Copy Number Variants Are Ovarian Cancer Risk Alleles at Known and Novel Risk Loci.


Journal

Journal of the National Cancer Institute
ISSN: 1460-2105
Titre abrégé: J Natl Cancer Inst
Pays: United States
ID NLM: 7503089

Informations de publication

Date de publication:
14 11 2022
Historique:
received: 28 01 2022
revised: 13 04 2022
accepted: 18 08 2022
pubmed: 11 10 2022
medline: 18 11 2022
entrez: 10 10 2022
Statut: ppublish

Résumé

Known risk alleles for epithelial ovarian cancer (EOC) account for approximately 40% of the heritability for EOC. Copy number variants (CNVs) have not been investigated as EOC risk alleles in a large population cohort. Single nucleotide polymorphism array data from 13 071 EOC cases and 17 306 controls of White European ancestry were used to identify CNVs associated with EOC risk using a rare admixture maximum likelihood test for gene burden and a by-probe ratio test. We performed enrichment analysis of CNVs at known EOC risk loci and functional biofeatures in ovarian cancer-related cell types. We identified statistically significant risk associations with CNVs at known EOC risk genes; BRCA1 (PEOC = 1.60E-21; OREOC = 8.24), RAD51C (Phigh-grade serous ovarian cancer [HGSOC] = 5.5E-4; odds ratio [OR]HGSOC = 5.74 del), and BRCA2 (PHGSOC = 7.0E-4; ORHGSOC = 3.31 deletion). Four suggestive associations (P < .001) were identified for rare CNVs. Risk-associated CNVs were enriched (P < .05) at known EOC risk loci identified by genome-wide association study. Noncoding CNVs were enriched in active promoters and insulators in EOC-related cell types. CNVs in BRCA1 have been previously reported in smaller studies, but their observed frequency in this large population-based cohort, along with the CNVs observed at BRCA2 and RAD51C gene loci in EOC cases, suggests that these CNVs are potentially pathogenic and may contribute to the spectrum of disease-causing mutations in these genes. CNVs are likely to occur in a wider set of susceptibility regions, with potential implications for clinical genetic testing and disease prevention.

Sections du résumé

BACKGROUND
Known risk alleles for epithelial ovarian cancer (EOC) account for approximately 40% of the heritability for EOC. Copy number variants (CNVs) have not been investigated as EOC risk alleles in a large population cohort.
METHODS
Single nucleotide polymorphism array data from 13 071 EOC cases and 17 306 controls of White European ancestry were used to identify CNVs associated with EOC risk using a rare admixture maximum likelihood test for gene burden and a by-probe ratio test. We performed enrichment analysis of CNVs at known EOC risk loci and functional biofeatures in ovarian cancer-related cell types.
RESULTS
We identified statistically significant risk associations with CNVs at known EOC risk genes; BRCA1 (PEOC = 1.60E-21; OREOC = 8.24), RAD51C (Phigh-grade serous ovarian cancer [HGSOC] = 5.5E-4; odds ratio [OR]HGSOC = 5.74 del), and BRCA2 (PHGSOC = 7.0E-4; ORHGSOC = 3.31 deletion). Four suggestive associations (P < .001) were identified for rare CNVs. Risk-associated CNVs were enriched (P < .05) at known EOC risk loci identified by genome-wide association study. Noncoding CNVs were enriched in active promoters and insulators in EOC-related cell types.
CONCLUSIONS
CNVs in BRCA1 have been previously reported in smaller studies, but their observed frequency in this large population-based cohort, along with the CNVs observed at BRCA2 and RAD51C gene loci in EOC cases, suggests that these CNVs are potentially pathogenic and may contribute to the spectrum of disease-causing mutations in these genes. CNVs are likely to occur in a wider set of susceptibility regions, with potential implications for clinical genetic testing and disease prevention.

Identifiants

pubmed: 36210504
pii: 6751998
doi: 10.1093/jnci/djac160
pmc: PMC9949586
doi:

Types de publication

Journal Article Research Support, N.I.H., Intramural Research Support, N.I.H., Extramural Research Support, U.S. Gov't, Non-P.H.S. Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

