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Grant Details

Grant Number: 5U01HG006485-06 Interpret this number
Primary Investigator: Plon, Sharon
Organization: Baylor College Of Medicine
Project Title: Evaluating Utility and Improving Implementation of Genomic Sequencing for Pediatric Cancer Patients in the Diverse Population and Healthcare Settings of Texas: the Kidscanseq Study
Fiscal Year: 2018
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Abstract

Through this Clinical Sequencing Evidence-Generating Research (CSER2) with Enhanced Diversity project we will complete a trial (The Texas KidsCanSeq Study) comparing the results of targeted cancer panel sequencing versus genome-scale testing in pediatric cancer patients across diverse clinical settings. We will compare the targeted cancer panel to germline whole exome sequencing (WES) of unselected childhood cancer patients (n=1100) and WES, transcriptome sequencing and copy number array of FFPE tumor samples for the subset of patients with high-risk tumors (n=360). We will build on our success completing the CSER program BASIC3 exome sequencing trial (which included 60% Hispanic and African-American patients from a single large academic center) in this large multi-institutional study of an even more diverse patient population from five heterogeneous healthcare settings across Texas. The trial will be led by an experienced multi-PI team of Drs. Plon (medical geneticist), Parsons (pediatric oncologist) and McGuire (ethicist and health policy expert). We will assess clinical utility of these tests by measuring the frequency of diagnostic and/or actionable germline and tumor findings and the effect on treatment decisions (Aim 1). We will compare uptake by first degree relatives for familial genetic testing and recommended cancer surveillance by race, ethnicity and clinical settings (Aim 2). We will describe perceived utility (clinical, psychological, and pragmatic) by surveying and interviewing parents and participating pediatric oncologists (n=40) (Aim 3). Working with our pediatric cancer stakeholders, including advocates, BASIC3 study parents, and national organizations, we will create and evaluate the use of culturally sensitive educational materials, including videos in English and Spanish, improved integrated genomic test reports and counseling materials, and will compare in-person versus telemedicine exome results disclosure (Aim 4). Finally, we will provide data to guide future application of clinical genomics through three innovative pilot projects focused on health economics, decision support for cancer surveillance and whole genome sequencing (Aim 5). Baylor College of Medicine, Texas Children?s Hospital, and our partner institutions across the state are ideally suited to conduct this study and play leadership roles in CSER2 consortium activities based on our longstanding pediatric oncology and cancer genetics expertise, extensive experience in CLIA-certified clinical germline and cancer genomic diagnostic testing, and a track record of scholarship in ethical and social implications of genomics and health disparities research.

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Publications

The Clinical Sequencing Evidence-Generating Research Consortium: Integrating Genomic Sequencing in Diverse and Medically Underserved Populations.
Authors: Amendola L.M. , Berg J.S. , Horowitz C.R. , Angelo F. , Bensen J.T. , Biesecker B.B. , Biesecker L.G. , Cooper G.M. , East K. , Filipski K. , et al. .
Source: American Journal Of Human Genetics, 2018-09-06 00:00:00.0; 103(3), p. 319-327.
PMID: 30193136
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Why Patients Decline Genomic Sequencing Studies: Experiences from the CSER Consortium.
Authors: Amendola L.M. , Robinson J.O. , Hart R. , Biswas S. , Lee K. , Bernhardt B.A. , East K. , Gilmore M.J. , Kauffman T.L. , Lewis K.L. , et al. .
Source: Journal Of Genetic Counseling, 2018-03-01 00:00:00.0; , .
EPub date: 2018-03-01 00:00:00.0.
PMID: 29497922
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Anticipated responses of early adopter genetic specialists and nongenetic specialists to unsolicited genomic secondary findings.
Authors: Christensen K.D. , Bernhardt B.A. , Jarvik G.P. , Hindorff L.A. , Ou J. , Biswas S. , Powell B.C. , Grundmeier R.W. , Machini K. , Karavite D.J. , et al. .
Source: Genetics In Medicine : Official Journal Of The American College Of Medical Genetics, 2018-02-01 00:00:00.0; , .
EPub date: 2018-02-01 00:00:00.0.
PMID: 29388940
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Characterizing reduced coverage regions through comparison of exome and genome sequencing data across 10 centers.
