Joint, multifaceted genomic analysis enables diagnosis of diverse, ultra-rare monogenic presentations

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

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

Volume / Issue Vol. 16, Issue 1
Published August 07, 2025
ISSN 2041-1723
Publisher Nature Portfolio

Journal Info

Nature Communications

Nature Portfolio

ISSN: 2041-1723 Open Access Life Sciences

Authors (342)

S

Shilpa Nadimpalli Kobren

M

Mikhail A. Moldovan

R

Rebecca Reimers

D

Daniel Traviglia

X

Xinyun Li

D

Danielle Barnum

A

Alexander Veit

R

Rosario I. Corona

G

George de V. Carvalho Neto

J

Julian Willett

M

Michele Berselli

W

William Ronchetti

S

Stanley F. Nelson

Department of Human Genetics, University of California, Los Angeles, Los Angeles

R

Richard Sherwood

J

Joel Krier

I

Isaac S. Kohane

J

Jose Abdenur

M

Maria T. Acosta

Office of the Clinical Director, National Human Genome Research Institute, Bethesda, MD

D

David R. Adams

B

Ben Afzali

A

Ali Al-Beshri

E

Eric Allenspach

R

Raquel L. Alvarez

J

Justin Alvey

A

Ashley Andrews

B

Beatriz Anguiano

E

Euan A. Ashley

S

Sanaz Attaripour

S

Suha Bachir

C

Carlos A. Bacino

G

Guney Bademci

A

Ashok Balasubramanyam

D

Dustin Baldridge

E

Erin E. Baldwin

A

Allen Bale

E

Elsa Balton

M

Manisha Balwani

M

Michael Bamshad

M

Mafalda Barbosa

D

Deborah Barbouth

R

Rebekah Barrick

D

Donald Basel

P

Pinar Bayrak-Toydemir

T

Taylor Beagle

A

Alan H. Beggs

Boston Children’s Hospital, Boston

E

Edward Behrens

M

Megan Bell

H

Hugo J. Bellen

P

Paul Berger

J

Jonathan A. Bernstein

G

Gerard T. Berry

L

Louise Bier

S

Stephanie Bivona

K

Kirsten Blanco

L

Lauren Blieden

E

Elizabeth Blue

D

Devon Bonner

B

Brett Bordini

N

Nicholas Borja

L

Lorenzo Botto

S

Steven Boyden

L

Lauren C. Briere

E

Elizabeth A. Burke

L

Lindsay C. Burrage

F

Francisco Bustos

M

Manish J. Butte

R

Russell Butterfield

P

Peter Byers

W

William E. Byrd

K

Kaitlin Callaway

J

John Carey

T

Thomas Cassini

C

Chun-Hung Chan

R

Richard Chang

S

Sirisak Chanprasert

H

Hsiao-Tuan Chao

E

Elizabeth C. Chao

I

Ivan Chinn

G

Gary D. Clark

T

Terra R. Coakley

L

Laurel A. Cobban

J

Joy D. Cogan

M

Matthew Coggins

Rocket Pharmaceuticals, Cranbury, NJ

F

F. Sessions Cole

E

Erin Conboy

B

Brian Corner

W

William J. Craigen

A

Andrew B. Crouse

V

Vishnu Cuddapah

C

Charlotte Cunningham-Rundles

P

Precilla D’Souza

Office of the Clinical Director, National Human Genome Research Institute, Bethesda, MD

