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Commonalities Across Computational Workflows for Uncovering Explanatory Variants in Undiagnosed Cases by Shilpa Nadimpalli Kobren; Dustin Baldridge; Matt Velinder; Joel B. Krier; Kimberly LeBlanc; Cecilia Esteves; Barbara N. Pusey; Stephan Züchner; Elizabeth Blue; Hane Lee; Alden Huang; Lisa Bastarache; Anna Bican; Joy Cogan; Shruti Marwaha; Anna Alkelai; David R. Murdock; Pengfei Liu; Daniel J. Wegner; Alexander J. Paul; Maria T. Acosta; Margaret Adam; David R. Adams; Pankaj B. Agrawal; Mercedes E. Alejandro; Justin Alvey; Laura Amendola; Ashley Andrews; Euan A. Ashley; Mahshid S. Azamian; Carlos A. Bacino; Guney Bademci; Eva Baker; Ashok Balasubramanyam; Dustin Baldridge; Jim Bale; Michael Bamshad; Deborah Barbouth; Pinar Bayrak-Toydemir; Anita Beck; Alan H. Beggs; Edward Behrens; Gill Bejerano; Jimmy Bennett; Beverly Berg-Rood; Jonathan A. Bernstein; Gerard T. Berry; Anna Bican; Stephanie Bivona; Elizabeth Blue; John Bohnsack; Carsten Bonnenmann; Devon Bonner; Lorenzo Botto; Brenna Boyd; Lauren C. Briere; Elly Brokamp; Gabrielle Brown; Elizabeth A. Burke; Lindsay C. Burrage; Manish J. Butte; Peter Byers; William E. Byrd; John Carey; Olveen Carrasquillo; Ta Chen Peter Chang; Sirisak Chanprasert; Hsiao-Tuan Chao; Gary D. Clark; Terra R. Coakley; Laurel A. Cobban; Joy D. Cogan; Matthew Coggins; F. Sessions Cole; Heather A. Colley; Cynthia M. Cooper; Heidi Cope; William J. Craigen; Andrew B. Crouse; Michael Cunningham; Precilla D’Souza; Hongzheng Dai; Surendra Dasari; Joie Davis; Jyoti G. Daya; Matthew Deardorff; Esteban C. Dell’Angelica; Shweta U. Dhar; Katrina Dipple; Daniel Doherty; Naghmeh Dorrani; Argenia L. Doss; Emilie D. Douine; David D. Draper; Laura Duncan; Dawn Earl; David J. Eckstein; Lisa T. Emrick; Christine M. Eng; Cecilia Esteves; Marni Falk; Liliana Fernandez; Carlos Ferreira; Elizabeth L. Fieg; Laurie C. Findley; Paul G. Fisher; Brent L. Fogel; Irman Forghani; Laure Fresard; William A. Gahl; Ian Glass; Bernadette Gochuico; Rena A. Godfrey; Katie Golden-Grant; Alica M. Goldman; Madison P. Goldrich; David B. Goldstein; Alana Grajewski; Catherine A. Groden; Irma Gutierrez; Sihoun Hahn; Rizwan Hamid; Neil A. Hanchard; Kelly Hassey; Nichole Hayes; Frances High; Anne Hing; Fuki M. Hisama; Ingrid A. Holm; Jason Hom; Martha Horike-Pyne; Alden Huang; Yong Huang; Laryssa Huryn; Rosario Isasi; Fariha Jamal; Gail P. Jarvik; Jeffrey Jarvik; Suman Jayadev; Lefkothea Karaviti; Jennifer Kennedy; Dana Kiley; Isaac S. Kohane; Jennefer N. Kohler; Susan Korrick; Mary Kozuira; Deborah Krakow; Donna M. Krasnewich; Elijah Kravets; Joel B. Krier; Grace L. LaMoure; Seema R. Lalani; Byron Lam; Christina