of Basic Medical Sciences, Southern Medical UniversityGuangzhouChina
- Precision Regenerative Medicine Research Centre, Division of Medical SciencesMacau University of Science and TechnologyMacaoChina
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Caeser R, Chiang J, Tan ES, Tai ES, Ngeow J. Cascade testing for hereditary cancer in Singapore: how population genomics help guide clinical policy. Fam Cancer 2024; 23:133-140. [PMID: 38662262 DOI: 10.1007/s10689-024-00376-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Accepted: 03/14/2024] [Indexed: 04/26/2024]
Abstract
Hereditary Cancer makes up around 5-10% of all cancers. It is important to diagnose hereditary cancer in a timely fashion, as not only do patients require long-term care from a young age, but their relatives also require management. The main approach to capture at-risk relatives is cascade testing. It involves genetic testing of relatives of the first detected carrier of a pathogenic variant in a family i.e. the proband. The current standard of care for cascade testing is a patient-mediated approach. Probands are then advised to inform and encourage family members to undergo genetic testing. In Singapore, cascade testing is inefficient, around 10-15%, lower than the 30% global average. Here, we describe the cascade testing process and its effort to increase testing in Singapore. Precision Health Research, Singapore (PRECISE), was set up to coordinate Singapore's National Precision Medicine strategy and has awarded five clinical implementation pilots, with one of them seeking to identify strategies for how cascade testing for hereditary cancer can be increased in a safe and cost-efficient manner. Achieving this will be done through addressing barriers such as cost, manpower shortages, exploring a digital channel for contacting at-risk relatives, and getting a deeper insight into why genetic testing gets declined. If successful, it will likely result in care pathways that are a cost-effective public health intervention for identifying individuals at risk. Surveillance and management of those unaffected at-risk individuals, if caught early, will result in improved patient outcomes, and further reduce the healthcare burden for the economy.
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Affiliation(s)
- Rebecca Caeser
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, 169610, Singapore
- Oncology Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore
| | - Jianbang Chiang
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, 169610, Singapore
- Oncology Academic Clinical Program, Duke-NUS Medical School, Singapore, Singapore
| | - Ee Shien Tan
- Duke-National University of Singapore (NUS) Medical School, National University of Singapore, Singapore, Singapore
- Genetics Service, Department of Pediatrics, Kadang Kerbau (KK) Women's and Children's Hospital, Singapore, Singapore
| | - E Shyong Tai
- Duke-National University of Singapore (NUS) Medical School, National University of Singapore, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Precision Health Research, Singapore, Singapore
| | - Joanne Ngeow
- Cancer Genetics Service, Division of Medical Oncology, National Cancer Centre Singapore, Singapore, 169610, Singapore.
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore.
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Sanabria-Salas MC, Pedroza-Duran A, Díaz-Casas SE, Nuñez Lemus M, Grillo-Ardila CF, Briceño-Morales X, García-Mora M, Ángel-Aristizábal J, Mariño Lozano IF, Suarez Rodríguez RA, Guzmán Abisaab LH. Management and Clinical Outcomes of Breast Cancer in Women Diagnosed with Hereditary Cancer Syndromes in a Clinic-Based Sample from Colombia. Cancers (Basel) 2024; 16:2020. [PMID: 38893140 PMCID: PMC11171067 DOI: 10.3390/cancers16112020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 05/08/2024] [Accepted: 05/09/2024] [Indexed: 06/21/2024] Open
Abstract
This study aimed to investigate prognosis and survival differences in 82 breast cancer patients with germline pathogenic/likely pathogenic variants (PVs) treated and followed at the Breast Unit of the Instituto Nacional de Cancerología, Colombia (INC-C) between 2018 and 2021. Median age at diagnosis was 46 years, with 62.2% presenting locally advanced tumors, 47.6% histological grade 3, and 35.4% with triple-negative breast cancer (TNBC) subtype. Most carriers, 74.4% (61/82), had PVs in known breast cancer susceptibility genes (i.e., "associated gene carriers" group, considered inherited breast cancer cases): BRCA2 (30), BRCA1 (14), BARD1 (4), RAD51D (3), TP53 (2), PALB2 (2), ATM (2), CHEK2 (1), RAD51C (1), NF1 (1), and PTEN (1). BRCA1-2 represented 53.7%, and homologous recombination DNA damage repair (HR-DDR) genes associated with breast cancer risk accounted for 15.9%. Patients with PVs in non-breast-cancer risk genes were combined in a different category (21/82; 25.6%) (i.e., "non-associated gene carriers" group, considered other breast cancer cases). Median follow-up was 38.1 months, and 24% experienced recurrence, with 90% being distant. The 5-year Disease-Free Survival (DFS) for inherited breast cancer cases was 66.5%, and for other breast cancer cases it was 88.2%. In particular, for carriers of PVs in the BRCA2 gene, it was 37.6%. The 5-year Overall Survival (OS) rates ranged from 68.8% for those with PVs in BRCA2 to 100% for those with PVs in other HR-DDR genes. Further studies are crucial for understanding tumor behavior and therapy response differences among Colombian breast cancer patients with germline PVs.
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Affiliation(s)
- María Carolina Sanabria-Salas
- Instituto Nacional de Cancerología, Calle 1 N. 9-85, Bogotá 111511, Colombia; (A.P.-D.); (S.E.D.-C.); (M.N.L.); (X.B.-M.); (M.G.-M.); (J.Á.-A.); (I.F.M.L.); (R.A.S.R.); (L.H.G.A.)
- Division of Medical Oncology and Hematology, Princess Margaret Cancer Centre, University Health Network, 610 University Avenue, Toronto, ON M5G 2C1, Canada
| | - Ana Pedroza-Duran
- Instituto Nacional de Cancerología, Calle 1 N. 9-85, Bogotá 111511, Colombia; (A.P.-D.); (S.E.D.-C.); (M.N.L.); (X.B.-M.); (M.G.-M.); (J.Á.-A.); (I.F.M.L.); (R.A.S.R.); (L.H.G.A.)
| | - Sandra E. Díaz-Casas
- Instituto Nacional de Cancerología, Calle 1 N. 9-85, Bogotá 111511, Colombia; (A.P.-D.); (S.E.D.-C.); (M.N.L.); (X.B.-M.); (M.G.-M.); (J.Á.-A.); (I.F.M.L.); (R.A.S.R.); (L.H.G.A.)
| | - Marcela Nuñez Lemus
- Instituto Nacional de Cancerología, Calle 1 N. 9-85, Bogotá 111511, Colombia; (A.P.-D.); (S.E.D.-C.); (M.N.L.); (X.B.-M.); (M.G.-M.); (J.Á.-A.); (I.F.M.L.); (R.A.S.R.); (L.H.G.A.)
| | - Carlos F. Grillo-Ardila
- Department of Obstetrics & Gynecology, School of Medicine, Universidad Nacional de Colombia, Avenida Carrera 30 N. 45-3, Bogotá 111321, Colombia;
| | - Ximena Briceño-Morales
- Instituto Nacional de Cancerología, Calle 1 N. 9-85, Bogotá 111511, Colombia; (A.P.-D.); (S.E.D.-C.); (M.N.L.); (X.B.-M.); (M.G.-M.); (J.Á.-A.); (I.F.M.L.); (R.A.S.R.); (L.H.G.A.)
| | - Mauricio García-Mora
- Instituto Nacional de Cancerología, Calle 1 N. 9-85, Bogotá 111511, Colombia; (A.P.-D.); (S.E.D.-C.); (M.N.L.); (X.B.-M.); (M.G.-M.); (J.Á.-A.); (I.F.M.L.); (R.A.S.R.); (L.H.G.A.)
| | - Javier Ángel-Aristizábal
- Instituto Nacional de Cancerología, Calle 1 N. 9-85, Bogotá 111511, Colombia; (A.P.-D.); (S.E.D.-C.); (M.N.L.); (X.B.-M.); (M.G.-M.); (J.Á.-A.); (I.F.M.L.); (R.A.S.R.); (L.H.G.A.)
| | - Iván Fernando Mariño Lozano
- Instituto Nacional de Cancerología, Calle 1 N. 9-85, Bogotá 111511, Colombia; (A.P.-D.); (S.E.D.-C.); (M.N.L.); (X.B.-M.); (M.G.-M.); (J.Á.-A.); (I.F.M.L.); (R.A.S.R.); (L.H.G.A.)
| | - Raúl Alexis Suarez Rodríguez
- Instituto Nacional de Cancerología, Calle 1 N. 9-85, Bogotá 111511, Colombia; (A.P.-D.); (S.E.D.-C.); (M.N.L.); (X.B.-M.); (M.G.-M.); (J.Á.-A.); (I.F.M.L.); (R.A.S.R.); (L.H.G.A.)
| | - Luis Hernán Guzmán Abisaab
- Instituto Nacional de Cancerología, Calle 1 N. 9-85, Bogotá 111511, Colombia; (A.P.-D.); (S.E.D.-C.); (M.N.L.); (X.B.-M.); (M.G.-M.); (J.Á.-A.); (I.F.M.L.); (R.A.S.R.); (L.H.G.A.)
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Kansuttiviwat C, Lertwilaiwittaya P, Roothumnong E, Nakthong P, Dungort P, Meesamarnpong C, Tansa-Nga W, Pongsuktavorn K, Wiboonthanasarn S, Tititumjariya W, Phuphuripan N, Lertbussarakam C, Wattanarangsan J, Sritun J, Punuch K, Kammarabutr J, Mutirangura P, Thongnoppakhun W, Limwongse C, Pithukpakorn M. Germline mutations of 4567 patients with hereditary breast-ovarian cancer spectrum in Thailand. NPJ Genom Med 2024; 9:9. [PMID: 38355628 PMCID: PMC10866978 DOI: 10.1038/s41525-024-00400-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 01/29/2024] [Indexed: 02/16/2024] Open
Abstract
Multi-gene panel testing has led to the detection of pathogenic/likely pathogenic (P/LP) variants in many cancer susceptibility genes in patients with breast-ovarian cancer spectrum. However, the clinical and genomic data of Asian populations, including Thai cancer patients, was underrepresented, and the clinical significance of multi-gene panel testing in Thailand remains undetermined. In this study, we collected the clinical and genetic data from 4567 Thai patients with cancer in the hereditary breast-ovarian cancer (HBOC) spectrum who underwent multi-gene panel testing. Six hundred and ten individuals (13.4%) had germline P/LP variants. Detection rates of germline P/LP variants in breast, ovarian, pancreatic, and prostate cancer were 11.8%, 19.8%, 14.0%, and 7.1%, respectively. Non-BRCA gene mutations accounted for 35% of patients with germline P/LP variants. ATM was the most common non-BRCA gene mutation. Four hundred and thirty-two breast cancer patients with germline P/LP variants (80.4%) met the current NCCN genetic testing criteria. The most common indication was early-onset breast cancer. Ten patients harbored double pathogenic variants in this cohort. Our result showed that a significant proportion of non-BRCA P/LP variants were identified in patients with HBOC-related cancers. These findings support the benefit of multi-gene panel testing for inherited cancer susceptibility among Thai HBOC patients. Some modifications of the testing policy may be appropriate for implementation in diverse populations.
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Affiliation(s)
- Chalermkiat Kansuttiviwat
- Division of Medical Genetics, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Pongtawat Lertwilaiwittaya
- Division of Medical Genetics, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Genomics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- University of Alabama at Birmingham, Birmingham, AL, USA
| | - Ekkapong Roothumnong
- Division of Medical Genetics, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Genomics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Panee Nakthong
- Siriraj Genomics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Peerawat Dungort
- Siriraj Genomics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Chutima Meesamarnpong
- Siriraj Genomics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Warisara Tansa-Nga
- Siriraj Genomics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Khontawan Pongsuktavorn
- Siriraj Genomics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Supakit Wiboonthanasarn
- Siriraj Genomics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Warunya Tititumjariya
- Siriraj Genomics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Nannipa Phuphuripan
- Siriraj Genomics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | | | - Jantanee Wattanarangsan
- Siriraj Genomics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Jiraporn Sritun
- Siriraj Genomics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Kittiporn Punuch
- Siriraj Genomics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Jirayu Kammarabutr
- Siriraj Genomics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Pornthira Mutirangura
- Department of Medicine, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Wanna Thongnoppakhun
- Siriraj Genomics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Chanin Limwongse
- Division of Medical Genetics, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Genomics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Manop Pithukpakorn
- Division of Medical Genetics, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
- Siriraj Genomics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
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Horton C, Hoang L, Zimmermann H, Young C, Grzybowski J, Durda K, Vuong H, Burks D, Cass A, LaDuca H, Richardson ME, Harrison S, Chao EC, Karam R. Diagnostic Outcomes of Concurrent DNA and RNA Sequencing in Individuals Undergoing Hereditary Cancer Testing. JAMA Oncol 2024; 10:212-219. [PMID: 37924330 PMCID: PMC10625669 DOI: 10.1001/jamaoncol.2023.5586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 09/04/2023] [Indexed: 11/06/2023]
Abstract
Importance Personalized surveillance, prophylaxis, and cancer treatment options for individuals with hereditary cancer predisposition are informed by results of germline genetic testing. Improvements to genomic technology, such as the availability of RNA sequencing, may increase identification of individuals eligible for personalized interventions by improving the accuracy and yield of germline testing. Objective To assess the cumulative association of paired DNA and RNA testing with detection of disease-causing germline genetic variants and resolution of variants of uncertain significance (VUS). Design, Setting, and Participants Paired DNA and RNA sequencing was performed on individuals undergoing germline testing for hereditary cancer indication at a single diagnostic laboratory from March 2019 through April 2020. Demographic characteristics, clinical data, and test results were curated as samples were received, and changes to variant classification were assessed over time. Data analysis was performed from May 2020 to June 2023. Main Outcomes and Measures Main outcomes were increase in diagnostic yield, decrease in VUS rate, the overall results by variant type, the association of RNA evidence with variant classification, and the corresponding predicted effect on cancer risk management. Results A total of 43 524 individuals were included (median [range] age at testing, 54 [2-101] years; 37 373 female individuals [85.7%], 6224 male individuals [14.3%], and 2 individuals of unknown sex [<0.1%]), with 43 599 tests. A total of 2197 (5.0%) were Ashkenazi Jewish, 1539 (3.5%) were Asian, 3077 (7.1%) were Black, 2437 (5.6%) were Hispanic, 27 793 (63.7%) were White, and 2049 (4.7%) were other race, and for 4507 individuals (10.3%), race and ethnicity were unknown. Variant classification was impacted in 549 individuals (1.3%). Medically significant upgrades were made in 97 individuals, including 70 individuals who had a variant reclassified from VUS to pathogenic/likely pathogenic (P/LP) and 27 individuals who had a novel deep intronic P/LP variant that would not have been detected using DNA sequencing alone. A total of 93 of 545 P/LP splicing variants (17.1%) were dependent on RNA evidence for classification, and 312 of 439 existing splicing VUS (71.1%) were resolved by RNA evidence. Notably, the increase in positive rate (3.1%) and decrease in VUS rate (-3.9%) was higher in Asian, Black, and Hispanic individuals combined compared to White individuals (1.6%; P = .02; and -2.5%; P < .001). Conclusions and Relevance Findings of this diagnostic study demonstrate that the ability to perform RNA sequencing concurrently with DNA sequencing represents an important advancement in germline genetic testing by improving detection of novel variants and classification of existing variants. This expands the identification of individuals with hereditary cancer predisposition and increases opportunities for personalization of therapeutics and surveillance.
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Affiliation(s)
| | | | | | | | | | | | - Huy Vuong
- Ambry Genetics, Aliso Viejo, California
| | | | | | | | | | | | - Elizabeth C Chao
- Ambry Genetics, Aliso Viejo, California
- University of California, Irvine, School of Medicine
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Oketch DJA, Giulietti M, Piva F. Copy Number Variations in Pancreatic Cancer: From Biological Significance to Clinical Utility. Int J Mol Sci 2023; 25:391. [PMID: 38203561 PMCID: PMC10779192 DOI: 10.3390/ijms25010391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 12/20/2023] [Accepted: 12/24/2023] [Indexed: 01/12/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is the most common type of pancreatic cancer, characterized by high tumor heterogeneity and a poor prognosis. Inter- and intra-tumoral heterogeneity in PDAC is a major obstacle to effective PDAC treatment; therefore, it is highly desirable to explore the tumor heterogeneity and underlying mechanisms for the improvement of PDAC prognosis. Gene copy number variations (CNVs) are increasingly recognized as a common and heritable source of inter-individual variation in genomic sequence. In this review, we outline the origin, main characteristics, and pathological aspects of CNVs. We then describe the occurrence of CNVs in PDAC, including those that have been clearly shown to have a pathogenic role, and further highlight some key examples of their involvement in tumor development and progression. The ability to efficiently identify and analyze CNVs in tumor samples is important to support translational research and foster precision oncology, as copy number variants can be utilized to guide clinical decisions. We provide insights into understanding the CNV landscapes and the role of both somatic and germline CNVs in PDAC, which could lead to significant advances in diagnosis, prognosis, and treatment. Although there has been significant progress in this field, understanding the full contribution of CNVs to the genetic basis of PDAC will require further research, with more accurate CNV assays such as single-cell techniques and larger cohorts than have been performed to date.
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Affiliation(s)
| | - Matteo Giulietti
- Department of Specialistic Clinical and Odontostomatological Sciences, Polytechnic University of Marche, 60131 Ancona, Italy
| | - Francesco Piva
- Department of Specialistic Clinical and Odontostomatological Sciences, Polytechnic University of Marche, 60131 Ancona, Italy
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Fernández-Castillejo S, Roig B, Melé M, Serrano S, Salvat M, Querol M, Brunet J, Pineda M, Cisneros A, Parada D, Badia J, Borràs J, Rodríguez-Balada M, Gumà J. Opportunistic genetic screening increases the diagnostic yield and is medically valuable for care of patients and their relatives with hereditary cancer. J Med Genet 2023; 61:69-77. [PMID: 37591735 PMCID: PMC10803988 DOI: 10.1136/jmg-2023-109389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 07/23/2023] [Indexed: 08/19/2023]
Abstract
BACKGROUND Multigene panel testing by next-generation sequencing (MGP-NGS) enables the detection of germline pathogenic or likely pathogenic variants (PVs/LPVs) in genes beyond those associated with a certain cancer phenotype. Opportunistic genetic screening based on MGP-NGS in patients with suspicion of hereditary cancer reveals these incidental findings (IFs). METHODS MGP-NGS was performed in patients who fulfilled the clinical criteria to undergo genetic testing according to the Catalan Health Service guidelines. Variants were classified following the American College of Medical Genetics and Genomics-Association for Molecular Pathology guidelines and the Cancer Variant Interpretation Group UK guidelines. RESULTS IFs were identified in 10 (1.22%) of the 817 patients who underwent MGP-NGS. The mean age at cancer diagnosis was 49.4±9.5 years. Three IFs (30.0%) were detected in PMS2, two (20.0%) in ATM and TP53 and one (10.0%) in MSH6, NTHL1 and VHL. Seven (70.0%) IFs were single-nucleotide substitutions, two (20.0%) were deletions and one (10.0%) was a duplication. Three (30.0) IFs were located in intronic regions, three (30.3%) were nonsense, two (20.0%) were frameshift and two (20.0%) were missense variations. Six (60.0%) IFs were classified as PVs and four (40.0%) as LPVs. CONCLUSIONS Opportunistic genetic screening increased the diagnostic yield by 1.22% in our cohort. Most of the identified IFs were present in clinically actionable genes (n=7; 70.0%), providing these families with an opportunity to join cancer early detection programmes, as well as secondary cancer prevention. IFs might facilitate the diagnosis of asymptomatic individuals and the early management of cancer once it develops.