H

Hongzheng Dai

N

Nitsuh K. Dargie

K

Kahlen Darr

S

Surendra Dasari

J

Joie Davis

M

Margaret Delgado

E

Esteban C. Dell’Angelica

N

Nada Derar

P

Patricia Dickson

K

Katrina Dipple

N

Naghmeh Dorrani

J

Jessica Douglas

A

Abdul Elkadri

S

Sara Emami

L

Lisa T. Emrick

C

Christine M. Eng

C

Cecilia Esteves

R

Rachel Evard

K

Kimberly Ezell

L

Layal F. Abi Farraj

E

Elizabeth L. Fieg

P

Paul G. Fisher

B

Brent L. Fogel

J

Jiayu Fu

W

William A. Gahl

Medical Genetics Branch, National Human Genome Research Institute, Bethesda, MD

R

Rebecca Ganetzky

E

Eric Gayle

B

Bruce Gelb

M

Mark Gerstein

E

Emily Glanton

I

Ian Glass

P

Page C. Goddard

J

Joanna M. Gonzalez

J

John E. Gorzynski

B

Brett H. Graham

A

Andrea Gropman

M

Meghan C. Halley

W

Winston Halstead

R

Rizwan Hamid

N

Neil Hanchard

K

Kelly Hassey

C

Caroline Hendry

F

Frances High

F

Fuki M. Hisama

I

Ingrid A. Holm

J

Jason Hom

M

Martha Horike-Pyne

Y

Yan Huang

A

Alden Huang

M

Monika Weisz Hubshman

A

Anna Hurst

J

John A. Phillips

W

Wendy Introne

A

Ayuko Iverson

G

Gail P. Jarvik

O

Orpa Jean-Marie

L

Lauren Jeffries

Pediatric Genomics Discovery Program, Department of Pediatrics, Yale University School of Medicine