1533-1544

Subventions

Organisme : NCI NIH HHS
ID : P01 CA017054
Pays : United States
Organisme : NCI NIH HHS
ID : UM1 CA176726
Pays : United States
Organisme : NCI NIH HHS
ID : R01 CA058860
Pays : United States
Organisme : NCI NIH HHS
ID : P50 CA105009
Pays : United States
Organisme : NIH HHS
ID : R01-CA122443
Pays : United States
Organisme : Wellcome Trust
ID : 076113
Pays : United Kingdom
Organisme : Medical Research Council
ID : G0401527
Pays : United Kingdom
Organisme : NCI NIH HHS
ID : U19-CA148112
Pays : United States
Organisme : NCI NIH HHS
ID : N01 CN025403
Pays : United States
Organisme : Intramural NIH HHS
ID : Z01 ES049033
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Organisme : NCI NIH HHS
ID : P50 CA136393
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Organisme : Cancer Research UK
ID : C490/A10119 C490/A10124
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Organisme : Medical Research Council
ID : 1000143
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Investigateurs

P Webb (P)
A DeFazio (A)
M Friedlander (M)
A Obermair (A)
P Grant (P)
C Nagle (C)
V Beesley (V)
G Chevenix-Trench (G)
D Bowtell (D)
P Blomfield (P)
A Brand (A)
A Davis (A)
Y Leung (Y)
J Nicklin (J)
M Quinn (M)
K Livingstone (K)
H O'Neill (H)
M Williams (M)
A Black (A)
A Hadley (A)
A Glasgow (A)
A Garrett (A)
A Rao (A)
C Shannon (C)
C Steer (C)
D Allen (D)
D Neesham (D)
G Otton (G)
G Au-Yeung (G)
G Goss (G)
G Wain (G)
G Gard (G)
G Robertson (G)
J Lombard (J)
J Tan (J)
J McNeilage (J)
J Power (J)
J Coward (J)
J Miller (J)
J Carter (J)
J Lamont (J)
K M Wong (KM)
K Reid (K)
L Perrin (L)
L Milishkin (L)
M Nascimento (M)
M Buck (M)
M Bunting (M)
M Harrison (M)
N Chetty (N)
N Hacker (N)
O McNally (O)
P Harnett (P)
P Beale (P)
R Awad (R)
R Mohan (R)
R Farrell (R)
R McIntosh (R)
R Rome (R)
R Sayer (R)
R Houghton (R)
R Hogg (R)
R Land (R)
S Baron-Hay (S)
S Paramasivum (S)
S Pather (S)
S Hyde (S)
S Salfinger (S)
S Valmadre (S)
T Jobling (T)
T Manolitsas (T)
T Bonaventura (T)
V Arora (V)
D Bowtell (D)
G Chenevix-Trench (G)
A Green (A)
P Webb (P)
A DeFazio (A)
D Gertig (D)
N Traficante (N)
S Fereday (S)
S Moore (S)
J Hung (J)
K Harrap (K)
T Sadkowsky (T)
N Pandeya (N)
M Malt (M)
R Robertson (R)
T Vanden Bergh (TV)
M Jones (M)
P McKenzie (P)
J Maidens (J)
K Nattress (K)
Y E Chiew (YE)
A Stenlake (A)
H Sullivan (H)
B Alexander (B)
P Ashover (P)
S Brown (S)
T Corrish (T)
L Green (L)
L Jackman (L)
K Ferguson (K)
K Martin (K)
A Martyn (A)
B Ranieri (B)
J White (J)
V Jayde (V)
L Bowes (L)
P Mamers (P)
L Galletta (L)
D Giles (D)
J Hendley (J)
K Alsop (K)
T Schmidt (T)
H Shirley (H)
C Ball (C)
C Young (C)
S Viduka (S)
H Tran (H)
S Bilic (S)
L Glavinas (L)
J Brooks (J)
R Stuart-Harris (R)
F Kirsten (F)
J Rutovitz (J)
P Clingan (P)
A Glasgow (A)
A Proietto (A)
S Braye (S)
G Otton (G)
J Shannon (J)
T Bonaventura (T)
J Stewart (J)
S Begbie (S)

Informations de copyright

© The Author(s) 2022. Published by Oxford University Press.

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Auteurs

Amber A DeVries (AA)

Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA.

Joe Dennis (J)

Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.

Jonathan P Tyrer (JP)

Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK.

Pei-Chen Peng (PC)

Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA.

Simon G Coetzee (SG)

Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA.

Alberto L Reyes (AL)

Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA.

Jasmine T Plummer (JT)

Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
Applied Genomics, Computation and Translational Core, Cedars-Sinai Medical Center, Los Angeles, CA, USA.

Brian D Davis (BD)

Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
Applied Genomics, Computation and Translational Core, Cedars-Sinai Medical Center, Los Angeles, CA, USA.

Stephanie S Chen (SS)

Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
Applied Genomics, Computation and Translational Core, Cedars-Sinai Medical Center, Los Angeles, CA, USA.

Felipe Segato Dezem (FS)

Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA.

Katja K H Aben (KKH)

Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.
Netherlands Comprehensive Cancer Organisation, Utrecht, The Netherlands.