Authors: Sanghvi R.V. , Buhay C.J. , Powell B.C. , Tsai E.A. , Dorschner M.O. , Hong C.S. , Lebo M.S. , Sasson A. , Hanna D.S. , McGee S. , et al. .
Source: Genetics In Medicine : Official Journal Of The American College Of Medical Genetics, 2017-11-16 00:00:00.0; , .
EPub date: 2017-11-16 00:00:00.0.
PMID: 29144510
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Haploinsufficiency of the Chromatin Remodeler BPTF Causes Syndromic Developmental and Speech Delay, Postnatal Microcephaly, and Dysmorphic Features.
Authors: Stankiewicz P. , Khan T.N. , Szafranski P. , Slattery L. , Streff H. , Vetrini F. , Bernstein J.A. , Brown C.W. , Rosenfeld J.A. , Rednam S. , et al. .
Source: American Journal Of Human Genetics, 2017-10-05 00:00:00.0; 101(4), p. 503-515.
EPub date: 2017-09-21 00:00:00.0.
PMID: 28942966
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Navigating the research-clinical interface in genomic medicine: analysis from the CSER Consortium.
Authors: Wolf S.M. , Amendola L.M. , Berg J.S. , Chung W.K. , Clayton E.W. , Green R.C. , Harris-Wai J. , Henderson G.E. , Jarvik G.P. , Koenig B.A. , et al. .
Source: Genetics In Medicine : Official Journal Of The American College Of Medical Genetics, 2017-08-31 00:00:00.0; , .
EPub date: 2017-08-31 00:00:00.0.
PMID: 28858330
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Pediatric Cancer Predisposition and Surveillance: An Overview, and a Tribute to Alfred G. Knudson Jr.
Authors: Brodeur G.M. , Nichols K.E. , Plon S.E. , Schiffman J.D. , Malkin D. .
Source: Clinical Cancer Research : An Official Journal Of The American Association For Cancer Research, 2017-06-01 00:00:00.0; 23(11), p. e1-e5.
PMID: 28572261
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Precision medicine in pediatric oncology: Lessons learned and next steps.
Authors: Mody R.J. , Prensner J.R. , Everett J. , Parsons D.W. , Chinnaiyan A.M. .
Source: Pediatric Blood & Cancer, 2017 Mar; 64(3), .
EPub date: 2016-10-17 00:00:00.0.
PMID: 27748023
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Resolution Of Disease Phenotypes Resulting From Multilocus Genomic Variation
Authors: Posey J.E. , Harel T. , Liu P. , Rosenfeld J.A. , James R.A. , Coban Akdemir Z.H. , Walkiewicz M. , Bi W. , Xiao R. , Ding Y. , et al. .
Source: The New England Journal Of Medicine, 2017-01-05 00:00:00.0; 376(1), p. 21-31.
PMID: 27959697
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Somatic Cancer Variant Curation And Harmonization Through Consensus Minimum Variant Level Data
Authors: Ritter D.I. , Roychowdhury S. , Roy A. , Rao S. , Landrum M.J. , Sonkin D. , Shekar M. , Davis C.F. , Hart R.K. , Micheel C. , et al. .
Source: Genome Medicine, 2016-11-04 00:00:00.0; 8(1), p. 117.
PMID: 27814769
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A Survey Of Current Practices For Genomic Sequencing Test Interpretation And Reporting Processes In Us Laboratories
Authors: O'Daniel J.M. , McLaughlin H.M. , Amendola L.M. , Bale S.J. , Berg J.S. , Bick D. , Bowling K.M. , Chao E.C. , Chung W.K. , Conlin L.K. , et al. .
Source: Genetics In Medicine : Official Journal Of The American College Of Medical Genetics, 2016-11-03 00:00:00.0; , .
PMID: 27811861
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Renal Cell Carcinoma Harboring Somatic Tsc2 Mutations In A Child With Methylmalonic Acidemia
Authors: Potter S.L. , Venkatramani R. , Wenderfer S. , Graham B.H. , Vasudevan S.A. , Sher A. , Wu H. , Wheeler D.A. , Yang Y. , Eng C.M. , et al. .
Source: Pediatric Blood & Cancer, 2016-10-17 00:00:00.0; , .