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Affiliation(s)
- Sara Fernández-Castillejo
- Institut d'Oncologia de la Catalunya Sud (IOCS), Hospital Universitari Sant Joan de Reus (HUSJR), Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain. Universitat Rovira i Virgili (URV), Reus, Spain
| | - Bàrbara Roig
- Institut d'Oncologia de la Catalunya Sud (IOCS), Hospital Universitari Sant Joan de Reus (HUSJR), Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain. Universitat Rovira i Virgili (URV), Reus, Spain
| | - Mireia Melé
- Institut d'Oncologia de la Catalunya Sud (IOCS), Hospital Universitari Sant Joan de Reus (HUSJR), Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain. Universitat Rovira i Virgili (URV), Reus, Spain
| | - Sara Serrano
- Institut d'Oncologia de la Catalunya Sud (IOCS), Hospital Universitari Sant Joan de Reus (HUSJR), Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain. Universitat Rovira i Virgili (URV), Reus, Spain
| | - Mònica Salvat
- Institut d'Oncologia de la Catalunya Sud (IOCS), Hospital Universitari Sant Joan de Reus (HUSJR), Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain. Universitat Rovira i Virgili (URV), Reus, Spain
| | - Montserrat Querol
- Institut d'Oncologia de la Catalunya Sud (IOCS), Hospital Universitari Sant Joan de Reus (HUSJR), Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain. Universitat Rovira i Virgili (URV), Reus, Spain
| | - Joan Brunet
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL and Biomedical Research Centre Network for Oncology (CIBERONC), L'Hospitalet de Llobregat, Spain
- Hereditary Cancer Program, Catalan Institute of Oncology-IDIBGI, Girona, Spain
| | - Marta Pineda
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL and Biomedical Research Centre Network for Oncology (CIBERONC), L'Hospitalet de Llobregat, Spain
| | - Adela Cisneros
- Hematology Department, ICO and Hospital Germans Trias i Pujol, Josep Carreras Leukaemia Research Institute, Badalona, Spain
| | - David Parada
- Pathology Molecular Unit, Department of Pathology, Hospital Universitari Sant Joan de Reus (HUSJR), Spain. Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain. Universitat Rovira i Virgili (URV), Reus, Spain
| | - Joan Badia
- Institut d'Oncologia de la Catalunya Sud (IOCS), Hospital Universitari Sant Joan de Reus (HUSJR), Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain. Universitat Rovira i Virgili (URV), Reus, Spain
| | - Joan Borràs
- Institut d'Oncologia de la Catalunya Sud (IOCS), Hospital Universitari Sant Joan de Reus (HUSJR), Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain. Universitat Rovira i Virgili (URV), Reus, Spain
| | - Marta Rodríguez-Balada
- Institut d'Oncologia de la Catalunya Sud (IOCS), Hospital Universitari Sant Joan de Reus (HUSJR), Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain. Universitat Rovira i Virgili (URV), Reus, Spain
| | - Josep Gumà
- Institut d'Oncologia de la Catalunya Sud (IOCS), Hospital Universitari Sant Joan de Reus (HUSJR), Institut d'Investigació Sanitària Pere Virgili (IISPV), Reus, Spain. Universitat Rovira i Virgili (URV), Reus, Spain
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Abdeltwab RM, Yacoub E, Rashad AH, Shohdy KS. Molecular Basis of Tumorigenesis of Bladder Cancer and Emerging Concepts in Developing Therapeutic Targets. Bladder Cancer 2023; 9:313-322. [PMID: 38994247 PMCID: PMC11165923 DOI: 10.3233/blc-230025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 09/15/2023] [Indexed: 07/13/2024]
Abstract
BACKGROUND Advanced urothelial carcinoma (UC) is an aggressive disease whose mutagenic processes are yet to be elucidated. Targeted therapies are urgently needed, but the road from bench to bedside is slowly progressing. In this review, we discuss urothelial carcinoma etiology, along with the most recent advances in UC candidate targeted therapies. METHODOLOGY A comprehensive database search was performed. We aimed to review the most recent updates on UC genomics and targeted therapies. Pre-clinical as well as clinical studies were included. RESULTS Our review highlights the advances in understanding the molecular basis of urothelial tumorigenesis, including smoking, chemical parasitic carcinogens, inheritance, and APOBEC3 editing enzymes. We discussed how these factors contributed to the current mutational landscape of UC. Therapeutic options for UC are still very limited. However, several promising therapeutic approaches are in development to leverage our knowledge of molecular targets, such as targeting fibroblast growth factor receptors (FGFR), DNA damage repair pathways, and HER2. CONCLUSIONS Blindly testing targeted therapies based on other cancer data is not sufficient. UC-specific biomarkers are needed to precisely use the appropriate drug for the appropriate population. More efforts to understand UC biology and evolution are urgently needed.
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Affiliation(s)
| | - Elaria Yacoub
- Department of Clinical Oncology, Cairo University, Cairo, Egypt
| | - Ahmed H. Rashad
- Department of Clinical Oncology, Cairo University, Cairo, Egypt
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10
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Nikmanesh A, Esmailizadeh A, Asadollahpour Nanaei H, Ezedinloo L, Asadi Fozi M. Comparison of genetic diversity and phylogenetic structure of BRCA1 gene of some domestic and wild sheep breeds in different countries. Anim Biotechnol 2023; 34:4746-4759. [PMID: 36927261 DOI: 10.1080/10495398.2023.2187410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
BRCA1 gene plays an important role in DNA damage repair, cell cycle, and transcription process regulation; hence it's called gate keeper. The current research aims to perform bioinformatics analyzes of the BRCA1 gene of different breeds of domestic and wild sheep from 49 breeds in 14 countries using the NCBI genome database. The desired sequences were aligned using MEGA11 software and a phylogenetic tree was drawn by Neighbor-Joining method. The number of mutations, nucleotide diversity, and haploid diversity were also analyzed using Dnaspv5 software. The analyses showed 296 polymorphisms, which led to the creation of 45 different haplotypes with a haplotype diversity of 0.035. Nucleotide diversity and average nucleotide differences among breeds were estimated as 0.259 and 0.052, respectively. The average genetic distance within the population of countries was calculated as 0.052. The amount of sequence conservation in this research was 0.313 on average, which indicates the high polymorphism of this gene and the emergence of new proteins. Tajima's D value in Tajima's neutrality test was -2.421, which was significant (p < 0.05). One of the reasons for the high genetic diversity in Iran's wild sheep population is the existence of forests and open environments, which prevent genetic drift and reduce inbreeding.
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Affiliation(s)
- Alireza Nikmanesh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
| | | | - Leila Ezedinloo
- Department of Environment (DOE), Natural History Museum & Genetic Resource, Bureau, Park Nature of Pardisan, Tehran, Iran
| | - Masood Asadi Fozi
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, Iran
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Cragun DL, Hunt PP, Dean M, Weidner A, Shields AK, Tezak A, Pal T. Applying the framework for developing and evaluating complex interventions to increase family communication about hereditary cancer. PEC INNOVATION 2023; 2:100133. [PMID: 37214492 PMCID: PMC10194404 DOI: 10.1016/j.pecinn.2023.100133] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 01/30/2023] [Accepted: 02/01/2023] [Indexed: 05/24/2023]
Abstract
Objective Evaluate an intervention to increase family communication (FC) of positive hereditary cancer test results using the Framework for Developing and Evaluating Complex Interventions (FDECI). Methods We developed 'programme theory' during the FDECI development phase by aligning intervention components with behavior change techniques (BCTs) and theoretical factors expected to improve FC. During the feasibility phase, we obtained feedback from 12 stakeholder interviews. Results Intervention components aligned with a total of 14 unique BCTs for which prior evidence links the BCT to theoretical factors that influence behavior change. Constructive stakeholder feedback included: more information desired, rewording to support autonomy by highlighting options, and improvements to navigation, visuals, and audio. Positive comments included: comprehensiveness of materials, modeling of conversations, and usefulness of the materials for helping a person prepare to share positive test results. Conclusion The first FDECI phases were helpful for improving the intervention and planning our ongoing effectiveness and future implementation phases. Innovation Our application of the FDECI is novel, including plans to test our 'programme theory' using coincidence analysis (CNA) to determine who accesses which intervention materials, how utilizing certain materials impact the aligned theoretical factors, and whether these in turn make a difference in the behavioral outcome.
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Affiliation(s)
- Deborah L. Cragun
- University of South Florida, College of Public Health, Tampa, FL, United States of America
| | - Paige Phillips Hunt
- University of South Florida, College of Public Health, Tampa, FL, United States of America
| | - Marleah Dean
- University of South Florida, Department of Communication, Tampa, FL; Health Outcomes & Behavior Program, Moffitt Cancer Center, Tampa, FL, United States of America
- Moffitt Cancer Center, Health Outcomes & Behavior Program, Tampa, FL, United States of America
| | - Anne Weidner
- Vanderbilt University Medical Center, Department of Medicine; Vanderbilt-Ingram Cancer Center, Nashville, TN, United States of America
| | - Andrea K. Shields
- University of South Florida, College of Public Health, Tampa, FL, United States of America
| | - Ann Tezak
- Vanderbilt University Medical Center, Department of Medicine; Vanderbilt-Ingram Cancer Center, Nashville, TN, United States of America
| | - Tuya Pal
- Vanderbilt University Medical Center, Department of Medicine; Vanderbilt-Ingram Cancer Center, Nashville, TN, United States of America
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Badran AR, Youngs A, Forman A, Elms M, Chang LL, Lebbe F, Reekie A, Short J, Hlaing MT, Watts E, Hipps D, Snape K. Proactive familial cancer risk assessment: a service development study in UK primary care. BJGP Open 2023; 7:BJGPO.2023.0076. [PMID: 37591554 PMCID: PMC11176673 DOI: 10.3399/bjgpo.2023.0076] [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: 04/28/2023] [Revised: 07/31/2023] [Accepted: 08/11/2023] [Indexed: 08/19/2023] Open
Abstract
BACKGROUND Family history assessment can identify individuals above population-risk for cancer to enable targeted Screening, Prevention, and Early Detection (SPED). Family History Questionnaire Service (FHQS) is a resource-efficient patient-facing online tool to facilitate this. In the UK, cancer risk assessment is usually only offered to concerned individuals proactively self-presenting to their GP, leading to inequity in accessing SPED in the community. AIM To improve access to community cancer genetic risk assessment and explore barriers to uptake. DESIGN & SETTING Service development project of a digital pathway using the FHQS for cancer risk assessment across four general practices within the clinical remit of the South West Thames Centre for Genomics (SWTCG). METHOD 3100 individuals aged 38-50 years were invited to complete the FHQS through either text message or email. A random selection of 100 non-responders were contacted to determine barriers to uptake. RESULTS In total, n = 304/3100 (10%) registered for the FHQS. Responders were more likely to be British (63% vs 47%, P<0.001), speak English as their main language (92% vs 76%, P<0.001), and not require an interpreter (99.6% vs 94.9%, P = 0.001). Of 304 responders, 158 (52%) were automatically identified as at population-risk without full family history review. Of the remaining 146 responders, 52 (36%) required either additional screening referral (n = 23), genetics referral (n = 15), and/or advice to relatives (n = 18). Of 100 non-responders contacted, eight had incorrect contact details and 53 were contactable. Reasons for not responding included not receiving invitation details (n = 26), losing the invitation (n = 5), or forgetting (n = 4). CONCLUSION The FHQS can be used as part of a low-resource primary care pathway to identify individuals in the community above population-risk for cancer requiring action. This study highlighted barriers to uptake requiring consideration to maximise impact and minimise inequity.
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Affiliation(s)
- Abdul Rahman Badran
- South West Thames Centre for Genomics, St George's University Hospitals NHS Foundation Trust, London, UK
- Fieldway Medical Centre, Danebury, New Addington, Croydon, UK
| | - Alice Youngs
- South West Thames Centre for Genomics, St George's University Hospitals NHS Foundation Trust, London, UK
| | - Andrea Forman
- South West Thames Centre for Genomics, St George's University Hospitals NHS Foundation Trust, London, UK
| | - Marisa Elms
- South West Thames Centre for Genomics, St George's University Hospitals NHS Foundation Trust, London, UK
| | | | - Fiyaz Lebbe
- Fieldway Medical Centre, Danebury, New Addington, Croydon, UK
| | - Adam Reekie
- South West Thames Centre for Genomics, St George's University Hospitals NHS Foundation Trust, London, UK
| | - John Short
- South West Thames Centre for Genomics, St George's University Hospitals NHS Foundation Trust, London, UK
| | - Min Theik Hlaing
- South West Thames Centre for Genomics, St George's University Hospitals NHS Foundation Trust, London, UK
| | - Emma Watts
- Shere Surgery, Gomshall Lane, Guildford, UK
| | - Deborah Hipps
- The Exchange Surgery, Gracefield Gardens, London, UK
| | - Katie Snape
- South West Thames Centre for Genomics, St George's University Hospitals NHS Foundation Trust, London, UK
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Chen C, Shi H, Niu W, Bao X, Yang J, Jin H, Song W, Sun Y. The preimplantation genetic testing for monogenic disorders strategy for blocking the transmission of hereditary cancers through haplotype linkage analysis by karyomapping. J Assist Reprod Genet 2023; 40:2933-2943. [PMID: 37751120 PMCID: PMC10656414 DOI: 10.1007/s10815-023-02939-0] [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: 05/12/2023] [Accepted: 09/09/2023] [Indexed: 09/27/2023] Open
Abstract
PURPOSE Providing feasible preimplantation genetic testing strategies for monogenic disorders (PGT-M) for prevention and control of genetic cancers. METHODS Inclusion of families with a specific pathogenic mutation or a clear family history of genetic cancers. Identification of the distribution of hereditary cancer-related mutations in families through genetic testing. After a series of assisted reproductive measures such as down-regulation, stimulation, egg retrieval, and in vitro fertilization, a biopsy of trophectoderm cells from a blastocyst was performed for single-cell level whole-genome amplification (WGA). Then, the detection of chromosomal aneuploidies was performed by karyomapping. Construction of a haplotype-based linkage analysis to determine whether the embryo carries the mutation. Meanwhile, we performed CNV testing. Finally, embryos can be selected for transfer, and the results will be verified in 18-22 weeks after pregnancy. RESULTS Six couples with a total of 7 cycles were included in our study. Except for cycle 1 of case 5 which did not result in a transferable embryo, the remaining 6 cycles produced transferable embryos and had a successful pregnancy. Four couples have had amniotic fluid tests to confirm that the fetus does not carry the mutation, while 1 couple was not tested due to insufficient pregnancy weeks. And the remaining couples had to induce labor due to fetal megacystis during pregnancy. CONCLUSION Our strategy has been proven to be feasible. It can effectively prevent transmission of hereditary cancer-related mutations to offspring during the prenatal stage.
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Affiliation(s)
- Chuanju Chen
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Key Laboratory of Reproduction and Cenetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Provincial Obstetrical and Gynecological Diseases (Reproductive Medicine) Clinical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Engineering Laboratory of Preimplantation Genetic Diagnosis and Screening, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Hao Shi
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Key Laboratory of Reproduction and Cenetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Provincial Obstetrical and Gynecological Diseases (Reproductive Medicine) Clinical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Engineering Laboratory of Preimplantation Genetic Diagnosis and Screening, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Wenbin Niu
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Key Laboratory of Reproduction and Cenetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Provincial Obstetrical and Gynecological Diseases (Reproductive Medicine) Clinical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Engineering Laboratory of Preimplantation Genetic Diagnosis and Screening, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Xiao Bao
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Key Laboratory of Reproduction and Cenetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Provincial Obstetrical and Gynecological Diseases (Reproductive Medicine) Clinical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Engineering Laboratory of Preimplantation Genetic Diagnosis and Screening, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Jingya Yang
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Key Laboratory of Reproduction and Cenetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Provincial Obstetrical and Gynecological Diseases (Reproductive Medicine) Clinical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Engineering Laboratory of Preimplantation Genetic Diagnosis and Screening, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Haixia Jin
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Key Laboratory of Reproduction and Cenetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Provincial Obstetrical and Gynecological Diseases (Reproductive Medicine) Clinical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Engineering Laboratory of Preimplantation Genetic Diagnosis and Screening, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Wenyan Song
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Key Laboratory of Reproduction and Cenetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Provincial Obstetrical and Gynecological Diseases (Reproductive Medicine) Clinical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
- Henan Engineering Laboratory of Preimplantation Genetic Diagnosis and Screening, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China
| | - Yingpu Sun
- Center for Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
- Henan Key Laboratory of Reproduction and Cenetics, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
- Henan Provincial Obstetrical and Gynecological Diseases (Reproductive Medicine) Clinical Research Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
- Henan Engineering Laboratory of Preimplantation Genetic Diagnosis and Screening, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, China.
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Watanabe T, Soeda S, Okoshi C, Fukuda T, Yasuda S, Fujimori K. Landscape of somatic mutated genes and inherited susceptibility genes in gynecological cancer. J Obstet Gynaecol Res 2023; 49:2629-2643. [PMID: 37632362 DOI: 10.1111/jog.15766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 07/26/2023] [Indexed: 08/28/2023]
Abstract
Traditionally, gynecological cancers have been classified based on histology. Since remarkable advancements in next-generation sequencing technology have enabled the exploration of somatic mutations in various cancer types, comprehensive sequencing efforts have revealed the genomic landscapes of some common forms of human cancer. The genomic features of various gynecological malignancies have been reported by several studies of large-scale genomic cohorts, including The Cancer Genome Atlas. Although recent comprehensive genomic profiling tests, which can detect hundreds of genetic mutations at a time from cancer tissues or blood samples, have been increasingly used as diagnostic clinical biomarkers and in therapeutic management decisions, germline pathogenic variants associated with hereditary cancers can also be detected using this test. Gynecological cancers are closely related to genetic factors, with approximately 5% of endometrial cancer cases and 20% of ovarian cancer cases being caused by germline pathogenic variants. Hereditary breast and ovarian cancer syndrome and Lynch syndrome are the two major cancer susceptibility syndromes among gynecological cancers. In addition, several other hereditary syndromes have been reported to be associated with gynecological cancers. In this review, we highlight the genes for somatic mutation and germline pathogenic variants commonly seen in gynecological cancers. We first describe the relationship between clinicopathological attributes and somatic mutated genes. Subsequently, we discuss the characteristics and clinical management of inherited cancer syndromes resulting from pathogenic germline variants in gynecological malignancies.
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Affiliation(s)
- Takafumi Watanabe
- Department of Obstetrics and Gynecology, Fukushima Medical University, Fukushima, Japan
| | - Shu Soeda
- Department of Obstetrics and Gynecology, Fukushima Medical University, Fukushima, Japan
| | - Chihiro Okoshi
- Department of Obstetrics and Gynecology, Fukushima Medical University, Fukushima, Japan
| | - Toma Fukuda
- Department of Obstetrics and Gynecology, Fukushima Medical University, Fukushima, Japan
| | - Shun Yasuda
- Department of Obstetrics and Gynecology, Fukushima Medical University, Fukushima, Japan
| | - Keiya Fujimori
- Department of Obstetrics and Gynecology, Fukushima Medical University, Fukushima, Japan
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Adaku N, Ostendorf BN, Mei W, Tavazoie SF. Apolipoprotein E2 Stimulates Protein Synthesis and Promotes Melanoma Progression and Metastasis. Cancer Res 2023; 83:3013-3025. [PMID: 37335131 PMCID: PMC10740391 DOI: 10.1158/0008-5472.can-23-1252] [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: 04/26/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 06/21/2023]
Abstract
The secreted lipid transporter apolipoprotein E (APOE) plays important roles in atherosclerosis and Alzheimer's disease and has been implicated as a suppressor of melanoma progression. The APOE germline genotype predicts human melanoma outcomes, with APOE4 and APOE2 allele carriers exhibiting prolonged and reduced survival, respectively, relative to APOE3 homozygotes. While the APOE4 variant was recently shown to suppress melanoma progression by enhancing antitumor immunity, further work is needed to fully characterize the melanoma cell-intrinsic effects of APOE variants on cancer progression. Using a genetically engineered mouse model, we showed that human germline APOE genetic variants differentially modulate melanoma growth and metastasis in an APOE2>APOE3>APOE4 manner. The low-density lipoprotein receptor-related protein 1 (LRP1) receptor mediated the cell-intrinsic effects of APOE variants on melanoma progression. Protein synthesis was a tumor cell-intrinsic process differentially modulated by APOE variants, with APOE2 promoting translation via LRP1. These findings reveal a gain-of-function role for the APOE2 variant in melanoma progression, which may aid in predicting melanoma patient outcomes and understanding the protective effect of APOE2 in Alzheimer's disease. SIGNIFICANCE APOE germline variants impact melanoma progression through disparate mechanisms, such as the protein synthesis-promoting function of the APOE2 variant, indicating that germline genetic variants are causal contributors to metastatic outcomes.
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Affiliation(s)
- Nneoma Adaku
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY 10065, USA
| | - Benjamin N. Ostendorf
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY 10065, USA
| | - Wenbin Mei
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY 10065, USA
| | - Sohail F. Tavazoie
- Laboratory of Systems Cancer Biology, The Rockefeller University, New York, NY 10065, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
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Le T, Rojas PS, Fakunle M, Huang FW. Racial disparity in the genomics of precision oncology of prostate cancer. Cancer Rep (Hoboken) 2023; 6 Suppl 1:e1867. [PMID: 37565547 PMCID: PMC10440844 DOI: 10.1002/cnr2.1867] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 06/15/2023] [Accepted: 06/30/2023] [Indexed: 08/12/2023] Open
Abstract
BACKGROUND Significant racial disparities in prostate cancer incidence and mortality have been reported between African American Men (AAM), who are at increased risk for prostate cancer, and European American Men (EAM). In most of the studies carried out on prostate cancer, this population is underrepresented. With the advancement of genome-wide association studies, several genetic predictor models of prostate cancer risk have been elaborated, as well as numerous studies that identify both germline and somatic mutations with clinical utility. RECENT FINDINGS Despite significant advances, the AAM population continues to be underrepresented in genomic studies, which can limit generalizability and potentially widen disparities. Here we outline racial disparities in currently available genomic applications that are used to estimate the risk of individuals developing prostate cancer and to identify personalized oncology treatment strategies. While the incidence and mortality of prostate cancer are different between AAM and EAM, samples from AAM remain to be unrepresented in different studies. CONCLUSION This disparity impacts the available genomic data on prostate cancer. As a result, the disparity can limit the predictive utility of the genomic applications and may lead to the widening of the existing disparities. More studies with substantially higher recruitment and engagement of African American patients are necessary to overcome this disparity.
