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Rafati M, McReynolds LJ, Wang Y, Hicks B, Jones K, Spellman SR, He M, Bolon YT, Arrieta-Bolaños E, Saultz JN, Lee SJ, Savage SA, Gadalla SM. Hemophagocytic Lymphohistiocytosis Gene Variants in Severe Aplastic Anemia and Their Impact on Hematopoietic Cell Transplantation Outcomes. Transplant Cell Ther 2024:S2666-6367(24)00427-5. [PMID: 38810947 DOI: 10.1016/j.jtct.2024.05.017] [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: 03/24/2024] [Revised: 05/20/2024] [Accepted: 05/23/2024] [Indexed: 05/31/2024]
Abstract
Germline genetic testing for patients with severe aplastic anemia (SAA) is recommended to guide treatment, including the use of immunosuppressive therapy and/or adjustment of hematopoietic cell transplantation (HCT) modalities. Hemophagocytic lymphohistiocytosis (HLH) is a life-threatening hyperinflammatory condition often associated with cytopenias with autosomal recessive (AR) or X-linked recessive (XLR) inheritance. HLH is part of the SAA differential diagnosis, and genetic testing may identify variants in HLH genes in patients with SAA. The impact of pathogenic/likely pathogenic (P/LP) variants in HLH genes on HCT outcomes in SAA is unclear. In this study, we aimed to determine the frequency of HLH gene variants in a large cohort of patients with acquired SAA and to evaluate their association(s) with HCT outcomes. The Transplant Outcomes in Aplastic Anemia project, a collaboration between the National Cancer Institute and the Center for International Blood and Marrow Transplant Research, collected genomic and clinical data from 824 patients who underwent HCT for SAA between 1989 and 2015. We excluded 140 patients with inherited bone marrow failure syndromes and used exome sequencing data from the remaining 684 patients with acquired SAA to identify P/LP variants in 14 HLH-associated genes (11 AR, 3 XLR) curated using American College of Medical Genetics and Genomics/Association of Molecular Pathology (ACMG/AMP) criteria. Deleterious variants of uncertain significance (del-VUS) were defined as those not meeting the ACMG/AMP P/LP criteria but with damaging predictions in ≥3 of 5 meta-predictors (BayesDel, REVEL, CADD, MetaSVM, and/or EIGEN). The Kaplan-Meier estimator was used to calculate the probability of overall survival (OS) after HCT, and the cumulative incidence calculator was used for other HCT outcomes, accounting for relevant competing risks. There were 46 HLH variants in 49 of the 684 patients (7.2%). Seventeen variants in 19 patients (2.8%) were P/LP; 8 of these were loss-of-function variants. Among the 19 patients with P/LP HLH variants, 16 (84%) had monoallelic variants in genes with AR inheritance, and 3 had variants in XLR genes. PRF1 was the most frequently affected gene (in 8 of the 19 patients). We found no statistically significant differences in transplantation-related factors between patients with and those without P/LP HLH variants. The 5-year survival probability was 89% (95% confidence interval [CI], 72% to 99%) in patients with P/LP HLH variants and 70% (95% CI, 53% to 85%) in those with del-VUS HLH variants, compared to 66% (95% CI, 62% to 70%) in those without variants (P = .16, log-rank test). The median time to neutrophil engraftment was 16 days for patients with P/LP HLH variants and 18 days in those with del-VUS HLH variants or without variants combined (P = .01, Gray's test). No statistically significant associations between P/LP HLH variants and the risk of acute or chronic graft-versus-host disease were noted. In this large cohort of patients with acquired SAA, we found that 2.8% of patients harbored a P/LP variant in an HLH gene. No negative effects of HLH gene variants on post-HCT survival were noted. The small number of patients with P/LP HLH variants limits the study's ability to provide conclusive evidence; nonetheless, our data suggest that there is no need for special transplantation considerations for patients with SAA carrying P/LP variants.
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Affiliation(s)
- Maryam Rafati
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland.