PMID: 27748010
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Practical Considerations For Implementing Genomic Information Resources. Experiences From Emerge And Cser
Authors: Rasmussen L.V. , Overby C.L. , Connolly J. , Chute C.G. , Denny J.C. , Freimuth R. , Hartzler A.L. , Holm I.A. , Manzi S. , Pathak J. , et al. .
Source: Applied Clinical Informatics, 2016-09-21 00:00:00.0; 7(3), p. 870-82.
PMID: 27652374
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Novel patient-derived xenograft and cell line models for therapeutic testing of pediatric liver cancer.
Authors: Bissig-Choisat B. , Kettlun-Leyton C. , Legras X.D. , Zorman B. , Barzi M. , Chen L.L. , Amin M.D. , Huang Y.H. , Pautler R.G. , Hampton O.A. , et al. .
Source: Journal Of Hepatology, 2016 Aug; 65(2), p. 325-33.
EPub date: 2016-04-23 00:00:00.0.
PMID: 27117591
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Performance of ACMG-AMP Variant-Interpretation Guidelines among Nine Laboratories in the Clinical Sequencing Exploratory Research Consortium.
Authors: Amendola L.M. , Jarvik G.P. , Leo M.C. , McLaughlin H.M. , Akkari Y. , Amaral M.D. , Berg J.S. , Biswas S. , Bowling K.M. , Conlin L.K. , et al. .
Source: American Journal Of Human Genetics, 2016-07-07 00:00:00.0; 99(1), p. 247.
PMID: 27392081
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Clinical Sequencing Exploratory Research Consortium: Accelerating Evidence-Based Practice of Genomic Medicine.
Authors: Green R.C. , Goddard K.A. , Jarvik G.P. , Amendola L.M. , Appelbaum P.S. , Berg J.S. , Bernhardt B.A. , Biesecker L.G. , Biswas S. , Blout C.L. , et al. .
Source: American Journal Of Human Genetics, 2016-06-02 00:00:00.0; 98(6), p. 1051-66.
EPub date: 2016-06-02 00:00:00.0.
PMID: 27181682
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Performance of ACMG-AMP Variant-Interpretation Guidelines among Nine Laboratories in the Clinical Sequencing Exploratory Research Consortium.
Authors: Amendola L.M. , Jarvik G.P. , Leo M.C. , McLaughlin H.M. , Akkari Y. , Amaral M.D. , Berg J.S. , Biswas S. , Bowling K.M. , Conlin L.K. , et al. .
Source: American Journal Of Human Genetics, 2016-06-02 00:00:00.0; 98(6), p. 1067-76.
EPub date: 2016-06-02 00:00:00.0.
PMID: 27181684
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Germline Findings In Tumor-only Sequencing: Points To Consider For Clinicians And Laboratories
Authors: Raymond V.M. , Gray S.W. , Roychowdhury S. , Joffe S. , Chinnaiyan A.M. , Parsons D.W. , Plon S.E. , Clinical Sequencing Exploratory Research Consortium Tumor Working Group .
Source: Journal Of The National Cancer Institute, 2016 Apr; 108(4), .
PMID: 26590952
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Is Whole-exome Sequencing An Ethically Disruptive Technology? Perspectives Of Pediatric Oncologists And Parents Of Pediatric Patients With Solid Tumors
Authors: McCullough L.B. , Slashinski M.J. , McGuire A.L. , Street R.L. , Eng C.M. , Gibbs R.A. , Parsons D.W. , Plon S.E. .
Source: Pediatric Blood & Cancer, 2016 Mar; 63(3), p. 511-5.
PMID: 26505993
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"not Tied Up Neatly With A Bow": Professionals' Challenging Cases In Informed Consent For Genomic Sequencing
Authors: Tomlinson A.N. , Skinner D. , Perry D.L. , Scollon S.R. , Roche M.I. , Bernhardt B.A. .
Source: Journal Of Genetic Counseling, 2016 Feb; 25(1), p. 62-72.
PMID: 25911622
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Diagnostic Yield Of Clinical Tumor And Germline Whole-exome Sequencing For Children With Solid Tumors
Authors: Parsons D.W. , Roy A. , Yang Y. , Wang T. , Scollon S. , Bergstrom K. , Kerstein R.A. , Gutierrez S. , Petersen A.K. , Bavle A. , et al. .
