S
Sai Chen
Researcher at University of Michigan
Publications - 25
Citations - 3136
Sai Chen is an academic researcher from University of Michigan. The author has contributed to research in topics: Genome-wide association study & Imputation (genetics). The author has an hindex of 13, co-authored 25 publications receiving 2081 citations. Previous affiliations of Sai Chen include Illumina & University of Virginia.
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Journal ArticleDOI
A reference panel of 64,976 haplotypes for genotype imputation
Shane A. McCarthy,Sayantan Das,Warren W. Kretzschmar,Olivier Delaneau,Andrew R. Wood,Alexander Teumer,Hyun Min Kang,Christian Fuchsberger,Petr Danecek,Kevin Sharp,Yang Luo,C Sidore,Alan Kwong,Nicholas J. Timpson,Seppo Koskinen,Scott I. Vrieze,Laura J. Scott,He Zhang,Anubha Mahajan,Jan H. Veldink,Ulrike Peters,Ulrike Peters,Carlos N. Pato,Cornelia M. van Duijn,Christopher E. Gillies,Ilaria Gandin,Massimo Mezzavilla,Arthur Gilly,Massimiliano Cocca,Michela Traglia,Andrea Angius,Jeffrey C. Barrett,D.I. Boomsma,Kari Branham,Gerome Breen,Gerome Breen,Chad M. Brummett,Fabio Busonero,Harry Campbell,Andrew T. Chan,Sai Chen,Emily Y. Chew,Francis S. Collins,Laura J Corbin,George Davey Smith,George Dedoussis,Marcus Dörr,Aliki-Eleni Farmaki,Luigi Ferrucci,Lukas Forer,Ross M. Fraser,Stacey Gabriel,Shawn Levy,Leif Groop,Leif Groop,Tabitha A. Harrison,Andrew T. Hattersley,Oddgeir L. Holmen,Kristian Hveem,Matthias Kretzler,James Lee,Matt McGue,Thomas Meitinger,David Melzer,Josine L. Min,Karen L. Mohlke,John B. Vincent,Matthias Nauck,Deborah A. Nickerson,Aarno Palotie,Aarno Palotie,Michele T. Pato,Nicola Pirastu,Melvin G. McInnis,J. Brent Richards,J. Brent Richards,Cinzia Sala,Veikko Salomaa,David Schlessinger,Sebastian Schoenherr,P. Eline Slagboom,Kerrin S. Small,Tim D. Spector,Dwight Stambolian,Marcus A. Tuke,Jaakko Tuomilehto,Leonard H. van den Berg,Wouter van Rheenen,Uwe Völker,Cisca Wijmenga,Daniela Toniolo,Eleftheria Zeggini,Paolo Gasparini,Matthew G. Sampson,James F. Wilson,Timothy M. Frayling,Paul I.W. de Bakker,Morris A. Swertz,Steven A. McCarroll,Charles Kooperberg,Annelot M. Dekker,David Altshuler,Cristen J. Willer,William G. Iacono,Samuli Ripatti,Nicole Soranzo,Nicole Soranzo,Klaudia Walter,Anand Swaroop,Francesco Cucca,Carl A. Anderson,Richard M. Myers,Michael Boehnke,Mark I. McCarthy,Mark I. McCarthy,Richard Durbin,Gonçalo R. Abecasis,Jonathan Marchini +117 more
TL;DR: A reference panel of 64,976 human haplotypes at 39,235,157 SNPs constructed using whole-genome sequence data from 20 studies of predominantly European ancestry leads to accurate genotype imputation at minor allele frequencies as low as 0.1% and a large increase in the number of SNPs tested in association studies.