J

Joanna Jen

T

Tanner D. Jensen

Y

Yong-Hui Jiang

V

Vaidehi Jobanputra

New York Genome Center

O

Oguz Kanca

Department of Molecular and Human Genetics, Baylor College of Medicine

Y

Yigit Karasozen

O

Odelya Kaufman

L

Laura Keehan

S

Shamika Ketkar

D

Dana Kiley

G

Gonench Kilich

E

Eric Klee

J

Jennefer N. Kohler

B

Bruce Korf

S

Susan Korrick

E

Elijah Kravets

R

Runjun Kumar

S

Seema R. Lalani

B

Brendan C. Lanpher

I

Ian R. Lanza

K

Kumarie Latchman

K

Kimberly LeBlanc

B

Brendan H. Lee

M

Miranda Leitheiser

M

Monkol Lek

Department of Genetics, Yale School of Medicine

K

Kathleen A. Leppig

M

Mia Levanto

R

Richard A. Lewis

R

Rachel Li

Department of Molecular and Cell Biology, University of California Berkeley

K

Khurram Liaqat

P

Pengfei Liu

N

Nicola Longo

J

Joseph Loscalzo

Department of Medicine, Brigham and Women’s Hospital, Boston

R

Richard L. Maas

E

Ellen F. Macnamara

C

Calum A. MacRae

V

Valerie V. Maduro

R

Rachel Mahoney

M

MayChristine V. Malicdan

T

Tarun K. K. Mamidi

S

Shrikant Mane

L

Lili Mantcheva

R

Rong Mao

R

Ronit Marom

G

Gabor Marth

B

Beth A. Martin

M

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

J

Julian A. Martinez-Agosto

S

Shruti Marwaha

T

Taylor Maurer

J

Julie McCarrier

A

Allyn McConkie-Rosell

A

Ashley McMinn

E

Erin McRoy

H

Hector Rodrigo Mendez

M

Matthew Might

M

Mohamad Mikati

D

Danny Miller

A

Alexander Miller

G

Ghayda Mirzaa

B

Breanna Mitchell

S

Stephen B. Montgomery

P

Paolo Moretti

J

Jennifer Morgan

M

Marie Morimoto

T

Tahseen Mozaffar

L

Lindsay Mulvihill

J

John J. Mulvihill

M

Michael Muriello

S

Sandesh Nagamani

M

Mariko Nakano-Okuno

S

Serena Neumann

T

Thomas J. Nicholas

D

Donna Novacic

D

Devin Oglesbee

C

Carol Oladele

J

James P. Orengo

R

Rebecca Overbury

L

Laura Pace

S

Stephen C. Pak

J

J. Carl Pallais

N

Neil H. Parker

A

Alex Paul

L

LéShon Peart

S

Seth Perlman

L

Leoyklang Petcharet

J

Jennifer E. Posey

L

Lorraine Potocki

R

Rakale C. Quarells

A

Aaron Quinlan

D

Daniel J. Rader

R

Ramakrishnan Rajagopalan

D

Deepak A. Rao

A

Anna Raper

W

Wendy Raskind

A

Adriana Rebelo

C

Chloe M. Reuter

L

Lynette Rives

L

Lance H. Rodan

M

Martin Rodriguez

M

María José Ortuño Romero

J

Jill A. Rosenfeld

E

Elisabeth Rosenthal

F

Francis Rossignol

B

Bianca E. Russell

M

Marla Sabaii

M

Mohamad Saifeddine

J

Jacinda B. Sampson

S

Suzanne Sandmeyer

T

Timothy Schedl

J

Jason Schend

L

Lisa Schimmenti

K

Kelly Schoch

J

Jennifer Schymick

D

Daryl A. Scott

T

Teodoro Jerves Serrano

E

Elaine Seto

M

Mariya Shadrina

V

Vandana Shashi

E

Emily Shelkowitz

S

Susan Shin

J

Jimann Shin

S

Saskia Shuman

E

Edwin K. Silverman

Channing Division of Network Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA.

G

Giorgio Sirugo

K

Kathy Sisco

T

Tammi Skelton

C

Cara Skraban

C

Carson A. Smith

K

Kevin S. Smith

J

Jared Sninsky

L

Lilianna Solnica-Krezel

B

Ben Solomon

A

Albert R. La Spada

M

Michele Spencer-Manzon

R

Rebecca C. Spillmann

M

Maija-Rikka Steenari

A

Andrew Stergachis

J

Joan M. Stoler

K

Kathleen Sullivan

D

David A. Sweetser

B

Barbara N. Pusey Swerdzewski

V

Virginia Sybert

H

Holly K. Tabor

Q

Queenie Tan

A

Arjun Tarakad

H

Herman Taylor

M

Mustafa Tekin

W

Willa Thorson

C

Cynthia J. Tifft

Office of the Clinical Director, National Human Genome Research Institute, Bethesda, MD

C

Camilo Toro

A

Alyssa A. Tran

K

Kayla M. Treat

B

Brianna Tucker

R

Rachel A. Ungar

F

Filippo Pinto e. Vairo

A

Adeline Vanderver

A

Andres Vargas

V

Vasilis Vasiliou

M

Matt Velinder

J

James Verbsky

F

Francesco Vetrini

E

Eric Vilain

D

Dave Viskochil

T

Tiphanie P. Vogel

C

Colleen E. Wahl

M

Melissa Walker

N

Nicole M. Walley

J

Jennifer Wambach

E

Emily Wang

M

Michael F. Wangler

P

Patricia A. Ward

I

Isum Ward

A

Alistair Ward

S

Stephanie M. Ware

D

Daniel Wegner

C

Corrine K. Welt

M

Mark Wener

M

Monte Westerfield

M

Matthew T. Wheeler

J

Jordan Whitlock

L

Laurens Wiel

B

Brandon M. Wilk

L

Lynne A. Wolfe

H

Heidi Wood

K

Kim Worley

E

Elizabeth A. Worthey

C

Changrui Xiao

H

Hua Xu

State Key Laboratory of Gene Function and Modulation Research, School of Life Sciences, and Biomedical Pioneering Innovation Center, Peking University

S

Shinya Yamamoto

H

Hui Zhang

The Fourth Hospital of Hebei Medical University Shijiazhuang China

M

Michael Zimmermann

S

Stephan Züchner

S

Shamil R. Sunyaev