Peter D Stenson

Peter D Stenson

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Peter D Stenson

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SeqTailor: a user-friendly webserver for the extraction of DNA or protein sequences from next-generation sequencing data.

Nucleic Acids Res 2019 Jul;47(W1):W623-W631

The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.

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http://dx.doi.org/10.1093/nar/gkz326DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6602489PMC
July 2019

S-CAP extends pathogenicity prediction to genetic variants that affect RNA splicing.

Nat Genet 2019 04 25;51(4):755-763. Epub 2019 Feb 25.

Department of Computer Science, Stanford University, Stanford, CA, USA.

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http://dx.doi.org/10.1038/s41588-019-0348-4DOI Listing
April 2019

M-CAP eliminates a majority of variants of uncertain significance in clinical exomes at high sensitivity.

Nat Genet 2016 12 24;48(12):1581-1586. Epub 2016 Oct 24.

Department of Computer Science, Stanford University, Stanford, California, USA.

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http://dx.doi.org/10.1038/ng.3703DOI Listing
December 2016

Analysis of protein-coding genetic variation in 60,706 humans.

Nature 2016 08;536(7616):285-91

Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.

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http://www.nature.com/articles/nature19057
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http://dx.doi.org/10.1038/nature19057DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5018207PMC
August 2016

Assessing the Pathogenicity of Insertion and Deletion Variants with the Variant Effect Scoring Tool (VEST-Indel).

Hum Mutat 2016 Jan 26;37(1):28-35. Epub 2015 Oct 26.

Department of Biomedical Engineering and Institute for Computational Medicine, The Johns Hopkins University, Baltimore, Maryland.

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http://doi.wiley.com/10.1002/humu.22911
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http://dx.doi.org/10.1002/humu.22911DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5057310PMC
January 2016

Proteins linked to autosomal dominant and autosomal recessive disorders harbor characteristic rare missense mutation distribution patterns.

Hum Mol Genet 2015 Nov 5;24(21):5995-6002. Epub 2015 Aug 5.

Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21210, USA and Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA,

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http://dx.doi.org/10.1093/hmg/ddv309DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6354780PMC
November 2015

The human gene damage index as a gene-level approach to prioritizing exome variants.

Proc Natl Acad Sci U S A 2015 Nov 19;112(44):13615-20. Epub 2015 Oct 19.

St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, NY 10065; Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U.1163, Necker Hospital for Sick Children, 75015 Paris, France; Paris Descartes University, Imagine Institute, 75015 Paris, France; Howard Hughes Medical Institute, New York, NY 10065; Pediatric Hematology-Immunology Unit, Necker Hospital for Sick Children, 75015 Paris, France

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http://dx.doi.org/10.1073/pnas.1518646112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4640721PMC
November 2015

The evaluation of tools used to predict the impact of missense variants is hindered by two types of circularity.

Hum Mutat 2015 May 26;36(5):513-23. Epub 2015 Mar 26.

Machine Learning and Computational Biology Research Group, Max Planck Institute for Intelligent Systems and Max Planck Institute for Developmental Biology, Tübingen, Germany; Zentrum für Bioinformatik, Eberhard Karls Universität Tübingen, Tübingen, Germany; Department for Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.

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https://orca-mwe.cf.ac.uk/84063/1/Grimm_et_al-2015-Human_Mut
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http://doi.wiley.com/10.1002/humu.22768
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http://dx.doi.org/10.1002/humu.22768DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4409520PMC
May 2015

A massively parallel pipeline to clone DNA variants and examine molecular phenotypes of human disease mutations.

PLoS Genet 2014 Dec 11;10(12):e1004819. Epub 2014 Dec 11.

Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, United States of America; Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America.

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http://files.figshare.com/1839935/Text_S1.pdf
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http://dx.plos.org/10.1371/journal.pgen.1004819
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http://dx.doi.org/10.1371/journal.pgen.1004819DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4263371PMC
December 2014

A probabilistic model to predict clinical phenotypic traits from genome sequencing.

PLoS Comput Biol 2014 Sep 4;10(9):e1003825. Epub 2014 Sep 4.