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Affiliation(s)
- Tu Le
- Division of Hematology and Oncology, Department of MedicineUniversity of CaliforniaSan FranciscoCaliforniaUSA
- Division of Hematology and Oncology, Department of MedicineSan Francisco Veterans Affairs Medical CenterSan FranciscoCaliforniaUSA
| | - Pilar Soto Rojas
- Division of Hematology and Oncology, Department of MedicineUniversity of CaliforniaSan FranciscoCaliforniaUSA
- Department of OncologyHospital Universitario Virgen MacarenaSevilleSpain
| | - Mary Fakunle
- Department of UrologyUniversity of CaliforniaSan FranciscoCaliforniaUSA
| | - Franklin W. Huang
- Division of Hematology and Oncology, Department of MedicineUniversity of CaliforniaSan FranciscoCaliforniaUSA
- Division of Hematology and Oncology, Department of MedicineSan Francisco Veterans Affairs Medical CenterSan FranciscoCaliforniaUSA
- Department of UrologyUniversity of CaliforniaSan FranciscoCaliforniaUSA
- Chan Zuckerberg BiohubSan FranciscoCaliforniaUSA
- Institute for Human GeneticsUniversity of California San FranciscoSan FranciscoCaliforniaUSA
- Bakar Computational Health Sciences InstituteUniversity of California San FranciscoSan FranciscoCaliforniaUSA
- Benioff Initiative for Prostate Cancer ResearchUniversity of California San FranciscoSan FranciscoCaliforniaUSA
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17
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Vavassori A, Mauri G, Mazzola GC, Mastroleo F, Bonomo G, Durante S, Zerini D, Marvaso G, Corrao G, Ferrari ED, Rondi E, Vigorito S, Cattani F, Orsi F, Jereczek-Fossa BA. Cyberknife Radiosurgery for Prostate Cancer after Abdominoperineal Resection (CYRANO): The Combined Computer Tomography and Electromagnetic Navigation Guided Transperineal Fiducial Markers Implantation Technique. Curr Oncol 2023; 30:7926-7935. [PMID: 37754491 PMCID: PMC10529393 DOI: 10.3390/curroncol30090576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/18/2023] [Accepted: 08/24/2023] [Indexed: 09/28/2023] Open
Abstract
In this technical development report, we present the strategic placement of fiducial markers within the prostate under the guidance of computed tomography (CT) and electromagnetic navigation (EMN) for the delivery of ultra-hypofractionated cyberknife (CK) therapy in a patient with localized prostate cancer (PCa) who had previously undergone chemo-radiotherapy for rectal cancer and subsequent abdominoperineal resection due to local recurrence. The patient was positioned in a prone position with a pillow under the pelvis to facilitate access, and an electromagnetic fiducial marker was placed on the patient's skin to establish a stable position. CT scans were performed to plan the procedure, mark virtual points, and simulate the needle trajectory using the navigation system. Local anesthesia was administered, and a 21G needle was used to place the fiducial markers according to the navigation system information. A confirmatory CT scan was obtained to ensure proper positioning. The implantation procedure was safe, without any acute side effects such as pain, hematuria, dysuria, or hematospermia. Our report highlights the ability to use EMN systems to virtually navigate within a pre-acquired imaging dataset in the interventional room, allowing for non-conventional approaches and potentially revolutionizing fiducial marker positioning, offering new perspectives for PCa treatment in selected cases.
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Affiliation(s)
- Andrea Vavassori
- Division of Radiation Oncology, IEO European Institute of Oncology IRCCS, 20141 Milan, Italy; (A.V.); (G.C.M.); (S.D.); (D.Z.); (G.M.); (G.C.); (E.D.F.); (B.A.J.-F.)
| | - Giovanni Mauri
- Division of Interventional Radiology, IEO European Institute of Oncology IRCCS, 20141 Milan, Italy; (G.M.); (G.B.); (F.O.)
- Department of Oncology and Hemato-Oncology, University of Milan, 20141 Milan, Italy
| | - Giovanni Carlo Mazzola
- Division of Radiation Oncology, IEO European Institute of Oncology IRCCS, 20141 Milan, Italy; (A.V.); (G.C.M.); (S.D.); (D.Z.); (G.M.); (G.C.); (E.D.F.); (B.A.J.-F.)
- Department of Oncology and Hemato-Oncology, University of Milan, 20141 Milan, Italy
| | - Federico Mastroleo
- Division of Radiation Oncology, IEO European Institute of Oncology IRCCS, 20141 Milan, Italy; (A.V.); (G.C.M.); (S.D.); (D.Z.); (G.M.); (G.C.); (E.D.F.); (B.A.J.-F.)
- Department of Translational Medicine, University of Piemonte Orientale (UPO), 20188 Novara, Italy
| | - Guido Bonomo
- Division of Interventional Radiology, IEO European Institute of Oncology IRCCS, 20141 Milan, Italy; (G.M.); (G.B.); (F.O.)
| | - Stefano Durante
- Division of Radiation Oncology, IEO European Institute of Oncology IRCCS, 20141 Milan, Italy; (A.V.); (G.C.M.); (S.D.); (D.Z.); (G.M.); (G.C.); (E.D.F.); (B.A.J.-F.)
| | - Dario Zerini
- Division of Radiation Oncology, IEO European Institute of Oncology IRCCS, 20141 Milan, Italy; (A.V.); (G.C.M.); (S.D.); (D.Z.); (G.M.); (G.C.); (E.D.F.); (B.A.J.-F.)
| | - Giulia Marvaso
- Division of Radiation Oncology, IEO European Institute of Oncology IRCCS, 20141 Milan, Italy; (A.V.); (G.C.M.); (S.D.); (D.Z.); (G.M.); (G.C.); (E.D.F.); (B.A.J.-F.)
- Department of Oncology and Hemato-Oncology, University of Milan, 20141 Milan, Italy
| | - Giulia Corrao
- Division of Radiation Oncology, IEO European Institute of Oncology IRCCS, 20141 Milan, Italy; (A.V.); (G.C.M.); (S.D.); (D.Z.); (G.M.); (G.C.); (E.D.F.); (B.A.J.-F.)
| | - Elettra Dorotea Ferrari
- Division of Radiation Oncology, IEO European Institute of Oncology IRCCS, 20141 Milan, Italy; (A.V.); (G.C.M.); (S.D.); (D.Z.); (G.M.); (G.C.); (E.D.F.); (B.A.J.-F.)
- Department of Oncology and Hemato-Oncology, University of Milan, 20141 Milan, Italy
| | - Elena Rondi
- Unit of Medical Physics, IEO European Institute of Oncology IRCCS, 20141 Milan, Italy; (E.R.); (S.V.); (F.C.)
| | - Sabrina Vigorito
- Unit of Medical Physics, IEO European Institute of Oncology IRCCS, 20141 Milan, Italy; (E.R.); (S.V.); (F.C.)
| | - Federica Cattani
- Unit of Medical Physics, IEO European Institute of Oncology IRCCS, 20141 Milan, Italy; (E.R.); (S.V.); (F.C.)
| | - Franco Orsi
- Division of Interventional Radiology, IEO European Institute of Oncology IRCCS, 20141 Milan, Italy; (G.M.); (G.B.); (F.O.)
| | - Barbara Alicja Jereczek-Fossa
- Division of Radiation Oncology, IEO European Institute of Oncology IRCCS, 20141 Milan, Italy; (A.V.); (G.C.M.); (S.D.); (D.Z.); (G.M.); (G.C.); (E.D.F.); (B.A.J.-F.)
- Department of Oncology and Hemato-Oncology, University of Milan, 20141 Milan, Italy
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Balinisteanu I, Panzaru MC, Caba L, Ungureanu MC, Florea A, Grigore AM, Gorduza EV. Cancer Predisposition Syndromes and Thyroid Cancer: Keys for a Short Two-Way Street. Biomedicines 2023; 11:2143. [PMID: 37626640 PMCID: PMC10452453 DOI: 10.3390/biomedicines11082143] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/20/2023] [Accepted: 07/26/2023] [Indexed: 08/27/2023] Open
Abstract
Cancer predisposition syndromes are entities determined especially by germinal pathogenic variants, with most of them autosomal dominantly inherited. The risk of a form of cancer is variable throughout life and affects various organs, including the thyroid. Knowing the heterogeneous clinical picture and the existing genotype-phenotype correlations in some forms of thyroid cancer associated with these syndromes is important for adequate and early management of patients and families. This review synthesizes the current knowledge on genes and proteins involved in cancer predisposition syndromes with thyroid cancer and the phenomena of heterogeneity (locus, allelic, mutational, and clinical).
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Affiliation(s)
- Ioana Balinisteanu
- Endocrinology Department, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania; (I.B.); (M.-C.U.)
- Endocrinology Department, “Sf. Spiridon” Hospital, 700106 Iasi, Romania
| | - Monica-Cristina Panzaru
- Department of Medical Genetics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania; (A.F.); (E.V.G.)
| | - Lavinia Caba
- Department of Medical Genetics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania; (A.F.); (E.V.G.)
| | - Maria-Christina Ungureanu
- Endocrinology Department, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania; (I.B.); (M.-C.U.)
- Endocrinology Department, “Sf. Spiridon” Hospital, 700106 Iasi, Romania
| | - Andreea Florea
- Department of Medical Genetics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania; (A.F.); (E.V.G.)
| | - Ana Maria Grigore
- Department of Medical Genetics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania; (A.F.); (E.V.G.)
| | - Eusebiu Vlad Gorduza
- Department of Medical Genetics, Faculty of Medicine, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania; (A.F.); (E.V.G.)
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19
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Özdemir Z, Çevik E, Öksüzoğlu ÖBÇ, Doğan M, Ateş Ö, Esin E, Bilgetekin İ, Demirci U, Köseoğlu Ç, Topal A, Karadurmuş N, Erdem HB, Bahsi T. Uncommon variants detected via hereditary cancer panel and suggestions for genetic counseling. Mutat Res 2023; 827:111831. [PMID: 37453313 DOI: 10.1016/j.mrfmmm.2023.111831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 06/08/2023] [Accepted: 07/01/2023] [Indexed: 07/18/2023]
Abstract
OBJECTIVE Hereditary cancer syndromes constitute 5-10% of all cancers. The development of next-generation sequencing technologies has made it possible to examine many hereditary cancer syndrome-causing genes in a single panel. This study's goal was to describe the prevalence and the variant spectrum using NGS in individuals who were thought to have a hereditary predisposition for cancer. MATERIAL AND METHOD Analysis was performed for 1254 who were thought to have a familial predisposition for cancer. We excluded 46 patients who were carrying BRCA1/2 variants in this study, for focusing on the rare gene mutations. Sequencing was performed using the Sophia Hereditary Cancer Solution v1.1 Panel and the Qiagen Large Hereditary Cancer Panel. The Illumina MiSeq system was used for the sequencing procedure. The software used for the data analyses was Sophia DDM and QIAGEN Clinical Insight (QCITM) Analyze. The resulting genomic changes were classified according to the current guidelines of ACMG/AMP. RESULTS Pathogenic/likely pathogenic variants were detected in 172 (13.7%) of 1254 patients. After excluding the 46 BRCA1/2-positive patients, among the remaining 126 patients; there were 60 (4.8%) breast cancer, 33 (2.6%) colorectal cancer, 9 (0.7%) ovarian cancer, 5 (0.4%) endometrium cancer, 5 (0.4%) stomach cancer, 3 (0.2%) prostate cancer patients. The most altered genes were MUTYH in 27 (2.1%) patients, MMR genes (MLH1, MSH6, MSH, MSH2, PMS2 and EPCAM) in 26 (2%) patients, and ATM in 25 (2%) patients. We also examined the genotype-phenotype correlation in rare variants. Additionally, we identified 11 novel variations. CONCLUSION This study provided significant information regarding rare variants observed in the Turkish population because it was carried out with a large patient group. Personalized treatment options and genetic counseling for the patients are therefore made facilitated.
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Affiliation(s)
- Zeynep Özdemir
- Ankara Etlik City Hospital, Department of Medical Genetics, Ankara, Turkiye.
| | - Ezgi Çevik
- Ankara Etlik City Hospital, Department of Medical Genetics, Ankara, Turkiye
| | | | - Mutlu Doğan
- University of Health Sciences, Ankara Oncology Training and Research Hospital, Department of Medical Oncology, Ankara, Turkiye
| | - Öztürk Ateş
- University of Health Sciences, Ankara Oncology Training and Research Hospital, Department of Medical Oncology, Ankara, Turkiye
| | - Ece Esin
- Bayındır Hospital, Department of Medical Oncology, Ankara, Turkiye
| | - İrem Bilgetekin
- Lösante Hospital, Department of Medical Oncology, Ankara, Türkiye
| | - Umut Demirci
- Memorial Hospital, Department of Medical Oncology, Ankara, Turkiye
| | - Çağlar Köseoğlu
- University of Health Sciences, Gülhane Training and Research Hospital, Department of Medical Oncology, Ankara, Turkiye
| | - Alper Topal
- University of Health Sciences, Gülhane Training and Research Hospital, Department of Medical Oncology, Ankara, Turkiye
| | - Nuri Karadurmuş
- University of Health Sciences, Gülhane Training and Research Hospital, Department of Medical Oncology, Ankara, Turkiye
| | - Haktan Bağış Erdem
- Ankara Etlik City Hospital, Department of Medical Genetics, Ankara, Turkiye
| | - Taha Bahsi
- Ankara Etlik City Hospital, Department of Medical Genetics, Ankara, Turkiye
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20
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Subasri V, Light N, Kanwar N, Brzezinski J, Luo P, Hansford JR, Cairney E, Portwine C, Elser C, Finlay JL, Nichols KE, Alon N, Brunga L, Anson J, Kohlmann W, de Andrade KC, Khincha PP, Savage SA, Schiffman JD, Weksberg R, Pugh TJ, Villani A, Shlien A, Goldenberg A, Malkin D. Multiple Germline Events Contribute to Cancer Development in Patients with Li-Fraumeni Syndrome. CANCER RESEARCH COMMUNICATIONS 2023; 3:738-754. [PMID: 37377903 PMCID: PMC10150777 DOI: 10.1158/2767-9764.crc-22-0402] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 01/19/2023] [Accepted: 03/29/2023] [Indexed: 06/29/2023]
Abstract
Li-Fraumeni syndrome (LFS) is an autosomal dominant cancer-predisposition disorder. Approximately 70% of individuals who fit the clinical definition of LFS harbor a pathogenic germline variant in the TP53 tumor suppressor gene. However, the remaining 30% of patients lack a TP53 variant and even among variant TP53 carriers, approximately 20% remain cancer-free. Understanding the variable cancer penetrance and phenotypic variability in LFS is critical to developing rational approaches to accurate, early tumor detection and risk-reduction strategies. We leveraged family-based whole-genome sequencing and DNA methylation to evaluate the germline genomes of a large, multi-institutional cohort of patients with LFS (n = 396) with variant (n = 374) or wildtype TP53 (n = 22). We identified alternative cancer-associated genetic aberrations in 8/14 wildtype TP53 carriers who developed cancer. Among variant TP53 carriers, 19/49 who developed cancer harbored a pathogenic variant in another cancer gene. Modifier variants in the WNT signaling pathway were associated with decreased cancer incidence. Furthermore, we leveraged the noncoding genome and methylome to identify inherited epimutations in genes including ASXL1, ETV6, and LEF1 that confer increased cancer risk. Using these epimutations, we built a machine learning model that can predict cancer risk in patients with LFS with an area under the receiver operator characteristic curve (AUROC) of 0.725 (0.633-0.810). Significance Our study clarifies the genomic basis for the phenotypic variability in LFS and highlights the immense benefits of expanding genetic and epigenetic testing of patients with LFS beyond TP53. More broadly, it necessitates the dissociation of hereditary cancer syndromes as single gene disorders and emphasizes the importance of understanding these diseases in a holistic manner as opposed to through the lens of a single gene.
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Affiliation(s)
- Vallijah Subasri
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Vector Institute, Toronto, Ontario, Canada
| | - Nicholas Light
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | - Nisha Kanwar
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jack Brzezinski
- Division of Haematology/Oncology, The Hospital for Sick Children, Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Ping Luo
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Jordan R. Hansford
- Children's Cancer Centre, Royal Children's Hospital, Melbourne, Victoria, Australia
- Murdoch Children's Research Institute, Parkville, Victoria, Australia
- Department of Pediatrics, University of Melbourne, Melbourne, Australia
- Michael Rice Cancer Centre, Women's and Children's Hospital, North Adelaide, South Australia, Australia
- South Australia Health and Medical Research Institute, Adelaide, South Australia, Australia
- South Australia Immunogenomics Cancer Institute, University of Adelaide, Adelaide, Australia
| | - Elizabeth Cairney
- Department of Paediatrics, London Health Sciences Centre and Western University, London, Ontario, Canada
| | - Carol Portwine
- Department of Paediatrics, McMaster University, Hamilton, Ontario, Canada
| | - Christine Elser
- Department of Medical Oncology, Princess Margaret Hospital and Mount Sinai Hospital, Toronto, Ontario, Canada
- Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Jonathan L. Finlay
- Neuro-Oncology Program, Nationwide Children's Hospital and The Ohio State University, Columbus, Ohio
| | - Kim E. Nichols
- Department of Oncology, St Jude Children's Research Hospital, Memphis, Tennessee
| | - Noa Alon
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Ledia Brunga
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jo Anson
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Wendy Kohlmann
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah
| | - Kelvin C. de Andrade
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, NCI, Bethesda, Maryland
| | - Payal P. Khincha
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, NCI, Bethesda, Maryland
| | - Sharon A. Savage
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, NCI, Bethesda, Maryland
| | - Joshua D. Schiffman
- Department of Pediatrics, University of Utah, Salt Lake City, Utah
- PEEL Therapeutics, Inc., Salt Lake City, Utah
| | - Rosanna Weksberg
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Trevor J. Pugh
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Anita Villani
- Division of Haematology/Oncology, The Hospital for Sick Children, Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Adam Shlien
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Anna Goldenberg
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Vector Institute, Toronto, Ontario, Canada
- CIFAR: Child and Brain Development, Toronto, Ontario, Canada
- Department of Computer Science, University of Toronto, Toronto, Ontario, Canada
| | - David Malkin
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Division of Haematology/Oncology, The Hospital for Sick Children, Department of Paediatrics, University of Toronto, Toronto, Ontario, Canada
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Hathaway F, Martins R, Sorscher S, Bzura A, Dudbridge F, Fennell DA. Family Matters: Germline Testing in Thoracic Cancers. Am Soc Clin Oncol Educ Book 2023; 43:e389956. [PMID: 37167572 DOI: 10.1200/edbk_389956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Most thoracic cancers arise via a series of stepwise somatic alterations driven by a well-defined carcinogen (ie, tobacco or asbestos for lung cancer and mesothelioma, respectively). A small proportion can emerge on a background of pathogenic germline variants (PGVs), which have the property of heritability. In general, PGVs may be initially suspected on the basis of the presence of specific clinical features. Such gene × environment interactions significantly increase the risk of developing lung cancer (1.5- to 3.2-fold). PGVs have been discovered involving the actionable driver oncogene, epidermal growth factor receptor (EGFR), with an EGFR T790M PGV rate of 0.3%-0.9% in the nonsquamous non-small-cell lung cancer subtype. Its appearance during routine somatic DNA sequencing in those patients who have not had a previous tyrosine kinase inhibitor should raise suspicion. In patients with sporadic mesothelioma, BAP1 is the most frequently mutated tumor driver, with a PGV rate between 2.8% and 8%, associated with a favorable prognosis. BAP1 PGVs accelerate mesothelioma tumorigenesis after asbestos exposure in preclinical models and may be partly predicted by clinical criteria. At present, routine germline genetic testing for thoracic cancers is not a standard practice. Expert genetic counseling is, therefore, required for patients who carry a PGV. Ongoing studies aim to better understand the natural history of patients harboring PGVs to underpin future cancer prevention, precise counseling, and cancer management with the goal of improving the quality and length of life.
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Affiliation(s)
- Feighanne Hathaway
- Department of Medicine, Section of Hematology/Oncology, The University of Chicago Comprehensive Cancer Center, Chicago, IL
| | - Renato Martins
- Department of Hematology, Oncology, Palliative Care, Virginia Commonwealth University, Richmond, VA
| | | | | | | | - Dean A Fennell
- The University of Leicester, Leicester, United Kingdom
- University Hospitals of Leicester NHS Trust, Leicester, United Kingdom
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22
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Majithia J, Mahajan A, Vaish R, Prakash G, Patwardhan S, Sarin R. Imaging Recommendations for Diagnosis, Staging, and Management of Hereditary Malignancies. Indian J Med Paediatr Oncol 2023. [DOI: 10.1055/s-0042-1760325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023] Open
Abstract
AbstractHereditary cancer syndromes, characterized by genetically distinct neoplasms developing in specific organs in more than one family members, predispose an individual to early onset of distinct site-specific tumors. Early age of onset, multiorgan involvement, multiple and bilateral tumors, advanced disease at presentation, and aggressive tumor histology are few characteristic features of hereditary cancer syndromes. A multidisciplinary approach to hereditary cancers has led to a paradigm shift in the field of preventive oncology and precision medicine. Imaging plays a pivotal role in the screening, testing, and follow-up of individuals and their first- and second-degree relatives with hereditary cancers. In fact, a radiologist is often the first to apprise the clinician about the possibility of an underlying hereditary cancer syndrome based on pathognomonic imaging findings. This article focuses on the imaging spectrum of few common hereditary cancer syndromes with specific mention of the imaging features of associated common and uncommon tumors in each syndrome. The screening and surveillance recommendations for each condition with specific management approaches, in contrast to sporadic cases, have also been described.