Hoda Anton-Culver (H)

Department of Medicine, Genetic Epidemiology Research Institute, University of California Irvine, Irvine, CA, USA.

Natalia N Antonenkova (NN)

N.N. Alexandrov Research Institute of Oncology and Medical Radiology, Minsk, Belarus.

Matthias W Beckmann (MW)

Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-European Metropolitan Region of Nuremberg, Friedrich-Alexander University Erlangen-Nuremberg, University Hospital Erlangen, Erlangen, Germany.

Alicia Beeghly-Fadiel (A)

Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA.

Andrew Berchuck (A)

Department of Gynecologic Oncology, Duke University Hospital, Durham, NC, USA.

Natalia V Bogdanova (NV)

N.N. Alexandrov Research Institute of Oncology and Medical Radiology, Minsk, Belarus.
Department of Radiation Oncology, Hannover Medical School, Hannover, Germany.
Gynaecology Research Unit, Hannover Medical School, Hannover, Germany.

Nadja Bogdanova-Markov (N)

Institute of Human Genetics, University of Münster, Münster, Germany.

James D Brenton (JD)

Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.

Ralf Butzow (R)

Department of Pathology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland.

Ian Campbell (I)

Cancer Genetics Laboratory, Research Division, Peter MacCallum Cancer Center, Melbourne, Victoria, Australia.
Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia.

Jenny Chang-Claude (J)

Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany.
Cancer Epidemiology Group, University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany.

Georgia Chenevix-Trench (G)

Department of Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.

Linda S Cook (LS)

Epidemiology, School of Public Health, University of Colorado, Aurora, CO, USA.
Community Health Sciences, University of Calgary, Calgary, AB, Canada.

Anna DeFazio (A)

Centre for Cancer Research, The Westmead Institute for Medical Research, Sydney, New South Wales, Australia.
Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia.
The Daffodil Centre, a joint venture with Cancer Council NSW, The University of Sydney, Sydney, New South Wales, Australia.

Jennifer A Doherty (JA)

Huntsman Cancer Institute, Department of Population Health Sciences, University of Utah, Salt Lake City, UT, USA.

Thilo Dörk (T)

Gynaecology Research Unit, Hannover Medical School, Hannover, Germany.

Diana M Eccles (DM)

Faculty of Medicine, University of Southampton, Southampton, UK.

A Heather Eliassen (AH)

Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA.

Peter A Fasching (PA)

Department of Gynecology and Obstetrics, Comprehensive Cancer Center Erlangen-European Metropolitan Region of Nuremberg, Friedrich-Alexander University Erlangen-Nuremberg, University Hospital Erlangen, Erlangen, Germany.
David Geffen School of Medicine, Department of Medicine Division of Hematology and Oncology, University of California at Los Angeles, Los Angeles, CA, USA.

Renée T Fortner (RT)

Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany.

Graham G Giles (GG)

Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia.
Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia.
Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia.

Ellen L Goode (EL)

Department of Quantitative Health Sciences, Division of Epidemiology, Mayo Clinic, Rochester, MN, USA.

Marc T Goodman (MT)

Samuel Oschin Comprehensive Cancer Institute, Cancer Prevention and Genetics Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA.

Jacek Gronwald (J)

Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland.

Niclas Håkansson (N)

Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.

Michelle A T Hildebrandt (MAT)

Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA.

Chad Huff (C)

Department of Epidemiology, University of Texas MD Anderson Cancer Center, Houston, TX, USA.

David G Huntsman (DG)

Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, BC, Canada.
Department of Molecular Oncology, BC Cancer Research Centre, Vancouver, BC, Canada.

Allan Jensen (A)

Department of Lifestyle, Reproduction and Cancer, Danish Cancer Society Research Center, Copenhagen, Denmark.

Siddhartha Kar (S)

Medical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK.
Section of Translational Epidemiology, Division of Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.

Beth Y Karlan (BY)

David Geffen School of Medicine, Department of Obstetrics and Gynecology, University of California at Los Angeles, Los Angeles, CA, USA.

Elza K Khusnutdinova (EK)

Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia.
Saint Petersburg State University, Saint Petersburg, Russia.

Lambertus A Kiemeney (LA)

Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, The Netherlands.

Susanne K Kjaer (SK)

Department of Lifestyle, Reproduction and Cancer, Danish Cancer Society Research Center, Copenhagen, Denmark.
Department of Gynaecology, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark.

Jolanta Kupryjanczyk (J)

Department of Pathology and Laboratory Diagnostics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland.

Marilyne Labrie (M)

Knight Cancer Institute, Oregon Health & Science University, Portland, OR, USA.