Department of Biomedical Engineering and Institute for Computational Medicine, The Johns Hopkins University, Baltimore, Maryland, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1003825DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4154636PMC
September 2014

Elucidating common structural features of human pathogenic variations using large-scale atomic-resolution protein networks.

Hum Mutat 2014 May 7;35(5):585-93. Epub 2014 Apr 7.

Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, 14853; Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York, 14853.

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http://dx.doi.org/10.1002/humu.22534DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4876038PMC
May 2014

MuPIT interactive: webserver for mapping variant positions to annotated, interactive 3D structures.

Hum Genet 2013 Nov 23;132(11):1235-43. Epub 2013 Jun 23.

Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD, USA.

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http://dx.doi.org/10.1007/s00439-013-1325-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3797853PMC
November 2013

Using exome data to identify malignant hyperthermia susceptibility mutations.

Anesthesiology 2013 Nov;119(5):1043-53

* Research Associate, † Clinical Specialty Consultant, ‡ Staff Scientist, ‡‡ Branch Chief, Genetic Disease Research Branch, †† Director, National Institutes of Health Intramural Sequencing Center, National Human Genome Research Institute (NHGRI), National Institutes of Health, Bethesda, Maryland. # Research Associate, ** Professor of Human Molecular Genetics, Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, United Kingdom. § Postdoctoral Fellow, Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health. Current position: Assistant Member, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida. ‖ Members of the National Institutes of Health Intramural Sequencing Center group are listed in the appendix.

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http://dx.doi.org/10.1097/ALN.0b013e3182a8a8e7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4077354PMC
November 2013

Identifying Mendelian disease genes with the variant effect scoring tool.

BMC Genomics 2013 28;14 Suppl 3:S3. Epub 2013 May 28.

Department of Biomedical Engineering and Institute for Computational Medicine, Johns Hopkins University, 3400 N, Charles St, Baltimore, Maryland USA.

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http://dx.doi.org/10.1186/1471-2164-14-S3-S3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3665549PMC
October 2013

Interpreting secondary cardiac disease variants in an exome cohort.

Circ Cardiovasc Genet 2013 Aug 16;6(4):337-46. Epub 2013 Jul 16.

Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA.

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http://dx.doi.org/10.1161/CIRCGENETICS.113.000039DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3887521PMC
August 2013

CRAVAT: cancer-related analysis of variants toolkit.

Bioinformatics 2013 Mar 16;29(5):647-8. Epub 2013 Jan 16.

Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3582272PMC
March 2013

Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models.

Hum Mutat 2013 Jan 2;34(1):57-65. Epub 2012 Nov 2.

Bristol Centre for Systems Biomedicine and MRC CAiTE Centre, School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom.

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http://dx.doi.org/10.1002/humu.22225DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3558800PMC
January 2013

Single base-pair substitutions at the translation initiation sites of human genes as a cause of inherited disease.

Hum Mutat 2011 Oct 8;32(10):1137-43. Epub 2011 Sep 8.

Institut für Medizinische Informatik und Statistik, Christian-Albrechts-Universität zu Kiel, Kiel, Germany.

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http://dx.doi.org/10.1002/humu.21547DOI Listing
October 2011

Comparative analysis of germline and somatic microlesion mutational spectra in 17 human tumor suppressor genes.

Hum Mutat 2011 Jun 22;32(6):620-32. Epub 2011 Mar 22.

Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff, United Kingdom.

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http://doi.wiley.com/10.1002/humu.21483
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http://dx.doi.org/10.1002/humu.21483DOI Listing
June 2011

Meiotic recombination favors the spreading of deleterious mutations in human populations.

Hum Mutat 2011 Feb 25;32(2):198-206. Epub 2011 Jan 25.

Université de Lyon, Université Lyon 1, CNRS, UMR 5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France.

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http://dx.doi.org/10.1002/humu.21407DOI Listing
February 2011

Genes, mutations, and human inherited disease at the dawn of the age of personalized genomics.

Hum Mutat 2010 Jun;31(6):631-55

Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, United Kingdom.

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http://dx.doi.org/10.1002/humu.21260DOI Listing
June 2010

The Human Gene Mutation Database: 2008 update.

Genome Med 2009 Jan 22;1(1):13. Epub 2009 Jan 22.