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Affiliation(s)
- Jinita Majithia
- Department of Radiodiagnosis, Tata Memorial Hospital, Mumbai, Maharashtra, India
| | - Abhishek Mahajan
- Department of Radiology, The Clatterbridge Cancer Centre NHS Foundation Trust, Liverpool, United Kingdom
| | - Richa Vaish
- Department of Head and Neck Oncology, Tata Memorial Hospital, Mumbai, Maharashtra, India
| | - Gagan Prakash
- Department of Uro-Oncology, Tata Memorial Hospital, Mumbai, Maharashtra, India
| | - Saket Patwardhan
- Department of Radiodiagnosis, Tata Memorial Hospital, Mumbai, Maharashtra, India
| | - Rajiv Sarin
- Department of Radiation Oncology and In-Charge Cancer Genetics, Tata Memorial Hospital and Advanced Centre for Treatment Research and Education in Cancer (ACTREC), Mumbai, Maharashtra, India
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23
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Espinoza Moya ME, Guertin JR, Dorval M, Lapointe J, Bouchard K, Nabi H, Laberge M. Examining interprofessional collaboration in oncogenetic service delivery models for hereditary cancers: a scoping review protocol. BMJ Open 2022; 12:e066802. [PMID: 36523215 PMCID: PMC9748975 DOI: 10.1136/bmjopen-2022-066802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
INTRODUCTION In a context of limited genetic specialists, collaborative models have been proposed to ensure timely access to high quality oncogenetic services for individuals with inherited cancer susceptibility. Yet, extensive variability in the terminology used and lack of a clear understanding of how interprofessional collaboration is operationalised and evaluated currently constrains the development of a robust evidence base on the value of different approaches used to optimise access to these services. To fill in this knowledge gap, this scoping review aims to systematically unpack the nature and extent of collaboration proposed by these interventions, and synthesise the evidence available on their implementation, effectiveness and economic impact. METHODS AND ANALYSIS Following the Joanna Briggs Institute guidelines for scoping reviews, a comprehensive literature search will be conducted to identify peer-reviewed and grey literature on collaborative models used for adult patients with, or at increased risk of, hereditary breast, ovarian, colorectal and prostate cancers. An initial search was developed for Medline, Embase, CINAHL (Cumulative Index to Nursing and Allied Health Literature), Cochrane and Web of Science on 13 June 2022 and will be complemented by searches in Google and relevant websites. Documents describing either the theory of change, planning, implementation and/or evaluation of these interventions will be considered for inclusion. Results will be summarised descriptively and used to compare relevant model characteristics and synthesise evidence available on their implementation, effectiveness and economic impact. This process is expected to guide the development of a definition and typology of collaborative models in oncogenetics that could help strengthen the knowledge base on these interventions. Moreover, because we will be mapping the existing evidence on collaborative models in oncogenetics, the proposed review will help us identify areas where additional research might be needed. ETHICS AND DISSEMINATION This research does not require ethics approval. Results from this review will be disseminated through peer-reviewed articles and conferences.
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Affiliation(s)
- Maria Eugenia Espinoza Moya
- Population Health and Optimal Health Practices Unit, Centre de Recherche du Centre hospitalier universitaire (CHU) de Québec-Université Laval, Quebec City, Quebec, Canada
- Département des opérations et systèmes de décision, Faculté des sciences de l'administration, Université Laval, Quebec City, Quebec, Canada
| | - Jason Robert Guertin
- Population Health and Optimal Health Practices Unit, Centre de Recherche du Centre hospitalier universitaire (CHU) de Québec-Université Laval, Quebec City, Quebec, Canada
- Department of Social and Preventive Medicine, Faculty of Medicine, Université Laval, Quebec City, Quebec, Canada
| | - Michel Dorval
- Oncology Division, Centre de Recherche du CHU de Québec-Université Laval, Quebec City, Quebec, Canada
- Faculty of Pharmacy, Université Laval, Quebec City, Quebec, Canada
- CISSS, Chaudière-Appalaches Research Center, Lévis, Québec, Canada
| | - Julie Lapointe
- Oncology Division, Centre de Recherche du CHU de Québec-Université Laval, Quebec City, Quebec, Canada
| | - Karine Bouchard
- Département de cancérologie, CHU de Québec-Université Laval, Quebec City, Quebec, Canada
| | - Hermann Nabi
- Department of Social and Preventive Medicine, Faculty of Medicine, Université Laval, Quebec City, Quebec, Canada
- Oncology Division, Centre de Recherche du CHU de Québec-Université Laval, Quebec City, Quebec, Canada
| | - Maude Laberge
- Population Health and Optimal Health Practices Unit, Centre de Recherche du Centre hospitalier universitaire (CHU) de Québec-Université Laval, Quebec City, Quebec, Canada
- Département des opérations et systèmes de décision, Faculté des sciences de l'administration, Université Laval, Quebec City, Quebec, Canada
- Vitam, Centre de recherche en santé durable, Laval University, Quebec City, Quebec, Canada
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Paduano F, Colao E, Fabiani F, Rocca V, Dinatolo F, Dattola A, D’Antona L, Amato R, Trapasso F, Baudi F, Perrotti N, Iuliano R. Germline Testing in a Cohort of Patients at High Risk of Hereditary Cancer Predisposition Syndromes: First Two-Year Results from South Italy. Genes (Basel) 2022; 13:1286. [PMID: 35886069 PMCID: PMC9319682 DOI: 10.3390/genes13071286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/15/2022] [Accepted: 07/18/2022] [Indexed: 12/04/2022] Open
Abstract
Germline pathogenic variants (PVs) in oncogenes and tumour suppressor genes are responsible for 5 to 10% of all diagnosed cancers, which are commonly known as hereditary cancer predisposition syndromes (HCPS). A total of 104 individuals at high risk of HCPS were selected by genetic counselling for genetic testing in the past 2 years. Most of them were subjects having a personal and family history of breast cancer (BC) selected according to current established criteria. Genes analysis involved in HCPS was assessed by next-generation sequencing (NGS) using a custom cancer panel with high- and moderate-risk susceptibility genes. Germline PVs were identified in 17 of 104 individuals (16.3%) analysed, while variants of uncertain significance (VUS) were identified in 21/104 (20.2%) cases. Concerning the germline PVs distribution among the 13 BC individuals with positive findings, 8/13 (61.5%) were in the BRCA1/2 genes, whereas 5/13 (38.4%) were in other high- or moderate-risk genes including PALB2, TP53, ATM and CHEK2. NGS genetic testing showed that 6/13 (46.1%) of the PVs observed in BC patients were detected in triple-negative BC. Interestingly, the likelihood of carrying the PVs in the moderate-to-high-risk genes calculated by the cancer risk model BOADICEA was significantly higher in pathogenic variant carriers than in negative subjects. Collectively, this study shows that multigene panel testing can offer an effective diagnostic approach for patients at high risk of hereditary cancers.
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Affiliation(s)
- Francesco Paduano
- Medical Genetics Unit, Mater Domini University Hospital, 88100 Catanzaro, Italy; (E.C.); (F.F.); (V.R.); (F.D.); (A.D.); (L.D.); (R.A.); (F.T.); (F.B.); (N.P.)
- Department of Health Sciences, Campus S. Venuta, University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
- Stem Cells and Medical Genetics Units, Tecnologica Research Institute and Marrelli Health, 88900 Crotone, Italy
| | - Emma Colao
- Medical Genetics Unit, Mater Domini University Hospital, 88100 Catanzaro, Italy; (E.C.); (F.F.); (V.R.); (F.D.); (A.D.); (L.D.); (R.A.); (F.T.); (F.B.); (N.P.)
| | - Fernanda Fabiani
- Medical Genetics Unit, Mater Domini University Hospital, 88100 Catanzaro, Italy; (E.C.); (F.F.); (V.R.); (F.D.); (A.D.); (L.D.); (R.A.); (F.T.); (F.B.); (N.P.)
| | - Valentina Rocca
- Medical Genetics Unit, Mater Domini University Hospital, 88100 Catanzaro, Italy; (E.C.); (F.F.); (V.R.); (F.D.); (A.D.); (L.D.); (R.A.); (F.T.); (F.B.); (N.P.)
- Department of Experimental and Clinical Medicine, Campus S. Venuta, University Magna Graecia of Catanzaro, Viale Europa, Località Germaneto, 88100 Catanzaro, Italy
| | - Francesca Dinatolo
- Medical Genetics Unit, Mater Domini University Hospital, 88100 Catanzaro, Italy; (E.C.); (F.F.); (V.R.); (F.D.); (A.D.); (L.D.); (R.A.); (F.T.); (F.B.); (N.P.)
| | - Adele Dattola
- Medical Genetics Unit, Mater Domini University Hospital, 88100 Catanzaro, Italy; (E.C.); (F.F.); (V.R.); (F.D.); (A.D.); (L.D.); (R.A.); (F.T.); (F.B.); (N.P.)
| | - Lucia D’Antona
- Medical Genetics Unit, Mater Domini University Hospital, 88100 Catanzaro, Italy; (E.C.); (F.F.); (V.R.); (F.D.); (A.D.); (L.D.); (R.A.); (F.T.); (F.B.); (N.P.)
- Department of Health Sciences, Campus S. Venuta, University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
| | - Rosario Amato
- Medical Genetics Unit, Mater Domini University Hospital, 88100 Catanzaro, Italy; (E.C.); (F.F.); (V.R.); (F.D.); (A.D.); (L.D.); (R.A.); (F.T.); (F.B.); (N.P.)
- Department of Health Sciences, Campus S. Venuta, University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
| | - Francesco Trapasso
- Medical Genetics Unit, Mater Domini University Hospital, 88100 Catanzaro, Italy; (E.C.); (F.F.); (V.R.); (F.D.); (A.D.); (L.D.); (R.A.); (F.T.); (F.B.); (N.P.)
- Department of Experimental and Clinical Medicine, Campus S. Venuta, University Magna Graecia of Catanzaro, Viale Europa, Località Germaneto, 88100 Catanzaro, Italy
| | - Francesco Baudi
- Medical Genetics Unit, Mater Domini University Hospital, 88100 Catanzaro, Italy; (E.C.); (F.F.); (V.R.); (F.D.); (A.D.); (L.D.); (R.A.); (F.T.); (F.B.); (N.P.)
- Department of Health Sciences, Campus S. Venuta, University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
| | - Nicola Perrotti
- Medical Genetics Unit, Mater Domini University Hospital, 88100 Catanzaro, Italy; (E.C.); (F.F.); (V.R.); (F.D.); (A.D.); (L.D.); (R.A.); (F.T.); (F.B.); (N.P.)
- Department of Health Sciences, Campus S. Venuta, University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
| | - Rodolfo Iuliano
- Medical Genetics Unit, Mater Domini University Hospital, 88100 Catanzaro, Italy; (E.C.); (F.F.); (V.R.); (F.D.); (A.D.); (L.D.); (R.A.); (F.T.); (F.B.); (N.P.)
- Department of Health Sciences, Campus S. Venuta, University Magna Graecia of Catanzaro, 88100 Catanzaro, Italy
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Chang Y, Chao D, Chung C, Chou Y, Chang C, Lin C, Chu H, Chen H, Liu T, Juan Y, Chang S, Chang J. Cancer carrier screening in the general population using whole-genome sequencing. Cancer Med 2022; 12:1972-1983. [PMID: 35861108 PMCID: PMC9883534 DOI: 10.1002/cam4.5034] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/27/2022] [Accepted: 06/29/2022] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Cancer is a major cause of death, and its early identification and intervention have potential for clinical actionability and benefits for human health. The studies using whole-genome sequencing (WGS) and large samples analysis of cancer-related genes have been rarely done. METHODS We performed WGS to explore germline mutations in coding and non-coding areas of cancer-related genes and non-coding driver genes and regulatory areas. Structural variants (SVs) was also analyzed. We used several tools and a subgrouping method to analyze the variants in 1491 healthy participants. Moreover, 275 cancer-related genes sequencing was carried out in 125 cancer patients. RESULTS The incidence of familial cancer in the Taiwanese general population is 8.79% (131/1491). Cancer carrier rate of cancer-related genes is about 7.04% (105/1491) for pathogenic/likely pathogenic variants (P/LP) on ClinVar database only, and 28.24% (421/1491) for P/LP and loss of function variants. The carrier frequencies of cancer-related genes P/LP on ClinVar database were as follows: 8.40% (11/131), 7.11% (28/394), and 6.83% (66/966) in FC, 1MC, and nMC, respectively. The SVs and non-coding driver gene variants are uncommon. There are 1.54% (23/1491) of actionable cancer genes in American College of Medical Genetics and Genomics (ACMG), and the germline mutation rate of 275 cancer-related genes is 7.2% (9/125) in cancer patients including 4.0% (5/125) of actionable cancer genes in ACMG. After analyzing the frequencies of P/LP variants on GJB2 and SLC25A13 genes, we suggest that these two genes may not be cancer-related genes and need be re-evaluated. CONCLUSIONS WGS analysis can completely detect germline mutations in cancer carriers. This study use subgrouping approach for samples provides a strategy to study whether a gene or variant is a cancer-related gene or variant in the future studies.
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Affiliation(s)
- Ya‐Sian Chang
- Center for Precision MedicineChina Medical University HospitalTaichungTaiwan
- Epigenome Research CenterChina Medical University HospitalTaichungTaiwan
- Department of Laboratory MedicineChina Medical University HospitalTaichungTaiwan
- School of MedicineChina Medical UniversityTaichungTaiwan
| | - Dy‐San Chao
- Center for Precision MedicineChina Medical University HospitalTaichungTaiwan
- Epigenome Research CenterChina Medical University HospitalTaichungTaiwan
- Department of Laboratory MedicineChina Medical University HospitalTaichungTaiwan
| | - Chin‐Chun Chung
- Center for Precision MedicineChina Medical University HospitalTaichungTaiwan
| | - Yu‐Pao Chou
- Center for Precision MedicineChina Medical University HospitalTaichungTaiwan
- Epigenome Research CenterChina Medical University HospitalTaichungTaiwan
- Department of Laboratory MedicineChina Medical University HospitalTaichungTaiwan
| | - Chieh‐Min Chang
- Center for Precision MedicineChina Medical University HospitalTaichungTaiwan
- Epigenome Research CenterChina Medical University HospitalTaichungTaiwan
- Department of Laboratory MedicineChina Medical University HospitalTaichungTaiwan
| | - Chia‐Li Lin
- Center for Precision MedicineChina Medical University HospitalTaichungTaiwan
| | - Hou‐Wei Chu
- Institute of Biomedical Sciences|Academia SinicaTaipeiTaiwan
| | - Hon‐Da Chen
- Center for Precision MedicineChina Medical University HospitalTaichungTaiwan
- Epigenome Research CenterChina Medical University HospitalTaichungTaiwan
- Department of Laboratory MedicineChina Medical University HospitalTaichungTaiwan
| | - Ting‐Yuan Liu
- Center for Precision MedicineChina Medical University HospitalTaichungTaiwan
| | - Yu‐Hsuan Juan
- Center for Precision MedicineChina Medical University HospitalTaichungTaiwan
| | - Shun‐Jen Chang
- Department of Kinesiology, Health and Leisure StudiesNational University of KaohsiungKaohsiungTaiwan
| | - Jan‐Gowth Chang
- Center for Precision MedicineChina Medical University HospitalTaichungTaiwan
- Epigenome Research CenterChina Medical University HospitalTaichungTaiwan
- Department of Laboratory MedicineChina Medical University HospitalTaichungTaiwan
- School of MedicineChina Medical UniversityTaichungTaiwan
- Department of Bioinformatics and Medical EngineeringAsia UniversityTaichungTaiwan
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Educational Programme for Cancer Nurses in Genetics, Health Behaviors and Cancer Prevention: A Multidisciplinary Consensus Study. J Pers Med 2022; 12:jpm12071104. [PMID: 35887601 PMCID: PMC9318790 DOI: 10.3390/jpm12071104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 06/26/2022] [Accepted: 07/01/2022] [Indexed: 11/21/2022] Open
Abstract
(1) Background: Most common hereditary cancers in Europe have been associated with lifestyle behaviors, and people affected are lacking follow up care. However, access to education programmes to increase knowledge on cancer and genetics and promote healthy lifestyle behaviors in people at high risk of cancer is scarce. This affects the quality of care of people with a hereditary risk of cancer. This study aimed to reach a multidisciplinary consensus on topics and competencies and competencies that cancer nurses need in relation to cancer, genetics, and health promotion. (2) Methods: A two-round online Delphi study was undertaken. Experts in cancer and genetics were asked to assess the relevance of eighteen items and to suggest additional terms. Consensus was defined as an overall agreement of at least 75%. (3) Results: A total of 74 multiprofessional experts from all around the world participated in this study including healthcare professionals working in genetics (39%), researchers in cancer and genetics (31%) and healthcare professionals with cancer patients (30%). Thirteen additional items were proposed. A total of thirty-one items reached consensus. (4) Conclusions: This multidisciplinary consensus study provide the essential elements to build an educational programme to increase cancer nurses’ skills to support the complex care of people living with a higher risk of cancer including addressing lifestyle behaviors. All professionals highlighted the importance of cancer nurses increasing their skills in cancer and genetics.
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de Oliveira JM, Zurro NB, Coelho AVC, Caraciolo MP, de Alexandre RB, Cervato MC, Minillo RM, de Vasconcelos Carvalho Neto G, Grivicich I, Oliveira JB. The genetics of hereditary cancer risk syndromes in Brazil: a comprehensive analysis of 1682 patients. Eur J Hum Genet 2022; 30:818-823. [PMID: 35534704 PMCID: PMC9259741 DOI: 10.1038/s41431-022-01098-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 02/02/2022] [Accepted: 03/31/2022] [Indexed: 02/08/2023] Open
Abstract
Hereditary cancer risk syndromes are caused by germline variants, commonly in tumor suppressor genes. Most studies on hereditary cancer have been conducted in white populations. We report the largest study in Brazilian individuals with multiple ethnicities. We genotyped 1682 individuals from all country regions with Next-generation sequencing (NGS) panels. Most were women with a personal/family history of cancer, mostly breast and ovarian. We identified 321 pathogenic/likely pathogenic (P/LP) variants in 305 people (18.1%) distributed among 32 genes. Most were on BRCA1 and BRCA2 (129 patients, 26.2% and 14.3% of all P/LP, respectively), MUTYH (42 monoallelic patients, 13.1%), PALB2 (25, 7.8%), Lynch syndrome genes (17, 5.3%), and TP53 (17, 5.3%). Transheterozygosity prevalence in our sample was 0.89% (15/1682). BRCA1/BRCA2 double heterozygosity rate was 0.78% (1/129) for BRCA variants carriers and 0.06% (1/1682) overall. We evaluated the performance of the genetic testing criteria by NCCN and the Brazilian National Health Agency (ANS). The inclusion criteria currently used in Brazil fail to identify 17%-25% of carriers of P/LP variants in hereditary cancer genes. Our results add knowledge on the Brazilian spectrum of cancer risk germline variants, demonstrate that large multigene panels have high positivity rates, and indicate that Brazilian inclusion criteria for genetic testing should be improved.
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Affiliation(s)
- Jarbas Maciel de Oliveira
- Hospital Memorial Arcoverde, Arcoverde, Pernambuco Brazil ,grid.411513.30000 0001 2111 8057Universidade Luterana do Brasil, Programa de Pós-Graduação em Biologia Celular e Molecular Aplicada à Saúde, Canoas, Rio Grande do Sul Brazil
| | - Nuria Bengala Zurro
- grid.413562.70000 0001 0385 1941Hospital Israelita Albert Einstein, São Paulo, Brazil
| | | | | | | | - Murilo Castro Cervato
- grid.413562.70000 0001 0385 1941Hospital Israelita Albert Einstein, São Paulo, Brazil
| | | | | | - Ivana Grivicich
- grid.411513.30000 0001 2111 8057Universidade Luterana do Brasil, Programa de Pós-Graduação em Biologia Celular e Molecular Aplicada à Saúde, Canoas, Rio Grande do Sul Brazil
| | - João Bosco Oliveira
- grid.413562.70000 0001 0385 1941Hospital Israelita Albert Einstein, São Paulo, Brazil
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28
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Mittendorf KF, Lewis HS, Duenas DM, Eubanks DJ, Gilmore MJ, Goddard KAB, Joseph G, Kauffman TL, Kraft SA, Lindberg NM, Reyes AA, Shuster E, Syngal S, Ukaegbu C, Zepp JM, Wilfond BS, Porter KM. Literacy-adapted, electronic family history assessment for genetics referral in primary care: patient user insights from qualitative interviews. Hered Cancer Clin Pract 2022; 20:22. [PMID: 35689290 PMCID: PMC9188215 DOI: 10.1186/s13053-022-00231-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 05/30/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Risk assessment for hereditary cancer syndromes is recommended in primary care, but family history is rarely collected in enough detail to facilitate risk assessment and referral - a roadblock that disproportionately impacts individuals with healthcare access barriers. We sought to qualitatively assess a literacy-adapted, electronic patient-facing family history tool developed for use in diverse, underserved patient populations recruited in the Cancer Health Assessments Reaching Many (CHARM) Study. METHODS Interview participants were recruited from a subpopulation of CHARM participants who experienced barriers to tool use in terms of spending a longer time to complete the tool, having incomplete attempts, and/or providing inaccurate family history in comparison to a genetic counselor-collected standard. We conducted semi-structured interviews with participants about barriers and facilitators to tool use and overall tool acceptability; interviews were recorded and professionally transcribed. Transcripts were coded based on a codebook developed using inductive techniques, and coded excerpts were reviewed to identify overarching themes related to barriers and facilitators to family history self-assessment and acceptability of the study tool. RESULTS Interviewees endorsed the tool as easy to navigate and understand. However, they described barriers related to family history information, literacy and language, and certain tool functions. Participants offered concrete, easy-to-implement solutions to each barrier. Despite experience barriers to use of the tool, most participants indicated that electronic family history self-assessment was acceptable or preferable in comparison to clinician-collected family history. CONCLUSIONS Even for participants who experienced barriers to tool use, family history self-assessment was considered an acceptable alternative to clinician-collected family history. Barriers experienced could be overcome with minor adaptations to the current family history tool. TRIAL REGISTRATION This study is a sub-study of the Cancer Health Assessments Reaching Many (CHARM) trial, ClinicalTrials.gov, NCT03426878. Registered 8 February 2018.