Diether Lambrechts (D)

VIB Center for Cancer Biology, VIB, Leuven, Belgium.
Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium.

Nhu D Le (ND)

Cancer Control Research, BC Cancer, Vancouver, BC, Canada.

Jan Lubiński (J)

Department of Genetics and Pathology, Pomeranian Medical University, Szczecin, Poland.

Taymaa May (T)

Division of Gynecologic Oncology, University Health Network, Princess Margaret Hospital, Toronto, Ontario, Canada.

Usha Menon (U)

MRC Clinical Trials Unit, Institute of Clinical Trials & Methodology, University College London, London, UK.

Roger L Milne (RL)

Cancer Epidemiology Division, Cancer Council Victoria, Melbourne, Victoria, Australia.
Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia.
Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, Victoria, Australia.

Francesmary Modugno (F)

Women's Cancer Research Center, Magee-Womens Research Institute and Hillman Cancer Center, Pittsburgh, PA, USA.
Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.

Alvaro N Monteiro (AN)

Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA.

Kirsten B Moysich (KB)

Department of Cancer Prevention and Control, Roswell Park Cancer Institute, Buffalo, NY, USA.

Kunle Odunsi (K)

Department of Oncology, University of Chicago Medicine Comprehensive Cancer Center, Chicago, IL, USA.
Department of Obstetrics and Gynecology, University of Chicago Medicine Comprehensive Cancer Center, Chicago, IL, USA.

Håkan Olsson (H)

Oncology, Department of Clinical Sciences, Lund University, Lund, Sweden.

Celeste L Pearce (CL)

Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MI, USA.
Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA, USA.

Tanja Pejovic (T)

Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium.
Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, OR, USA.

Susan J Ramus (SJ)

School of Women's and Children's Health, Faculty of Medicine and Health, University of NSW Sydney, Sydney, New South Wales, Australia.
Adult Cancer Program, Lowy Cancer Research Centre, University of NSW Sydney, Sydney, New South Wales, Australia.

Elio Riboli (E)

Imperial College London, London, UK.

Marjorie J Riggan (MJ)

Department of Gynecologic Oncology, Duke University Hospital, Durham, NC, USA.

Isabelle Romieu (I)

Nutrition and Metabolism Section, International Agency for Research on Cancer (IARC-WHO), Lyon, France.

Dale P Sandler (DP)

Epidemiology Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA.

Joellen M Schildkraut (JM)

Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA.

V Wendy Setiawan (VW)

Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.

Weiva Sieh (W)

Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.

Honglin Song (H)

Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.

Rebecca Sutphen (R)

Epidemiology Center, College of Medicine, University of South Florida, Tampa, FL, USA.

Kathryn L Terry (KL)

Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.
Obstetrics and Gynecology Epidemiology Center, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.

Pamela J Thompson (PJ)

Samuel Oschin Comprehensive Cancer Institute, Cancer Prevention and Genetics Program, Cedars-Sinai Medical Center, Los Angeles, CA, USA.

Linda Titus (L)

Muskie School of Public Policy, Public Health, Portland, ME, USA.

Shelley S Tworoger (SS)

Department of Cancer Epidemiology, Moffitt Cancer Center, Tampa, FL, USA.

Els Van Nieuwenhuysen (E)

Division of Gynecologic Oncology, Department of Gynecology and Obstetrics, Leuven Cancer Institute, Leuven, Belgium.

Digna Velez Edwards (DV)

Division of Quantitative Sciences, Department of Obstetrics and Gynecology, Department of Biomedical Sciences, Women's Health Research, Vanderbilt University Medical Center, Nashville, TN, USA.

Penelope M Webb (PM)

Population Health Department, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia.

Nicolas Wentzensen (N)

Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA.

Alice S Whittemore (AS)

Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, USA.
Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA, USA.

Alicja Wolk (A)

Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.
Department of Surgical Sciences, Uppsala University, Uppsala, Sweden.

Anna H Wu (AH)

Department of Preventive Medicine, Keck School of Medicine, University of Southern California Norris Comprehensive Cancer Center, Los Angeles, CA, USA.

Argyrios Ziogas (A)

Department of Medicine, Genetic Epidemiology Research Institute, University of California Irvine, Irvine, CA, USA.

Matthew L Freedman (ML)

Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.

Kate Lawrenson (K)

Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Women's Cancer Program at the Samuel Oschin Cancer Institute Cedars-Sinai Medical Center, Los Angeles, CA, USA.

Paul D P Pharoah (PDP)

Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK.

Douglas F Easton (DF)

Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK.

Simon A Gayther (SA)

Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA.

Michelle R Jones (MR)

Center for Bioinformatics and Functional Genomics, Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA.

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