Lam; Brendan C. Lanpher; Ian R. Lanza; Lea Latham; Kimberly LeBlanc; Brendan H. Lee; Hane Lee; Roy Levitt; Richard A. Lewis; Sharyn A. Lincoln; Pengfei Liu; Xue Zhong Liu; Nicola Longo; Sandra K. Loo; Joseph Loscalzo; Richard L. Maas; John MacDowall; Calum A. MacRae; Ellen F. Macnamara; Valerie V. Maduro; Marta M. Majcherska; Bryan C. Mak; May Christine V. Malicdan; Laura A. Mamounas; Teri A. Manolio; Rong Mao; Kenneth Maravilla; Thomas C. Markello; Ronit Marom; Gabor Marth; Beth A. Martin; Martin G. Martin; Julian A. Martinez-Agosto; Shruti Marwaha; Jacob McCauley; Allyn McConkie-Rosell; Colleen E. McCormack; Alexa T. McCray; Elisabeth McGee; Heather Mefford; J. Lawrence Merritt; Matthew Might; Ghayda Mirzaa; Eva Morava; Paolo M. Moretti; Paolo Moretti; Deborah Mosbrook-Davis; John J. Mulvihill; David R. Murdock; Anna Nagy; Mariko Nakano-Okuno; Avi Nath; Stanley F. Nelson; John H. Newman; Sarah K. Nicholas; Deborah Nickerson; Shirley Nieves-Rodriguez; Donna Novacic; Devin Oglesbee; James P. Orengo; Laura Pace; Stephen Pak; J. Carl Pallais; Christina G.S. Palmer; Jeanette C. Papp; Neil H. Parker; John A. Phillips; Jennifer E. Posey; Lorraine Potocki; Bradley Power; Barbara N. Pusey; Aaron Quinlan; Archana N. Raja; Deepak A. Rao; Wendy Raskind; Genecee Renteria; Chloe M. Reuter; Lynette Rives; Amy K. Robertson; Lance H. Rodan; Jill A. Rosenfeld; Natalie Rosenwasser; Francis Rossignol; Maura Ruzhnikov; Ralph Sacco; Jacinda B. Sampson; Susan L. Samson; Mario Saporta; Judy Schaechter; Timothy Schedl; Kelly Schoch; C. Ron Scott; Daryl A. Scott; Vandana Shashi; Jimann Shin; Rebecca H. Signer; Edwin K. Silverman; Janet S. Sinsheimer; Kathy Sisco; Edward C. Smith; Kevin S. Smith; Emily Solem; Lilianna Solnica-Krezel; Ben Solomon; Rebecca C. Spillmann; Joan M. Stoler; Jennifer A. Sullivan; Kathleen Sullivan; Angela Sun; Shirley Sutton; David A. Sweetser; Virginia Sybert; Holly K. Tabor; Amelia L.M. Tan; Queenie K.-G. Tan; Mustafa Tekin; Fred Telischi; Willa Thorson; Audrey Thurm; Cynthia J. Tifft; Camilo Toro; Alyssa A. Tran; Brianna M. Tucker; Tiina K. Urv; Adeline Vanderver; Matt Velinder; Dave Viskochil; Tiphanie P. Vogel; Colleen E. Wahl; Melissa Walker; Stephanie Wallace; Nicole M. Walley; Chris A. Walsh; Jennifer Wambach; Jijun Wan; Lee-kai Wang; Michael F. Wangler; Patricia A. Ward; Daniel Wegner; Mark Wener; Tara Wenger; Katherine Wesseling Perry; Monte Westerfield; Matthew T. Wheeler; Jordan Whitlock; Lynne A. Wolfe; Jeremy D. Woods; Shinya Yamamoto; John Yang; Muhammad Yousef; Diane B. Zastrow; Wadih Zein; Chunli Zhao; Stephan Zuchner; Shamil R. Sunyaev; Isaac S. Kohane is a Biochemistry, Genetics and Molecular Biology article available to read on EtoBox.