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Affiliation(s)
- Kathleen F Mittendorf
- Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, 2525 West End Avenue, Nashville, TN, 37203, USA
| | - Hannah S Lewis
- Treuman Katz Center for Pediatric Bioethics, Seattle Children's Research Institute, 1900 9th Ave, Seattle, WA, 98101, USA
| | - Devan M Duenas
- Treuman Katz Center for Pediatric Bioethics, Seattle Children's Research Institute, 1900 9th Ave, Seattle, WA, 98101, USA
| | - Donna J Eubanks
- Center for Health Research, Kaiser Permanente Northwest, 3800 N. Interstate Ave, Portland, OR, 97227, USA
| | - Marian J Gilmore
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, 3800 N. Interstate Ave, Portland, OR, 97227, USA
| | - Katrina A B Goddard
- Division of Cancer Control and Population Sciences, National Cancer Institute, 9609 Medical Center Drive, Bethesda, MD, 20892, USA
| | - Galen Joseph
- Department of Humanities and Social Sciences, University of California San Francisco, 490 Illinois Street, 7th Floor, San Francisco, CA, 94143, USA
| | - Tia L Kauffman
- Center for Health Research, Kaiser Permanente Northwest, 3800 N. Interstate Ave, Portland, OR, 97227, USA
| | - Stephanie A Kraft
- Treuman Katz Center for Pediatric Bioethics, Seattle Children's Research Institute, 1900 9th Ave, Seattle, WA, 98101, USA
- Department of Pediatrics, Division of Bioethics and Palliative Care, University of Washington, 1959 NE. Pacific St, Seattle, WA, 98195, USA
| | - Nangel M Lindberg
- Center for Health Research, Kaiser Permanente Northwest, 3800 N. Interstate Ave, Portland, OR, 97227, USA
| | - Ana A Reyes
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, 3800 N. Interstate Ave, Portland, OR, 97227, USA
| | - Elizabeth Shuster
- Center for Health Research, Kaiser Permanente Northwest, 3800 N. Interstate Ave, Portland, OR, 97227, USA
| | - Sapna Syngal
- Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA
- Harvard Medical School, 25 Shattuck St, Boston, MA, 02115, USA
- Brigham and Women's Hospital, 75 Francis St, Boston, MA, 02115, USA
| | - Chinedu Ukaegbu
- Dana-Farber Cancer Institute, 450 Brookline Ave, Boston, MA, 02215, USA
- Harvard Medical School, 25 Shattuck St, Boston, MA, 02115, USA
| | - Jamilyn M Zepp
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, 3800 N. Interstate Ave, Portland, OR, 97227, USA
| | - Benjamin S Wilfond
- Treuman Katz Center for Pediatric Bioethics, Seattle Children's Research Institute, 1900 9th Ave, Seattle, WA, 98101, USA
- Department of Pediatrics, Division of Bioethics and Palliative Care, University of Washington, 1959 NE. Pacific St, Seattle, WA, 98195, USA
| | - Kathryn M Porter
- Treuman Katz Center for Pediatric Bioethics, Seattle Children's Research Institute, 1900 9th Ave, Seattle, WA, 98101, USA.
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Mardani P, Fallahi M, Kamran H, Shahriarirad R, Anbardar MH, Soleimani N. Mediastinal thymoma in a patient with previous rectal and breast cancers: A report of a case with multiple primary cancers and review of literature. Clin Case Rep 2022; 10:e5987. [PMID: 35769240 PMCID: PMC9210131 DOI: 10.1002/ccr3.5987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/25/2022] [Accepted: 06/05/2022] [Indexed: 12/04/2022] Open
Abstract
A 42-year-old female patient with intellectual disability was presented to us as a newly diagnosed case of thymoma. She was identified as a case of multiple primary cancers, including adenocarcinoma of the rectum, carcinoma of the breast, and mediastinal thymoma, in a 15-year period, who underwent chemotherapy, radiotherapy, and surgical resection.
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Affiliation(s)
- Parviz Mardani
- Thoracic and Vascular Surgery Research CenterShiraz University of Medical ScienceShirazIran
| | - Mohammadmehdi Fallahi
- Students Research Committee, School of MedicineShiraz University of Medical SciencesShirazIran
| | - Hooman Kamran
- Thoracic and Vascular Surgery Research CenterShiraz University of Medical ScienceShirazIran
- Students Research Committee, School of MedicineShiraz University of Medical SciencesShirazIran
| | - Reza Shahriarirad
- Thoracic and Vascular Surgery Research CenterShiraz University of Medical ScienceShirazIran
- Students Research Committee, School of MedicineShiraz University of Medical SciencesShirazIran
| | - Mohammad Hossein Anbardar
- Department of PathologyAbu Ali Sina HospitalShiraz Medical SchoolShiraz University of Medical SciencesShirazIran
| | - Neda Soleimani
- Department of PathologyAbu Ali Sina HospitalShiraz Medical SchoolShiraz University of Medical SciencesShirazIran
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Pallonen TAS, Lempiäinen SMM, Joutsiniemi TK, Aaltonen RI, Pohjola PE, Kankuri-Tammilehto MK. Genetic, clinic and histopathologic characterization of BRCA-associated hereditary breast and ovarian cancer in southwestern Finland. Sci Rep 2022; 12:6704. [PMID: 35469032 PMCID: PMC9038668 DOI: 10.1038/s41598-022-10519-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 04/07/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractWe have analyzed the histopathological, clinical, and genetic characteristics in hereditary breast and ovarian cancer patients of counselled families from 1996 up to today in the southwestern Finland population. In this study we analyzed the incidence of different BRCA1 and BRCA2 pathogenic variants (PV). 1211 families were evaluated, and the families were classified as 38 BRCA1 families, 48 BRCA2 families, 689 non-BRCA families and 436 other counselled families (criteria for genetic testing was not met). In those families, the study consisted of 44 BRCA1 breast and/or ovarian cancer patients, 58 BRCA2 cancer patients, 602 non-BRCA patients and 328 other counselled patients. Breast cancer mean onset was 4.6 years earlier in BRCA1 carriers compared to BRCA2 (p = 0.07, a trend) and ovarian cancer onset almost 11 years earlier in BRCA1 families (p < 0.05). In BRCA families the onset of ovarian cancer was later than 40 years, and BRCA2-origin breast cancer was seen as late as 78 years. The BRCA PV (9%) increases the risk for same patient having both ovarian and breast cancer with a twofold risk when compared to non-BRCA group (4%) (95% CI p < 0.05). Triple-negativity in BRCA1 (42%) carriers is approximately 2.6 times vs more common than in BRCA2 carriers (16%) (p < 0.05). The risk ratio for bilateral breast cancer is approximately four times when compared BRCA2 (17%) and other counselled patients’ group (4%) (p < 0.05). 27% southwestern BRCA2-families have a unique PV, and correspondingly 39% of BRCA1-families. The results of this analysis allow improved prediction of cancer risk in high-risk hereditary breast and ovarian families in southwestern Finland and improve long term follow-up programs. According to the result it could be justified to have the discussion about prophylactic salpingo-oophorectomy by the age of 40 years. The possibility of late breast cancer onset in BRCA2 carriers supports the lifelong follow-up in BRCA carriers. Cancer onset is similar between BRCA2 carries and non-BRCA high-risk families. This study evaluated mutation profile of BRCA in southwestern Finland. In this study genotype–phenotype correlation was not found
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31
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Mighton C, Lerner‐Ellis J. Principles of molecular testing for hereditary cancer. Genes Chromosomes Cancer 2022; 61:356-381. [DOI: 10.1002/gcc.23048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 04/03/2022] [Accepted: 04/06/2022] [Indexed: 11/10/2022] Open
Affiliation(s)
- Chloe Mighton
- Laboratory Medicine and Pathology, Mount Sinai Hospital, Sinai Health Toronto ON Canada
- Lunenfeld Tanenbaum Research Institute, Sinai Health Toronto ON Canada
- Genomics Health Services Research Program Li Ka Shing Knowledge Institute, St. Michael's Hospital, Unity Health Toronto Toronto ON Canada
- Institute of Health Policy, Management and Evaluation, Dalla Lana School of Public Health University of Toronto Toronto ON Canada
| | - Jordan Lerner‐Ellis
- Laboratory Medicine and Pathology, Mount Sinai Hospital, Sinai Health Toronto ON Canada
- Lunenfeld Tanenbaum Research Institute, Sinai Health Toronto ON Canada
- Department of Laboratory Medicine and Pathobiology University of Toronto Toronto ON Canada
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Dzung A, Saltari A, Tiso N, Lyck R, Dummer R, Levesque MP. STK11 Prevents Invasion through Signal Transducer and Activator of Transcription 3/5 and FAK Repression in Cutaneous Melanoma. J Invest Dermatol 2022; 142:1171-1182.e10. [PMID: 34757069 DOI: 10.1016/j.jid.2021.09.035] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 08/23/2021] [Accepted: 09/01/2021] [Indexed: 11/18/2022]
Abstract
The STK11/LKB1 is a tumor suppressor involved in metabolism and cell motility. In BRAFV600E melanoma, STK11 is inactivated by extracellular signal‒regulated kinase and RSK, preventing it from binding and activating adenosine monophosphate-activated protein kinase and promoting melanoma cell proliferation. Although STK11 mutations occur in 5‒10% of cutaneous melanoma, few functional studies have been performed. By knocking out STK11 with CRISPR/Cas9 in two human BRAF-mutant melanoma cell lines, we found that STK11 loss reduced the sensitivity to a BRAF inhibitor. More strikingly, STK11 loss led to an increased invasive phenotype in both three-dimensional spheroids and in vivo zebrafish xenograft models. STK11 overexpression consistently reversed the invasive phenotype. Interestingly, STK11 knockout increased invasion also in an NRAS-mutant melanoma cell line. Furthermore, although STK11 was expressed in primary human melanoma tumors, its expression significantly decreased in melanoma metastases, especially in brain metastases. In the STK11-knockout cells, we observed increased activating phosphorylation of signal transducer and activator of transcription 3/5 and FAK. Using inhibitors of signal transducer and activator of transcription 3/5 and FAK, we reversed the invasive phenotype in both BRAF- and NRAS-mutated cells. Our findings confirm an increased invasive phenotype on STK11 inactivation in BRAF- and NRAS-mutant cutaneous melanoma that can be targeted by signal transducer and activator of transcription 3/5 and FAK inhibition.
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Affiliation(s)
- Andreas Dzung
- Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Annalisa Saltari
- Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Natascia Tiso
- Laboratory of Developmental Genetics, Department of Biology, University of Padova, Padova, Italy
| | - Ruth Lyck
- Theodor Kocher Institute, University of Bern, Bern, Switzerland
| | - Reinhard Dummer
- Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Mitchell P Levesque
- Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland.
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Leite Rocha D, Ashton-Prolla P, Rosset C. Reviewing the occurrence of large genomic rearrangements in patients with inherited cancer predisposing syndromes: importance of a comprehensive molecular diagnosis. Expert Rev Mol Diagn 2022; 22:319-346. [PMID: 35234551 DOI: 10.1080/14737159.2022.2049247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Hereditary cancer predisposition syndromes are caused by germline pathogenic or likely pathogenic variants in cancer predisposition genes (CPG). The majority of pathogenic variants in CPGs are point mutations, but large gene rearrangements (LGRs) are present in several CPGs. LGRs can be much more difficult to characterize and perhaps they may have been neglected in molecular diagnoses. AREAS COVERED We aimed to evaluate the frequencies of germline LGRs in studies conducted in different populations worldwide through a qualitative systematic review based on an online literature research in PubMed. Two reviewers independently extracted data from published studies between 2009 and 2020. In total, 126 studies from 37 countries and 5 continents were included in the analysis. The number of studies in different continents ranged from 3 to 48 and for several countries there was an absolute lack of information. Asia and Europe represented most of the studies, and LGR frequencies varied from 3.04 to 15.06% in different continents. MLPA was one of the methods of choice in most studies (93%). EXPERT OPINION The LGR frequencies found in this review reinforce the need for comprehensive molecular testing regardless of the population of origin and should be considered by genetic counseling providers.
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Affiliation(s)
- Débora Leite Rocha
- Laboratório de Medicina Genômica, Serviço de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Rua Ramiro Barcelos, 2350, CEP: 90035-930, Porto Alegre, Rio Grande do Sul, Brazil
| | - Patrícia Ashton-Prolla
- Laboratório de Medicina Genômica, Serviço de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Rua Ramiro Barcelos, 2350, CEP: 90035-930, Porto Alegre, Rio Grande do Sul, Brazil.,Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil. Av. Bento Gonçalves, 9500 - Prédio 43312 M, CEP: 91501-970, Caixa Postal 1505, Porto Alegre, Rio Grande do Sul, Brazil.,Serviço de Genética Médica, HCPA, Rio Grande do Sul, Brazil. Rua Ramiro Barcelos, 2350, CEP: 90035-930, Porto Alegre, Rio Grande do Sul, Brazil
| | - Clévia Rosset
- Laboratório de Medicina Genômica, Serviço de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre (HCPA), Rua Ramiro Barcelos, 2350, CEP: 90035-930, Porto Alegre, Rio Grande do Sul, Brazil
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Kryklyva V, Brosens LAA, Marijnissen‐van Zanten MAJ, Ligtenberg MJL, Nagtegaal ID. Mismatch repair deficiency in early‐onset duodenal, ampullary, and pancreatic carcinomas is a strong indicator for a hereditary defect. J Pathol Clin Res 2022; 8:181-190. [PMID: 34873870 PMCID: PMC8822371 DOI: 10.1002/cjp2.252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 10/05/2021] [Accepted: 11/09/2021] [Indexed: 11/15/2022]
Abstract
Mismatch repair deficiency (dMMR) is a hallmark of Lynch syndrome (LS), but its prevalence in early‐onset (diagnosed under the age of 50 years) duodenal, ampullary, and pancreatic carcinomas (DC, AC, and PC, respectively) is largely unknown. We explored the prevalence of dMMR and the underlying molecular mechanisms in a retrospectively collected cohort of 90 early‐onset carcinomas of duodenal, ampullary, and pancreatic origin. dMMR was most prevalent in early‐onset DCs (47.8%); more than half of those were associated with hereditary cancer syndromes (LS or constitutional mismatch repair deficiency syndrome). All dMMR AC and PC were due to LS. Concordance of dMMR with underlying hereditary condition warrants ubiquitous dMMR testing in all early‐onset DC, AC, and PC.
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Affiliation(s)
- Valentyna Kryklyva
- Department of Pathology Radboud Institute for Molecular Life Sciences, Radboud University Medical Center Nijmegen The Netherlands
| | - Lodewijk AA Brosens
- Department of Pathology Radboud Institute for Molecular Life Sciences, Radboud University Medical Center Nijmegen The Netherlands
- Department of Pathology University Medical Center Utrecht, Utrecht University Utrecht The Netherlands
| | - Monica AJ Marijnissen‐van Zanten
- Department of Pathology Radboud Institute for Molecular Life Sciences, Radboud University Medical Center Nijmegen The Netherlands
| | - Marjolijn JL Ligtenberg
- Department of Pathology Radboud Institute for Molecular Life Sciences, Radboud University Medical Center Nijmegen The Netherlands
- Department of Human Genetics Radboud Institute for Molecular Life Sciences, Radboud University Medical Center Nijmegen The Netherlands
| | - Iris D Nagtegaal
- Department of Pathology Radboud Institute for Molecular Life Sciences, Radboud University Medical Center Nijmegen The Netherlands
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Metabolomics and the Multi-Omics View of Cancer. Metabolites 2022; 12:metabo12020154. [PMID: 35208228 PMCID: PMC8880085 DOI: 10.3390/metabo12020154] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 01/29/2022] [Accepted: 01/31/2022] [Indexed: 11/17/2022] Open
Abstract
Cancer is widely regarded to be a genetic disease. Indeed, over the past five decades, the genomic perspective on cancer has come to almost completely dominate the field. However, this genome-only view is incomplete and tends to portray cancer as a disease that is highly heritable, driven by hundreds of complex genetic interactions and, consequently, difficult to prevent or treat. New evidence suggests that cancer is not as heritable or purely genetic as once thought and that it really is a multi-omics disease. As highlighted in this review, the genome, the exposome, and the metabolome all play roles in cancer’s development and manifestation. The data presented here show that >90% of cancers are initiated by environmental exposures (the exposome) which lead to cancer-inducing genetic changes. The resulting genetic changes are, then, propagated through the altered DNA of the proliferating cancer cells (the genome). Finally, the dividing cancer cells are nourished and sustained by genetically reprogrammed, cancer-specific metabolism (the metabolome). As shown in this review, all three “omes” play roles in initiating cancer. Likewise, all three “omes” interact closely, often providing feedback to each other to sustain or enhance tumor development. Thanks to metabolomics, these multi-omics feedback loops are now much more evident and their roles in explaining the hallmarks of cancer are much better understood. Importantly, this more holistic, multi-omics view portrays cancer as a disease that is much more preventable, easier to understand, and potentially, far more treatable.
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Watanabe T, Soeda S, Endo Y, Okabe C, Sato T, Kamo N, Ueda M, Kojima M, Furukawa S, Nishigori H, Takahashi T, Fujimori K. Rare Hereditary Gynecological Cancer Syndromes. Int J Mol Sci 2022; 23:1563. [PMID: 35163487 PMCID: PMC8835983 DOI: 10.3390/ijms23031563] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/25/2022] [Accepted: 01/28/2022] [Indexed: 12/04/2022] Open
Abstract
Hereditary cancer syndromes, which are characterized by onset at an early age and an increased risk of developing certain tumors, are caused by germline pathogenic variants in tumor suppressor genes and are mostly inherited in an autosomal dominant manner. Therefore, hereditary cancer syndromes have been used as powerful models to identify and characterize susceptibility genes associated with cancer. Furthermore, clarification of the association between genotypes and phenotypes in one disease has provided insights into the etiology of other seemingly different diseases. Molecular genetic discoveries from the study of hereditary cancer syndrome have not only changed the methods of diagnosis and management, but have also shed light on the molecular regulatory pathways that are important in the development and treatment of sporadic tumors. The main cancer susceptibility syndromes that involve gynecologic cancers include hereditary breast and ovarian cancer syndrome as well as Lynch syndrome. However, in addition to these two hereditary cancer syndromes, there are several other hereditary syndromes associated with gynecologic cancers. In the present review, we provide an overview of the clinical features, and discuss the molecular genetics, of four rare hereditary gynecological cancer syndromes; Cowden syndrome, Peutz-Jeghers syndrome, DICER1 syndrome and rhabdoid tumor predisposition syndrome 2.
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Affiliation(s)
- Takafumi Watanabe
- Department of Obstetrics and Gynecology, Fukushima Medical University, Fukushima 960-1295, Japan; (S.S.); (Y.E.); (C.O.); (T.S.); (N.K.); (M.U.); (M.K.); (S.F.); (K.F.)
| | - Shu Soeda
- Department of Obstetrics and Gynecology, Fukushima Medical University, Fukushima 960-1295, Japan; (S.S.); (Y.E.); (C.O.); (T.S.); (N.K.); (M.U.); (M.K.); (S.F.); (K.F.)
| | - Yuta Endo
- Department of Obstetrics and Gynecology, Fukushima Medical University, Fukushima 960-1295, Japan; (S.S.); (Y.E.); (C.O.); (T.S.); (N.K.); (M.U.); (M.K.); (S.F.); (K.F.)
| | - Chikako Okabe
- Department of Obstetrics and Gynecology, Fukushima Medical University, Fukushima 960-1295, Japan; (S.S.); (Y.E.); (C.O.); (T.S.); (N.K.); (M.U.); (M.K.); (S.F.); (K.F.)
| | - Tetsu Sato
- Department of Obstetrics and Gynecology, Fukushima Medical University, Fukushima 960-1295, Japan; (S.S.); (Y.E.); (C.O.); (T.S.); (N.K.); (M.U.); (M.K.); (S.F.); (K.F.)
| | - Norihito Kamo
- Department of Obstetrics and Gynecology, Fukushima Medical University, Fukushima 960-1295, Japan; (S.S.); (Y.E.); (C.O.); (T.S.); (N.K.); (M.U.); (M.K.); (S.F.); (K.F.)
| | - Makiko Ueda
- Department of Obstetrics and Gynecology, Fukushima Medical University, Fukushima 960-1295, Japan; (S.S.); (Y.E.); (C.O.); (T.S.); (N.K.); (M.U.); (M.K.); (S.F.); (K.F.)
| | - Manabu Kojima
- Department of Obstetrics and Gynecology, Fukushima Medical University, Fukushima 960-1295, Japan; (S.S.); (Y.E.); (C.O.); (T.S.); (N.K.); (M.U.); (M.K.); (S.F.); (K.F.)
| | - Shigenori Furukawa
- Department of Obstetrics and Gynecology, Fukushima Medical University, Fukushima 960-1295, Japan; (S.S.); (Y.E.); (C.O.); (T.S.); (N.K.); (M.U.); (M.K.); (S.F.); (K.F.)
| | - Hidekazu Nishigori
- Fukushima Medical Center for Children and Women, Fukushima Medical University, 1 Hikarigaoka, Fukushima 960-1295, Japan; (H.N.); (T.T.)
| | - Toshifumi Takahashi
- Fukushima Medical Center for Children and Women, Fukushima Medical University, 1 Hikarigaoka, Fukushima 960-1295, Japan; (H.N.); (T.T.)
| | - Keiya Fujimori
- Department of Obstetrics and Gynecology, Fukushima Medical University, Fukushima 960-1295, Japan; (S.S.); (Y.E.); (C.O.); (T.S.); (N.K.); (M.U.); (M.K.); (S.F.); (K.F.)
