Joint, multifaceted genomic analysis enables diagnosis of diverse, ultra-rare monogenic presentations
Abstract
Abstract Genomics for rare disease diagnosis has advanced at a rapid pace due to our ability to perform in-depth analyses on individual patients with ultra-rare diseases. The increasing sizes of ultra-rare disease cohorts internationally newly enables cohort-wide analyses for new discoveries, but well-calibrated statistical genetics approaches for jointly analyzing these patients are still under development. The Undiagnosed Diseases Network (UDN) brings multiple clinical, research and experimental centers under the same umbrella across the United States to facilitate and scale case-based diagnostic analyses. Here, we present the first joint analysis of whole genome sequencing data of UDN patients across the network. We introduce new, well-calibrated statistical methods for prioritizing disease genes with de novo recurrence and compound heterozygosity. We also detect pathways enriched with candidate and known diagnostic genes. Our computational analysis, coupled with a systematic clinical review, recapitulated known diagnoses and revealed new disease associations. We further release a software package, RaMeDiES, enabling automated cross-analysis of deidentified sequenced cohorts for new diagnostic and research discoveries. Gene-level findings and variant-level information across the cohort are available in a public-facing browser ( https://dbmi-bgm.github.io/udn-browser/ ). These results show that case-level diagnostic efforts should be supplemented by a joint genomic analysis across cohorts.
Article Details
Authors (342)
Shilpa Nadimpalli Kobren
Mikhail A. Moldovan
Rebecca Reimers
Daniel Traviglia
Xinyun Li
Danielle Barnum
Alexander Veit
Rosario I. Corona
George de V. Carvalho Neto
Julian Willett
Michele Berselli
William Ronchetti
Stanley F. Nelson
Department of Human Genetics, University of California, Los Angeles, Los Angeles
Richard Sherwood
Joel Krier
Isaac S. Kohane
Jose Abdenur
Maria T. Acosta
Office of the Clinical Director, National Human Genome Research Institute, Bethesda, MD
David R. Adams
Ben Afzali
Ali Al-Beshri
Eric Allenspach
Raquel L. Alvarez
Justin Alvey
Ashley Andrews
Beatriz Anguiano
Euan A. Ashley
Sanaz Attaripour
Suha Bachir
Carlos A. Bacino
Guney Bademci
Ashok Balasubramanyam
Dustin Baldridge
Erin E. Baldwin
Allen Bale
Elsa Balton
Manisha Balwani
Michael Bamshad
Mafalda Barbosa
Deborah Barbouth
Rebekah Barrick
Donald Basel
Pinar Bayrak-Toydemir
Taylor Beagle
Alan H. Beggs
Boston Children’s Hospital, Boston
Edward Behrens
Megan Bell
Hugo J. Bellen
Paul Berger
Jonathan A. Bernstein
Gerard T. Berry
Louise Bier
Stephanie Bivona
Kirsten Blanco
Lauren Blieden
Elizabeth Blue
Devon Bonner
Brett Bordini
Nicholas Borja
Lorenzo Botto
Steven Boyden
Lauren C. Briere
Elizabeth A. Burke
Lindsay C. Burrage
Francisco Bustos
Manish J. Butte
Russell Butterfield
Peter Byers
William E. Byrd
Kaitlin Callaway
John Carey
Thomas Cassini
Chun-Hung Chan
Richard Chang
Sirisak Chanprasert
Hsiao-Tuan Chao
Elizabeth C. Chao
Ivan Chinn
Gary D. Clark
Terra R. Coakley
Laurel A. Cobban
Joy D. Cogan
Matthew Coggins
Rocket Pharmaceuticals, Cranbury, NJ
F. Sessions Cole
Erin Conboy
Brian Corner
William J. Craigen
Andrew B. Crouse
Vishnu Cuddapah
Charlotte Cunningham-Rundles
Precilla D’Souza
Office of the Clinical Director, National Human Genome Research Institute, Bethesda, MD
Hongzheng Dai
Nitsuh K. Dargie
Kahlen Darr
Surendra Dasari
Joie Davis
Margaret Delgado
Esteban C. Dell’Angelica
Nada Derar
Patricia Dickson
Katrina Dipple
Naghmeh Dorrani
Jessica Douglas
Abdul Elkadri
Sara Emami
Lisa T. Emrick
Christine M. Eng
Cecilia Esteves
Rachel Evard
Kimberly Ezell
Layal F. Abi Farraj
Elizabeth L. Fieg
Paul G. Fisher
Brent L. Fogel
Jiayu Fu
William A. Gahl
Medical Genetics Branch, National Human Genome Research Institute, Bethesda, MD
Rebecca Ganetzky
Eric Gayle
Bruce Gelb
Mark Gerstein
Emily Glanton
Ian Glass
Page C. Goddard
Joanna M. Gonzalez
John E. Gorzynski
Brett H. Graham
Andrea Gropman
Meghan C. Halley
Winston Halstead
Rizwan Hamid
Neil Hanchard
Kelly Hassey
Caroline Hendry
Frances High
Fuki M. Hisama