Source: Jama Oncology, 2016-01-28 00:00:00.0; , .
PMID: 26822237
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When Participants in Genomic Research Grow Up: Contact and Consent at the Age of Majority.
Authors: Brothers K.B. , Holm I.A. , Childerhose J.E. , Antommaria A.H. , Bernhardt B.A. , Clayton E.W. , Gelb B.D. , Joffe S. , Lynch J.A. , McCormick J.B. , et al. .
Source: The Journal Of Pediatrics, 2016 Jan; 168, p. 226-31.e1.
PMID: 26477867
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Molecular Diagnostic Experience Of Whole-exome Sequencing In Adult Patients
Authors: Posey J.E. , Rosenfeld J.A. , James R.A. , Bainbridge M. , Niu Z. , Wang X. , Dhar S. , Wiszniewski W. , Akdemir Z.H. , Gambin T. , et al. .
Source: Genetics In Medicine : Official Journal Of The American College Of Medical Genetics, 2015-12-03 00:00:00.0; , .
PMID: 26633545
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Hepatocellular Carcinoma Associated With Tight-junction Protein 2 Deficiency
Authors: Zhou S. , Hertel P.M. , Finegold M.J. , Wang L. , Kerkar N. , Wang J. , Wong L.J. , Plon S.E. , Sambrotta M. , Foskett P. , et al. .
Source: Hepatology (baltimore, Md.), 2015 Dec; 62(6), p. 1914-6.
PMID: 25921221
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Experiences With Obtaining Informed Consent For Genomic Sequencing
Authors: Bernhardt B.A. , Roche M.I. , Perry D.L. , Scollon S.R. , Tomlinson A.N. , Skinner D. .
Source: American Journal Of Medical Genetics. Part A, 2015 Nov; 167A(11), p. 2635-46.
PMID: 26198374
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Professionally Responsible Disclosure Of Genomic Sequencing Results In Pediatric Practice
Authors: McCullough L.B. , Brothers K.B. , Chung W.K. , Joffe S. , Koenig B.A. , Wilfond B. , Yu J.H. , Clinical Sequencing Exploratory Research (CSER) Consortium Pediatrics Working Group .
Source: Pediatrics, 2015 Oct; 136(4), p. e974-82.
PMID: 26371191
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Pediatric Cancer Genetics Research And An Evolving Preventive Ethics Approach For Return Of Results After Death Of The Subject
Authors: Scollon S. , Bergstrom K. , McCullough L.B. , McGuire A.L. , Gutierrez S. , Kerstein R. , Parsons D.W. , Plon S.E. .
Source: The Journal Of Law, Medicine & Ethics : A Journal Of The American Society Of Law, Medicine & Ethics, 2015 Fall; 43(3), p. 529-37.
PMID: 26479562
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Bcor-ccnb3 Fusions Are Frequent In Undifferentiated Sarcomas Of Male Children
Authors: Peters T.L. , Kumar V. , Polikepahad S. , Lin F.Y. , Sarabia S.F. , Liang Y. , Wang W.L. , Lazar A.J. , Doddapaneni H. , Chao H. , et al. .
Source: Modern Pathology : An Official Journal Of The United States And Canadian Academy Of Pathology, Inc, 2015 Apr; 28(4), p. 575-86.
PMID: 25360585
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Actionable exomic incidental findings in 6503 participants: challenges of variant classification.
Authors: Amendola L.M. , Dorschner M.O. , Robertson P.D. , Salama J.S. , Hart R. , Shirts B.H. , Murray M.L. , Tokita M.J. , Gallego C.J. , Kim D.S. , et al. .
Source: Genome Research, 2015 Mar; 25(3), p. 305-15.
PMID: 25637381
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How Behavioral Economics Can Help To Avoid 'the Last Mile Problem' In Whole Genome Sequencing
Authors: Blumenthal-Barby J.S. , McGuire A.L. , Green R.C. , Ubel P.A. .
Source: Genome Medicine, 2015; 7(1), p. 3.
PMID: 25614766
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Illustrative case studies in the return of exome and genome sequencing results.
