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Danielle Perrin
Researcher at Broad Institute
Publications - 11
Citations - 4606
Danielle Perrin is an academic researcher from Broad Institute. The author has contributed to research in topics: Genomics & Genome. The author has an hindex of 8, co-authored 11 publications receiving 4177 citations.
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Journal ArticleDOI
Genome sequence, comparative analysis and haplotype structure of the domestic dog
Kerstin Lindblad-Toh,Claire M. Wade,Claire M. Wade,Tarjei S. Mikkelsen,Tarjei S. Mikkelsen,Elinor K. Karlsson,Elinor K. Karlsson,David B. Jaffe,Michael Kamal,Michele Clamp,Jean L. Chang,Edward J. Kulbokas,Michael C. Zody,Evan Mauceli,Xiaohui Xie,Matthew Breen,Robert K. Wayne,Elaine A. Ostrander,Chris P. Ponting,Francis Galibert,Douglas Smith,Pieter J. deJong,Ewen F. Kirkness,Pablo Alvarez,Tara Biagi,William Brockman,Jonathan Butler,Chee-Wye Chin,April Cook,James Cuff,Mark J. Daly,Mark J. Daly,David DeCaprio,Sante Gnerre,Manfred Grabherr,Manolis Kellis,Michael Kleber,Carolyne Bardeleben,Leo Goodstadt,Andreas Heger,Christophe Hitte,Lisa Kim,Klaus-Peter Koepfli,Heidi G. Parker,John P. Pollinger,Stephen M. J. Searle,Nathan B. Sutter,Rachael Thomas,Caleb Webber,Jennifer Baldwin,Jennifer Baldwin,Adal Abebe,Amr Abouelleil,Lynne Aftuck,Mostafa Ait-zahra,Tyler Aldredge,Nicole R. Allen,Peter An,Scott Anderson,Claudel Antoine,Harindra Arachchi,Ali Aslam,Laura Ayotte,Pasang Bachantsang,Andrew Barry,Tashi Bayul,Mostafa Benamara,Aaron M. Berlin,Daniel Bessette,Berta Blitshteyn,Toby Bloom,Jason Blye,Leonid Boguslavskiy,Claude Bonnet,Boris Boukhgalter,Adam Brown,Patrick Cahill,Nadia Calixte,Jody Camarata,Yama Cheshatsang,Jeffrey Chu,Mieke Citroen,Alville Collymore,Patrick Cooke,Tenzin Dawoe,Riza M. Daza,Karin Decktor,Stuart DeGray,Norbu Dhargay,Kimberly Dooley,Kathleen Dooley,Passang Dorje,Kunsang Dorjee,Lester Dorris,Noah Duffey,Alan Dupes,Osebhajajeme Egbiremolen,Richard Elong,Jill Falk,Abderrahim Farina,Susan Faro,Diallo Ferguson,Patricia Ferreira,Sheila A. Fisher,Michael Fitzgerald,Karen Foley,Chelsea D. Foley,Alicia Franke,Dennis C. Friedrich,Diane Gage,Manuel Garber,Gary Gearin,Georgia Giannoukos,Tina Goode,Audra Goyette,Joseph Graham,Edward Grandbois,Kunsang Gyaltsen,Nabil Hafez,Daniel S. Hagopian,Birhane Hagos,Jennifer Ruth Sadler Hall,Claire M. Healy,Ryan Hegarty,Tracey Honan,Andrea Horn,Nathan Houde,Leanne Hughes,Leigh Anne Hunnicutt,M. Husby,Benjamin Jester,Charlien Jones,Asha Kamat,Ben Kanga,Cristyn Kells,Dmitry Khazanovich,Alix Chinh Kieu,Peter Kisner,Mayank Kumar,Krista Lance,Thomas E. Landers,Marcia Lara,William H. Lee,Jean-Pierre Leger,Niall J. Lennon,Lisa Leuper,Sarah LeVine,Jinlei Liu,Xiaohong Liu,Yeshi Lokyitsang,Tashi Lokyitsang,Annie Lui,Jan Macdonald,John E. Major,Richard Marabella,Kebede Maru,Charles Matthews,Susan McDonough,Teena Mehta,James Meldrim,Alexandre Melnikov,Louis Meneus,Atanas Mihalev,Tanya Mihova,Karen Hughes Miller,Rachel Mittelman,Valentine Mlenga,Leonidas Mulrain,Glen Munson,Adam Navidi,Jerome Naylor,Tuyen T. Nguyen,Nga Nguyen,Cindy Nguyen,Thu Nguyen,Robert Nicol,Nyima Norbu,Choe Norbu,Nathaniel Novod,Tenchoe Nyima,Peter Olandt,Barry O'Neill,Keith O'Neill,Sahal Osman,Lucien Oyono,Christopher Patti,Danielle Perrin,Pema Phunkhang,Fritz Pierre,Margaret Priest,Anthony Rachupka,Sujaa Raghuraman,Rayale Rameau,Verneda Ray,Christina Raymond,Filip Rege,Cecil Rise,Julie Rogers,Peter Rogov,Julie Sahalie,Sampath Settipalli,Ted Sharpe,Terrance Shea,Mechele Sheehan,Ngawang Sherpa,Jianying Shi,Diana M. Shih,Jessie Sloan,Cherylyn Smith,Todd Sparrow,John Stalker,Nicole Stange-Thomann,Sharon Stavropoulos,Catherine Stone,Sabrina M. Stone,Sean M. Sykes,Pierre Tchuinga,Pema Tenzing,Senait Tesfaye,Dawa Thoulutsang,Yama Thoulutsang,Kerri Topham,Ira Topping,Tsamla Tsamla,Helen Vassiliev,Vijay Venkataraman,Andy Vo,Tsering Wangchuk,Tsering Wangdi,Michael Weiand,Jane E. Wilkinson,Adam Wilson,Shailendra Yadav,Shuli Yang,Xiaoping Yang,Geneva Young,Qing Yu,Joanne Zainoun,Lisa Zembek,Andrew Zimmer,Eric S. Lander,Eric S. Lander +241 more
TL;DR: A high-quality draft genome sequence of the domestic dog is reported, together with a dense map of single nucleotide polymorphisms (SNPs) across breeds, to shed light on the structure and evolution of genomes and genes.