Ingrid A. Holm
Jason Hom
Martha Horike-Pyne
Yan Huang
Alden Huang
Monika Weisz Hubshman
Anna Hurst
John A. Phillips
Wendy Introne
Ayuko Iverson
Gail P. Jarvik
Orpa Jean-Marie
Lauren Jeffries
Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine
Joanna Jen
Tanner D. Jensen
Yong-Hui Jiang
Vaidehi Jobanputra
New York Genome Center
Oguz Kanca
Department of Molecular and Human Genetics, Baylor College of Medicine
Yigit Karasozen
Odelya Kaufman
Laura Keehan
Shamika Ketkar
Dana Kiley
Gonench Kilich
Eric Klee
Jennefer N. Kohler
Bruce Korf
Susan Korrick
Elijah Kravets
Runjun Kumar
Seema R. Lalani
Brendan C. Lanpher
Ian R. Lanza
Kumarie Latchman
Kimberly LeBlanc
Brendan H. Lee
Miranda Leitheiser
Monkol Lek
Department of Genetics, Yale School of Medicine
Kathleen A. Leppig
Mia Levanto
Richard A. Lewis
Rachel Li
Department of Molecular and Cell Biology, University of California Berkeley
Khurram Liaqat
Pengfei Liu
Nicola Longo
Joseph Loscalzo
Department of Medicine, Brigham and Women’s Hospital, Boston
Richard L. Maas
Ellen F. Macnamara
Calum A. MacRae
Valerie V. Maduro
Rachel Mahoney
MayChristine V. Malicdan
Tarun K. K. Mamidi
Shrikant Mane
Lili Mantcheva
Rong Mao
Ronit Marom
Gabor Marth
Beth A. Martin
Martín G. Martín
Department of Pediatrics, Division of Gastroenterology and Nutrition, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Mattel Children’s Hospital, and the David Geffen School of Medicine, University of California, Los Angeles, Los Angeles
Julian A. Martinez-Agosto
Shruti Marwaha
Taylor Maurer
Julie McCarrier
Allyn McConkie-Rosell
Ashley McMinn
Erin McRoy
Hector Rodrigo Mendez
Matthew Might
Mohamad Mikati
Danny Miller
Alexander Miller
Ghayda Mirzaa
Breanna Mitchell
Stephen B. Montgomery
Paolo Moretti
Jennifer Morgan
Marie Morimoto
Tahseen Mozaffar
Lindsay Mulvihill
John J. Mulvihill
Michael Muriello
Sandesh Nagamani
Mariko Nakano-Okuno
Serena Neumann
Thomas J. Nicholas
Donna Novacic
Devin Oglesbee
Carol Oladele
James P. Orengo
Rebecca Overbury
Laura Pace
Stephen C. Pak
J. Carl Pallais
Neil H. Parker
Alex Paul
LéShon Peart
Seth Perlman
Leoyklang Petcharet
Jennifer E. Posey
Lorraine Potocki
Rakale C. Quarells
Aaron Quinlan
Daniel J. Rader
Ramakrishnan Rajagopalan
Deepak A. Rao
Anna Raper
Wendy Raskind
Adriana Rebelo
Chloe M. Reuter
Lynette Rives
Lance H. Rodan
Martin Rodriguez
María José Ortuño Romero
Jill A. Rosenfeld
Elisabeth Rosenthal
Francis Rossignol
Bianca E. Russell
Marla Sabaii
Mohamad Saifeddine
Jacinda B. Sampson
Suzanne Sandmeyer
Timothy Schedl
Jason Schend
Lisa Schimmenti
Kelly Schoch
Jennifer Schymick
Daryl A. Scott
Teodoro Jerves Serrano
Elaine Seto
Mariya Shadrina
Vandana Shashi
Emily Shelkowitz
Susan Shin
Jimann Shin
Saskia Shuman
Edwin K. Silverman
Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA.
Giorgio Sirugo
Kathy Sisco
Tammi Skelton
Cara Skraban
Carson A. Smith
Kevin S. Smith
Jared Sninsky
Lilianna Solnica-Krezel
Ben Solomon
Albert R. La Spada
Michele Spencer-Manzon
Rebecca C. Spillmann
Maija-Rikka Steenari
Andrew Stergachis
Joan M. Stoler
Kathleen Sullivan
David A. Sweetser
Barbara N. Pusey Swerdzewski
Virginia Sybert
Holly K. Tabor
Queenie Tan
Arjun Tarakad
Herman Taylor
Mustafa Tekin
Willa Thorson
Cynthia J. Tifft
Office of the Clinical Director, National Human Genome Research Institute, Bethesda, MD
Camilo Toro
Alyssa A. Tran
Kayla M. Treat
Brianna Tucker
Rachel A. Ungar
Filippo Pinto e. Vairo
Adeline Vanderver
Andres Vargas
Vasilis Vasiliou
Matt Velinder
James Verbsky
Francesco Vetrini
Eric Vilain
Dave Viskochil
Tiphanie P. Vogel
Colleen E. Wahl
Melissa Walker
Nicole M. Walley
Jennifer Wambach
Emily Wang
Michael F. Wangler
Patricia A. Ward
Isum Ward
Alistair Ward
Stephanie M. Ware
Daniel Wegner
Corrine K. Welt
Mark Wener
Monte Westerfield
Matthew T. Wheeler
Jordan Whitlock
Laurens Wiel
Brandon M. Wilk
Lynne A. Wolfe
Heidi Wood
Kim Worley
Elizabeth A. Worthey
Changrui Xiao
Hua Xu
State Key Laboratory of Gene Function and Modulation Research, School of Life Sciences, and Biomedical Pioneering Innovation Center, Peking University
Shinya Yamamoto
Hui Zhang
The Fourth Hospital of Hebei Medical University Shijiazhuang China
Michael Zimmermann
Stephan Züchner
Shamil R. Sunyaev