Critical assessment of variant prioritization methods for rare disease diagnosis within the rare genomes project

Autor: Sarah L. Stenton, Melanie C. O’Leary, Gabrielle Lemire, Grace E. VanNoy, Stephanie DiTroia, Vijay S. Ganesh, Emily Groopman, Emily O’Heir, Brian Mangilog, Ikeoluwa Osei-Owusu, Lynn S. Pais, Jillian Serrano, Moriel Singer-Berk, Ben Weisburd, Michael W. Wilson, Christina Austin-Tse, Marwa Abdelhakim, Azza Althagafi, Giulia Babbi, Riccardo Bellazzi, Samuele Bovo, Maria Giulia Carta, Rita Casadio, Pieter-Jan Coenen, Federica De Paoli, Matteo Floris, Manavalan Gajapathy, Robert Hoehndorf, Julius O. B. Jacobsen, Thomas Joseph, Akash Kamandula, Panagiotis Katsonis, Cyrielle Kint, Olivier Lichtarge, Ivan Limongelli, Yulan Lu, Paolo Magni, Tarun Karthik Kumar Mamidi, Pier Luigi Martelli, Marta Mulargia, Giovanna Nicora, Keith Nykamp, Vikas Pejaver, Yisu Peng, Thi Hong Cam Pham, Maurizio S. Podda, Aditya Rao, Ettore Rizzo, Vangala G. Saipradeep, Castrense Savojardo, Peter Schols, Yang Shen, Naveen Sivadasan, Damian Smedley, Dorian Soru, Rajgopal Srinivasan, Yuanfei Sun, Uma Sunderam, Wuwei Tan, Naina Tiwari, Xiao Wang, Yaqiong Wang, Amanda Williams, Elizabeth A. Worthey, Rujie Yin, Yuning You, Daniel Zeiberg, Susanna Zucca, Constantina Bakolitsa, Steven E. Brenner, Stephanie M. Fullerton, Predrag Radivojac, Heidi L. Rehm, Anne O’Donnell-Luria

Publikováno v: Human Genomics, Vol 18, Iss 1, Pp 1-25 (2024)

Abstract Background A major obstacle faced by families with rare diseases is obtaining a genetic diagnosis. The average "diagnostic odyssey" lasts over five years and causal variants are identified in under 50%, even when capturing variants genome-wi

Externí odkaz: https://doaj.org/article/29fbe7d26d88463789f004c8908aa4a7

GA4GH Phenopackets: A Practical Introduction

Autor: Markus S. Ladewig, Julius O. B. Jacobsen, Alex H. Wagner, Daniel Danis, Baha El Kassaby, Michael Gargano, Tudor Groza, Michael Baudis, Robin Steinhaus, Dominik Seelow, Nikolaos E. Bechrakis, Christopher J. Mungall, Paul N. Schofield, Olivier Elemento, Lindsay Smith, Julie A. McMurry, Monica Munoz‐Torres, Melissa A. Haendel, Peter N. Robinson

Publikováno v: Advanced Genetics, Vol 4, Iss 1, Pp n/a-n/a (2023)

Abstract The Global Alliance for Genomics and Health (GA4GH) is developing a suite of coordinated standards for genomics for healthcare. The Phenopacket is a new GA4GH standard for sharing disease and phenotype information that characterizes an indiv

Externí odkaz: https://doaj.org/article/8b38a05352e2438485566a378a383583

Phenotype‐driven approaches to enhance variant prioritization and diagnosis of rare disease

Autor: Julius O. B. Jacobsen, Catherine Kelly, Valentina Cipriani, Genomics England Research Consortium, Christopher J. Mungall, Justin Reese, Daniel Danis, Peter N. Robinson, Damian Smedley

Publikováno v: Human Mutation. 43:1071-1081

Rare disease diagnostics and disease gene discovery have been revolutionized by whole-exome and genome sequencing but identifying the causative variant(s) from the millions in each individual remains challenging. The use of deep phenotyping of patien

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::778de45099578134043a940fd99fb21d
https://doi.org/10.1002/humu.24380

Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases

Autor: Julius O B Jacobsen, Catherine Kelly, Valentina Cipriani, Peter N Robinson, Damian Smedley

Publikováno v: Briefings in Bioinformatics. 23

Yuan et al. recently described an independent evaluation of several phenotype-driven gene prioritization methods for Mendelian disease on two separate, clinical datasets. Although they attempted to use default settings for each tool, we describe thre

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::9b5921deedd49c827c5668fe034c2b77
https://doi.org/10.1093/bib/bbac188

SvAnna: efficient and accurate pathogenicity prediction of coding and regulatory structural variants in long-read genome sequencing

Autor: Daniel Danis, Julius O. B. Jacobsen, Parithi Balachandran, Qihui Zhu, Feyza Yilmaz, Justin Reese, Matthias Haimel, Gholson J. Lyon, Ingo Helbig, Christopher J. Mungall, Christine R. Beck, Charles Lee, Damian Smedley, Peter N. Robinson

Publikováno v: Genome Medicine
Genome medicine, vol 14, iss 1

Structural variants (SVs) are implicated in the etiology of Mendelian diseases but have been systematically underascertained owing to sequencing technology limitations. Long-read sequencing enables comprehensive detection of SVs, but approaches for p

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::79c2f263c4dfd514eb87ba2fc07105cd