Journal ArticleDOI
Whole-exome sequencing and clinical interpretation of formalin-fixed, paraffin-embedded tumor samples to guide precision cancer medicine
Eliezer M. Van Allen,Nikhil Wagle,Petar Stojanov,Danielle Perrin,Kristian Cibulskis,Sara Marlow,Judit Jané-Valbuena,Dennis C. Friedrich,Gregory V. Kryukov,Scott L. Carter,Aaron McKenna,Andrey Sivachenko,Mara Rosenberg,Adam Kiezun,Douglas Voet,Michael S. Lawrence,Lee Lichtenstein,Jeff Gentry,Franklin W. Huang,Jennifer L. Fostel,Deborah N. Farlow,David A. Barbie,Leena Gandhi,Eric S. Lander,Stacy W. Gray,Steven Joffe,Pasi A. Jänne,Judy Garber,Laura E. MacConaill,Neal I. Lindeman,Barrett J. Rollins,Philip W. Kantoff,Sheila Fisher,Stacey Gabriel,Gad Getz,Levi A. Garraway +35 more
TL;DR: A prospective clinical WES platform for archival formalin-fixed, paraffin-embedded tumor samples that employs computational methods for effective clinical analysis and interpretation of WES data and may inform the widespread implementation of precision cancer medicine.
Journal ArticleDOI
Discovery and characterization of artifactual mutations in deep coverage targeted capture sequencing data due to oxidative DNA damage during sample preparation
Maura Costello,Trevor J. Pugh,Timothy Fennell,Chip Stewart,Lee Lichtenstein,James Meldrim,Jennifer L. Fostel,Dennis C. Friedrich,Danielle Perrin,Danielle Dionne,Sharon Kim,Stacey Gabriel,Eric S. Lander,Sheila Fisher,Gad Getz +14 more
TL;DR: The discovery of novel C > A/G > T transversion artifacts found at low allelic fractions in targeted capture data is described and informatics methods are presented to confidently filter these artifacts from sequencing data sets.
Journal ArticleDOI
MAP Kinase Pathway Alterations in BRAF-Mutant Melanoma Patients with Acquired Resistance to Combined RAF/MEK Inhibition
Nikhil Wagle,Nikhil Wagle,Eliezer M. Van Allen,Eliezer M. Van Allen,Daniel J. Treacy,Dennie T. Frederick,Zachary A. Cooper,Amaro Taylor-Weiner,Mara Rosenberg,Eva M. Goetz,Ryan J. Sullivan,Deborah N. Farlow,Dennis C. Friedrich,Kristin Anderka,Danielle Perrin,Cory M. Johannessen,Aaron McKenna,Kristian Cibulskis,Gregory V. Kryukov,Eran Hodis,Eran Hodis,Eran Hodis,Donald P. Lawrence,Sheila Fisher,Gad Getz,Gad Getz,Stacey Gabriel,Scott L. Carter,Keith T. Flaherty,Jennifer A. Wargo,Levi A. Garraway,Levi A. Garraway +31 more
TL;DR: The continued MAPK signaling-based resistance identified in patients suggests that alternative dosing of current agents, more potent RAF/MEK inhibitors, and/or inhibition of the downstream kinase ERK may be needed for durable control of BRAF-mutant melanoma.
Journal ArticleDOI
Mutations causing medullary cystic kidney disease type 1 lie in a large VNTR in MUC1 missed by massively parallel sequencing
Andrew Kirby,Andreas Gnirke,David B. Jaffe,Veronika Baresova,Nathalie Pochet,Nathalie Pochet,Brendan Blumenstiel,Chun Ye,Daniel Aird,Christine Stevens,James T. Robinson,Moran N. Cabili,Moran N. Cabili,Irit Gat-Viks,Irit Gat-Viks,Edward Kelliher,Riza M. Daza,Matthew Defelice,Helena Hůlková,Jana Sovová,Petr Vylet'al,Corinne Antignac,Corinne Antignac,Corinne Antignac,Mitchell Guttman,Robert E. Handsaker,Robert E. Handsaker,Danielle Perrin,Scott Steelman,Snaevar Sigurdsson,Steven J. Scheinman,Carrie Sougnez,Kristian Cibulskis,Melissa Parkin,Todd Green,Elizabeth J. Rossin,Michael C. Zody,Ramnik J. Xavier,Ramnik J. Xavier,Martin R. Pollak,Martin R. Pollak,Seth L. Alper,Seth L. Alper,Kerstin Lindblad-Toh,Kerstin Lindblad-Toh,Stacey Gabriel,P. Suzanne Hart,Aviv Regev,Chad Nusbaum,Stanislav Kmoch,Anthony J. Bleyer,Eric S. Lander,Mark J. Daly,Mark J. Daly +53 more
TL;DR: The illustrative case of the simple mendelian disorder medullary cystic kidney disease type 1 (MCKD1), mapped more than a decade ago to a 2-Mb region on chromosome 1, is described to provide a cautionary tale about the challenges in identifying the genes responsible for mendelians, let alone more complex, disorders through massively parallel sequencing.