Institute of Medical Genetics, Cardiff University, Heath Park, Cardiff CF14 4XN, UK.

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http://dx.doi.org/10.1186/gm13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2651586PMC
January 2009

Abundance and length of simple repeats in vertebrate genomes are determined by their structural properties.

Genome Res 2008 Oct 7;18(10):1545-53. Epub 2008 Aug 7.

Institute of Biosciences and Technology, Center for Genome Research, Texas A&M University Health Science Center, Houston, Texas 77030, USA.

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http://dx.doi.org/10.1101/gr.078303.108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2556271PMC
October 2008

Evolutionary and biomedical insights from the rhesus macaque genome.

Authors:
Richard A Gibbs Jeffrey Rogers Michael G Katze Roger Bumgarner George M Weinstock Elaine R Mardis Karin A Remington Robert L Strausberg J Craig Venter Richard K Wilson Mark A Batzer Carlos D Bustamante Evan E Eichler Matthew W Hahn Ross C Hardison Kateryna D Makova Webb Miller Aleksandar Milosavljevic Robert E Palermo Adam Siepel James M Sikela Tony Attaway Stephanie Bell Kelly E Bernard Christian J Buhay Mimi N Chandrabose Marvin Dao Clay Davis Kimberly D Delehaunty Yan Ding Huyen H Dinh Shannon Dugan-Rocha Lucinda A Fulton Ramatu Ayiesha Gabisi Toni T Garner Jennifer Godfrey Alicia C Hawes Judith Hernandez Sandra Hines Michael Holder Jennifer Hume Shalini N Jhangiani Vandita Joshi Ziad Mohid Khan Ewen F Kirkness Andrew Cree R Gerald Fowler Sandra Lee Lora R Lewis Zhangwan Li Yih-Shin Liu Stephanie M Moore Donna Muzny Lynne V Nazareth Dinh Ngoc Ngo Geoffrey O Okwuonu Grace Pai David Parker Heidie A Paul Cynthia Pfannkoch Craig S Pohl Yu-Hui Rogers San Juana Ruiz Aniko Sabo Jireh Santibanez Brian W Schneider Scott M Smith Erica Sodergren Amanda F Svatek Teresa R Utterback Selina Vattathil Wesley Warren Courtney Sherell White Asif T Chinwalla Yucheng Feng Aaron L Halpern Ladeana W Hillier Xiaoqiu Huang Pat Minx Joanne O Nelson Kymberlie H Pepin Xiang Qin Granger G Sutton Eli Venter Brian P Walenz John W Wallis Kim C Worley Shiaw-Pyng Yang Steven M Jones Marco A Marra Mariano Rocchi Jacqueline E Schein Robert Baertsch Laura Clarke Miklós Csürös Jarret Glasscock R Alan Harris Paul Havlak Andrew R Jackson Huaiyang Jiang Yue Liu David N Messina Yufeng Shen Henry Xing-Zhi Song Todd Wylie Lan Zhang Ewan Birney Kyudong Han Miriam K Konkel Jungnam Lee Arian F A Smit Brygg Ullmer Hui Wang Jinchuan Xing Richard Burhans Ze Cheng John E Karro Jian Ma Brian Raney Xinwei She Michael J Cox Jeffery P Demuth Laura J Dumas Sang-Gook Han Janet Hopkins Anis Karimpour-Fard Young H Kim Jonathan R Pollack Tomas Vinar Charles Addo-Quaye Jeremiah Degenhardt Alexandra Denby Melissa J Hubisz Amit Indap Carolin Kosiol Bruce T Lahn Heather A Lawson Alison Marklein Rasmus Nielsen Eric J Vallender Andrew G Clark Betsy Ferguson Ryan D Hernandez Kashif Hirani Hildegard Kehrer-Sawatzki Jessica Kolb Shobha Patil Ling-Ling Pu Yanru Ren David Glenn Smith David A Wheeler Ian Schenck Edward V Ball Rui Chen David N Cooper Belinda Giardine Fan Hsu W James Kent Arthur Lesk David L Nelson William E O'brien Kay Prüfer Peter D Stenson James C Wallace Hui Ke Xiao-Ming Liu Peng Wang Andy Peng Xiang Fan Yang Galt P Barber David Haussler Donna Karolchik Andy D Kern Robert M Kuhn Kayla E Smith Ann S Zwieg

Science 2007 Apr;316(5822):222-34

Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.