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Seibel E, Gunn G, Ali N, Jordan E, Kenneson A. Primary Care Providers' Use of Genetic Services in the Southeast United States: Barriers, Facilitators, and Strategies. J Prim Care Community Health 2022; 13:21501319221134752. [PMID: 36345220 PMCID: PMC9647281 DOI: 10.1177/21501319221134752] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 10/06/2022] [Accepted: 10/07/2022] [Indexed: 07/14/2024] Open
Abstract
INTRODUCTION/OBJECTIVES Collectively, genetic diseases are not that rare, and with increasing availability of genetics-informed healthcare management, primary care providers (PCPs) are more often asked to screen for or provide genetic services. Previous studies have identified barriers that impact PCPs' ability to provide genetic services, including limited knowledge, training, and time/resources. This study set out to identify specific barriers limiting genetics service provision by PCPs within the Southeastern Regional Genetics Network (SERN) and resources that would help eliminate those barriers. METHODS PCPs were recruited through provider networks and invited to participate in semi-structured interviews, conducted via Zoom, recorded, and transcribed verbatim. Interview transcripts were independently coded by 2 coders using MAXQDA software. Thematic analysis was conducted. RESULTS Eleven interviews were conducted. Three predominant themes emerged from the data regarding factors impacting use of genetic services: system-wide factors, provider-specific factors, and patient factors. System-wide barriers included a lack of genetics providers and logistic challenges, which led to some PCPs coordinating referrals with other specialists or independently managing patients. Regarding provider-specific barriers, PCPs reported lack of genetics knowledge making referrals challenging. When possible, many PCPs contacted genetics providers for assistance. When not possible, some PCPs reached out to other colleagues or specialists for guidance. Patient-specific barriers included concerns or lack of information regarding genetics and unmet social needs. Many PCPs provided additional education regarding genetics appointments or testing benefits to their patients. Assistance from genetic counselors, electronic medical record systems that support referral to genetics, prior experience referring to genetics, established communication channels with genetics professionals, and highly motivated patients all facilitated improved collaboration with genetic services. PCPs provided suggestions for future resources to support interactions with genetics, including clear referral guidelines, increased access to genetics providers, improved test ordering processes, increased access to genetic education, and communication systems. CONCLUSIONS PCPs face barriers at 3 different levels when engaging with genetic services: systems, providers, and patients. This study identified strategies that PCPs use to address these barriers, which are dependent on individual resources and practice settings. These strategies demonstrate resourcefulness in working to incorporate genetics into clinics operating at maximum capacity. By targeting barriers that uniquely impact providers, systems, and patients, as well as building upon strategies that PCPs are already using, medical providers can support PCPs to help with the provision of genetic services.
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Affiliation(s)
- Erin Seibel
- Department of Human Genetics, Emory
University School of Medicine, Atlanta, GA, USA
| | - Gwen Gunn
- Department of Human Genetics, Emory
University School of Medicine, Atlanta, GA, USA
| | - Nadia Ali
- Department of Human Genetics, Emory
University School of Medicine, Atlanta, GA, USA
| | - Ellen Jordan
- Rollins School of Public Health, Emory
University, Atlanta, GA, USA
| | - Aileen Kenneson
- Department of Human Genetics, Emory
University School of Medicine, Atlanta, GA, USA
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Cancer Genetics and Breast Cancer. Best Pract Res Clin Obstet Gynaecol 2022; 82:3-11. [DOI: 10.1016/j.bpobgyn.2022.01.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 01/19/2022] [Accepted: 01/21/2022] [Indexed: 12/15/2022]
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Sánchez A, Bujanda L, Cuatrecasas M, Bofill A, Alvarez-Urturi C, Hernandez G, Aguilera L, Carballal S, Llach J, Herrera-Pariente C, Iglesias M, Rivero-Sánchez L, Jung G, Moreno L, Ocaña T, Bayarri C, Pellise M, Castells A, Castellví-Bel S, Balaguer F, Moreira L. Identification of Lynch Syndrome Carriers among Patients with Small Bowel Adenocarcinoma. Cancers (Basel) 2021; 13:cancers13246378. [PMID: 34944998 PMCID: PMC8699558 DOI: 10.3390/cancers13246378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 12/14/2021] [Indexed: 12/03/2022] Open
Abstract
Simple Summary Small bowel adenocarcinoma (SBA) is associated with Lynch syndrome (LS). This is the first study to evaluate the identification of LS patients based on mismatch repair deficiency (MMRd) tumor among SBA. The authors found a 21.3% prevalence of MMRd tumors and a 10.1% prevalence of LS. A germline mutation was identified in 60% of patients with a MMRd tumor. This data suggests that universal tumor MMR testing among SBA patients should be implemented for the identification of LS. Abstract Background: Small bowel adenocarcinoma (SBA) is a rare disease which can be associated with Lynch syndrome (LS). LS tumors are characterized by the presence of microsatellite instability (MSI) and/or the loss of mismatch repair (MMR) protein expression. In SBA, the frequency of MMR deficient (MMRd) tumors varies from 5% to 35%. This study aims to describe the prevalence of LS carriers among patients with MMRd small bowel adenocarcinomas. Methods: A multicenter retrospective study with identification and MMR testing of all consecutive SBA between 2004 and 2020 in a multicenter Spanish study. Demographical data, tumor characteristics, follow-up and survival information were collected. Germline testing was driven by identification of MMRd tumors. Results: A total of 94 individuals diagnosed with SBA were recruited. We observed 20 (21.3%) MMRd tumors. In 9/15 (60%) patients with MMRd tumors, a pathogenic variant was identified (three MLH1, four MSH2, one MSH6 and one PMS2). Accordingly, the prevalence of LS among all SBA cases was 10.1%. Conclusions: More than one-fifth of SBA display MMRd and in more than a half is due to LS. Our data supports the implementation of universal MMR tumor testing among SBA for the identification of LS families.
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Affiliation(s)
- Ariadna Sánchez
- Department of Gastroenterology, Hospital Clínic Barcelona, Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBEREHD), IDIBAPS (Institut d’Investigacions Biomèdiques August Pi i Sunyer), University of Barcelona, 08036 Barcelona, Spain; (A.S.); (A.B.); (S.C.); (J.L.); (C.H.-P.); (L.R.-S.); (G.J.); (L.M.); (T.O.); (C.B.); (M.P.); (A.C.); (S.C.-B.); (F.B.)
| | - Luis Bujanda
- Department of Gastroenterology, Biodonostia Health Research Institute, Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBEREHD), Universidad del País Vasco (UPV/EHU), 20014 San Sebastián, Spain;
| | - Miriam Cuatrecasas
- Department of Pathology, Hospital Clínic Barcelona, Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBEREHD), IDIBAPS (Institut d’Investigacions Biomèdiques August Pi i Sunyer), University of Barcelona, 08036 Barcelona, Spain;
| | - Alex Bofill
- Department of Gastroenterology, Hospital Clínic Barcelona, Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBEREHD), IDIBAPS (Institut d’Investigacions Biomèdiques August Pi i Sunyer), University of Barcelona, 08036 Barcelona, Spain; (A.S.); (A.B.); (S.C.); (J.L.); (C.H.-P.); (L.R.-S.); (G.J.); (L.M.); (T.O.); (C.B.); (M.P.); (A.C.); (S.C.-B.); (F.B.)
| | - Cristina Alvarez-Urturi
- Department of Gastroenterology, IMIM (Hospital del Mar Medical Research Institute), Barcelona Hospital del Mar, 08003 Barcelona, Spain;
| | - Goretti Hernandez
- Department of Gastroenterology, Hospital Universitario de Canarias, 38320 Tenerife, Spain;
| | - Lara Aguilera
- Department of Gastroenterology, Vall d’Hebron Research Institute, 08035 Barcelona, Spain;
| | - Sabela Carballal
- Department of Gastroenterology, Hospital Clínic Barcelona, Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBEREHD), IDIBAPS (Institut d’Investigacions Biomèdiques August Pi i Sunyer), University of Barcelona, 08036 Barcelona, Spain; (A.S.); (A.B.); (S.C.); (J.L.); (C.H.-P.); (L.R.-S.); (G.J.); (L.M.); (T.O.); (C.B.); (M.P.); (A.C.); (S.C.-B.); (F.B.)
| | - Joan Llach
- Department of Gastroenterology, Hospital Clínic Barcelona, Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBEREHD), IDIBAPS (Institut d’Investigacions Biomèdiques August Pi i Sunyer), University of Barcelona, 08036 Barcelona, Spain; (A.S.); (A.B.); (S.C.); (J.L.); (C.H.-P.); (L.R.-S.); (G.J.); (L.M.); (T.O.); (C.B.); (M.P.); (A.C.); (S.C.-B.); (F.B.)
| | - Cristina Herrera-Pariente
- Department of Gastroenterology, Hospital Clínic Barcelona, Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBEREHD), IDIBAPS (Institut d’Investigacions Biomèdiques August Pi i Sunyer), University of Barcelona, 08036 Barcelona, Spain; (A.S.); (A.B.); (S.C.); (J.L.); (C.H.-P.); (L.R.-S.); (G.J.); (L.M.); (T.O.); (C.B.); (M.P.); (A.C.); (S.C.-B.); (F.B.)
| | - Mar Iglesias
- Department of Pathology, IMIM (Hospital del Mar Medical Research Institute), Barcelona Hospital del Mar, 08003 Barcelona, Spain;
| | - Liseth Rivero-Sánchez
- Department of Gastroenterology, Hospital Clínic Barcelona, Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBEREHD), IDIBAPS (Institut d’Investigacions Biomèdiques August Pi i Sunyer), University of Barcelona, 08036 Barcelona, Spain; (A.S.); (A.B.); (S.C.); (J.L.); (C.H.-P.); (L.R.-S.); (G.J.); (L.M.); (T.O.); (C.B.); (M.P.); (A.C.); (S.C.-B.); (F.B.)
| | - Gerhard Jung
- Department of Gastroenterology, Hospital Clínic Barcelona, Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBEREHD), IDIBAPS (Institut d’Investigacions Biomèdiques August Pi i Sunyer), University of Barcelona, 08036 Barcelona, Spain; (A.S.); (A.B.); (S.C.); (J.L.); (C.H.-P.); (L.R.-S.); (G.J.); (L.M.); (T.O.); (C.B.); (M.P.); (A.C.); (S.C.-B.); (F.B.)
| | - Lorena Moreno
- Department of Gastroenterology, Hospital Clínic Barcelona, Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBEREHD), IDIBAPS (Institut d’Investigacions Biomèdiques August Pi i Sunyer), University of Barcelona, 08036 Barcelona, Spain; (A.S.); (A.B.); (S.C.); (J.L.); (C.H.-P.); (L.R.-S.); (G.J.); (L.M.); (T.O.); (C.B.); (M.P.); (A.C.); (S.C.-B.); (F.B.)
| | - Teresa Ocaña
- Department of Gastroenterology, Hospital Clínic Barcelona, Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBEREHD), IDIBAPS (Institut d’Investigacions Biomèdiques August Pi i Sunyer), University of Barcelona, 08036 Barcelona, Spain; (A.S.); (A.B.); (S.C.); (J.L.); (C.H.-P.); (L.R.-S.); (G.J.); (L.M.); (T.O.); (C.B.); (M.P.); (A.C.); (S.C.-B.); (F.B.)
| | - Carolina Bayarri
- Department of Gastroenterology, Hospital Clínic Barcelona, Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBEREHD), IDIBAPS (Institut d’Investigacions Biomèdiques August Pi i Sunyer), University of Barcelona, 08036 Barcelona, Spain; (A.S.); (A.B.); (S.C.); (J.L.); (C.H.-P.); (L.R.-S.); (G.J.); (L.M.); (T.O.); (C.B.); (M.P.); (A.C.); (S.C.-B.); (F.B.)
| | - Maria Pellise
- Department of Gastroenterology, Hospital Clínic Barcelona, Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBEREHD), IDIBAPS (Institut d’Investigacions Biomèdiques August Pi i Sunyer), University of Barcelona, 08036 Barcelona, Spain; (A.S.); (A.B.); (S.C.); (J.L.); (C.H.-P.); (L.R.-S.); (G.J.); (L.M.); (T.O.); (C.B.); (M.P.); (A.C.); (S.C.-B.); (F.B.)
| | - Antoni Castells
- Department of Gastroenterology, Hospital Clínic Barcelona, Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBEREHD), IDIBAPS (Institut d’Investigacions Biomèdiques August Pi i Sunyer), University of Barcelona, 08036 Barcelona, Spain; (A.S.); (A.B.); (S.C.); (J.L.); (C.H.-P.); (L.R.-S.); (G.J.); (L.M.); (T.O.); (C.B.); (M.P.); (A.C.); (S.C.-B.); (F.B.)
| | - Sergi Castellví-Bel
- Department of Gastroenterology, Hospital Clínic Barcelona, Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBEREHD), IDIBAPS (Institut d’Investigacions Biomèdiques August Pi i Sunyer), University of Barcelona, 08036 Barcelona, Spain; (A.S.); (A.B.); (S.C.); (J.L.); (C.H.-P.); (L.R.-S.); (G.J.); (L.M.); (T.O.); (C.B.); (M.P.); (A.C.); (S.C.-B.); (F.B.)
| | - Francesc Balaguer
- Department of Gastroenterology, Hospital Clínic Barcelona, Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBEREHD), IDIBAPS (Institut d’Investigacions Biomèdiques August Pi i Sunyer), University of Barcelona, 08036 Barcelona, Spain; (A.S.); (A.B.); (S.C.); (J.L.); (C.H.-P.); (L.R.-S.); (G.J.); (L.M.); (T.O.); (C.B.); (M.P.); (A.C.); (S.C.-B.); (F.B.)
| | - Leticia Moreira
- Department of Gastroenterology, Hospital Clínic Barcelona, Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBEREHD), IDIBAPS (Institut d’Investigacions Biomèdiques August Pi i Sunyer), University of Barcelona, 08036 Barcelona, Spain; (A.S.); (A.B.); (S.C.); (J.L.); (C.H.-P.); (L.R.-S.); (G.J.); (L.M.); (T.O.); (C.B.); (M.P.); (A.C.); (S.C.-B.); (F.B.)
- Correspondence: ; Tel.: +34-93-227-5739; Fax: +34-93-227-5589
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Bree KK, Hensley PJ, Pettaway CA. Germline Mutations in African American Men With Prostate Cancer: Incidence, Implications and Diagnostic Disparities. Urology 2021; 163:148-155. [PMID: 34453957 DOI: 10.1016/j.urology.2021.08.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 08/03/2021] [Accepted: 08/12/2021] [Indexed: 12/17/2022]
Abstract
Recent data suggests that African American men (AAM) with prostate cancer (PCa) exhibit genetic alterations in highly penetrant germline genes, as well as low penetrant single nucleotide polymorphisms. The importance of germline variants of uncertain significance (VUS) remain poorly elucidated and given the elevated rates of VUS in AAM compared to Caucasians with PCa, further studies are needed to facilitate potential reclassification of VUS. Ongoing efforts to include AAM in genomics research is of paramount importance in order to ensure applicability of discoveries across diverse populations and potentially reduce PCa disparities as we embark on the era of precision medicine.
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Affiliation(s)
- Kelly K Bree
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Patrick J Hensley
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Curtis A Pettaway
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, TX.
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Porphyromonas gingivalis infection exacerbates oesophageal cancer and promotes resistance to neoadjuvant chemotherapy. Br J Cancer 2021; 125:433-444. [PMID: 33981017 PMCID: PMC8329259 DOI: 10.1038/s41416-021-01419-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 03/30/2021] [Accepted: 04/22/2021] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND The effect of Porphyromonas gingivalis (Pg) infection on oesophageal squamous cell carcinoma (ESCC) prognosis, chemotherapeutic efficacy, and oesophageal cancer cell apoptosis resistance and proliferation remain poorly understood. METHODS Clinicopathological data from 312 ESCC oesophagectomy patients, along with the computed tomography imaging results and longitudinal cancerous tissue samples from a patient subset (n = 85) who received neoadjuvant chemotherapy (NACT), were analysed. Comparison of overall survival and response rate to NACT between Pg-infected and Pg-uninfected patients was made by multivariate Cox analysis and Response Evaluation Criteria in Solid Tumours v.1.1 criteria. The influence of Pg on cell proliferation and drug-induced apoptosis was examined in ESCC patients and validated in vitro and in vivo. RESULTS The 5-year overall survival was lower in Pg-positive patients, and infection was associated with multiple clinicopathological factors and pathologic tumour, node, metastasis stage. Of the 85 patients who received NACT, Pg infection was associated with a lower response rate and 5-year overall survival. Infection with Pg resulted in apoptosis resistance in ESCC and promoted ESCC cell viability, which was confirmed in longitudinal cancerous tissue samples. Pg-induced apoptosis resistance was dependent on fimbriae and STAT3. CONCLUSIONS Pg infection is associated with a worse ESCC prognosis, reduced chemotherapy efficacy, and can potentiate the aggressive behaviour of ESCC cells.
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Weitzel JN, Kidd J, Bernhisel R, Shehayeb S, Frankel P, Blazer KR, Turco D, Nehoray B, McGreevy K, Svirsky K, Brown K, Gardiner A, Daly M, Hughes E, Cummings S, Saam J, Slavin TP. Multigene assessment of genetic risk for women for two or more breast cancers. Breast Cancer Res Treat 2021; 188:759-768. [PMID: 33826040 PMCID: PMC8803157 DOI: 10.1007/s10549-021-06201-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 03/16/2021] [Indexed: 10/21/2022]
Abstract
PURPOSE The prevalence, penetrance, and spectrum of pathogenic variants that predispose women to two or more breast cancers is largely unknown. METHODS We queried clinical and genetic data from women with one or more breast cancer diagnosis who received multigene panel testing between 2013 and 2018. Clinical data were obtained from provider-completed test request forms. For each gene on the panel, a multivariable logistic regression model was constructed to test for association with risk of multiple breast cancer diagnoses. Models accounted for age of diagnosis, personal and family cancer history, and ancestry. Results are reported as odds ratios (ORs) with 95% confidence intervals (CIs). RESULTS This study included 98,979 patients: 88,759 (89.7%) with a single breast cancer and 10,220 (10.3%) with ≥ 2 breast cancers. Of women with two or more breast cancers, 13.2% had a pathogenic variant in a cancer predisposition gene compared to 9.4% with a single breast cancer. BRCA1, BRCA2, CDH1, CHEK2, MSH6, PALB2, PTEN, and TP53 were significantly associated with two or more breast cancers, with ORs ranging from 1.35 for CHEK2 to 3.80 for PTEN. Overall, pathogenic variants in all breast cancer risk genes combined were associated with both metachronous (OR 1.65, 95% CI 1.53-1.79, p = 7.2 × 10-33) and synchronous (OR 1.33, 95% CI 1.19-1.50, p = 2.4 × 10-6) breast cancers. CONCLUSIONS This study demonstrated that several high and moderate penetrance breast cancer susceptibility genes are associated with ≥ 2 breast cancers, affirming the association of two or more breast cancers with diverse genetic etiologies.
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Affiliation(s)
- Jeffrey N Weitzel
- City of Hope Cancer Center, 1500 East Duarte Road, Duarte, CA, 91010, USA.
- , 578 Acacia Street, Sierra Madre, CA, 91024, USA.
| | - John Kidd
- Myriad Genetics, Inc., Salt Lake City, UT, USA
| | | | - Susan Shehayeb
- City of Hope Cancer Center, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Paul Frankel
- City of Hope Cancer Center, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Kathleen R Blazer
- City of Hope Cancer Center, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | - Diana Turco
- Myriad Genetics, Inc., Salt Lake City, UT, USA
| | - Bita Nehoray
- City of Hope Cancer Center, 1500 East Duarte Road, Duarte, CA, 91010, USA
| | | | | | | | | | - Mary Daly
- Fox Chase Cancer Center, Philadelphia, PA, USA
| | | | | | - Jennifer Saam
- Myriad Genetics, Inc., Salt Lake City, UT, USA
- Castle Biosciences, Inc., Phoenix, AZ, USA
| | - Thomas P Slavin
- City of Hope Cancer Center, 1500 East Duarte Road, Duarte, CA, 91010, USA
- Myriad Genetics, Inc., Salt Lake City, UT, USA
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Katabathina VS, Marji H, Khanna L, Ramani N, Yedururi S, Dasyam A, Menias CO, Prasad SR. Decoding Genes: Current Update on Radiogenomics of Select Abdominal Malignancies. Radiographics 2021; 40:1600-1626. [PMID: 33001791 DOI: 10.1148/rg.2020200042] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Technologic advances in chromosomal analysis and DNA sequencing have enabled genome-wide analysis of cancer cells, yielding considerable data on the genetic basis of malignancies. Evolving knowledge of tumor genetics and oncologic pathways has led to a better understanding of histopathologic features, tumor classification, tumor biologic characteristics, and imaging findings and discovery of targeted therapeutic agents. Radiogenomics is a rapidly evolving field of imaging research aimed at correlating imaging features with gene mutations and gene expression patterns, and it may provide surrogate imaging biomarkers that may supplant genetic tests and be used to predict treatment response and prognosis and guide personalized treatment options. Multidetector CT, multiparametric MRI, and PET with use of multiple radiotracers are some of the imaging techniques commonly used to assess radiogenomic associations. Select abdominal malignancies demonstrate characteristic imaging features that correspond to gene mutations. Recent advances have enabled us to understand the genetics of steatotic and nonsteatotic hepatocellular adenomas, a plethora of morphologic-molecular subtypes of hepatic malignancies, a variety of clear cell and non-clear cell renal cell carcinomas, a myriad of hereditary and sporadic exocrine and neuroendocrine tumors of the pancreas, and the development of targeted therapeutic agents for gastrointestinal stromal tumors based on characteristic KIT gene mutations. Mutations associated with aggressive phenotypes of these malignancies can sometimes be predicted on the basis of their imaging characteristics. Radiologists should be familiar with the genetics and pathogenesis of common cancers that have associated imaging biomarkers, which can help them be integral members of the cancer management team and guide clinicians and pathologists. Online supplemental material is available for this article. ©RSNA, 2020 See discussion on this article by Luna (pp 1627-1630).