| | - Lisa J McReynolds
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Youjin Wang
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Belynda Hicks
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland; Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Kristine Jones
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland; Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Stephen R Spellman
- Center for International Blood and Marrow Transplant Research, National Marrow Donor Program, Minneapolis, Minnesota
| | - Meilun He
- Center for International Blood and Marrow Transplant Research, National Marrow Donor Program, Minneapolis, Minnesota
| | - Yung-Tsi Bolon
- Center for International Blood and Marrow Transplant Research, National Marrow Donor Program, Minneapolis, Minnesota
| | - Esteban Arrieta-Bolaños
- Institute for Experimental Cellular Therapy, University Hospital Essen, Essen, Germany; German Cancer Consortium (DKTK), partner site Essen/Düsseldorf, Heidelberg, Germany
| | - Jennifer N Saultz
- Division of Hematology/Medical Oncology, Oregon Health & Science University, Portland, Oregon
| | - Stephanie J Lee
- Center for International Blood and Marrow Transplant Research, Medical College of Wisconsin, Milwaukee, Wisconsin; Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Sharon A Savage
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Shahinaz M Gadalla
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
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Deng J, Altintas B, Haley JS, Kim J, Ramos M, Carey DJ, Stewart DR, McReynolds LJ. Most Fanconi anemia heterozygotes are not at increased cancer risk: A genome-first DiscovEHR cohort population study. Genet Med 2024; 26:101042. [PMID: 38063144 PMCID: PMC10939803 DOI: 10.1016/j.gim.2023.101042] [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: 06/22/2023] [Revised: 12/01/2023] [Accepted: 12/01/2023] [Indexed: 01/23/2024] Open
Abstract
PURPOSE Fanconi anemia (FA) is a bone marrow failure and cancer predisposition syndrome caused primarily by biallelic pathogenic variants in 1 of 22 genes involved in DNA interstrand cross-link repair. An enduring question concerns cancer risk of those with a single pathogenic FA gene variant. To investigate all FA genes, this study utilized the DiscovEHR cohort of 170,503 individuals with exome sequencing and electronic health data. METHODS 5822 subjects with a single pathogenic variant in an FA gene were identified. Two control groups were used in primary analysis deriving cancer risk signals. Secondary exploratory analysis was conducted using the UK Biobank and The Cancer Genome Atlas. RESULTS Signals for elevated cancer risk were found in all 5 known cancer predisposition genes. Among the remaining 15 genes associated with autosomal recessive inheritance cancer risk signals were found for 4 cancers across 3 genes in the primary cohort but were not validated in secondary cohorts. CONCLUSION To our knowledge, this is the first and largest FA heterozygote study to use genomic ascertainment and validates well-established cancer predispositions in 5 genes, whereas finding insufficient evidence of predisposition in 15 others. Our findings inform clinical surveillance given how common pathogenic FA variants are in the population.
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Affiliation(s)
- Joseph Deng
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD
| | - Burak Altintas
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD; Washington University, St. Louis Children's Hospital, St. Louis, MO
| | - Jeremy S Haley
- Department of Genomic Health, Weis Center for Research, Geisinger Medical Center, Danville, PA
| | - Jung Kim
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD
| | - Mark Ramos
- Biostatistics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD
| | - David J Carey
- Department of Genomic Health, Weis Center for Research, Geisinger Medical Center, Danville, PA
| | - Douglas R Stewart
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD
| | - Lisa J McReynolds
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD.
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Kocagil S, Şafak İN, Saraç E, Aydın C, Artan S, Kırel B. Further Evidence for RFWD3 Gene Causing Fanconi Anemia Complementation Group W: Detailed Clinical Report of the Second Case in the Literature. Mol Syndromol 2023; 14:509-515. [PMID: 38058754 PMCID: PMC10697762 DOI: 10.1159/000531429] [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: 05/17/2022] [Accepted: 06/03/2023] [Indexed: 12/08/2023] Open
Abstract
Introduction Fanconi anemia (FA) is a heterogeneous genetic disorder that is characterized by progressive bone marrow failure, congenital malformations, predisposition to malignancy, and short stature. The RFWD3 gene was recently associated with FA complementation group W, and only 1 patient is reported in the literature so far. Case Presentation Here, we report the second patient, a 10-year-old male, who has failure to thrive, central nervous system abnormalities, bilateral radial ray defects, urogenital anomalies, facial dysmorphism, and thrombocytopenia. The patient was suspected to have FA according to the aforementioned findings, and the homozygous c.1501C>T variant in the RFWD3 gene was detected by whole-exome sequencing. The diepoxybutane test and mitomycin C-induced peripheral blood cultures revealed 0.46 and 0.90 chromosomal breaks, respectively. Conclusion In this article, clinical findings of the second patient with FA complementation group W are discussed in detail, aiming to expand the clinical and molecular spectrums of the disease.