Journal ArticleDOI
Discovery of common and rare genetic risk variants for colorectal cancer
Jeroen R. Huyghe,Stephanie A. Bien,Tabitha A. Harrison,Hyun Min Kang,Sai Chen,Stephanie L. Schmit,David V. Conti,Conghui Qu,Jihyoun Jeon,Christopher K. Edlund,Peyton Greenside,Michael Wainberg,Fredrick R. Schumacher,Joshua D. Smith,David M. Levine,Sarah C. Nelson,Nasa Sinnott-Armstrong,Demetrius Albanes,M. Henar Alonso,Kristin E. Anderson,Coral Arnau-Collell,Volker Arndt,Christina Bamia,Barbara L. Banbury,John A. Baron,Sonja I. Berndt,Stéphane Bézieau,D. Timothy Bishop,Juergen Boehm,Heiner Boeing,Hermann Brenner,Stefanie Brezina,Stephan Buch,Daniel D. Buchanan,Daniel D. Buchanan,Andrea N. Burnett-Hartman,Katja Butterbach,Bette J. Caan,Peter T. Campbell,Christopher S. Carlson,Christopher S. Carlson,Sergi Castellví-Bel,Andrew T. Chan,Andrew T. Chan,Jenny Chang-Claude,Jenny Chang-Claude,Stephen J. Chanock,Maria Dolores Chirlaque,Sang-Hee Cho,Charles M. Connolly,Amanda J. Cross,Katarina Cuk,Keith R. Curtis,Albert de la Chapelle,Kimberly F. Doheny,David Duggan,Douglas F. Easton,Sjoerd G. Elias,Faye Elliott,Dallas R. English,Dallas R. English,Edith J. M. Feskens,Jane C. Figueiredo,Jane C. Figueiredo,Rocky Fischer,Liesel M. FitzGerald,Liesel M. FitzGerald,David Forman,Manish Gala,Steven Gallinger,W. James Gauderman,Graham G. Giles,Graham G. Giles,Elizabeth M. Gillanders,Jian Gong,Phyllis J. Goodman,William M. Grady,John S. Grove,Andrea Gsur,Marc J. Gunter,Robert W. Haile,Jochen Hampe,Heather Hampel,Sophia Harlid,Richard B. Hayes,Philipp Hofer,Michael Hoffmeister,John L. Hopper,John L. Hopper,Wan-Ling Hsu,Wen Yi Huang,Thomas J. Hudson,David J. Hunter,David J. Hunter,Gemma Ibáñez-Sanz,Gregory Idos,Roxann G. Ingersoll,Rebecca D. Jackson,Eric J. Jacobs,Mark A. Jenkins,Amit Joshi,Corinne E. Joshu,Temitope O. Keku,Timothy J. Key,Hyeong Rok Kim,Emiko Kobayashi,Laurence N. Kolonel,Charles Kooperberg,Tilman Kühn,Sébastien Küry,Sun-Seog Kweon,Susanna C. Larsson,Cecelia A. Laurie,Loic Le Marchand,Suzanne M. Leal,Soo-Chin Lee,Flavio Lejbkowicz,Mathieu Lemire,Christopher I. Li,Li Li,Wolfgang Lieb,Yi Lin,Annika Lindblom,Noralane M. Lindor,Hua Ling,Tin Louie,Satu Männistö,Sanford D. Markowitz,Vicente Martín,Giovanna Masala,Caroline McNeil,Marilena Melas,Roger L. Milne,Roger L. Milne,Lorena Moreno,Neil Murphy,Robin Myte,Alessio Naccarati,Polly A. Newcomb,Polly A. Newcomb,Kenneth Offit,Kenneth Offit,Shuji Ogino,Shuji Ogino,N. Charlotte Onland-Moret,Barbara Pardini,Patrick S. Parfrey,Rachel Pearlman,Vittorio Perduca,Vittorio Perduca,Paul D.P. Pharoah,Mila Pinchev,Elizabeth A. Platz,Ross L. Prentice,Elizabeth W. Pugh,Leon Raskin,Gad Rennert,Gad Rennert,Hedy S. Rennert,Hedy S. Rennert,Elio Riboli,Miguel Rodríguez-Barranco,Jane Romm,Lori C. Sakoda,Lori C. Sakoda,Clemens Schafmayer,Robert E. Schoen,Daniela Seminara,Mitul Shah,Tameka Shelford,Min-Ho Shin,Katerina Shulman,Sabina Sieri,Martha L. Slattery,Melissa C. Southey,Zsofia K. Stadler,Christa Stegmaier,Yu Ru Su,Catherine M. Tangen,Stephen N. Thibodeau,Duncan