What is Commonalities Across Computational Workflows for Uncovering Explanatory Variants in Undiagnosed Cases about?

## Purpose Genomic sequencing has become an increasingly powerful and relevant tool to be leveraged for the discovery of genetic aberrations underlying rare, Mendelian conditions. Although the computational tools incorporated into diagnostic workflows for this task are continually evolving and improving, we nevertheless sought to investigate commonalities across sequencing processing workflows to reveal consensus and standard practice tools and highlight exploratory analyses where technical and theoretical method improvements would be most impactful. ## Methods We collected details regarding the computational approaches used by a genetic testing laboratory and 11 clinical research sites in the United States participating in the Undiagnosed Diseases Network via meetings with bioinformaticians, online survey forms, and analyses of internal protocols. ## Results We found that tools for processing genomic sequencing data can be grouped into four distinct categories. Whereas well-established practices exist for initial variant calling and quality control steps, there is substantial divergence across sites in later stages for variant prioritization and multimodal data integration, demons

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Author

Shilpa Nadimpalli Kobren; Dustin Baldridge; Matt Velinder; Joel B. Krier; Kimberly LeBlanc; Cecilia Esteves; Barbara N. Pusey; Stephan Züchner; Elizabeth Blue; Hane Lee; Alden Huang; Lisa Bastarache; Anna Bican; Joy Cogan; Shruti Marwaha; Anna Alkelai; David R. Murdock; Pengfei Liu; Daniel J. Wegner; Alexander J. Paul; Maria T. Acosta; Margaret Adam; David R. Adams; Pankaj B. Agrawal; Mercedes E. Alejandro; Justin Alvey; Laura Amendola; Ashley Andrews; Euan A. Ashley; Mahshid S. Azamian; Carlos A. Bacino; Guney Bademci; Eva Baker; Ashok Balasubramanyam; Dustin Baldridge; Jim Bale; Michael Bamshad; Deborah Barbouth; Pinar Bayrak-Toydemir; Anita Beck; Alan H. Beggs; Edward Behrens; Gill Bejerano; Jimmy Bennett; Beverly Berg-Rood; Jonathan A. Bernstein; Gerard T. Berry; Anna Bican; Stephanie Bivona; Elizabeth Blue; John Bohnsack; Carsten Bonnenmann; Devon Bonner; Lorenzo Botto; Brenna Boyd; Lauren C. Briere; Elly Brokamp; Gabrielle Brown; Elizabeth A. Burke; Lindsay C. Burrage; Manish J. Butte; Peter Byers; William E. Byrd; John Carey; Olveen Carrasquillo; Ta Chen Peter Chang; Sirisak Chanprasert; Hsiao-Tuan Chao; Gary D. Clark; Terra R. Coakley; Laurel A. Cobban; Joy D. Cogan; Matthew Coggins; F. Sessions Cole; Heather A. Colley; Cynthia M. Cooper; Heidi Cope; William J. Craigen; Andrew B. Crouse; Michael Cunningham; Precilla D’Souza; Hongzheng Dai; Surendra Dasari; Joie Davis; Jyoti G. Daya; Matthew Deardorff; Esteban C. Dell’Angelica; Shweta U. Dhar; Katrina Dipple; Daniel Doherty; Naghmeh Dorrani; Argenia L. Doss; Emilie D. Douine; David D. Draper; Laura Duncan; Dawn Earl; David J. Eckstein; Lisa T. Emrick; Christine M. Eng; Cecilia Esteves; Marni Falk; Liliana Fernandez; Carlos Ferreira; Elizabeth L. Fieg; Laurie C. Findley; Paul G. Fisher; Brent L. Fogel; Irman Forghani; Laure Fresard; William A. Gahl; Ian Glass; Bernadette Gochuico; Rena A. Godfrey; Katie Golden-Grant; Alica M. Goldman; Madison P. Goldrich; David