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http://dx.doi.org/10.1126/science.1139247DOI Listing
April 2007

The Human Gene Mutation Database (HGMD) and its exploitation in the study of mutational mechanisms.

Curr Protoc Bioinformatics 2006 Jan;Chapter 1:Unit 1.13

Cardiff University, Cardiff, United Kingdom.

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http://dx.doi.org/10.1002/0471250953.bi0113s12DOI Listing
January 2006

Intrachromosomal serial replication slippage in trans gives rise to diverse genomic rearrangements involving inversions.

Hum Mutat 2005 Oct;26(4):362-73

Institut National de la Santé et de la Recherche Médicale U613, Etablissement Français du Sang-Bretagne, Université de Bretagne Occidentale, Centre Hospitalier Universitaire, Brest, France.

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http://dx.doi.org/10.1002/humu.20230DOI Listing
October 2005

A systematic analysis of LINE-1 endonuclease-dependent retrotranspositional events causing human genetic disease.

Hum Genet 2005 Sep 28;117(5):411-27. Epub 2005 Jun 28.

INSERM U613-Génétique Moléculaire et Génétique Epidémiologique, Etablissement Français du Sang-Bretagne, Université de Bretagne Occidentale, Centre Hospitalier Universitaire, Brest, 29220, France.

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http://dx.doi.org/10.1007/s00439-005-1321-0DOI Listing
September 2005

Complex gene rearrangements caused by serial replication slippage.

Hum Mutat 2005 Aug;26(2):125-34

INSERM U613 - Génétique Moléculaire et Génétique Epidémiologique, Etablissement Français du Sang - Bretagne, Université de Bretagne Occidentale, Centre Hospitalier Universitaire, Brest, France.

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http://dx.doi.org/10.1002/humu.20202DOI Listing
August 2005

Meta-analysis of gross insertions causing human genetic disease: novel mutational mechanisms and the role of replication slippage.

Hum Mutat 2005 Feb;25(2):207-21

INSERM (Institut National de la Santé et de la Recherche Médicale) U613-Génétique Moléculaire et Génétique Epidémiologique, Université de Bretagne Occidentale, Centre Hospitalier Universitaire, Brest, France.

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http://dx.doi.org/10.1002/humu.20133DOI Listing
February 2005

Genome sequence of the Brown Norway rat yields insights into mammalian evolution.