C. Thomas,Sushma S. Thomas,Amanda E. Toland,Antonia Trichopoulou,Cornelia M. Ulrich,David Van Den Berg,Fränzel J.B. Van Duijnhoven,Bethany Van Guelpen,Henk J. van Kranen,Joseph Vijai,Kala Visvanathan,Pavel Vodicka,Pavel Vodicka,Ludmila Vodickova,Ludmila Vodickova,Veronika Vymetalkova,Veronika Vymetalkova,Korbinian Weigl,Korbinian Weigl,Stephanie J. Weinstein,Emily White,Aung Ko Win,Aung Ko Win,C. Roland Wolf,Alicja Wolk,Alicja Wolk,Michael O. Woods,Anna H. Wu,Syed H.E. Zaidi,Brent W. Zanke,Qing Zhang,Wei Zheng,Peter C. Scacheri,John D. Potter,Michael C. Bassik,Anshul Kundaje,Graham Casey,Victor Moreno,Gonçalo R. Abecasis,Deborah A. Nickerson,Stephen B. Gruber,Li Hsu,Li Hsu,Ulrike Peters,Ulrike Peters +224 more
TL;DR: Genome-wide association analyses based on whole-genome sequencing and imputation identify 40 new risk variants for colorectal cancer, including a strongly protective low-frequency variant at CHD1 and loci implicating signaling and immune function in disease etiology.
Journal ArticleDOI
ExpansionHunter: A sequence-graph based tool to analyze variation in short tandem repeat regions.
Egor Dolzhenko,Viraj Deshpande,Felix Schlesinger,Peter Krusche,Roman Petrovski,Sai Chen,Dorothea Emig-Agius,Andrew M. Gross,Giuseppe Narzisi,Brett Bowman,Konrad Scheffler,Joke J.F.A. van Vugt,Courtney E. French,Alba Sanchis-Juan,Alba Sanchis-Juan,Kristina Ibáñez,Arianna Tucci,Bryan R. Lajoie,Jan H. Veldink,Lucy Raymond,Ryan J. Taft,David R. Bentley,Michael A. Eberle +22 more
TL;DR: A new version of Illumina's repeat genotyping software, ExpansionHunter, is introduced that uses a novel computational method to perform targeted genotypes of a broad class of such loci.
Journal ArticleDOI
Paragraph: a graph-based structural variant genotyper for short-read sequence data
Sai Chen,Peter Krusche,Peter Krusche,Egor Dolzhenko,Rachel M. Sherman,Roman Petrovski,Felix Schlesinger,Melanie Kirsche,David R. Bentley,Michael C. Schatz,Michael C. Schatz,Fritz J. Sedlazeck,Michael A. Eberle +12 more
TL;DR: This work introduces Paragraph, an accurate genotyper that models SVs using sequence graphs and SV annotations and shows that Paragraph has better accuracy than other existing genotypers and can be applied to population-scale studies.
Journal ArticleDOI
ExpansionHunter Denovo: a computational method for locating known and novel repeat expansions in short-read sequencing data
Egor Dolzhenko,Mark F. Bennett,Mark F. Bennett,Phillip A. Richmond,Brett Trost,Sai Chen,Joke J.F.A. van Vugt,Charlotte Nguyen,Charlotte Nguyen,Giuseppe Narzisi,Vladimir G. Gainullin,Andrew M. Gross,Bryan R. Lajoie,Ryan J. Taft,Wyeth W. Wasserman,Stephen W. Scherer,Jan H. Veldink,David R. Bentley,Ryan K. C. Yuen,Ryan K. C. Yuen,Melanie Bahlo,Melanie Bahlo,Michael A. Eberle +22 more
TL;DR: Analysis of real and simulated data shows that the ExpansionHunter Denovo method can identify large expansions of 41 out of 44 pathogenic repeats, including nine recently reported non-reference repeat expansions not discoverable via existing methods.