B. Goldstein; Alana Grajewski; Catherine A. Groden; Irma Gutierrez; Sihoun Hahn; Rizwan Hamid; Neil A. Hanchard; Kelly Hassey; Nichole Hayes; Frances High; Anne Hing; Fuki M. Hisama; Ingrid A. Holm; Jason Hom; Martha Horike-Pyne; Alden Huang; Yong Huang; Laryssa Huryn; Rosario Isasi; Fariha Jamal; Gail P. Jarvik; Jeffrey Jarvik; Suman Jayadev; Lefkothea Karaviti; Jennifer Kennedy; Dana Kiley; Isaac S. Kohane; Jennefer N. Kohler; Susan Korrick; Mary Kozuira; Deborah Krakow; Donna M. Krasnewich; Elijah Kravets; Joel B. Krier; Grace L. LaMoure; Seema R. Lalani; Byron Lam; Christina Lam; Brendan C. Lanpher; Ian R. Lanza; Lea Latham; Kimberly LeBlanc; Brendan H. Lee; Hane Lee; Roy Levitt; Richard A. Lewis; Sharyn A. Lincoln; Pengfei Liu; Xue Zhong Liu; Nicola Longo; Sandra K. Loo; Joseph Loscalzo; Richard L. Maas; John MacDowall; Calum A. MacRae; Ellen F. Macnamara; Valerie V. Maduro; Marta M. Majcherska; Bryan C. Mak; May Christine V. Malicdan; Laura A. Mamounas; Teri A. Manolio; Rong Mao; Kenneth Maravilla; Thomas C. Markello; Ronit Marom; Gabor Marth; Beth A. Martin; Martin G. Martin; Julian A. Martinez-Agosto; Shruti Marwaha; Jacob McCauley; Allyn McConkie-Rosell; Colleen E. McCormack; Alexa T. McCray; Elisabeth McGee; Heather Mefford; J. Lawrence Merritt; Matthew Might; Ghayda Mirzaa; Eva Morava; Paolo M. Moretti; Paolo Moretti; Deborah Mosbrook-Davis; John J. Mulvihill; David R. Murdock; Anna Nagy; Mariko Nakano-Okuno; Avi Nath; Stanley F. Nelson; John H. Newman; Sarah K. Nicholas; Deborah Nickerson; Shirley Nieves-Rodriguez; Donna Novacic; Devin Oglesbee; James P. Orengo; Laura Pace; Stephen Pak; J. Carl Pallais; Christina G.S. Palmer; Jeanette C. Papp; Neil H. Parker; John A. Phillips; Jennifer E. Posey; Lorraine Potocki; Bradley Power; Barbara N. Pusey; Aaron Quinlan; Archana N. Raja; Deepak A. Rao; Wendy Raskind; Genecee Renteria; Chloe M. Reuter; Lynette Rives; Amy K. Robertson; Lance H. Rodan; Jill A. Rosenfeld; Natalie Rosenwasser; Francis Rossignol; Maura Ruzhnikov; Ralph Sacco; Jacinda B. Sampson; Susan L. Samson; Mario Saporta; Judy Schaechter; Timothy Schedl; Kelly Schoch; C. Ron Scott; Daryl A. Scott; Vandana Shashi; Jimann Shin; Rebecca H. Signer; Edwin K. Silverman; Janet S. Sinsheimer; Kathy Sisco; Edward C. Smith; Kevin S. Smith; Emily Solem; Lilianna Solnica-Krezel; Ben Solomon; Rebecca C. Spillmann; Joan M. Stoler; Jennifer A. Sullivan; Kathleen Sullivan; Angela Sun; Shirley Sutton; David A. Sweetser; Virginia Sybert; Holly K. Tabor; Amelia L.M. Tan; Queenie K.-G. Tan; Mustafa Tekin; Fred Telischi; Willa Thorson; Audrey Thurm; Cynthia J. Tifft; Camilo Toro; Alyssa A. Tran; Brianna M. Tucker; Tiina K. Urv; Adeline Vanderver; Matt Velinder; Dave Viskochil; Tiphanie P. Vogel; Colleen E. Wahl; Melissa Walker; Stephanie Wallace; Nicole M. Walley; Chris A. Walsh; Jennifer Wambach; Jijun Wan; Lee-kai Wang; Michael F. Wangler; Patricia A. Ward; Daniel Wegner; Mark Wener; Tara Wenger; Katherine Wesseling Perry; Monte Westerfield; Matthew T. Wheeler; Jordan Whitlock; Lynne A. Wolfe; Jeremy D. Woods; Shinya Yamamoto; John Yang; Muhammad Yousef; Diane B. Zastrow; Wadih Zein; Chunli Zhao; Stephan Zuchner; Shamil R. Sunyaev; Isaac S. Kohane

Publisher

Elsevier BV

Published

2021

Language

EN

Field

Biochemistry, Genetics and Molecular Biology (Life Sciences)