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Affiliation(s)
- Sinem Kocagil
- Department of Medical Genetics, Faculty of Medicine, Eskisehir Osmangazi University, Eskisehir, Turkey
| | - İkbal Nur Şafak
- Department of Pediatrics, Faculty of Medicine, Eskisehir Osmangazi University, Eskisehir, Turkey
| | - Elif Saraç
- Department of Medical Genetics, Faculty of Medicine, Eskisehir Osmangazi University, Eskisehir, Turkey
| | - Can Aydın
- Department of Pediatrics, Faculty of Medicine, Eskisehir Osmangazi University, Eskisehir, Turkey
| | - Sevilhan Artan
- Department of Medical Genetics, Faculty of Medicine, Eskisehir Osmangazi University, Eskisehir, Turkey
| | - Birgül Kırel
- Department of Pediatrics, Faculty of Medicine, Eskisehir Osmangazi University, Eskisehir, Turkey
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Fink O, Even-Or E, Avni B, Grisariu S, Zaidman I, Schejter YD, NaserEddin A, Najajreh M, Stepensky P. Two decades of stem cell transplantation in patients with Fanconi anemia: Analysis of factors affecting transplant outcomes. Clin Transplant 2023; 37:e14835. [PMID: 36259220 PMCID: PMC10078339 DOI: 10.1111/ctr.14835] [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: 07/23/2022] [Revised: 10/10/2022] [Accepted: 10/11/2022] [Indexed: 01/18/2023]
Abstract
Allogeneic hematopoietic stem cell transplantation (HSCT) is currently the only curative treatment for the hematological complications of patients with Fanconi anemia (FA). Over the last two decades, HSCT outcomes have improved dramatically following the development of regimens tailored for FA patients. In this study, we analyzed genetic, clinical, and transplant data of 41 patients with FA who underwent HSCT at Hadassah Medical Center between November 1996 and September 2020. Overall survival (OS) was 82.9% with a median follow-up time of 2.11-years (95% CI, .48-16.56). Thirteen patients (31.7%) developed acute graft-versus-host disease (GVHD), three of them with grades 3-4. Nine patients developed chronic GVHD, five had extensive disease. Twelve patients (29.3%) developed stable mixed-chimerism with complete resolution of bone marrow failure (BMF); none of them had acute nor chronic GVHD. Significantly higher GVHD rates were observed in transplants from peripheral blood stem cell grafts as compared to other stem cell sources (p = .002 for acute and p = .004 for chronic GVHD). Outcome parameters were comparable between HSCT from matched-sibling (n = 20) to other donors (n = 21), including survival rates (p = .1), time to engraftment (p = .69 and p = .14 for neutrophil and platelet engraftment time, respectively), chimerism status (p = .36 and p = .83 for full-donor and mixed chimerism, respectively), and GVHD prevalence (p = 1). Our results demonstrate the vast improvements in HSCT outcomes of patients with FA, narrowing the gap between matched-sibling versus alternative donor transplantations. Our data identifies factors that may significantly affect transplant outcomes such as graft source and chimerism status.
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Affiliation(s)
- Orly Fink
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Ehud Even-Or
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.,Department of Bone Marrow Transplantation and Cancer Immunotherapy, Hadassah Medical Center, Jerusalem, Israel
| | - Batia Avni
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.,Department of Bone Marrow Transplantation and Cancer Immunotherapy, Hadassah Medical Center, Jerusalem, Israel
| | - Sigal Grisariu
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.,Department of Bone Marrow Transplantation and Cancer Immunotherapy, Hadassah Medical Center, Jerusalem, Israel
| | - Irina Zaidman
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.,Department of Bone Marrow Transplantation and Cancer Immunotherapy, Hadassah Medical Center, Jerusalem, Israel
| | - Yael Dinur Schejter
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.,Department of Bone Marrow Transplantation and Cancer Immunotherapy, Hadassah Medical Center, Jerusalem, Israel
| | - Adeeb NaserEddin
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.,Department of Bone Marrow Transplantation and Cancer Immunotherapy, Hadassah Medical Center, Jerusalem, Israel
| | - Mohammad Najajreh
- The Huda Al Masri Pediatric Cancer Department, Beit Jala Hospital, Beit Jala, Palestine
| | - Polina Stepensky
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.,Department of Bone Marrow Transplantation and Cancer Immunotherapy, Hadassah Medical Center, Jerusalem, Israel
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McReynolds LJ, Rafati M, Wang Y, Ballew BJ, Kim J, Williams VV, Zhou W, Hendricks RM, Dagnall C, Freedman ND, Carter B, Strollo S, Hicks B, Zhu B, Jones K, Paczesny S, Marsh SGE, Spellman SR, He M, Wang T, Lee SJ, Savage SA, Gadalla SM. Genetic testing in severe aplastic anemia is required for optimal hematopoietic cell transplant outcomes. Blood 2022; 140:909-921. [PMID: 35776903 PMCID: PMC9412004 DOI: 10.1182/blood.2022016508] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 06/17/2022] [Indexed: 11/20/2022] Open
Abstract
Patients with severe aplastic anemia (SAA) can have an unrecognized inherited bone marrow failure syndrome (IBMFS) because of phenotypic heterogeneity. We curated germline genetic variants in 104 IBMFS-associated genes from exome sequencing performed on 732 patients who underwent hematopoietic cell transplant (HCT) between 1989 and 2015 for acquired SAA. Patients with pathogenic or likely pathogenic (P/LP) variants fitting known disease zygosity patterns were deemed unrecognized IBMFS. Carriers were defined as patients with a single P/LP variant in an autosomal recessive gene or females with an X-linked recessive P/LP variant. Cox proportional hazard models were used for survival analysis with follow-up until 2017. We identified 113 P/LP single-nucleotide variants or small insertions/deletions and 10 copy number variants across 42 genes in 121 patients. Ninety-one patients had 105 in silico predicted deleterious variants of uncertain significance (dVUS). Forty-eight patients (6.6%) had an unrecognized IBMFS (33% adults), and 73 (10%) were carriers. No survival difference between dVUS and acquired SAA was noted. Compared with acquired SAA (no P/LP variants), patients with unrecognized IBMFS, but not carriers, had worse survival after HCT (IBMFS hazard ratio [HR], 2.13; 95% confidence interval[CI], 1.40-3.24; P = .0004; carriers HR, 0.96; 95% CI, 0.62-1.50; P = .86). Results were similar in analyses restricted to patients receiving reduced-intensity conditioning (n = 448; HR IBMFS = 2.39; P = .01). The excess mortality risk in unrecognized IBMFS attributed to death from organ failure (HR = 4.88; P < .0001). Genetic testing should be part of the diagnostic evaluation for all patients with SAA to tailor therapeutic regimens. Carriers of a pathogenic variant in an IBMFS gene can follow HCT regimens for acquired SAA.