Authors:
Richard A Gibbs George M Weinstock Michael L Metzker Donna M Muzny Erica J Sodergren Steven Scherer Graham Scott David Steffen Kim C Worley Paula E Burch Geoffrey Okwuonu Sandra Hines Lora Lewis Christine DeRamo Oliver Delgado Shannon Dugan-Rocha George Miner Margaret Morgan Alicia Hawes Rachel Gill Celera Robert A Holt Mark D Adams Peter G Amanatides Holly Baden-Tillson Mary Barnstead Soo Chin Cheryl A Evans Steve Ferriera Carl Fosler Anna Glodek Zhiping Gu Don Jennings Cheryl L Kraft Trixie Nguyen Cynthia M Pfannkoch Cynthia Sitter Granger G Sutton J Craig Venter Trevor Woodage Douglas Smith Hong-Mei Lee Erik Gustafson Patrick Cahill Arnold Kana Lynn Doucette-Stamm Keith Weinstock Kim Fechtel Robert B Weiss Diane M Dunn Eric D Green Robert W Blakesley Gerard G Bouffard Pieter J De Jong Kazutoyo Osoegawa Baoli Zhu Marco Marra Jacqueline Schein Ian Bosdet Chris Fjell Steven Jones Martin Krzywinski Carrie Mathewson Asim Siddiqui Natasja Wye John McPherson Shaying Zhao Claire M Fraser Jyoti Shetty Sofiya Shatsman Keita Geer Yixin Chen Sofyia Abramzon William C Nierman Paul H Havlak Rui Chen K James Durbin Amy Egan Yanru Ren Xing-Zhi Song Bingshan Li Yue Liu Xiang Qin Simon Cawley Kim C Worley A J Cooney Lisa M D'Souza Kirt Martin Jia Qian Wu Manuel L Gonzalez-Garay Andrew R Jackson Kenneth J Kalafus Michael P McLeod Aleksandar Milosavljevic Davinder Virk Andrei Volkov David A Wheeler Zhengdong Zhang Jeffrey A Bailey Evan E Eichler Eray Tuzun Ewan Birney Emmanuel Mongin Abel Ureta-Vidal Cara Woodwark Evgeny Zdobnov Peer Bork Mikita Suyama David Torrents Marina Alexandersson Barbara J Trask Janet M Young Hui Huang Huajun Wang Heming Xing Sue Daniels Darryl Gietzen Jeanette Schmidt Kristian Stevens Ursula Vitt Jim Wingrove Francisco Camara M Mar Albà Josep F Abril Roderic Guigo Arian Smit Inna Dubchak Edward M Rubin Olivier Couronne Alexander Poliakov Norbert Hübner Detlev Ganten Claudia Goesele Oliver Hummel Thomas Kreitler Young-Ae Lee Jan Monti Herbert Schulz Heike Zimdahl Heinz Himmelbauer Hans Lehrach Howard J Jacob Susan Bromberg Jo Gullings-Handley Michael I Jensen-Seaman Anne E Kwitek Jozef Lazar Dean Pasko Peter J Tonellato Simon Twigger Chris P Ponting Jose M Duarte Stephen Rice Leo Goodstadt Scott A Beatson Richard D Emes Eitan E Winter Caleb Webber Petra Brandt Gerald Nyakatura Margaret Adetobi Francesca Chiaromonte Laura Elnitski Pallavi Eswara Ross C Hardison Minmei Hou Diana Kolbe Kateryna Makova Webb Miller Anton Nekrutenko Cathy Riemer Scott Schwartz James Taylor Shan Yang Yi Zhang Klaus Lindpaintner T Dan Andrews Mario Caccamo Michele Clamp Laura Clarke Valerie Curwen Richard Durbin Eduardo Eyras Stephen M Searle Gregory M Cooper Serafim Batzoglou Michael Brudno Arend Sidow Eric A Stone J Craig Venter Bret A Payseur Guillaume Bourque Carlos López-Otín Xose S Puente Kushal Chakrabarti Sourav Chatterji Colin Dewey Lior Pachter Nicolas Bray Von Bing Yap Anat Caspi Glenn Tesler Pavel A Pevzner David Haussler Krishna M Roskin Robert Baertsch Hiram Clawson Terrence S Furey Angie S Hinrichs Donna Karolchik William J Kent Kate R Rosenbloom Heather Trumbower Matt Weirauch David N Cooper Peter D Stenson Bin Ma Michael Brent Manimozhiyan Arumugam David Shteynberg Richard R Copley Martin S Taylor Harold Riethman Uma Mudunuri Jane Peterson Mark Guyer Adam Felsenfeld Susan Old Stephen Mockrin Francis Collins

Nature 2004 Apr;428(6982):493-521

Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, MS BCM226, One Baylor Plaza, Houston, Texas 77030, USA. http://www.hgsc.bcm.tmc.edu

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http://dx.doi.org/10.1038/nature02426DOI Listing
April 2004

Gross Rearrangement Breakpoint Database (GRaBD).

Hum Mutat 2004 Mar;23(3):219-21

Institute of Medical Genetics, University of Wales College of Medicine, Cardiff, United Kingdom.

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http://doi.wiley.com/10.1002/humu.20006
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http://dx.doi.org/10.1002/humu.20006DOI Listing
March 2004

Human Gene Mutation Database (HGMD): 2003 update.

Hum Mutat 2003 Jun;21(6):577-81

Institute of Medical Genetics, University of Wales College of Medicine, Heath Park, Cardiff, UK.

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http://doi.wiley.com/10.1002/humu.10212
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http://dx.doi.org/10.1002/humu.10212DOI Listing
June 2003