Authors: Amendola L.M. , Lautenbach D. , Scollon S. , Bernhardt B. , Biswas S. , East K. , Everett J. , Gilmore M.J. , Himes P. , Raymond V.M. , et al. .
Source: Personalized Medicine, 2015; 12(3), p. 283-295.
PMID: 26478737
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Recurrent Internal Tandem Duplications Of Bcor In Clear Cell Sarcoma Of The Kidney
Authors: Roy A. , Kumar V. , Zorman B. , Fang E. , Haines K.M. , Doddapaneni H. , Hampton O.A. , White S. , Bavle A.A. , Patel N.R. , et al. .
Source: Nature Communications, 2015; 6, p. 8891.
PMID: 26573325
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Molecular Findings Among Patients Referred For Clinical Whole-exome Sequencing
Authors: Yang Y. , Muzny D.M. , Xia F. , Niu Z. , Person R. , Ding Y. , Ward P. , Braxton A. , Wang M. , Buhay C. , et al. .
Source: Jama, 2014-11-12 00:00:00.0; 312(18), p. 1870-9.
PMID: 25326635
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Social and behavioral research in genomic sequencing: approaches from the Clinical Sequencing Exploratory Research Consortium Outcomes and Measures Working Group.
Authors: Gray S.W. , Martins Y. , Feuerman L.Z. , Bernhardt B.A. , Biesecker B.B. , Christensen K.D. , Joffe S. , Rini C. , Veenstra D. , McGuire A.L. , et al. .
Source: Genetics In Medicine : Official Journal Of The American College Of Medical Genetics, 2014 Oct; 16(10), p. 727-35.
PMID: 24625446
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The Challenge Of Informed Consent And Return Of Results In Translational Genomics: Empirical Analysis And Recommendations
Authors: Henderson G.E. , Wolf S.M. , Kuczynski K.J. , Joffe S. , Sharp R.R. , Parsons D.W. , Knoppers B.M. , Yu J.H. , Appelbaum P.S. .
Source: The Journal Of Law, Medicine & Ethics : A Journal Of The American Society Of Law, Medicine & Ethics, 2014 Fall; 42(3), p. 344-55.
PMID: 25264092
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Clinical Tumor Sequencing: An Incidental Casualty Of The American College Of Medical Genetics And Genomics Recommendations For Reporting Of Incidental Findings
Authors: Parsons D.W. , Roy A. , Plon S.E. , Roychowdhury S. , Chinnaiyan A.M. .
Source: Journal Of Clinical Oncology : Official Journal Of The American Society Of Clinical Oncology, 2014-07-20 00:00:00.0; 32(21), p. 2203-5.
PMID: 24958819
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De Novo Truncating Mutations In Ahdc1 In Individuals With Syndromic Expressive Language Delay, Hypotonia, And Sleep Apnea
Authors: Xia F. , Bainbridge M.N. , Tan T.Y. , Wangler M.F. , Scheuerle A.E. , Zackai E.H. , Harr M.H. , Sutton V.R. , Nalam R.L. , Zhu W. , et al. .
Source: American Journal Of Human Genetics, 2014-05-01 00:00:00.0; 94(5), p. 784-9.
PMID: 24791903
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Addressing The Ethical Challenges In Genetic Testing And Sequencing Of Children
Authors: Clayton E.W. , McCullough L.B. , Biesecker L.G. , Joffe S. , Ross L.F. , Wolf S.M. , Clinical Sequencing Exploratory Research (CSER) Consortium Pediatrics Working Group .
Source: The American Journal Of Bioethics : Ajob, 2014; 14(3), p. 3-9.
PMID: 24592828
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Obtaining Informed Consent For Clinical Tumor And Germline Exome Sequencing Of Newly Diagnosed Childhood Cancer Patients
Authors: Scollon S. , Bergstrom K. , Kerstein R.A. , Wang T. , Hilsenbeck S.G. , Ramamurthy U. , Gibbs R.A. , Eng C.M. , Chintagumpala M.M. , Berg S.L. , et al. .
Source: Genome Medicine, 2014; 6(9), p. 69.
PMID: 25317207
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Experiences And Attitudes Of Genome Investigators Regarding Return Of Individual Genetic Test Results
Authors: Ramoni R.B. , McGuire A.L. , Robinson J.O. , Morley D.S. , Plon S.E. , Joffe S. .