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Affiliation(s)
| | | | | | - Bari J Ballew
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD
| | | | | | - Weiyin Zhou
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD
| | | | - Casey Dagnall
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Neal D Freedman
- Metabolic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
| | - Brian Carter
- Department of Population Science, American Cancer Society, Atlanta, GA
| | - Sara Strollo
- Department of Population Science, American Cancer Society, Atlanta, GA
| | - Belynda Hicks
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Bin Zhu
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Kristine Jones
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD
| | - Sophie Paczesny
- Department of Microbiology and Immunology, Medical University of South Carolina, Charleston, SC
| | - Steven G E Marsh
- Anthony Nolan Research Institute and University College London Cancer Institute, London, United Kingdom
| | - Stephen R Spellman
- Center for International Blood and Marrow Transplant Research, National Marrow Donor Program, Minneapolis, MN
| | - Meilun He
- Center for International Blood and Marrow Transplant Research, National Marrow Donor Program, Minneapolis, MN
| | - Tao Wang
- Center for International Blood and Marrow Transplant Research and
- Division of Biostatistics, Medical College of Wisconsin, Milwaukee, WI; and
| | - Stephanie J Lee
- Center for International Blood and Marrow Transplant Research and
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
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McReynolds LJ, Biswas K, Giri N, Sharan SK, Alter BP. Genotype-cancer association in patients with Fanconi anemia due to pathogenic variants in FANCD1 (BRCA2) or FANCN (PALB2). Cancer Genet 2021; 258-259:101-109. [PMID: 34687993 DOI: 10.1016/j.cancergen.2021.10.001] [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: 03/02/2021] [Revised: 08/28/2021] [Accepted: 10/02/2021] [Indexed: 02/07/2023]
Abstract
Fanconi anemia (FA) is the most common inherited bone marrow failure syndrome and a cancer predisposition disorder. Cancers in FA include acute leukemia and solid tumors; the most frequent solid tumor is head and neck squamous cell carcinoma. FA is a primarily autosomal recessive disorder. Several of the genes in which biallelic pathogenic variants cause FA are also autosomal monoallelic cancer predisposition genes e.g. FANCD1 (BRCA2) and FANCN (PALB2). We observed that patients with FA due to biallelic or homozygous pathogenic variants in FANCD1 and FANCN have a unique cancer association. We curated published cases plus our NCI cohort cases, including 71 patients in the FANCD1 group (94 cancers and 69 variants) and 16 patients in the FANCN group (23 cancers and 20 variants). Only patients in FANCD1 and FANCN groups had one or more of these tumors: brain tumors (primarily medulloblastoma), Wilms tumor and neuroblastoma; this is a genotype-specific cancer combination of tumors of embryonal origin. Acute leukemias, seen in all FA genotypes, also occurred in FANCD1 and FANCN group patients at young ages. In silico predictions of pathogenicity for FANCD1 variants were compared with results from a mouse embryonic stem cell-based functional assay. Patients with two null FANCD1 variants did not have an increased frequency of cancer nor earlier onset of cancer compared with those with hypomorphic variants. Patients with FA and these specific cancers should consider genetic testing focused on FANCD1 and FANCN, and patients with these genotypes may consider ongoing surveillance for these specific cancers.
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Affiliation(s)
- Lisa J McReynolds
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA.
| | - Kajal Biswas
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Neelam Giri
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Shyam K Sharan
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, USA
| | - Blanche P Alter
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
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