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Affiliation(s)
- Venkata S Katabathina
- From the Department of Radiology, University of Texas Health at San Antonio, 7703 Floyd Curl Dr, San Antonio, TX 78229 (V.S.K., H.M., L.K.); Departments of Radiology (S.Y., S.R.P.) and Pathology (N.R.), University of Texas MD Anderson Cancer Center, Houston, Tex; Department of Radiology, University of Pittsburgh Medical Center, Pittsburgh, Pa (A.D.); and Department of Radiology, Mayo Clinic, Scottsdale, Ariz (C.O.M.)
| | - Haneen Marji
- From the Department of Radiology, University of Texas Health at San Antonio, 7703 Floyd Curl Dr, San Antonio, TX 78229 (V.S.K., H.M., L.K.); Departments of Radiology (S.Y., S.R.P.) and Pathology (N.R.), University of Texas MD Anderson Cancer Center, Houston, Tex; Department of Radiology, University of Pittsburgh Medical Center, Pittsburgh, Pa (A.D.); and Department of Radiology, Mayo Clinic, Scottsdale, Ariz (C.O.M.)
| | - Lokesh Khanna
- From the Department of Radiology, University of Texas Health at San Antonio, 7703 Floyd Curl Dr, San Antonio, TX 78229 (V.S.K., H.M., L.K.); Departments of Radiology (S.Y., S.R.P.) and Pathology (N.R.), University of Texas MD Anderson Cancer Center, Houston, Tex; Department of Radiology, University of Pittsburgh Medical Center, Pittsburgh, Pa (A.D.); and Department of Radiology, Mayo Clinic, Scottsdale, Ariz (C.O.M.)
| | - Nisha Ramani
- From the Department of Radiology, University of Texas Health at San Antonio, 7703 Floyd Curl Dr, San Antonio, TX 78229 (V.S.K., H.M., L.K.); Departments of Radiology (S.Y., S.R.P.) and Pathology (N.R.), University of Texas MD Anderson Cancer Center, Houston, Tex; Department of Radiology, University of Pittsburgh Medical Center, Pittsburgh, Pa (A.D.); and Department of Radiology, Mayo Clinic, Scottsdale, Ariz (C.O.M.)
| | - Sireesha Yedururi
- From the Department of Radiology, University of Texas Health at San Antonio, 7703 Floyd Curl Dr, San Antonio, TX 78229 (V.S.K., H.M., L.K.); Departments of Radiology (S.Y., S.R.P.) and Pathology (N.R.), University of Texas MD Anderson Cancer Center, Houston, Tex; Department of Radiology, University of Pittsburgh Medical Center, Pittsburgh, Pa (A.D.); and Department of Radiology, Mayo Clinic, Scottsdale, Ariz (C.O.M.)
| | - Anil Dasyam
- From the Department of Radiology, University of Texas Health at San Antonio, 7703 Floyd Curl Dr, San Antonio, TX 78229 (V.S.K., H.M., L.K.); Departments of Radiology (S.Y., S.R.P.) and Pathology (N.R.), University of Texas MD Anderson Cancer Center, Houston, Tex; Department of Radiology, University of Pittsburgh Medical Center, Pittsburgh, Pa (A.D.); and Department of Radiology, Mayo Clinic, Scottsdale, Ariz (C.O.M.)
| | - Christine O Menias
- From the Department of Radiology, University of Texas Health at San Antonio, 7703 Floyd Curl Dr, San Antonio, TX 78229 (V.S.K., H.M., L.K.); Departments of Radiology (S.Y., S.R.P.) and Pathology (N.R.), University of Texas MD Anderson Cancer Center, Houston, Tex; Department of Radiology, University of Pittsburgh Medical Center, Pittsburgh, Pa (A.D.); and Department of Radiology, Mayo Clinic, Scottsdale, Ariz (C.O.M.)
| | - Srinivasa R Prasad
- From the Department of Radiology, University of Texas Health at San Antonio, 7703 Floyd Curl Dr, San Antonio, TX 78229 (V.S.K., H.M., L.K.); Departments of Radiology (S.Y., S.R.P.) and Pathology (N.R.), University of Texas MD Anderson Cancer Center, Houston, Tex; Department of Radiology, University of Pittsburgh Medical Center, Pittsburgh, Pa (A.D.); and Department of Radiology, Mayo Clinic, Scottsdale, Ariz (C.O.M.)
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Mittendorf KF, Kauffman TL, Amendola LM, Anderson KP, Biesecker BB, Dorschner MO, Duenas DM, Eubanks DJ, Feigelson HS, Gilmore MJ, Hunter JE, Joseph G, Kraft SA, Lee SSJ, Leo MC, Liles EG, Lindberg NM, Muessig KR, Okuyama S, Porter KM, Riddle LS, Rolf BA, Rope AF, Zepp JM, Jarvik GP, Wilfond BS, Goddard KAB. Cancer Health Assessments Reaching Many (CHARM): A clinical trial assessing a multimodal cancer genetics services delivery program and its impact on diverse populations. Contemp Clin Trials 2021; 106:106432. [PMID: 33984519 PMCID: PMC8336568 DOI: 10.1016/j.cct.2021.106432] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 12/11/2022]
Abstract
Advances in the application of genomic technologies in clinical care have the potential to increase existing healthcare disparities. Studies have consistently shown that only a fraction of eligible patients with a family history of cancer receive recommended cancer genetic counseling and subsequent genetic testing. Care delivery models using pre-test and post-test counseling are not scalable, which contributes to barriers in accessing genetics services. These barriers are even more pronounced for patients in historically underserved populations. We have designed a multimodal intervention to improve subsequent cancer surveillance, by improving the identification of patients at risk for familial cancer syndromes, reducing barriers to genetic counseling/testing, and increasing patient understanding of complex genetic results. We are evaluating this intervention in two large, integrated healthcare systems that serve diverse patient populations (NCT03426878). The primary outcome is the number of diagnostic (hereditary cancer syndrome) findings. We are examining the clinical and personal utility of streamlined pathways to genetic testing using electronic medical record data, surveys, and qualitative interviews. We will assess downstream care utilization of individuals receiving usual clinical care vs. genetic testing through the study. We will evaluate the impacts of a literacy-focused genetic counseling approach versus usual care genetic counseling on care utilization and participant understanding, satisfaction, and family communication. By recruiting participants belonging to historically underserved populations, this study is uniquely positioned to evaluate the potential of a novel genetics care delivery program to reduce care disparities.
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Affiliation(s)
- Kathleen F Mittendorf
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, 3800 N. Interstate Ave, Portland, OR 97227, USA.
| | - Tia L Kauffman
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, 3800 N. Interstate Ave, Portland, OR 97227, USA.
| | - Laura M Amendola
- Department of Medicine, Division of Medical Genetics, University of Washington Medical Center, 1705 NE Pacific St., Seattle, WA 98195, USA
| | | | | | - Michael O Dorschner
- Department of Medicine, Division of Medical Genetics, University of Washington Medical Center, 1705 NE Pacific St., Seattle, WA 98195, USA
| | - Devan M Duenas
- Treuman Katz Center for Pediatric Bioethics, Seattle Children's Research Institute and Hospital, 1900 9(th) Ave, M/S JMB-6, Seattle, WA 98101, USA
| | - Donna J Eubanks
- Center for Health Research, Kaiser Permanente Northwest, 3800 N Interstate Ave, Portland, OR 97227, USA
| | - Heather Spencer Feigelson
- Institute for Health Research, Kaiser Permanente Colorado, 2550 S Parker Rd, Suite 200, Aurora, CO 80014, USA
| | - Marian J Gilmore
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, 3800 N. Interstate Ave, Portland, OR 97227, USA
| | - Jessica Ezzell Hunter
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, 3800 N. Interstate Ave, Portland, OR 97227, USA
| | - Galen Joseph
- Department of Humanities and Social Sciences, University of California, San Francisco, 1450 3rd Street, Rm 551 & 556, San Francisco, CA 94143, USA
| | - Stephanie A Kraft
- Treuman Katz Center for Pediatric Bioethics, Seattle Children's Research Institute and Hospital, 1900 9(th) Ave, M/S JMB-6, Seattle, WA 98101, USA; Department of Pediatrics, Division of Bioethics and Palliative Care, University of Washington, 1959 NE Pacific St, Seattle, WA 98195, USA
| | - Sandra Soo Jin Lee
- Division of Ethics, Department of Medical Humanities and Ethics, Columbia University, 630 West 168(th) St, PH15E-1525, New York, NY 10032, USA
| | - Michael C Leo
- Center for Health Research, Kaiser Permanente Northwest, 3800 N Interstate Ave, Portland, OR 97227, USA
| | - Elizabeth G Liles
- Center for Health Research, Kaiser Permanente Northwest, 3800 N Interstate Ave, Portland, OR 97227, USA
| | - Nangel M Lindberg
- Center for Health Research, Kaiser Permanente Northwest, 3800 N Interstate Ave, Portland, OR 97227, USA
| | - Kristin R Muessig
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, 3800 N. Interstate Ave, Portland, OR 97227, USA
| | - Sonia Okuyama
- Denver Health and Hospital Authority, 777 Bannock Denver, CO 80204, USA
| | - Kathryn M Porter
- Treuman Katz Center for Pediatric Bioethics, Seattle Children's Research Institute and Hospital, 1900 9(th) Ave, M/S JMB-6, Seattle, WA 98101, USA
| | - Leslie S Riddle
- Department of Humanities and Social Sciences, University of California, San Francisco, 1450 3rd Street, Rm 551 & 556, San Francisco, CA 94143, USA
| | - Bradley A Rolf
- Department of Medicine, Division of Medical Genetics, University of Washington Medical Center, 1705 NE Pacific St., Seattle, WA 98195, USA
| | - Alan F Rope
- Center for Health Research, Kaiser Permanente Northwest, 3800 N Interstate Ave, Portland, OR 97227, USA; Genome Medical, 701 Gateway Blvd, Suite 380, San Francisco, CA 94080, USA
| | - Jamilyn M Zepp
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, 3800 N. Interstate Ave, Portland, OR 97227, USA
| | - Gail P Jarvik
- Department of Medicine, Division of Medical Genetics, University of Washington Medical Center, 1705 NE Pacific St., Seattle, WA 98195, USA
| | - Benjamin S Wilfond
- Treuman Katz Center for Pediatric Bioethics, Seattle Children's Research Institute and Hospital, 1900 9(th) Ave, M/S JMB-6, Seattle, WA 98101, USA; Department of Pediatrics, Division of Bioethics and Palliative Care, University of Washington, 1959 NE Pacific St, Seattle, WA 98195, USA
| | - Katrina A B Goddard
- Department of Translational and Applied Genomics, Center for Health Research, Kaiser Permanente Northwest, 3800 N. Interstate Ave, Portland, OR 97227, USA
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Wijesiriwardhana P, Wetthasinghe K, Dissanayake VHW. Copy Number Variants Captured by the Array Comparative Genomic Hybridization in a Cohort of Patients Affected with Hereditary Colorectal Cancer in Sri Lanka: The First CNV Analysis Study of the Hereditary Colorectal Cancer in the Sri Lankan Population. Asian Pac J Cancer Prev 2021; 22:1957-1966. [PMID: 34181357 PMCID: PMC8418865 DOI: 10.31557/apjcp.2021.22.6.1957] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 06/08/2021] [Indexed: 11/25/2022] Open
Abstract
INTRODUCTION Hereditary non-polyposis colorectal cancer (HNPCC), is an autosomal dominant disorder characterized by the development of multiple cancer types. Molecular diagnosis of HNPCC requires the precise identification of pathogenic germline variants in DNA mismatch repair (MMR) genes. Next Generation Sequencing (NGS) is now the gold standard test in practice, to identify these variants. However, large genomic rearrangements (LGR) in cancer predisposing genes (CPGs) are missed by NGS. This may lead to underestimation of the frequency of the variants, misleading the genetic diagnosis and delaying intervention in high risk individuals. Hence this study was aimed at identifying the presence of large genomic alterations that could explain the missing heritable risk of colon cancer in affected patients with family history strongly suggestive of hereditary colorectal cancer in Sri Lanka. METHODS A cohort of six patients affected with hereditary colorectal cancer who tested negative for pathogenic variants in next generation sequencing studies was investigated using Sure Print G3 Human CGH 4x180K microarray platform. Agilent Genomic-Workbench-v7.0.4.0 software was used to identify the Copy Number Variants (CNV). Four healthy individuals (>55years) were used as controls. Annotations of the CNV regions which were observed were done using the database of Genomic Variants. RESULTS We identified 150 CNVs including regions of both genomic gains and losses in the patient cohort. There was no difference in the average number or the average genomic burden of CNVs identified in the patients versus the controls. CNVs were residing on the positions of 1q21.2, 2q37.3, 2p11.2-p11.1, 5q13.2, 6p12.3, 7q31.33, 7p14.1, 14q32.33, 15q11.1-11.2, 16p11.2, 22q11.22, 22q13.1 that were assessed by the array platform used in the study. CNVs in any of the well-known common CPG s or CNVs that reside on or in close proximity to genes corresponding to MMR pathway were not identified. We found several distinct pathways that have previously been identified as having a direct association with the progression of HNPCC. CONCLUSION This study shows that CNVs are likely contributors to the colorectal cancer predisposition in a small but significant proportion of patients affected with hereditary colorectal cancer in this cohort. Further studies have to perform to get a better understanding on the contribution of CNVs to the cancer predisposition in this cohort of patients in the Sri Lankan population.
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Affiliation(s)
- Prabhavi Wijesiriwardhana
- Department of Medical Laboratory Science, Faculty of Allied Health Sciences, University of Ruhuna, Sri Lanka.
- Human Genetics Unit, Faculty of Medicine, University of Colombo, Sri Lanka.
| | - Kalum Wetthasinghe
- Human Genetics Unit, Faculty of Medicine, University of Colombo, Sri Lanka.
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Mantilla WA, Sanabria-Salas MC, Baldion AM, Sua LF, Gonzalez DM, Lema M. NGS in Lung, Breast, and Unknown Primary Cancer in Colombia: A Multidisciplinary Consensus on Challenges and Opportunities. JCO Glob Oncol 2021; 7:1012-1023. [PMID: 34185572 PMCID: PMC8457807 DOI: 10.1200/go.21.00046] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 04/16/2021] [Accepted: 05/25/2021] [Indexed: 12/24/2022] Open
Abstract
Given the benefits and likely future applications, there is an urgent need to expand the use of next-generation sequencing (NGS) in breast, lung, and unknown primary cancers in Colombia. The objective of this review is to address the barriers limiting access to the use of NGS in Colombia, specifically for patients with breast, lung, and unknown primary cancers in the public health care system. A selected Panel of Colombian experts in NGS were provided with a series of relevant questions to address in a multiday conference. Each narrative was discussed and edited by the Panel through numerous drafts and rounds of discussion until consensus was achieved. There are limitations to the widespread adoption of innovative technology inherent to the Colombian health care system. Barriers identified to implementing NGS in Colombia include availability, accessibility, and affordability; limited infrastructure; training and awareness of health personnel; quality-control procedures; and collection of local data. Stakeholders must align to adapt the implementation of NGS to the constraints of resource-limited environments. Diagnostic algorithms were developed to guide molecular testing for lung, breast, and unknown primary cancers. Recommendations on overcoming the barriers to the widespread adoption of NGS include country-specific molecular testing guidelines, creating a national genetic registry, improving infrastructure, and creating health policy that favors the adoption of innovative technology.
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Affiliation(s)
| | | | - Ana Margarita Baldion
- Head of the Pathology Section, Department of Pathology and Laboratory Medicine, Hospital Universitario Fundacion Santa Fe de Bogota, Bogotá, Colombia
| | - Luz F. Sua
- Department of Pathology and Laboratory Medicine, Fundación Valle del Lili, and Faculty of Health Sciences, Universidad ICESI, Cali, Colombia
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Lapointe J, Dorval M, Chiquette J, Joly Y, Guertin JR, Laberge M, Gekas J, Hébert J, Pomey MP, Cruz-Marino T, Touhami O, Blanchet Saint-Pierre A, Gagnon S, Bouchard K, Rhéaume J, Boisvert K, Brousseau C, Castonguay L, Fortier S, Gosselin I, Lachapelle P, Lavoie S, Poirier B, Renaud MC, Ruizmangas MG, Sebastianelli A, Roy S, Côté M, Racine MM, Roy MC, Côté N, Brisson C, Charette N, Faucher V, Leblanc J, Dubeau MÈ, Plante M, Desbiens C, Beaumont M, Simard J, Nabi H. A Collaborative Model to Implement Flexible, Accessible and Efficient Oncogenetic Services for Hereditary Breast and Ovarian Cancer: The C-MOnGene Study. Cancers (Basel) 2021; 13:cancers13112729. [PMID: 34072979 PMCID: PMC8198545 DOI: 10.3390/cancers13112729] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 05/12/2021] [Accepted: 05/25/2021] [Indexed: 01/04/2023] Open
Abstract
Simple Summary We recently developed an oncogenetic model to overcome the unprecedented demand for genetic counseling and testing for hereditary breast and ovarian cancer. Quality and performance indicators showed that the implementation of this model improved access to genetic counseling and minimized delays for genetic tests for patients, who reported to be overwhelmingly satisfied with the process. However, it remains unknown whether this model is robust and sustainable or requires adjustments. In addition, whether the model could be deployed elsewhere remains also to be elucidated. The C-MOnGene study was therefore designed to gain an in-depth understanding of the context in which the model was developed and implemented, and document the lessons that can be learned to optimize oncogenetic services delivery in other settings. Abstract Medical genetic services are facing an unprecedented demand for counseling and testing for hereditary breast and ovarian cancer (HBOC) in a context of limited resources. To help resolve this issue, a collaborative oncogenetic model was recently developed and implemented at the CHU de Québec-Université Laval; Quebec; Canada. Here, we present the protocol of the C-MOnGene (Collaborative Model in OncoGenetics) study, funded to examine the context in which the model was implemented and document the lessons that can be learned to optimize the delivery of oncogenetic services. Within three years of implementation, the model allowed researchers to double the annual number of patients seen in genetic counseling. The average number of days between genetic counseling and disclosure of test results significantly decreased. Group counseling sessions improved participants’ understanding of breast cancer risk and increased knowledge of breast cancer and genetics and a large majority of them reported to be overwhelmingly satisfied with the process. These quality and performance indicators suggest this oncogenetic model offers a flexible, patient-centered and efficient genetic counseling and testing for HBOC. By identifying the critical facilitating factors and barriers, our study will provide an evidence base for organizations interested in transitioning to an oncogenetic model integrated into oncology care; including teams that are not specialized but are trained in genetics.
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Affiliation(s)
- Julie Lapointe
- Centre de Recherche du CHU de Québec-Université Laval, Hôpital du Saint-Sacrement, 1050, Chemin Ste-Foy, Local J0-01, Québec, QC G1S 4L8, Canada; (J.L.); (M.D.); (J.C.); (J.R.G.); (M.L.); (K.B.); (J.S.)
| | - Michel Dorval
- Centre de Recherche du CHU de Québec-Université Laval, Hôpital du Saint-Sacrement, 1050, Chemin Ste-Foy, Local J0-01, Québec, QC G1S 4L8, Canada; (J.L.); (M.D.); (J.C.); (J.R.G.); (M.L.); (K.B.); (J.S.)
- Centre de Recherche CISSS Chaudière-Appalaches, 143 Rue Wolfe, Lévis, QC G6V 3Z1, Canada;
- Faculté de Pharmacie, Université Laval, 1050 Av de la Médecine, Québec, QC G1V 0A6, Canada
| | - Jocelyne Chiquette
- Centre de Recherche du CHU de Québec-Université Laval, Hôpital du Saint-Sacrement, 1050, Chemin Ste-Foy, Local J0-01, Québec, QC G1S 4L8, Canada; (J.L.); (M.D.); (J.C.); (J.R.G.); (M.L.); (K.B.); (J.S.)
- CHU de Québec-Université Laval, 1050, Chemin Ste-Foy, Québec, QC G1S 4L8, Canada; (J.G.); (J.R.); (K.B.); (C.B.); (L.C.); (S.F.); (I.G.); (P.L.); (S.L.); (B.P.); (M.-C.R.); (M.-G.R.); (A.S.); (S.R.); (M.C.); (M.P.); (C.D.); (M.B.)
| | - Yann Joly
- Institut de Recherche du Centre Universitaire de Santé McGill, 2155 Rue Guy, 5e étage, Montréal, QC H3H 2R9, Canada;
- Département de Génétique Humaine et Unité de Bioéthique, Faculté de Médecine, Université McGill, 3605 Rue de la Montagne Montréal, Montréal, QC H3G 2M1, Canada
| | - Jason Robert Guertin
- Centre de Recherche du CHU de Québec-Université Laval, Hôpital du Saint-Sacrement, 1050, Chemin Ste-Foy, Local J0-01, Québec, QC G1S 4L8, Canada; (J.L.); (M.D.); (J.C.); (J.R.G.); (M.L.); (K.B.); (J.S.)