Source: Genetics In Medicine : Official Journal Of The American College Of Medical Genetics, 2013 Nov; 15(11), p. 882-7.
PMID: 23639901
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Processes and preliminary outputs for identification of actionable genes as incidental findings in genomic sequence data in the Clinical Sequencing Exploratory Research Consortium.
Authors: Berg J.S. , Amendola L.M. , Eng C. , Van Allen E. , Gray S.W. , Wagle N. , Rehm H.L. , DeChene E.T. , Dulik M.C. , Hisama F.M. , et al. .
Source: Genetics In Medicine : Official Journal Of The American College Of Medical Genetics, 2013 Nov; 15(11), p. 860-7.
PMID: 24195999
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Clinical Whole-exome Sequencing For The Diagnosis Of Mendelian Disorders
Authors: Yang Y. , Muzny D.M. , Reid J.G. , Bainbridge M.N. , Willis A. , Ward P.A. , Braxton A. , Beuten J. , Xia F. , Niu Z. , et al. .
Source: The New England Journal Of Medicine, 2013-10-17 00:00:00.0; 369(16), p. 1502-11.
PMID: 24088041
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A survey of informatics approaches to whole-exome and whole-genome clinical reporting in the electronic health record.
Authors: Tarczy-Hornoch P. , Amendola L. , Aronson S.J. , Garraway L. , Gray S. , Grundmeier R.W. , Hindorff L.A. , Jarvik G. , Karavite D. , Lebo M. , et al. .
Source: Genetics In Medicine : Official Journal Of The American College Of Medical Genetics, 2013 Oct; 15(10), p. 824-32.
PMID: 24071794
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Acmg Recommendations For Reporting Of Incidental Findings In Clinical Exome And Genome Sequencing
Authors: Green R.C. , Berg J.S. , Grody W.W. , Kalia S.S. , Korf B.R. , Martin C.L. , McGuire A.L. , Nussbaum R.L. , O'Daniel J.M. , Ormond K.E. , et al. .
Source: Genetics In Medicine : Official Journal Of The American College Of Medical Genetics, 2013 Jul; 15(7), p. 565-74.
PMID: 23788249
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Point-counterpoint. Ethics And Genomic Incidental Findings
Authors: McGuire A.L. , Joffe S. , Koenig B.A. , Biesecker B.B. , McCullough L.B. , Blumenthal-Barby J.S. , Caulfield T. , Terry S.F. , Green R.C. .
Source: Science (new York, N.y.), 2013-05-31 00:00:00.0; 340(6136), p. 1047-8.
PMID: 23686340
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The Indispensable Role Of Professional Judgment In Genomic Medicine
Authors: McGuire A.L. , McCullough L.B. , Evans J.P. .
Source: Jama, 2013-04-10 00:00:00.0; 309(14), p. 1465-6.
PMID: 23571582
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Returning Genetic Research Results: Study Type Matters
Authors: McGuire A.L. , Robinson J.O. , Ramoni R.B. , Morley D.S. , Jofe S. , Plon S.E. .
Source: Personalized Medicine, 2013 Jan; 10(1), p. 27-34.
PMID: 24077424
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Next-generation Sequencing In The Clinic: Are We Ready?
Authors: Biesecker L.G. , Burke W. , Kohane I. , Plon S.E. , Zimmern R. .
Source: Nature Reviews. Genetics, 2012 Nov; 13(11), p. 818-24.
PMID: 23076269
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Neuroscience. Preventable Forms Of Autism?
Authors: Beaudet,A.L. .
Source: Science (new York, N.y.), 2012-10-19 00:00:00.0; 338(6105), p. 342-3.
PMID: 23087240
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Exploring concordance and discordance for return of incidental findings from clinical sequencing.
Authors: Green R.C. , Berg J.S. , Berry G.T. , Biesecker L.G. , Dimmock D.P. , Evans J.P. , Grody W.W. , Hegde M.R. , Kalia S. , Korf B.R. , et al. .
Source: Genetics In Medicine : Official Journal Of The American College Of Medical Genetics, 2012 Apr; 14(4), p. 405-10.
PMID: 22422049
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