- Département de Médecine Sociale et Préventive, Faculté de Médecine, Université Laval, 1050 Avenue de la Médecine, Université Laval, Québec, QC G1V 0A6, Canada
| | - Maude Laberge
- Centre de Recherche du CHU de Québec-Université Laval, Hôpital du Saint-Sacrement, 1050, Chemin Ste-Foy, Local J0-01, Québec, QC G1S 4L8, Canada; (J.L.); (M.D.); (J.C.); (J.R.G.); (M.L.); (K.B.); (J.S.)
- Vitam, Centre de Recherche en Santé Durable, Université Laval, 2525, Chemin de la Canardière, Québec, QC G1J 0A4, Canada
- Département des Opérations et Systèmes de Décision, Faculté des Sciences de l’Administration, Université Laval, 2325 Rue de la Terrasse Université Laval, Québec, QC G1V 0A6, Canada
| | - Jean Gekas
- CHU de Québec-Université Laval, 1050, Chemin Ste-Foy, Québec, QC G1S 4L8, Canada; (J.G.); (J.R.); (K.B.); (C.B.); (L.C.); (S.F.); (I.G.); (P.L.); (S.L.); (B.P.); (M.-C.R.); (M.-G.R.); (A.S.); (S.R.); (M.C.); (M.P.); (C.D.); (M.B.)
| | - Johanne Hébert
- Centre de Recherche CISSS Chaudière-Appalaches, 143 Rue Wolfe, Lévis, QC G6V 3Z1, Canada;
- Département des Sciences Infirmières, Université du Québec à Rimouski (UQAR), Campus de Lévis, 1595 Boulevard Alphonse-Desjardins, Lévis, QC G6V 0A6, Canada
| | - Marie-Pascale Pomey
- Centre de Recherche du CHUM, 900, Rue Saint-Denis, Montréal, QC H2X 0A9, Canada;
- Département de Gestion, Évaluation et Politique de Santé, Faculté de Médecine, Université de Montréal, 7101 Avenue du Parc, 3e Étage, Montréal, QC H3N 1X9, Canada
| | - Tania Cruz-Marino
- CIUSSS Saguenay Lac-St-Jean, 930 Rue Jacques-Cartier Est, Chicoutimi, QC G7H 7K9, Canada; (T.C.-M.); (O.T.); (S.G.); (V.F.); (J.L.); (M.-È.D.)
| | - Omar Touhami
- CIUSSS Saguenay Lac-St-Jean, 930 Rue Jacques-Cartier Est, Chicoutimi, QC G7H 7K9, Canada; (T.C.-M.); (O.T.); (S.G.); (V.F.); (J.L.); (M.-È.D.)
| | - Arnaud Blanchet Saint-Pierre
- CISSS Bas St-Laurent, 150 Av Rouleau, Rimouski, QC G5L 5T1, Canada; (A.B.S.-P.); (M.-C.R.); (N.C.); (C.B.); (N.C.)
| | - Sylvain Gagnon
- CIUSSS Saguenay Lac-St-Jean, 930 Rue Jacques-Cartier Est, Chicoutimi, QC G7H 7K9, Canada; (T.C.-M.); (O.T.); (S.G.); (V.F.); (J.L.); (M.-È.D.)
| | - Karine Bouchard
- Centre de Recherche du CHU de Québec-Université Laval, Hôpital du Saint-Sacrement, 1050, Chemin Ste-Foy, Local J0-01, Québec, QC G1S 4L8, Canada; (J.L.); (M.D.); (J.C.); (J.R.G.); (M.L.); (K.B.); (J.S.)
| | - Josée Rhéaume
- CHU de Québec-Université Laval, 1050, Chemin Ste-Foy, Québec, QC G1S 4L8, Canada; (J.G.); (J.R.); (K.B.); (C.B.); (L.C.); (S.F.); (I.G.); (P.L.); (S.L.); (B.P.); (M.-C.R.); (M.-G.R.); (A.S.); (S.R.); (M.C.); (M.P.); (C.D.); (M.B.)
| | - Karine Boisvert
- CHU de Québec-Université Laval, 1050, Chemin Ste-Foy, Québec, QC G1S 4L8, Canada; (J.G.); (J.R.); (K.B.); (C.B.); (L.C.); (S.F.); (I.G.); (P.L.); (S.L.); (B.P.); (M.-C.R.); (M.-G.R.); (A.S.); (S.R.); (M.C.); (M.P.); (C.D.); (M.B.)
| | - Claire Brousseau
- CHU de Québec-Université Laval, 1050, Chemin Ste-Foy, Québec, QC G1S 4L8, Canada; (J.G.); (J.R.); (K.B.); (C.B.); (L.C.); (S.F.); (I.G.); (P.L.); (S.L.); (B.P.); (M.-C.R.); (M.-G.R.); (A.S.); (S.R.); (M.C.); (M.P.); (C.D.); (M.B.)
| | - Lysanne Castonguay
- CHU de Québec-Université Laval, 1050, Chemin Ste-Foy, Québec, QC G1S 4L8, Canada; (J.G.); (J.R.); (K.B.); (C.B.); (L.C.); (S.F.); (I.G.); (P.L.); (S.L.); (B.P.); (M.-C.R.); (M.-G.R.); (A.S.); (S.R.); (M.C.); (M.P.); (C.D.); (M.B.)
| | - Sylvain Fortier
- CHU de Québec-Université Laval, 1050, Chemin Ste-Foy, Québec, QC G1S 4L8, Canada; (J.G.); (J.R.); (K.B.); (C.B.); (L.C.); (S.F.); (I.G.); (P.L.); (S.L.); (B.P.); (M.-C.R.); (M.-G.R.); (A.S.); (S.R.); (M.C.); (M.P.); (C.D.); (M.B.)
| | - Isabelle Gosselin
- CHU de Québec-Université Laval, 1050, Chemin Ste-Foy, Québec, QC G1S 4L8, Canada; (J.G.); (J.R.); (K.B.); (C.B.); (L.C.); (S.F.); (I.G.); (P.L.); (S.L.); (B.P.); (M.-C.R.); (M.-G.R.); (A.S.); (S.R.); (M.C.); (M.P.); (C.D.); (M.B.)
| | - Philippe Lachapelle
- CHU de Québec-Université Laval, 1050, Chemin Ste-Foy, Québec, QC G1S 4L8, Canada; (J.G.); (J.R.); (K.B.); (C.B.); (L.C.); (S.F.); (I.G.); (P.L.); (S.L.); (B.P.); (M.-C.R.); (M.-G.R.); (A.S.); (S.R.); (M.C.); (M.P.); (C.D.); (M.B.)
| | - Sabrina Lavoie
- CHU de Québec-Université Laval, 1050, Chemin Ste-Foy, Québec, QC G1S 4L8, Canada; (J.G.); (J.R.); (K.B.); (C.B.); (L.C.); (S.F.); (I.G.); (P.L.); (S.L.); (B.P.); (M.-C.R.); (M.-G.R.); (A.S.); (S.R.); (M.C.); (M.P.); (C.D.); (M.B.)
| | - Brigitte Poirier
- CHU de Québec-Université Laval, 1050, Chemin Ste-Foy, Québec, QC G1S 4L8, Canada; (J.G.); (J.R.); (K.B.); (C.B.); (L.C.); (S.F.); (I.G.); (P.L.); (S.L.); (B.P.); (M.-C.R.); (M.-G.R.); (A.S.); (S.R.); (M.C.); (M.P.); (C.D.); (M.B.)
| | - Marie-Claude Renaud
- CHU de Québec-Université Laval, 1050, Chemin Ste-Foy, Québec, QC G1S 4L8, Canada; (J.G.); (J.R.); (K.B.); (C.B.); (L.C.); (S.F.); (I.G.); (P.L.); (S.L.); (B.P.); (M.-C.R.); (M.-G.R.); (A.S.); (S.R.); (M.C.); (M.P.); (C.D.); (M.B.)
| | - Maria-Gabriela Ruizmangas
- CHU de Québec-Université Laval, 1050, Chemin Ste-Foy, Québec, QC G1S 4L8, Canada; (J.G.); (J.R.); (K.B.); (C.B.); (L.C.); (S.F.); (I.G.); (P.L.); (S.L.); (B.P.); (M.-C.R.); (M.-G.R.); (A.S.); (S.R.); (M.C.); (M.P.); (C.D.); (M.B.)
| | - Alexandra Sebastianelli
- CHU de Québec-Université Laval, 1050, Chemin Ste-Foy, Québec, QC G1S 4L8, Canada; (J.G.); (J.R.); (K.B.); (C.B.); (L.C.); (S.F.); (I.G.); (P.L.); (S.L.); (B.P.); (M.-C.R.); (M.-G.R.); (A.S.); (S.R.); (M.C.); (M.P.); (C.D.); (M.B.)
| | - Stéphane Roy
- CHU de Québec-Université Laval, 1050, Chemin Ste-Foy, Québec, QC G1S 4L8, Canada; (J.G.); (J.R.); (K.B.); (C.B.); (L.C.); (S.F.); (I.G.); (P.L.); (S.L.); (B.P.); (M.-C.R.); (M.-G.R.); (A.S.); (S.R.); (M.C.); (M.P.); (C.D.); (M.B.)
| | - Madeleine Côté
- CHU de Québec-Université Laval, 1050, Chemin Ste-Foy, Québec, QC G1S 4L8, Canada; (J.G.); (J.R.); (K.B.); (C.B.); (L.C.); (S.F.); (I.G.); (P.L.); (S.L.); (B.P.); (M.-C.R.); (M.-G.R.); (A.S.); (S.R.); (M.C.); (M.P.); (C.D.); (M.B.)
| | | | - Marie-Claude Roy
- CISSS Bas St-Laurent, 150 Av Rouleau, Rimouski, QC G5L 5T1, Canada; (A.B.S.-P.); (M.-C.R.); (N.C.); (C.B.); (N.C.)
| | - Nathalie Côté
- CISSS Bas St-Laurent, 150 Av Rouleau, Rimouski, QC G5L 5T1, Canada; (A.B.S.-P.); (M.-C.R.); (N.C.); (C.B.); (N.C.)
| | - Carmen Brisson
- CISSS Bas St-Laurent, 150 Av Rouleau, Rimouski, QC G5L 5T1, Canada; (A.B.S.-P.); (M.-C.R.); (N.C.); (C.B.); (N.C.)
| | - Nelson Charette
- CISSS Bas St-Laurent, 150 Av Rouleau, Rimouski, QC G5L 5T1, Canada; (A.B.S.-P.); (M.-C.R.); (N.C.); (C.B.); (N.C.)
| | - Valérie Faucher
- CIUSSS Saguenay Lac-St-Jean, 930 Rue Jacques-Cartier Est, Chicoutimi, QC G7H 7K9, Canada; (T.C.-M.); (O.T.); (S.G.); (V.F.); (J.L.); (M.-È.D.)
| | - Josianne Leblanc
- CIUSSS Saguenay Lac-St-Jean, 930 Rue Jacques-Cartier Est, Chicoutimi, QC G7H 7K9, Canada; (T.C.-M.); (O.T.); (S.G.); (V.F.); (J.L.); (M.-È.D.)
| | - Marie-Ève Dubeau
- CIUSSS Saguenay Lac-St-Jean, 930 Rue Jacques-Cartier Est, Chicoutimi, QC G7H 7K9, Canada; (T.C.-M.); (O.T.); (S.G.); (V.F.); (J.L.); (M.-È.D.)
| | - Marie Plante
- CHU de Québec-Université Laval, 1050, Chemin Ste-Foy, Québec, QC G1S 4L8, Canada; (J.G.); (J.R.); (K.B.); (C.B.); (L.C.); (S.F.); (I.G.); (P.L.); (S.L.); (B.P.); (M.-C.R.); (M.-G.R.); (A.S.); (S.R.); (M.C.); (M.P.); (C.D.); (M.B.)
| | - Christine Desbiens
- CHU de Québec-Université Laval, 1050, Chemin Ste-Foy, Québec, QC G1S 4L8, Canada; (J.G.); (J.R.); (K.B.); (C.B.); (L.C.); (S.F.); (I.G.); (P.L.); (S.L.); (B.P.); (M.-C.R.); (M.-G.R.); (A.S.); (S.R.); (M.C.); (M.P.); (C.D.); (M.B.)
| | - Martin Beaumont
- CHU de Québec-Université Laval, 1050, Chemin Ste-Foy, Québec, QC G1S 4L8, Canada; (J.G.); (J.R.); (K.B.); (C.B.); (L.C.); (S.F.); (I.G.); (P.L.); (S.L.); (B.P.); (M.-C.R.); (M.-G.R.); (A.S.); (S.R.); (M.C.); (M.P.); (C.D.); (M.B.)
| | - Jacques Simard
- Centre de Recherche du CHU de Québec-Université Laval, Hôpital du Saint-Sacrement, 1050, Chemin Ste-Foy, Local J0-01, Québec, QC G1S 4L8, Canada; (J.L.); (M.D.); (J.C.); (J.R.G.); (M.L.); (K.B.); (J.S.)
- Département de Médecine moléculaire, Faculté de Médecine, Université Laval, 1050 Avenue de la Médecine, Québec, QC G1V 0A6, Canada
| | - Hermann Nabi
- Centre de Recherche du CHU de Québec-Université Laval, Hôpital du Saint-Sacrement, 1050, Chemin Ste-Foy, Local J0-01, Québec, QC G1S 4L8, Canada; (J.L.); (M.D.); (J.C.); (J.R.G.); (M.L.); (K.B.); (J.S.)
- Département de Médecine Sociale et Préventive, Faculté de Médecine, Université Laval, 1050 Avenue de la Médecine, Université Laval, Québec, QC G1V 0A6, Canada
- Correspondence: ; Tel.: +1-418-525-4444 (ext. 82800)
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Min YK, Park KS. The Application of Control Materials for Ongoing Quality Management of Next-Generation Sequencing in a Clinical Genetic Laboratory. MEDICINA (KAUNAS, LITHUANIA) 2021; 57:543. [PMID: 34071304 PMCID: PMC8227145 DOI: 10.3390/medicina57060543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 05/25/2021] [Accepted: 05/25/2021] [Indexed: 11/16/2022]
Abstract
Next-generation sequencing (NGS) has played an important role in detecting genetic variants with pathologic and therapeutic potential. The advantages of NGS, such as high-throughput sequencing capacity and massively parallel sequencing, have a significant impact on realization of genetic profiling in clinical genetic laboratories. These changes have enabled clinicians to execute precision medicine in diagnosis, prognosis, and treatment for patients. However, to adapt targeted gene panels in diagnostic use, analytical validation and ongoing quality control should be implemented and applied with both practical guidelines and appropriate control materials. Several guidelines for NGS quality control recommend usage of control materials such as HapMap cell lines, synthetic DNA fragments, and genetically characterized cell lines; however, specifications or applications of such usage are insufficient to guideline method development. This review focuses on what factors should be considered before control material selection for NGS assay and practical methods of how they could be developed in clinical genetic laboratories. This review also provides the detailed sources of critical information related to control materials.
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Affiliation(s)
- Young-Kyu Min
- Department of Medical Laser, Dankook University, Chungnam 31116, Korea;
- Department of Laboratory Medicine, Severance Hospital, 50-1 Yonsei-ro, Seodaemun-gu, Seoul 03722, Korea
| | - Kyung-Sun Park
- Department of Laboratory Medicine, Kyung Hee University School of Medicine and Kyung Hee University Medical Center, Seoul 02447, Korea
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Zong N, Ngo V, Stone DJ, Wen A, Zhao Y, Yu Y, Liu S, Huang M, Wang C, Jiang G. Leveraging Genetic Reports and Electronic Health Records for the Prediction of Primary Cancers: Algorithm Development and Validation Study. JMIR Med Inform 2021; 9:e23586. [PMID: 34032581 PMCID: PMC8188315 DOI: 10.2196/23586] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 01/07/2021] [Accepted: 01/27/2021] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Precision oncology has the potential to leverage clinical and genomic data in advancing disease prevention, diagnosis, and treatment. A key research area focuses on the early detection of primary cancers and potential prediction of cancers of unknown primary in order to facilitate optimal treatment decisions. OBJECTIVE This study presents a methodology to harmonize phenotypic and genetic data features to classify primary cancer types and predict cancers of unknown primaries. METHODS We extracted genetic data elements from oncology genetic reports of 1011 patients with cancer and their corresponding phenotypical data from Mayo Clinic's electronic health records. We modeled both genetic and electronic health record data with HL7 Fast Healthcare Interoperability Resources. The semantic web Resource Description Framework was employed to generate the network-based data representation (ie, patient-phenotypic-genetic network). Based on the Resource Description Framework data graph, Node2vec graph-embedding algorithm was applied to generate features. Multiple machine learning and deep learning backbone models were compared for cancer prediction performance. RESULTS With 6 machine learning tasks designed in the experiment, we demonstrated the proposed method achieved favorable results in classifying primary cancer types (area under the receiver operating characteristic curve [AUROC] 96.56% for all 9 cancer predictions on average based on the cross-validation) and predicting unknown primaries (AUROC 80.77% for all 8 cancer predictions on average for real-patient validation). To demonstrate the interpretability, 17 phenotypic and genetic features that contributed the most to the prediction of each cancer were identified and validated based on a literature review. CONCLUSIONS Accurate prediction of cancer types can be achieved with existing electronic health record data with satisfactory precision. The integration of genetic reports improves prediction, illustrating the translational values of incorporating genetic tests early at the diagnosis stage for patients with cancer.
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Affiliation(s)
- Nansu Zong
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, United States
| | - Victoria Ngo
- University of California Davis Health, Sacramento, CA, United States
| | - Daniel J Stone
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, United States
| | - Andrew Wen
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, United States
| | - Yiqing Zhao
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, United States
| | - Yue Yu
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, United States
| | - Sijia Liu
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, United States
| | - Ming Huang
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, United States
| | - Chen Wang
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, United States
| | - Guoqian Jiang
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, United States
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Li H, Liu S, Wang S, Zeng Q, Chen Y, Fang T, Zhang Y, Zhou Y, Zhang Y, Wang K, Yan Z, Qiang C, Xu M, Chai X, Yuan Y, Huang M, Zhang H, Xiong Y. Cancer SIGVAR: A semiautomated interpretation tool for germline variants of hereditary cancer-related genes. Hum Mutat 2021; 42:359-372. [PMID: 33565189 DOI: 10.1002/humu.24177] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 12/27/2020] [Accepted: 02/05/2021] [Indexed: 01/21/2023]
Abstract
Cancer is one of the most important health issues globally and the accuracy of interpretation of cancer-related variants is critical for the clinical management of hereditary cancer. ClinGen Sequence Variant Interpretation Working Groups have developed many adaptations of American College of Medical Genetics and Genomics and the Association of Molecular Pathologists guidelines to improve the consistency of interpretation. We combined the most recent adaptations to expand the number of the criteria from 28 to 48 and developed a tool called Cancer SIGVAR to help genetic counselors interpret the clinical significance of cancer germline variants. Our tool can accept VCF files as input and realize fully automated interpretation based on 21 criteria and semiautomated interpretation based on 48 criteria. We validated the performance of our tool with the ClinVar and CLINVITAE benchmark databases, achieving an average consistency for pathogenic and benign assessment up to 93.71% and 79.38%, respectively. We compared Cancer SIGVAR with two similar tools, InterVar and PathoMAN, and analyzed the main differences in criteria and implementation. Furthermore, we selected 911 variants from another two in-house benchmark databases, and semiautomated interpretation reached an average classification consistency of 98.35%. Our findings highlight the need to optimize automated interpretation tools based on constantly updated guidelines. Cancer SIGVAR is publicly available at http://cancersigvar.bgi.com/.
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Affiliation(s)
- Hong Li
- BGI-Wuhan Clinical Laboratories, BGI-Shenzhen, WuHan, China
| | - Shuixia Liu
- BGI-Wuhan Clinical Laboratories, BGI-Shenzhen, WuHan, China
| | | | - Quanlei Zeng
- BGI-Wuhan Clinical Laboratories, BGI-Shenzhen, WuHan, China
| | - Yulan Chen
- BGI Genomics, BGI-Shenzhen, ShenZhen, China
| | - Ting Fang
- BGI-Wuhan Clinical Laboratories, BGI-Shenzhen, WuHan, China
| | - Yi Zhang
- BGI-Wuhan Clinical Laboratories, BGI-Shenzhen, WuHan, China
| | - Ying Zhou
- BGI-Wuhan Clinical Laboratories, BGI-Shenzhen, WuHan, China
| | - Yu Zhang
- BGI-Wuhan Clinical Laboratories, BGI-Shenzhen, WuHan, China
| | - Kaiyue Wang
- BGI-Wuhan Clinical Laboratories, BGI-Shenzhen, WuHan, China
| | - Zhangwei Yan
- BGI-Wuhan Clinical Laboratories, BGI-Shenzhen, WuHan, China
| | - Cuicui Qiang
- BGI-Wuhan Clinical Laboratories, BGI-Shenzhen, WuHan, China
| | - Meng Xu
- BGI-Wuhan Clinical Laboratories, BGI-Shenzhen, WuHan, China
| | | | | | - Ming Huang
- BGI-Wuhan Clinical Laboratories, BGI-Shenzhen, WuHan, China
| | | | - Yun Xiong
- BGI-Wuhan Clinical Laboratories, BGI-Shenzhen, WuHan, China
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